1
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Valbuena A, Strobl K, Gil-Redondo JC, Valiente L, de Pablo PJ, Mateu MG. Single-Molecule Analysis of Genome Uncoating from Individual Human Rhinovirus Particles, and Modulation by Antiviral Drugs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304722. [PMID: 37806749 DOI: 10.1002/smll.202304722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Infection of humans by many viruses is typically initiated by the internalization of a single virion in each of a few susceptible cells. Thus, the outcome of the infection process may depend on stochastic single-molecule events. A crucial process for viral infection, and thus a target for developing antiviral drugs, is the uncoating of the viral genome. Here a force spectroscopy procedure using an atomic force microscope is implemented to study uncoating for individual human rhinovirus particles. Application of an increasing mechanical force on a virion led to a high force-induced structural transition that facilitated extrusion of the viral RNA molecule without loss of capsid integrity. Application of force to virions that h ad previously extruded the RNA, or to RNA-free capsids, led to a lower force-induced event associated with capsid disruption. The kinetic parameters are determined for each reaction. The high-force event is a stochastic process governed by a moderate free energy barrier (≈20 kcal mol-1 ), which results in a heterogeneous population of structurally weakened virions in which different fractions of the RNA molecule are externalized. The effects of antiviral compounds or capsid mutation on the kinetics of this reaction reveal a correlation between the reaction rate and virus infectivity.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Carlos Gil-Redondo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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2
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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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3
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Rao VB, Fokine A, Fang Q, Shao Q. Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging. Viruses 2023; 15:527. [PMID: 36851741 PMCID: PMC9958956 DOI: 10.3390/v15020527] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Bacteriophage (phage) T4 has served as an extraordinary model to elucidate biological structures and mechanisms. Recent discoveries on the T4 head (capsid) structure, portal vertex, and genome packaging add a significant body of new literature to phage biology. Head structures in unexpanded and expanded conformations show dramatic domain movements, structural remodeling, and a ~70% increase in inner volume while creating high-affinity binding sites for the outer decoration proteins Soc and Hoc. Small changes in intercapsomer interactions modulate angles between capsomer planes, leading to profound alterations in head length. The in situ cryo-EM structure of the symmetry-mismatched portal vertex shows the remarkable structural morphing of local regions of the portal protein, allowing similar interactions with the capsid protein in different structural environments. Conformational changes in these interactions trigger the structural remodeling of capsid protein subunits surrounding the portal vertex, which propagate as a wave of expansion throughout the capsid. A second symmetry mismatch is created when a pentameric packaging motor assembles at the outer "clip" domains of the dodecameric portal vertex. The single-molecule dynamics of the packaging machine suggests a continuous burst mechanism in which the motor subunits adjusted to the shape of the DNA fire ATP hydrolysis, generating speeds as high as 2000 bp/s.
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Affiliation(s)
- Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Qianglin Fang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Qianqian Shao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
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4
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Ramoji A, Pahlow S, Pistiki A, Rueger J, Shaik TA, Shen H, Wichmann C, Krafft C, Popp J. Understanding Viruses and Viral Infections by Biophotonic Methods. TRANSLATIONAL BIOPHOTONICS 2022. [DOI: 10.1002/tbio.202100008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Anuradha Ramoji
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4 Jena Germany
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
- Center for Sepsis Control and Care Jena University Hospital, Am Klinikum 1, 07747 Jena Germany
| | - Susanne Pahlow
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4 Jena Germany
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
- InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4 Jena Germany
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
| | - Jan Rueger
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
| | - Tanveer Ahmed Shaik
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
| | - Haodong Shen
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4 Jena Germany
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
- InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena Germany
| | - Christina Wichmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4 Jena Germany
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
- InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
| | - Juergen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4 Jena Germany
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies) , Albert‐Einstein Str. 9 Jena Germany
- Center for Sepsis Control and Care Jena University Hospital, Am Klinikum 1, 07747 Jena Germany
- InfectoGnostics Research Campus Jena, Philosophenweg 7, 07743 Jena Germany
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5
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Abstract
Although the process of genome encapsidation is highly conserved in tailed bacteriophages and eukaryotic double-stranded DNA viruses, there are two distinct packaging pathways that these viruses use to catalyze ATP-driven translocation of the viral genome into a preassembled procapsid shell. One pathway is used by ϕ29-like phages and adenoviruses, which replicate and subsequently package a monomeric, unit-length genome covalently attached to a virus/phage-encoded protein at each 5'-end of the dsDNA genome. In a second, more ubiquitous packaging pathway characterized by phage lambda and the herpesviruses, the viral DNA is replicated as multigenome concatemers linked in a head-to-tail fashion. Genome packaging in these viruses thus requires excision of individual genomes from the concatemer that are then translocated into a preassembled procapsid. Hence, the ATPases that power packaging in these viruses also possess nuclease activities that cut the genome from the concatemer at the beginning and end of packaging. This review focuses on proposed mechanisms of genome packaging in the dsDNA viruses using unit-length ϕ29 and concatemeric λ genome packaging motors as representative model systems.
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Affiliation(s)
- Carlos E Catalano
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States.
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, TX, United States
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Wangchuk J, Chatterjee A, Patil S, Madugula SK, Kondabagil K. The coevolution of large and small terminases of bacteriophages is a result of purifying selection leading to phenotypic stabilization. Virology 2021; 564:13-25. [PMID: 34598064 DOI: 10.1016/j.virol.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Genome packaging in many dsDNA phages requires a series of precisely coordinated actions of two phage-coded proteins, namely, large terminase (TerL) and small terminase (TerS) with DNA and ATP, and with each other. Despite the strict functional conservation, TerL and TerS homologs exhibit large sequence variations. We investigated the sequence variability across eight phage types and observed a coevolutionary framework wherein the genealogy of TerL homologs mirrored that of the corresponding TerS homologs. Furthermore, a high purifying selection observed (dN/dS«1) indicated strong structural constraints on both TerL and TerS, and identify coevolving residues in TerL and TerS of phage T4 and lambda. Using the highly coevolving (correlation coefficient of 0.99) TerL and TerS of phage N4, we show that their biochemical features are similar to the phylogenetically divergent phage λ terminases. We also demonstrate using the Surface Plasma Resonance (SPR) technique that phage N4 TerL transiently interacts with TerS.
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Affiliation(s)
- Jigme Wangchuk
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Supriya Patil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Santhosh Kumar Madugula
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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7
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Mo Y, Fizari M, Koharchik K, Smith DE. Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers. Front Mol Biosci 2021; 8:605102. [PMID: 33829038 PMCID: PMC8019724 DOI: 10.3389/fmolb.2021.605102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25-45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.
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Affiliation(s)
| | | | | | - Douglas E. Smith
- Department of Physics, University of California San Diego, La Jolla, CA, United States
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8
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Mo Y, Keller N, delToro D, Ananthaswamy N, Harvey SC, Rao VB, Smith DE. Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence. Nucleic Acids Res 2021; 48:11602-11614. [PMID: 33119757 PMCID: PMC7672480 DOI: 10.1093/nar/gkaa875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/12/2020] [Accepted: 09/29/2020] [Indexed: 01/20/2023] Open
Abstract
Many viruses employ ATP-powered motors during assembly to translocate DNA into procapsid shells. Previous reports raise the question if motor function is modulated by substrate DNA sequence: (i) the phage T4 motor exhibits large translocation rate fluctuations and pauses and slips; (ii) evidence suggests that the phage phi29 motor contacts DNA bases during translocation; and (iii) one theoretical model, the ‘B-A scrunchworm’, predicts that ‘A-philic’ sequences that transition more easily to A-form would alter motor function. Here, we use single-molecule optical tweezers measurements to compare translocation of phage, plasmid, and synthetic A-philic, GC rich sequences by the T4 motor. We observed no significant differences in motor velocities, even with A-philic sequences predicted to show higher translocation rate at high applied force. We also observed no significant changes in motor pausing and only modest changes in slipping. To more generally test for sequence dependence, we conducted correlation analyses across pairs of packaging events. No significant correlations in packaging rate, pausing or slipping versus sequence position were detected across repeated measurements with several different DNA sequences. These studies suggest that viral genome packaging is insensitive to DNA sequence and fluctuations in packaging motor velocity, pausing and slipping are primarily stochastic temporal events.
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Affiliation(s)
- Youbin Mo
- 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
| | - Damian delToro
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neeti Ananthaswamy
- Department of Biology, The Catholic University of America, District of Columbia, 20064, USA
| | - Stephen C Harvey
- Department of Biochemistry and Biophysics, Univ. of Pennsylvania, Philadelphia, PA 19104, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, District of Columbia, 20064, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
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9
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Ortiz D, delToro D, Ordyan M, Pajak J, Sippy J, Catala A, Oh CS, Vu A, Arya G, Feiss M, Smith DE, Catalano CE. Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor. Nucleic Acids Res 2019; 47:1404-1415. [PMID: 30541105 PMCID: PMC6379665 DOI: 10.1093/nar/gky1217] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/09/2018] [Accepted: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
ASCE ATPases include ring-translocases such as cellular helicases and viral DNA packaging motors (terminases). These motors have conserved Walker A and B motifs that bind Mg2+-ATP and a catalytic carboxylate that activates water for hydrolysis. Here we demonstrate that Glu179 serves as the catalytic carboxylate in bacteriophage λ terminase and probe its mechanistic role. All changes of Glu179 are lethal: non-conservative changes abrogate ATP hydrolysis and DNA translocation, while the conservative E179D change attenuates ATP hydrolysis and alters single molecule translocation dynamics, consistent with a slowed chemical hydrolysis step. Molecular dynamics simulations of several homologous terminases suggest a novel mechanism, supported by experiments, wherein the conserved Walker A arginine ‘toggles’ between interacting with a glutamate residue in the ‘lid’ subdomain and the catalytic glutamate upon ATP binding; this switch helps mediate a transition from an ‘open’ state to a ‘closed’ state that tightly binds nucleotide and DNA, and also positions the catalytic glutamate next to the γ-phosphate to align the hydrolysis transition state. Concomitant reorientation of the lid subdomain may mediate mechanochemical coupling of ATP hydrolysis and DNA translocation. Given the strong conservation of these structural elements in terminase enzymes, this mechanism may be universal for viral packaging motors.
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Affiliation(s)
- David Ortiz
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Damian delToro
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam Ordyan
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Jean Sippy
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Alexis Catala
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Choon-Seok Oh
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Amber Vu
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Michael Feiss
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carlos E Catalano
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
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10
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Sharp KA, Lu XJ, Cingolani G, Harvey SC. DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging. Biophys J 2019; 116:2172-2180. [PMID: 31103227 DOI: 10.1016/j.bpj.2019.02.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/11/2019] [Accepted: 02/22/2019] [Indexed: 11/19/2022] Open
Abstract
Motors that move DNA, or that move along DNA, play essential roles in DNA replication, transcription, recombination, and chromosome segregation. The mechanisms by which these DNA translocases operate remain largely unknown. Some double-stranded DNA (dsDNA) viruses use an ATP-dependent motor to drive DNA into preformed capsids. These include several human pathogens as well as dsDNA bacteriophages-viruses that infect bacteria. We previously proposed that DNA is not a passive substrate of bacteriophage packaging motors but is instead an active component of the machinery. We carried out computational studies on dsDNA in the channels of viral portal proteins, and they reveal DNA conformational changes consistent with that hypothesis. dsDNA becomes longer ("stretched") in regions of high negative electrostatic potential and shorter ("scrunched") in regions of high positive potential. These results suggest a mechanism that electrostatically couples the energy released by ATP hydrolysis to DNA translocation: The chemical cycle of ATP binding, hydrolysis, and product release drives a cycle of protein conformational changes. This produces changes in the electrostatic potential in the channel through the portal, and these drive cyclic changes in the length of dsDNA as the phosphate groups respond to the protein's electrostatic potential. The DNA motions are captured by a coordinated protein-DNA grip-and-release cycle to produce DNA translocation. In short, the ATPase, portal, and dsDNA work synergistically to promote genome packaging.
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Affiliation(s)
- Kim A Sharp
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, New York
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Stephen C Harvey
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania.
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11
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Jardine PJ. Slow and steady wins the race: physical limits on the rate of viral DNA packaging. Curr Opin Virol 2019; 36:32-37. [PMID: 31003199 DOI: 10.1016/j.coviro.2019.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/19/2022]
Abstract
During the assembly of dsDNA viruses such as the tailed bacteriophages and herpesviruses, the viral chromosome is compacted to near crystalline density inside a preformed head shell. DNA translocation is driven by powerful ring ATPase motors that couple ATP binding, hydrolysis, and release to force generation and movement. Studies of the motor of the bacteriophage phi29 have revealed a complex mechanochemistry behind this process that slows as the head fills. Recent studies of the physical behavior of packaging DNA suggest that surprisingly long-time scales of relaxation of DNA inside the head and jamming phenomena during packaging create the physical need for regulation of the rate of packaging. Studies of DNA packaging in viral systems have, therefore, revealed fundamental insight into the complex behavior of DNA and the need for biological systems to accommodate these physical constraints.
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Affiliation(s)
- Paul J Jardine
- Department of Diagnostic and Biological Sciences, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN 55455, United States.
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12
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Ordyan M, Alam I, Mahalingam M, Rao VB, Smith DE. Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor. Nat Commun 2018; 9:5434. [PMID: 30575768 PMCID: PMC6303390 DOI: 10.1038/s41467-018-07834-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/23/2018] [Indexed: 11/24/2022] Open
Abstract
ATP-powered viral packaging motors are among the most powerful biomotors known. Motor subunits arranged in a ring repeatedly grip and translocate the DNA to package viral genomes into capsids. Here, we use single DNA manipulation and rapid solution exchange to quantify how nucleotide binding regulates interactions between the bacteriophage T4 motor and DNA substrate. With no nucleotides, there is virtually no gripping and rapid slipping occurs with only minimal friction resisting. In contrast, binding of an ATP analog engages nearly continuous gripping. Occasional slips occur due to dissociation of the analog from a gripping motor subunit, or force-induced rupture of grip, but multiple other analog-bound subunits exert high friction that limits slipping. ADP induces comparably infrequent gripping and variable friction. Independent of nucleotides, slipping arrests when the end of the DNA is about to exit the capsid. This end-clamp mechanism increases the efficiency of packaging by making it essentially irreversible. Packaging of viral DNA depends on strong molecular motors that are powered by ATP hydrolysis. Here, the authors develop a single-molecule assay to monitor how nucleotide binding regulates motor-DNA interactions and reveal a generic mechanism that prevents exit of the whole DNA from the viral capsid during packaging.
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Affiliation(s)
- Mariam Ordyan
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, Mail Code 0379, La Jolla, CA, 92093-0379, USA
| | - Istiaq Alam
- Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064, USA
| | - Marthandan Mahalingam
- Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064, USA.
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, Mail Code 0379, La Jolla, CA, 92093-0379, USA.
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13
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Mustafa G, Chuang CY, Roy WA, Farhath MM, Pokhrel N, Ma Y, Nagasawa K, Antony E, Comstock MJ, Basu S, Balci H. A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. Biosens Bioelectron 2018; 121:34-40. [PMID: 30195120 DOI: 10.1016/j.bios.2018.08.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 01/27/2023]
Abstract
A force sensor concept is presented where fluorescence signal is converted into force information via single-molecule Förster resonance energy transfer (smFRET). The basic design of the sensor is a ~100 base pair (bp) long double stranded DNA (dsDNA) that is restricted to a looped conformation by a nucleic acid secondary structure (NAS) that bridges its ends. The looped dsDNA generates a tension across the NAS and unfolds it when the tension is high enough. The FRET efficiency between donor and acceptor (D&A) fluorophores placed across the NAS reports on its folding state. Three dsDNA constructs with different lengths were bridged by a DNA hairpin and KCl was titrated to change the applied force. After these proof-of-principle measurements, one of the dsDNA constructs was used to maintain the G-quadruplex (GQ) construct formed by thrombin binding aptamer (TBA) under tension while it interacted with a destabilizing protein and stabilizing small molecule. The force required to unfold TBA-GQ was independently investigated with high-resolution optical tweezers (OT) measurements that established the relevant force to be a few pN, which is consistent with the force generated by the looped dsDNA. The proposed method is particularly promising as it enables studying NAS, protein, and small molecule interactions using a highly-parallel FRET-based assay while the NAS is kept under an approximately constant force.
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Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Cho-Ying Chuang
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - William A Roy
- Department of Physics, Kent State University, Kent, OH 44242, United States
| | - Mohamed M Farhath
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, United States
| | - Matthew J Comstock
- Department of Physics, Michigan State University, East Lansing, MI 48824, United States
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, United States.
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14
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Abstract
Many icosahedral viruses use a specialized portal vertex for genome encapsidation in the viral capsid (or head). This structure then controls release of the viral genetic information to the host cell at the beginning of infection. In tailed bacteriophages, the portal system is connected to a tail device that delivers their genome to the bacterial cytoplasm. The head-to-tail interface is a multiprotein complex that locks the viral DNA inside the phage capsid correctly positioned for egress and that controls its ejection when the viral particle interacts with the host cell receptor. Here we review the molecular mechanisms how this interface is assembled and how it carries out those two critical steps in the life cycle of tailed phages.
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Affiliation(s)
- Paulo Tavares
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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15
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Keller N, delToro DJ, Smith DE. Single-Molecule Measurements of Motor-Driven Viral DNA Packaging in Bacteriophages Phi29, Lambda, and T4 with Optical Tweezers. Methods Mol Biol 2018; 1805:393-422. [PMID: 29971729 DOI: 10.1007/978-1-4939-8556-2_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Viral DNA packaging is a required step in the assembly of many dsDNA viruses. A molecular motor fueled by ATP hydrolysis packages the viral genome to near crystalline density inside a preformed prohead shell in ~5 min at room temperature. We describe procedures for measuring the packaging of single DNA molecules into single viral proheads with optical tweezers. Three viral packaging systems are described in detail: bacteriophages phi29 (φ29), lambda (λ), and T4. Two different approaches are described: (1) With φ29 and T4, prohead-motor complexes can be preassembled in bulk and packaging can be initiated in the optical tweezers by "feeding" a single DNA molecule to one of the complexes; (2) With φ29 and λ, packaging can be initiated in bulk then stalled, and a single prohead-motor-DNA complex can then be captured with optical tweezers and restarted. In both cases, the prohead is ultimately attached to one trapped microsphere and the end of the DNA being packaged is attached to a second trapped microsphere such that packaging of the DNA pulls the two microspheres together and the rate of packaging and force generated by the motor is directly measured in real time. These protocols allow for the effect of many experimental parameters on packaging dynamics to be studied such as temperature, ATP concentration, ionic conditions, structural changes to the DNA substrate, and mutations in the motor proteins. Procedures for capturing microspheres with the optical traps and different measurement modes are also described.
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Affiliation(s)
- Nicholas Keller
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Damian J delToro
- Department of Physics, University of California San Diego, La Jolla, CA, USA
| | - Douglas E Smith
- Department of Physics, University of California San Diego, La Jolla, CA, USA.
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16
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Serwer P, Wright ET, Demeler B, Jiang W. States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM. Biophys Rev 2017; 10:583-596. [PMID: 29243090 DOI: 10.1007/s12551-017-0372-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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17
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Lin S, Alam TI, Kottadiel VI, VanGessel CJ, Tang WC, Chemla YR, Rao VB. Altering the speed of a DNA packaging motor from bacteriophage T4. Nucleic Acids Res 2017; 45:11437-11448. [PMID: 28981683 PMCID: PMC5737356 DOI: 10.1093/nar/gkx809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The speed at which a molecular motor operates is critically important for the survival of a virus or an organism but very little is known about the underlying mechanisms. Tailed bacteriophage T4 employs one of the fastest and most powerful packaging motors, a pentamer of gp17 that translocates DNA at a rate of up to ∼2000-bp/s. We hypothesize, guided by structural and genetic analyses, that a unique hydrophobic environment in the catalytic space of gp17-adenosine triphosphatase (ATPase) determines the rate at which the 'lytic water' molecule is activated and OH- nucleophile is generated, in turn determining the speed of the motor. We tested this hypothesis by identifying two hydrophobic amino acids, M195 and F259, in the catalytic space of gp17-ATPase that are in a position to modulate motor speed. Combinatorial mutagenesis demonstrated that hydrophobic substitutions were tolerated but polar or charged substitutions resulted in null or cold-sensitive/small-plaque phenotypes. Quantitative biochemical and single-molecule analyses showed that the mutant motors exhibited 1.8- to 2.5-fold lower rate of ATP hydrolysis, 2.5- to 4.5-fold lower DNA packaging velocity, and required an activator protein, gp16 for rapid firing of ATPases. These studies uncover a speed control mechanism that might allow selection of motors with optimal performance for organisms' survival.
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Affiliation(s)
- Siying Lin
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Tanfis I Alam
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Vishal I Kottadiel
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Carl J VanGessel
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Wei-Chun Tang
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Yann R Chemla
- Department of Physics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
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18
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A DNA-centered explanation of the DNA polymerase translocation mechanism. Sci Rep 2017; 7:7566. [PMID: 28790383 PMCID: PMC5548866 DOI: 10.1038/s41598-017-08038-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022] Open
Abstract
DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle. Here, we propose a translocation mechanism that points to the flexibility of the DNA, including its overstretching transition, as the principal responsible for the DNA polymerase ratcheting motion. By using thermodynamic analyses, we then find that an external load hardly affects the fidelity of the copying process and, consequently, that translocation and fidelity maintenance are loosely coupled processes. The proposed translocation mechanism is compatible with single-molecule experiments, structural data and stereochemical details of the DNA-protein complex that is formed during replication, and may be extended to RNA transcription.
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19
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Sysoeva TA. Assessing heterogeneity in oligomeric AAA+ machines. Cell Mol Life Sci 2017; 74:1001-1018. [PMID: 27669691 PMCID: PMC11107579 DOI: 10.1007/s00018-016-2374-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.
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Affiliation(s)
- Tatyana A Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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20
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Hanhijärvi KJ, Ziedaite G, Bamford DH, Hæggström E, Poranen MM. Single-molecule measurements of viral ssRNA packaging. RNA (NEW YORK, N.Y.) 2017; 23:119-129. [PMID: 27803153 PMCID: PMC5159644 DOI: 10.1261/rna.057471.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Genome packaging of double-stranded RNA (dsRNA) phages has been widely studied using biochemical and molecular biology methods. We adapted the existing in vitro packaging system of one such phage for single-molecule experimentation. To our knowledge, this is the first attempt to study the details of viral RNA packaging using optical tweezers. Pseudomonas phage φ6 is a dsRNA virus with a tripartite genome. Positive-sense (+) single-stranded RNA (ssRNA) genome precursors are packaged into a preformed procapsid (PC), where negative strands are synthesized. We present single-molecule measurements of the viral ssRNA packaging by the φ6 PC. Our data show that packaging proceeds intermittently in slow and fast phases, which likely reflects differences in the unfolding of the RNA secondary structures of the ssRNA being packaged. Although the mean packaging velocity was relatively low (0.07-0.54 nm/sec), packaging could reach 4.62 nm/sec during the fast packaging phase.
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Affiliation(s)
| | - Gabija Ziedaite
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Edward Hæggström
- Department of Physics, University of Helsinki, Helsinki 00014, Finland
| | - Minna M Poranen
- Department of Biosciences, University of Helsinki, Helsinki 00014, Finland
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21
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Keller N, Grimes S, Jardine PJ, Smith DE. Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging. NATURE PHYSICS 2016; 12:757-761. [PMID: 27540410 PMCID: PMC4982518 DOI: 10.1038/nphys3740] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/23/2016] [Indexed: 05/26/2023]
Abstract
In many viruses molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50-100 nm prohead shells1, 2. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions3. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems4-8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles5 we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.9, 10.
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Affiliation(s)
- Nicholas Keller
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0379
| | - Shelley Grimes
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455
| | - Paul J. Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455
| | - Douglas E. Smith
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0379
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22
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Waters JT, Kim HD, Gumbart JC, Lu XJ, Harvey SC. DNA Scrunching in the Packaging of Viral Genomes. J Phys Chem B 2016; 120:6200-7. [PMID: 27214211 DOI: 10.1021/acs.jpcb.6b02149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The motors that drive double-stranded DNA (dsDNA) genomes into viral capsids are among the strongest of all biological motors for which forces have been measured, but it is not known how they generate force. We previously proposed that the DNA is not a passive substrate but that it plays an active role in force generation. This "scrunchworm hypothesis" holds that the motor proteins repeatedly dehydrate and rehydrate the DNA, which then undergoes cyclic shortening and lengthening motions. These are captured by a coupled protein-DNA grip-and-release cycle to rectify the motion and translocate the DNA into the capsid. In this study, we examined the interactions of dsDNA with the dodecameric connector protein of bacteriophage ϕ29, using molecular dynamics simulations on four different DNA sequences, starting from two different conformations (A-DNA and B-DNA). In all four simulations starting with the protein equilibrated with A-DNA in the channel, we observed transitions to a common, metastable, highly scrunched conformation, designated A*. This conformation is very similar to one recently reported by Kumar and Grubmüller in much longer MD simulations on B-DNA docked into the ϕ29 connector. These results are significant for four reasons. First, the scrunched conformations occur spontaneously, without requiring lever-like protein motions often believed to be necessary for DNA translocation. Second, the transition takes place within the connector, providing the location of the putative "dehydrator". Third, the protein has more contacts with one strand of the DNA than with the other; the former was identified in single-molecule laser tweezer experiments as the "load-bearing strand". Finally, the spontaneity of the DNA-protein interaction suggests that it may play a role in the initial docking of DNA in motors like that of T4 that can load and package any sequence.
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Affiliation(s)
- James T Waters
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Stephen C Harvey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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23
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Gao S, Zhang L, Rao VB. Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4. Nucleic Acids Res 2016; 44:4425-39. [PMID: 26984529 PMCID: PMC4872099 DOI: 10.1093/nar/gkw184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022] Open
Abstract
Tailed bacteriophages and herpes viruses use powerful molecular machines to package their genomes. The packaging machine consists of three components: portal, motor (large terminase; TerL) and regulator (small terminase; TerS). Portal, a dodecamer, and motor, a pentamer, form two concentric rings at the special five-fold vertex of the icosahedral capsid. Powered by ATPase, the motor ratchets DNA into the capsid through the portal channel. TerS is essential for packaging, particularly for genome recognition, but its mechanism is unknown and controversial. Structures of gear-shaped TerS rings inspired models that invoke DNA threading through the central channel. Here, we report that mutations of basic residues that line phage T4 TerS (gp16) channel do not disrupt DNA binding. Even deletion of the entire channel helix retained DNA binding and produced progeny phage in vivo. On the other hand, large oligomers of TerS (11-mers/12-mers), but not small oligomers (trimers to hexamers), bind DNA. These results suggest that TerS oligomerization creates a large outer surface, which, but not the interior of the channel, is critical for function, probably to wrap viral genome around the ring during packaging initiation. Hence, models involving TerS-mediated DNA threading may be excluded as an essential mechanism for viral genome packaging.
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Affiliation(s)
- Song Gao
- Department of Biology, The Catholic University of America, 620 Michigan Avenue Northeast, Washington, DC 20064, USA Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang 222005, China
| | - Liang Zhang
- Department of Biology, The Catholic University of America, 620 Michigan Avenue Northeast, Washington, DC 20064, USA
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, 620 Michigan Avenue Northeast, Washington, DC 20064, USA
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24
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Abstract
Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and translocase activities. TerL, following endonucleolytic cleavage of immature viral DNA concatemer recognized by TerS, assembles into a pentameric ring motor on the prohead's portal vertex and uses ATP hydrolysis energy for DNA translocation. TerL's N-terminal ATPase is connected by a hinge to the C-terminal endonuclease. Inchworm models propose that modest domain motions accompanying ATP hydrolysis are amplified, through changes in electrostatic interactions, into larger movements of the C-terminal domain bound to DNA. In phage ϕ29, four of the five TerL subunits sequentially hydrolyze ATP, each powering translocation of 2.5 bp. After one viral genome is encapsidated, the internal pressure signals termination of packaging and ejection of the motor. Current focus is on the structures of packaging complexes and the dynamics of TerL during DNA packaging, endonuclease regulation, and motor mechanics.
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Affiliation(s)
- Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC 20064;
| | - Michael Feiss
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242;
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25
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Walder R, Paik DH, Bull MS, Sauer C, Perkins TT. Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature. OPTICS EXPRESS 2015; 23:16554-16564. [PMID: 26191667 DOI: 10.1364/oe.23.016554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Advanced optical traps can probe single molecules with Ångstrom-scale precision, but drift limits the utility of these instruments. To achieve Å-scale stability, a differential measurement scheme between a pair of laser foci was introduced that substantially exceeds the inherent mechanical stability of various types of microscopes at room temperature. By using lock-in detection to measure both lasers with a single quadrant photodiode, we enhanced the differential stability of this optical reference frame and thereby stabilized an optical-trapping microscope to 0.2 Å laterally over 100 s based on the Allan deviation. In three dimensions, we achieved stabilities of 1 Å over 1,000 s and 1 nm over 15 h. This stability was complemented by high measurement bandwidth (100 kHz). Overall, our compact back-scattered detection enables an ultrastable measurement platform compatible with optical traps, atomic force microscopy, and optical microscopy, including super-resolution techniques.
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26
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Affiliation(s)
- Yann R Chemla
- Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
| | - Taekjip Ha
- Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA. Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
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27
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Harvey SC. The scrunchworm hypothesis: transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages. J Struct Biol 2014; 189:1-8. [PMID: 25486612 DOI: 10.1016/j.jsb.2014.11.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/14/2014] [Accepted: 11/30/2014] [Indexed: 11/17/2022]
Abstract
Double-stranded DNA bacteriophages have motors that drive the genome into preformed capsids, using the energy released by hydrolysis of ATP to overcome the forces opposing DNA packaging. Viral packaging motors are the strongest of all biological motors, but it is not known how they generate these forces. Several models for the process of mechanochemical force generation have been put forward, but there is no consensus on which, if any, of these is correct. All the existing models assume that protein-generated forces drive the DNA forward. The scrunchworm hypothesis proposes that the DNA molecule is the active force-generating core of the motor, not simply a substrate on which the motor operates. The protein components of the motor dehydrate a section of the DNA, converting it from the B form to the A form and shortening it by about 23%. The proteins then rehydrate the DNA, which converts back to the B form. Other regions of the motor grip and release the DNA to capture the shortening-lengthening motions of the B→A→B cycle ("scrunching"), so that DNA is pulled into the motor and pushed forward into the capsid. This DNA-centric mechanism provides a quantitative physical explanation for the magnitude of the forces generated by viral packaging motors. It also provides a simple explanation for the fact that each of the steps in the burst cycle advances the DNA by 2.5 base pairs. The scrunchworm hypothesis is consistent with a large body of published data, and it makes four experimentally testable predictions.
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Affiliation(s)
- Stephen C Harvey
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.
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28
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Abstract
The DNA packaging motors of double-stranded DNA phages are models for analysis of all multi-molecular motors and for analysis of several fundamental aspects of biology, including early evolution, relationship of in vivo to in vitro biochemistry and targets for anti-virals. Work on phage DNA packaging motors both has produced and is producing dualities in the interpretation of data obtained by use of both traditional techniques and the more recently developed procedures of single-molecule analysis. The dualities include (1) reductive vs. accretive evolution, (2) rotation vs. stasis of sub-assemblies of the motor, (3) thermal ratcheting vs. power stroking in generating force, (4) complete motor vs. spark plug role for the packaging ATPase, (5) use of previously isolated vs. new intermediates for analysis of the intermediate states of the motor and (6) a motor with one cycle vs. a motor with two cycles. We provide background for these dualities, some of which are under-emphasized in the literature. We suggest directions for future research.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry; The University of Texas Health Science Center; San Antonio, TX USA
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29
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Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4. Proc Natl Acad Sci U S A 2014; 111:15096-101. [PMID: 25288726 DOI: 10.1073/pnas.1407235111] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viral DNA packaging motors are among the most powerful molecular motors known. A variety of structural, biochemical, and single-molecule biophysical approaches have been used to understand their mechanochemistry. However, packaging initiation has been difficult to analyze because of its transient and highly dynamic nature. Here, we developed a single-molecule fluorescence assay that allowed visualization of packaging initiation and reinitiation in real time and quantification of motor assembly and initiation kinetics. We observed that a single bacteriophage T4 packaging machine can package multiple DNA molecules in bursts of activity separated by long pauses, suggesting that it switches between active and quiescent states. Multiple initiation pathways were discovered including, unexpectedly, direct DNA binding to the capsid portal followed by recruitment of motor subunits. Rapid succession of ATP hydrolysis was essential for efficient initiation. These observations have implications for the evolution of icosahedral viruses and regulation of virus assembly.
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30
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Keller N, delToro D, Grimes S, Jardine PJ, Smith DE. Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29. PHYSICAL REVIEW LETTERS 2014; 112:248101. [PMID: 24996111 PMCID: PMC5001848 DOI: 10.1103/physrevlett.112.248101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 05/12/2023]
Abstract
We use optical tweezers to study the effect of attractive versus repulsive DNA-DNA interactions on motor-driven viral packaging. Screening of repulsive interactions accelerates packaging, but induction of attractive interactions by spermidine(3+) causes heterogeneous dynamics. Acceleration is observed in a fraction of complexes, but most exhibit slowing and stalling, suggesting that attractive interactions promote nonequilibrium DNA conformations that impede the motor. Thus, repulsive interactions facilitate packaging despite increasing the energy of the theoretical optimum spooled DNA conformation.
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Affiliation(s)
- Nicholas Keller
- Department of Physics, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093, USA
| | - Damian delToro
- Department of Physics, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093, USA
| | - Shelley Grimes
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, 515 Delaware Street SE, Minneapolis, Minnesota 55455, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota, 515 Delaware Street SE, Minneapolis, Minnesota 55455, USA
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, 9500 Gilman Dr., La Jolla, California 92093, USA
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Migliori AD, Keller N, Alam TI, Mahalingam M, Rao VB, Arya G, Smith DE. Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor. Nat Commun 2014; 5:4173. [PMID: 24937091 PMCID: PMC4157569 DOI: 10.1038/ncomms5173] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 05/20/2014] [Indexed: 11/09/2022] Open
Abstract
How viral packaging motors generate enormous forces to translocate DNA into viral capsids remains unknown. Recent structural studies of the bacteriophage T4 packaging motor have led to a proposed mechanism wherein the gp17 motor protein translocates DNA by transitioning between extended and compact states, orchestrated by electrostatic interactions between complimentarily charged residues across the interface between the N- and C-terminal subdomains. Here we show that site-directed alterations in these residues cause force dependent impairments of motor function including lower translocation velocity, lower stall force and higher frequency of pauses and slips. We further show that the measured impairments correlate with computed changes in free-energy differences between the two states. These findings support the proposed structural mechanism and further suggest an energy landscape model of motor activity that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle.
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Affiliation(s)
- Amy D. Migliori
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0379
| | - Nicholas Keller
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0379
| | - Tanfis I. Alam
- Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064
| | - Marthandan Mahalingam
- Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064
| | - Venigalla B. Rao
- Department of Biology, The Catholic University of America, 620 Michigan Ave. NE, Washington, DC, 20064
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Douglas E Smith
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0379
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Affiliation(s)
- Thomas T. Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309;
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309
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Abstract
A virus is a complex molecular machine that propagates by channeling its genetic information from cell to cell. Unlike macroscopic engines, it operates in a nanoscopic world under continuous thermal agitation. Viruses have developed efficient passive and active strategies to pack and release nucleic acids. Some aspects of the dynamic behavior of viruses and their substrates can be studied using structural and biochemical techniques. Recently, physical techniques have been applied to dynamic studies of viruses in which their intrinsic mechanical activity can be measured directly. Optical tweezers are a technology that can be used to measure the force, torque and strain produced by molecular motors, as a function of time and at the single-molecule level. Thanks to this technique, some bacteriophages are now known to be powerful nanomachines; they exert force in the piconewton range and their motors work in a highly coordinated fashion for packaging the viral nucleic acid genome. Nucleic acids, whose elasticity and condensation behavior are inherently coupled to the viral packaging mechanisms, are also amenable to examination with optical tweezers. In this chapter, we provide a comprehensive analysis of this laser-based tool, its combination with imaging methods and its application to the study of viruses and viral molecules.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), c/Faraday 9, Campus de Cantoblanco, 28049, Madrid, Spain,
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Abstract
Viruses protect their genetic information by enclosing the viral nucleic acid inside a protein shell (capsid), in a process known as genome packaging. Viruses follow essentially two main strategies to package their genome: Either they co-assemble their genetic material together with the capsid protein, or they assemble first an empty shell (procapsid) and then pump the genome inside the capsid with a molecular motor that uses the energy released by ATP hydrolysis. During packaging the viral nucleic acid is condensed to very high concentration by its careful arrangement in concentric layers inside the capsid. In this chapter we will first give an overview of the different strategies used for genome packaging to discuss later some specific virus models where the structures of the main proteins involved, and the biophysics underlying the packaging mechanism, have been well documented.
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Affiliation(s)
- Ana Cuervo
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CSIC), c/Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
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Mateu MG. Assembly, stability and dynamics of virus capsids. Arch Biochem Biophys 2012; 531:65-79. [PMID: 23142681 DOI: 10.1016/j.abb.2012.10.015] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/18/2012] [Accepted: 10/28/2012] [Indexed: 12/13/2022]
Abstract
Most viruses use a hollow protein shell, the capsid, to enclose the viral genome. Virus capsids are large, symmetric oligomers made of many copies of one or a few types of protein subunits. Self-assembly of a viral capsid is a complex oligomerization process that proceeds along a pathway regulated by ordered interactions between the participating protein subunits, and that involves a series of (usually transient) assembly intermediates. Assembly of many virus capsids requires the assistance of scaffolding proteins or the viral nucleic acid, which interact with the capsid subunits to promote and direct the process. Once assembled, many capsids undergo a maturation reaction that involves covalent modification and/or conformational rearrangements, which may increase the stability of the particle. The final, mature capsid is a relatively robust protein complex able to protect the viral genome from physicochemical aggressions; however, it is also a metastable, dynamic structure poised to undergo controlled conformational transitions required to perform biologically critical functions during virus entry into cells, intracellular trafficking, and viral genome uncoating. This article provides an updated general overview on structural, biophysical and biochemical aspects of the assembly, stability and dynamics of virus capsids.
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Affiliation(s)
- Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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