1
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Fizari M, Keller N, Jardine PJ, Smith DE. Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging. Nucleic Acids Res 2023; 51:8060-8069. [PMID: 37449417 PMCID: PMC10450192 DOI: 10.1093/nar/gkad582] [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: 04/04/2023] [Revised: 06/17/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA-DNA sliding friction, consistent with a Frenkel-Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest that it is connected to the phenomenon of 'clogging' in soft matter systems. Our results provide evidence that DNA-DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.
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Affiliation(s)
- Mounir Fizari
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas Keller
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
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2
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Nguyen TVP, Wu Y, Yao T, Trinh JT, Zeng L, Chemla YR, Golding I. CO-INFECTING PHAGES IMPEDE EACH OTHER'S ENTRY INTO THE CELL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543643. [PMID: 37333217 PMCID: PMC10274716 DOI: 10.1101/2023.06.05.543643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Bacteriophage lambda tunes its propensity to lysogenize based on the number of viral genome copies inside the infected cell. Viral self-counting is believed to serve as a way of inferring the abundance of available hosts in the environment. This interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). However, here we show this premise to be untrue. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, followed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of individual phage entries decrease with MOI. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage landing, evidenced by compromised membrane integrity and loss of membrane potential. The dependence of phage entry dynamics on the surrounding medium is found to result in a strong impact of environmental conditions on the infection outcome, while the protracted entry of co-infecting phages increases the cell-to-cell variability in infection outcome at a given MOI. Our findings demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.
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Affiliation(s)
- Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
| | - Yuchen Wu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Jimmy T. Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yann R. Chemla
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
- Department of Microbiology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
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3
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Fizari M, Keller N, Jardine PJ, Smith DE. Role of DNA-DNA sliding friction and non-equilibrium dynamics in viral genome ejection and packaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535472. [PMID: 37066220 PMCID: PMC10104077 DOI: 10.1101/2023.04.03.535472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics, and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA-DNA sliding friction, consistent with a Frenkel-Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest it is connected to the phenomenon of "clogging" in soft-matter systems. Our results provide evidence that DNA-DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.
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4
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Park CB, Sung BJ. Effects of Packaging History on the Ejection of a Polymer Chain from a Small Confinement. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Chung Bin Park
- Department of Chemistry and Research Institute for Basic Science, Sogang University, Seoul 04107, Republic of Korea
| | - Bong June Sung
- Department of Chemistry and Research Institute for Basic Science, Sogang University, Seoul 04107, Republic of Korea
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5
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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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6
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Kiss B, Mudra D, Török G, Mártonfalvi Z, Csík G, Herényi L, Kellermayer M. Single-particle virology. Biophys Rev 2020; 12:1141-1154. [PMID: 32880826 PMCID: PMC7471434 DOI: 10.1007/s12551-020-00747-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023] Open
Abstract
The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Dorottya Mudra
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - György Török
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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7
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Park CB, Kwon S, Sung BJ. The effects of a knot and its conformational relaxation on the ejection of a single polymer chain from confinement. J Chem Phys 2019. [DOI: 10.1063/1.5110428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chung Bin Park
- Department of Chemistry, Sogang University, Seoul 04107, South Korea
| | - Seulki Kwon
- Department of Chemistry, Sogang University, Seoul 04107, South Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, South Korea
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8
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Broeker NK, Roske Y, Valleriani A, Stephan MS, Andres D, Koetz J, Heinemann U, Barbirz S. Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail. J Biol Chem 2019; 294:11751-11761. [PMID: 31189652 PMCID: PMC6682738 DOI: 10.1074/jbc.ra119.008133] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/11/2019] [Indexed: 12/20/2022] Open
Abstract
Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Å resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.
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Affiliation(s)
- Nina K Broeker
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mareike S Stephan
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Dorothee Andres
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Joachim Koetz
- Kolloidchemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustrasse 6, 14195 Berlin, Germany
| | - Stefanie Barbirz
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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9
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Silva-Valenzuela CA, Camilli A. Niche adaptation limits bacteriophage predation of Vibrio cholerae in a nutrient-poor aquatic environment. Proc Natl Acad Sci U S A 2019; 116:1627-1632. [PMID: 30635420 PMCID: PMC6358685 DOI: 10.1073/pnas.1810138116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Vibrio cholerae, the causative agent of cholera, has reservoirs in fresh and brackish water where it interacts with virulent bacteriophages. Phages are the most abundant biological entity on earth and coevolve with bacteria. It was reported that concentrations of phage and V. cholerae inversely correlate in aquatic reservoirs and in the human small intestine, and therefore that phages may quench cholera outbreaks. Although there is strong evidence for phage predation in cholera patients, evidence is lacking for phage predation of V. cholerae in aquatic environments. Here, we used three virulent phages, ICP1, ICP2, and ICP3, commonly shed by cholera patients in Bangladesh, as models to understand the predation dynamics in microcosms simulating aquatic environments. None of the phages were capable of predation in fresh water, and only ICP1 was able to prey on V. cholerae in estuarine water due to a requirement for salt. We conclude that ICP2 and ICP3 are better adapted for predation in a nutrient rich environment. Our results point to the evolution of niche-specific predation by V. cholerae-specific virulent phages, which complicates their use in predicting or monitoring cholera outbreaks as well as their potential use in reducing aquatic reservoirs of V. cholerae in endemic areas.
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Affiliation(s)
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111
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10
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Shao Q, Trinh JT, Zeng L. High-resolution studies of lysis-lysogeny decision-making in bacteriophage lambda. J Biol Chem 2018; 294:3343-3349. [PMID: 30242122 DOI: 10.1074/jbc.tm118.003209] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cellular decision-making guides complex development such as cell differentiation and disease progression. Much of our knowledge about decision-making is derived from simple models, such as bacteriophage lambda infection, in which lambda chooses between the vegetative lytic fate and the dormant lysogenic fate. This paradigmatic system is broadly understood but lacking mechanistic details, partly due to limited resolution of past studies. Here, we discuss how modern technologies have enabled high-resolution examination of lambda decision-making to provide new insights and exciting possibilities in studying this classical system. The advent of techniques for labeling specific DNA, RNA, and proteins in cells allows for molecular-level characterization of events in lambda development. These capabilities yield both new answers and new questions regarding how the isolated lambda genetic circuit acts, what biological events transpire among phages in their natural context, and how the synergy of simple phage macromolecules brings about complex behaviors.
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Affiliation(s)
- Qiuyan Shao
- From the Department of Biochemistry and Biophysics and.,the Center for Phage Technology, Texas A&M University, College Station, Texas 77843
| | - Jimmy T Trinh
- From the Department of Biochemistry and Biophysics and.,the Center for Phage Technology, Texas A&M University, College Station, Texas 77843
| | - Lanying Zeng
- From the Department of Biochemistry and Biophysics and .,the Center for Phage Technology, Texas A&M University, College Station, Texas 77843
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11
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In Vitro Studies of Lipopolysaccharide-Mediated DNA Release of Podovirus HK620. Viruses 2018; 10:v10060289. [PMID: 29843473 PMCID: PMC6024685 DOI: 10.3390/v10060289] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022] Open
Abstract
Gram-negative bacteria protect themselves with an outermost layer containing lipopolysaccharide (LPS). O-antigen-specific bacteriophages use tailspike proteins (TSP) to recognize and cleave the O-polysaccharide part of LPS. However, O-antigen composition and structure can be highly variable depending on the environmental conditions. It is important to understand how these changes may influence the early steps of the bacteriophage infection cycle because they can be linked to changes in host range or the occurrence of phage resistance. In this work, we have analyzed how LPS preparations in vitro trigger particle opening and DNA ejection from the E. coli podovirus HK620. Fluorescence-based monitoring of DNA release showed that HK620 phage particles in vitro ejected their genome at velocities comparable to those found for other podoviruses. Moreover, we found that HK620 irreversibly adsorbed to the LPS receptor via its TSP at restrictive low temperatures, without opening the particle but could eject its DNA at permissive temperatures. DNA ejection was solely stimulated by LPS, however, the composition of the O-antigen dictated whether the LPS receptor could start the DNA release from E. coli phage HK620 in vitro. This finding can be significant when optimizing bacteriophage mixtures for therapy, where in natural environments O-antigen structures may rapidly change.
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12
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Freeman KG, Behrens MA, Streletzky KA, Olsson U, Evilevitch A. Portal Stability Controls Dynamics of DNA Ejection from Phage. J Phys Chem B 2016; 120:6421-9. [PMID: 27176921 DOI: 10.1021/acs.jpcb.6b04172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Through a unique combination of time-resolved single-molecule (cryo-TEM) and bulk measurements (light scattering and small-angle X-ray scattering), we provide a detailed study of the dynamics of stochastic DNA ejection events from phage λ. We reveal that both binding with the specific phage receptor, LamB, and thermo-mechanical destabilization of the portal vertex on the capsid are required for initiation of ejection of the pressurized λ-DNA from the phage. Specifically, we found that a measurable activation energy barrier for initiation of DNA ejection with LamB present, Ea = (1.2 ± 0.1) × 10(-19) J/phage (corresponding to ∼28 kTbody/phage at Tbody = 37 °C), results in 15 times increased rate of ejection event dynamics when the temperature is raised from 15 to 45 °C (7.5 min versus 30 s average lag time for initiation of ejection). This suggests that phages have a double fail-safe mechanism for ejection-in addition to receptor binding, phage must also overcome (through thermal energy and internal DNA pressure) an energy barrier for DNA ejection. This energy barrier ensures that viral genome ejection into cells occurs with high efficiency only when the temperature conditions are favorable for genome replication. At lower suboptimal temperatures, the infectious phage titer is preserved over much longer times, since DNA ejection dynamics is strongly inhibited even in the presence of solubilized receptor or susceptible cells. This work also establishes a light scattering based approach to investigate the influence of external solution conditions, mimicking those of the bacterial cytoplasm, on the stability of the viral capsid portal, which is directly linked to dynamics of virion deactivation.
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Affiliation(s)
- Krista G Freeman
- Carnegie Mellon University , Department of Physics, Pittsburgh, Pennsylvania, United States
| | - Manja A Behrens
- Lund University , Division of Physical Chemistry, Lund, Sweden
| | - Kiril A Streletzky
- Cleveland State University , Department of Physics, Cleveland, Ohio, United States
| | - Ulf Olsson
- Lund University , Division of Physical Chemistry, Lund, Sweden
| | - Alex Evilevitch
- Carnegie Mellon University , Department of Physics, Pittsburgh, Pennsylvania, United States.,Lund University , Division of Biochemistry and Structural Biology, Lund, Sweden
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13
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Frutos MD, Leforestier A, Degrouard J, Zambrano N, Wien F, Boulanger P, Brasilès S, Renouard M, Durand D, Livolant F. Can Changes in Temperature or Ionic Conditions Modify the DNA Organization in the Full Bacteriophage Capsid? J Phys Chem B 2016; 120:5975-86. [PMID: 27152667 DOI: 10.1021/acs.jpcb.6b01783] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We compared four bacteriophage species, T5, λ, T7, and Φ29, to explore the possibilities of DNA reorganization in the capsid where the chain is highly concentrated and confined. First, we did not detect any change in DNA organization as a function of temperature between 20 to 40 °C. Second, the presence of spermine (4+) induces a significant enlargement of the typical size of the hexagonal domains in all phages. We interpret these changes as a reorganization of DNA by slight movements of defects in the structure, triggered by a partial screening of repulsive interactions. We did not detect any signal characteristic of a long-range chiral organization of the encapsidated DNA in the presence and in the absence of spermine.
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Affiliation(s)
- Marta de Frutos
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Amélie Leforestier
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Jéril Degrouard
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Nebraska Zambrano
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
| | - Frank Wien
- Synchrotron SOLEIL, DISCO, L'Orme des Merisiers , 91190 St Aubin, France
| | - Pascale Boulanger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Sandrine Brasilès
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Madalena Renouard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay , 91198 Gif sur Yvette Cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay , 91405 Orsay Cedex, France
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14
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Goldfain AM, Garmann RF, Jin Y, Lahini Y, Manoharan VN. Dynamic Measurements of the Position, Orientation, and DNA Content of Individual Unlabeled Bacteriophages. J Phys Chem B 2016; 120:6130-8. [DOI: 10.1021/acs.jpcb.6b02153] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Yan Jin
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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15
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DE FRUTOS M, LEFORESTIER A, LIVOLANT F. RELATIONSHIP BETWEEN THE GENOME PACKING IN THE BACTERIOPHAGE CAPSID AND THE KINETICS OF DNA EJECTION. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013500069] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present a general survey of experimental and theoretical observations of DNA structure and in vitro ejection kinetics for different bacteriophage species. In some species, like T5, the ejection may present pauses and arrests that have not been detected in others species like Lambda. We propose hypotheses to explain such differences and we discuss how the experimental conditions may be important for their detection. Our work highlights the role of DNA organization inside the bacteriophage capsid on the stochastic and out of equilibrium nature of the ejection process.
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Affiliation(s)
- M. DE FRUTOS
- Institut de Biologie et Biochimie Moléculaire et Cellulaire, UMR CNRS 8619, Bât 430, Université Paris Sud, 91405 Orsay cedex, France
| | - A. LEFORESTIER
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris-Sud, Bât 510, Orsay 91405, France
| | - F. LIVOLANT
- Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris-Sud, Bât 510, Orsay 91405, France
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16
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Chiaruttini N, Letellier L, Viasnoff V. A novel method to couple electrophysiological measurements and fluorescence imaging of suspended lipid membranes: the example of T5 bacteriophage DNA ejection. PLoS One 2013; 8:e84376. [PMID: 24376806 PMCID: PMC3871697 DOI: 10.1371/journal.pone.0084376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/22/2013] [Indexed: 12/21/2022] Open
Abstract
We present an innovative method to couple electrophysiological measurements with fluorescence imaging of functionalized suspended bilayers. Our method combines several advantages: it is well suited to study transmembrane proteins that are difficult to incorporate in suspended bilayers, it allows single molecule resolution both in terms of electrophysiological measurements and fluorescence imaging, and it enables mechanical stimulations of the membrane. The approach comprises of two steps: first the reconstitution of membrane proteins in giant unilamellar vesicles; then the formation of a suspended bilayer spanning a 5 to 15 micron-wide aperture that can be visualized by high NA microscope objectives. We exemplified how the technique can be used to detect in real time the translocation of T5 DNA across the bilayer during its ejection from the bacteriophage capsid.
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Affiliation(s)
- Nicolas Chiaruttini
- ESPCI Paristech, CNRS, Paris, France
- Aurélien Roux Lab, Biochemistry Department, University of Geneva, Geneva, Switzerland
| | - Lucienne Letellier
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud-11, CNRS, Orsay, France
| | - Virgile Viasnoff
- ESPCI Paristech, CNRS, Paris, France
- Aurélien Roux Lab, Biochemistry Department, University of Geneva, Geneva, Switzerland
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud-11, CNRS, Orsay, France
- MechanoBiology Institute of Singapore, Singapore, Singapore
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17
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Abstract
Sticky ends are unpaired nucleotides at the ends of DNA molecules that can associate to link DNA segments. Self-assembly of DNA molecules via sticky ends is currently used to grow DNA structures with desired architectures. The sticky end links are the weakest parts of such structures. In this work, the strength of sticky end links is studied by computational means. The number of basepairs in the sticky end and the sequence are varied, and the response to tension along the axis of the molecule is evaluated using a full atomistic model. It is observed that, generally, increasing the number of basepairs in the sticky end increases the strength, but the central factor controlling this parameter is the basepair sequence. The sticky ends are divided into two classes of low and high strength. The second class has strength comparable with that of a double stranded molecule with one nick in one of the strands. The strength of the first class is roughly half that of the strong sticky ends. For all strong sticky ends tested, the enhanced stability is associated with the formation of an unusually stable complex composed from two basepairs and two flanking bases of certain sequence. This complex rotates and aligns with the direction of the force allowing significant deformation and providing enhanced strength. This is similar to a mechanism recently suggested to enhance the mechanical stability of an RNA kissing loop from the Moloney murine leukemia virus. The model is tested against experimental structural data for sticky ends and against published simulation results for the stretch of double stranded DNA. The results provide guidance for the design of DNA self-assembled structures and indicate the types of sticky ends desirable if maximizing the strength and stability of these structures is targeted.
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Affiliation(s)
- Ehsan Ban
- Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute , Troy, New York, United States
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18
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Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity. Biophys J 2013; 104:2058-67. [PMID: 23663849 DOI: 10.1016/j.bpj.2013.03.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 01/14/2023] Open
Abstract
In the bacteriophage ϕ29, DNA is packed into a preassembled capsid from which it ejects under high pressure. A recent cryo-EM reconstruction of ϕ29 revealed a compact toroidal DNA structure (30-40 basepairs) lodged within the exit cavity formed by the connector-lower collar protein complex. Using multiscale models, we compute a detailed structural ensemble of intriguing DNA toroids of various lengths, all highly compatible with experimental observations. In particular, coarse-grained (elastic rod) and atomistic (molecular dynamics) models predict the formation of DNA toroids under significant compression, a largely unexplored state of DNA. Model predictions confirm that a biologically attainable compressive force of 25 pN sustains the toroid and yields DNA electron density maps highly consistent with the experimental reconstruction. The subsequent simulation of dynamic toroid ejection reveals large reactions on the connector that may signal genome release.
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19
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Identification and characterization of a novel flagellum-dependent Salmonella-infecting bacteriophage, iEPS5. Appl Environ Microbiol 2013; 79:4829-37. [PMID: 23747700 DOI: 10.1128/aem.00706-13] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel flagellatropic phage of Salmonella enterica serovar Typhimurium, called iEPS5, was isolated and characterized. iEPS5 has an icosahedral head and a long noncontractile tail with a tail fiber. Genome sequencing revealed a double-stranded DNA of 59,254 bp having 73 open reading frames (ORFs). To identify the receptor for iEPS5, Tn5 transposon insertion mutants of S. Typhimurium SL1344 that were resistant to the phage were isolated. All of the phage-resistant mutants were found to have mutations in genes involved in flagellar formation, suggesting that the flagellum is the adsorption target of this phage. Analysis of phage infection using the ΔmotA mutant, which is flagellated but nonmotile, demonstrated the requirement of flagellar rotation for iEPS5 infection. Further analysis of phage infection using the ΔcheY mutant revealed that iEPS5 could infect host bacteria only when the flagellum is rotating counterclockwise (CCW). These results suggested that the CCW-rotating flagellar filament is essential for phage adsorption and required for successful infection by iEPS5. In contrast to the well-studied flagellatropic phage Chi, iEPS5 cannot infect the ΔfliK mutant that makes a polyhook without a flagellar filament, suggesting that these two flagellatropic phages utilize different infection mechanisms. Here, we present evidence that iEPS5 injects its DNA into the flagellar filament for infection by assessing DNA transfer from SYBR gold-labeled iEPS5 to the host bacteria.
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20
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Mahalik JP, Hildebrandt B, Muthukumar M. Langevin dynamics simulation of DNA ejection from a phage. J Biol Phys 2013; 39:229-45. [PMID: 23860871 DOI: 10.1007/s10867-013-9316-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/22/2013] [Indexed: 11/30/2022] Open
Abstract
We have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from Φ29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages.
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Affiliation(s)
- J P Mahalik
- Department of Polymer Science and Engineering, Department of Physics, University of Massachusetts, Amherst, MA 01003, USA
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21
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Leforestier A. Polymorphism of DNA conformation inside the bacteriophage capsid. J Biol Phys 2013; 39:201-13. [PMID: 23860869 PMCID: PMC3662419 DOI: 10.1007/s10867-013-9315-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/20/2013] [Indexed: 10/27/2022] Open
Abstract
Double-stranded DNA bacteriophage genomes are packaged into their icosahedral capsids at the highest densities known so far (about 50 % w:v). How the molecule is folded at such density and how its conformation changes upon ejection or packaging are fascinating questions still largely open. We review cryo-TEM analyses of DNA conformation inside partially filled capsids as a function of the physico-chemical environment (ions, osmotic pressure, temperature). We show that there exists a wide variety of DNA conformations. Strikingly, the different observed structures can be described by some of the different models proposed over the years for DNA organisation inside bacteriophage capsids: either spool-like structures with axial or concentric symmetries, or liquid crystalline structures characterised by a DNA homogeneous density. The relevance of these conformations for the understanding of DNA folding and unfolding upon ejection and packaging in vivo is discussed.
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Affiliation(s)
- Amélie Leforestier
- Laboratoire de Physqiue des Solides, CNRS, UMR 8502, Université Paris Sud, Orsay, France.
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22
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Abstract
Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo.
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Affiliation(s)
- Ian J Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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23
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Lemay SG, Panja D, Molineux IJ. Role of osmotic and hydrostatic pressures in bacteriophage genome ejection. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022714. [PMID: 23496555 DOI: 10.1103/physreve.87.022714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 06/01/2023]
Abstract
A critical step in the bacteriophage life cycle is genome ejection into host bacteria. The ejection process for double-stranded DNA phages has been studied thoroughly in vitro, where after triggering with the cellular receptor the genome ejects into a buffer. The experimental data have been interpreted in terms of the decrease in free energy of the densely packed DNA associated with genome ejection. Here we detail a simple model of genome ejection in terms of the hydrostatic and osmotic pressures inside the phage, a bacterium, and a buffer solution or culture medium. We argue that the hydrodynamic flow associated with the water movement from the buffer solution into the phage capsid and further drainage into the bacterial cytoplasm, driven by the osmotic gradient between the bacterial cytoplasm and culture medium, provides an alternative mechanism for phage genome ejection in vivo; the mechanism is perfectly consistent with phage genome ejection in vitro.
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Affiliation(s)
- Serge G Lemay
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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24
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Van Valen D, Wu D, Chen YJ, Tuson H, Wiggins P, Phillips R. A single-molecule Hershey-Chase experiment. Curr Biol 2012; 22:1339-43. [PMID: 22727695 DOI: 10.1016/j.cub.2012.05.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/18/2012] [Accepted: 05/10/2012] [Indexed: 02/02/2023]
Abstract
Ever since Hershey and Chase used phages to establish DNA as the carrier of genetic information in 1952, the precise mechanisms of phage DNA translocation have been a mystery. Although bulk measurements have set a timescale for in vivo DNA translocation during bacteriophage infection, measurements of DNA ejection by single bacteriophages have only been made in vitro. Here, we present direct visualization of single bacteriophages infecting individual Escherichia coli cells. For bacteriophage λ, we establish a mean ejection time of roughly 5 min with significant cell-to-cell variability, including pausing events. In contrast, corresponding in vitro single-molecule ejections are more uniform and finish within 10 s. Our data reveal that when plotted against the amount of DNA ejected, the velocity of ejection for two different genome lengths collapses onto a single curve. This suggests that in vivo ejections are controlled by the amount of DNA ejected. In contrast, in vitro DNA ejections are governed by the amount of DNA left inside the capsid. This analysis provides evidence against a purely intrastrand repulsion-based mechanism and suggests that cell-internal processes dominate. This provides a picture of the early stages of phage infection and sheds light on the problem of polymer translocation.
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Affiliation(s)
- David Van Valen
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
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25
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Abstract
Bacteriophage λ, rediscovered in the early 1950s, has served as a model in molecular biology studies for decades. Although currently more complex organisms and more complicated biological systems can be studied, this phage is still an excellent model to investigate principles of biological processes occurring at the molecular level. In fact, very few other biological models provide possibilities to examine regulations of biological mechanisms as detailed as performed with λ. In this chapter, recent advances in our understanding of mechanisms of bacteriophage λ development are summarized and discussed. Particularly, studies on (i) phage DNA injection, (ii) molecular bases of the lysis-versus-lysogenization decision and the lysogenization process itself, (iii) prophage maintenance and induction, (iv), λ DNA replication, (v) phage-encoded recombination systems, (vi) transcription antitermination, (vii) formation of the virion structure, and (viii) lysis of the host cell, as published during several past years, will be presented.
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26
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Bertin A, de Frutos M, Letellier L. Bacteriophage-host interactions leading to genome internalization. Curr Opin Microbiol 2011; 14:492-6. [PMID: 21783404 DOI: 10.1016/j.mib.2011.07.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/02/2011] [Accepted: 07/05/2011] [Indexed: 01/18/2023]
Abstract
Bacteriophage infection is initiated by binding of the virion to a specific receptor located on the host surface. The genome is then released from the capsid and delivered to the host cytoplasm. Our knowledge of these early steps of infection has recently improved. The three-dimensional structure of numerous receptor binding proteins of tailed phages has been solved. Cryo-electron tomography has allowed characterization of the phage-host interactions in a cellular context and at nanometric resolution. The localization and motions of fluorescently labelled phages, receptors and viral DNA were monitored on individual bacteria. Altogether these approaches have revealed the intricacy of these early events and emphasize the link between infection and microbial architecture.
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Affiliation(s)
- Aurélie Bertin
- Institut de Biochimie Biophysique Moléculaire et Cellulaire, Univ Paris-Sud 11, UMR CNRS 8619, F- 91405, Orsay, France
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27
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Rüger W. Die Transkription der genetischen Information und ihre Regulation durch Proteinfaktoren. Angew Chem Int Ed Engl 1972. [DOI: 10.1002/ange.19720842002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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