1
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Hawkins DEDP, Godwin OC, Antson AA. Viral Genomic DNA Packaging Machinery. Subcell Biochem 2024; 104:181-205. [PMID: 38963488 DOI: 10.1007/978-3-031-58843-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Tailed double-stranded DNA bacteriophage employs a protein terminase motor to package their genome into a preformed protein shell-a system shared with eukaryotic dsDNA viruses such as herpesviruses. DNA packaging motor proteins represent excellent targets for antiviral therapy, with Letermovir, which binds Cytomegalovirus terminase, already licensed as an effective prophylaxis. In the realm of bacterial viruses, these DNA packaging motors comprise three protein constituents: the portal protein, small terminase and large terminase. The portal protein guards the passage of DNA into the preformed protein shell and acts as a protein interaction hub throughout viral assembly. Small terminase recognises the viral DNA and recruits large terminase, which in turn pumps DNA in an ATP-dependent manner. Large terminase also cleaves DNA at the termination of packaging. Multiple high-resolution structures of each component have been resolved for different phages, but it is only more recently that the field has moved towards cryo-EM reconstructions of protein complexes. In conjunction with highly informative single-particle studies of packaging kinetics, these structures have begun to inspire models for the packaging process and its place among other DNA machines.
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Affiliation(s)
- Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Owen C Godwin
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Structural Biology, The Francis Crick Institute, London, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
- Structural Biology, The Francis Crick Institute, London, UK.
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2
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Kiss B, Kellermayer M. Packing up the genome. eLife 2023; 12:e94128. [PMID: 38095555 PMCID: PMC10721213 DOI: 10.7554/elife.94128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Nucleotide and force-dependent mechanisms control how the viral genome of lambda bacteriophage is inserted into capsids.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis UniversityBudapestHungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis UniversityBudapestHungary
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3
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Hawkins DEDP, Bayfield O, Fung HKH, Grba DN, Huet A, Conway J, Antson AA. Insights into a viral motor: the structure of the HK97 packaging termination assembly. Nucleic Acids Res 2023; 51:7025-7035. [PMID: 37293963 PMCID: PMC10359639 DOI: 10.1093/nar/gkad480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023] Open
Abstract
Double-stranded DNA viruses utilise machinery, made of terminase proteins, to package viral DNA into the capsid. For cos bacteriophage, a defined signal, recognised by small terminase, flanks each genome unit. Here we present the first structural data for a cos virus DNA packaging motor, assembled from the bacteriophage HK97 terminase proteins, procapsids encompassing the portal protein, and DNA containing a cos site. The cryo-EM structure is consistent with the packaging termination state adopted after DNA cleavage, with DNA density within the large terminase assembly ending abruptly at the portal protein entrance. Retention of the large terminase complex after cleavage of the short DNA substrate suggests that motor dissociation from the capsid requires headful pressure, in common with pac viruses. Interestingly, the clip domain of the 12-subunit portal protein does not adhere to C12 symmetry, indicating asymmetry induced by binding of the large terminase/DNA. The motor assembly is also highly asymmetric, showing a ring of 5 large terminase monomers, tilted against the portal. Variable degrees of extension between N- and C-terminal domains of individual subunits suggest a mechanism of DNA translocation driven by inter-domain contraction and relaxation.
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Affiliation(s)
- Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117Heidelberg, Germany
| | - Daniel N Grba
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Alexis Huet
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - James F Conway
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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4
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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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5
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Ji C, Yu C, Song M, Pei H, Fu P, Lin Y, Wang J. Construction of Molecular Transporter Based on DNA Structure Regulation. ACS APPLIED BIO MATERIALS 2022; 5:2122-2129. [PMID: 35481744 DOI: 10.1021/acsabm.2c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study aims to build a molecular transporter machine that is based on the microstructure regulation of DNA triplets, which can automatically search, load, target delivery, and unload target protein molecules. The design of the molecular transporter includes: (1) a DNA triplet, which can recognize and load of the target protein; (2) a similar DNA triplet realizing the target transport; and (3) the signal-indicating DNA, which is connected at the target destination to achieve fixation of the target protein at the target destination. The molecular transporter machine would provide research practice and theoretical guidance for the development of DNA-based molecular machines.
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Affiliation(s)
- Chengdong Ji
- Zybio Inc, Chongqing, 400082, China.,Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | - Min Song
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | | | | | - Jing Wang
- Zybio Inc, Chongqing, 400082, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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6
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Tong AB, Bustamante C. Helical inchworming: a novel translocation mechanism for a ring ATPase. Biophys Rev 2022; 13:885-888. [PMID: 35047087 PMCID: PMC8724481 DOI: 10.1007/s12551-021-00883-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 01/29/2023] Open
Abstract
Ring ATPases perform a variety of tasks in the cell. Their function involves complex communication and coordination among the often identical subunits. Translocases in this group are of particular interest as they involve both chemical and mechanical actions in their operation. We study the DNA packaging motor of bacteriophage φ29, and using single-molecule optical tweezers and single-particle cryo-electron microscopy, have discovered a novel translocation mechanism for a molecular motor.
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Affiliation(s)
- Alexander B Tong
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA USA.,Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA USA.,Chemistry Graduate Group, University of California, Berkeley, Berkeley, CA USA
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA USA.,Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA USA.,Chemistry Graduate Group, University of California, Berkeley, Berkeley, CA USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA USA.,Department of Physics, University of California, Berkeley, Berkeley, CA USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA USA.,Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA USA
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7
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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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8
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A viral genome packaging ring-ATPase is a flexibly coordinated pentamer. Nat Commun 2021; 12:6548. [PMID: 34772936 PMCID: PMC8589836 DOI: 10.1038/s41467-021-26800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023] Open
Abstract
Multi-subunit ring-ATPases carry out a myriad of biological functions, including genome packaging in viruses. Though the basic structures and functions of these motors have been well-established, the mechanisms of ATPase firing and motor coordination are poorly understood. Here, using single-molecule fluorescence, we determine that the active bacteriophage T4 DNA packaging motor consists of five subunits of gp17. By systematically doping motors with an ATPase-defective subunit and selecting single motors containing a precise number of active or inactive subunits, we find that the packaging motor can tolerate an inactive subunit. However, motors containing one or more inactive subunits exhibit fewer DNA engagements, a higher failure rate in encapsidation, reduced packaging velocity, and increased pausing. These findings suggest a DNA packaging model in which the motor, by re-adjusting its grip on DNA, can skip an inactive subunit and resume DNA translocation, suggesting that strict coordination amongst motor subunits of packaging motors is not crucial for function.
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9
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A DNA packaging motor inchworms along one strand allowing it to adapt to alternative double-helical structures. Nat Commun 2021; 12:3439. [PMID: 34103515 PMCID: PMC8187434 DOI: 10.1038/s41467-021-23725-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/22/2021] [Indexed: 01/29/2023] Open
Abstract
Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism. Here, we investigate the operation of ring motors that transport ordered, helical substrates, such as the bacteriophage ϕ29 dsDNA packaging motor. This pentameric motor alternates between an ATP loading dwell and a hydrolysis burst wherein it packages one turn of DNA in four steps. When challenged with DNA-RNA hybrids and dsRNA, the motor matches its burst to the shorter helical pitches, keeping three power strokes invariant while shortening the fourth. Intermittently, the motor loses grip on the RNA-containing substrates, indicating that it makes optimal load-bearing contacts with dsDNA. To rationalize these observations, we propose a helical inchworm translocation mechanism in which, during each cycle, the motor increasingly adopts a lock-washer structure during the ATP loading dwell and successively regains its planar form with each power stroke during the burst. Ring ATPase translocases that operate on disordered substrates adopt lockwasher architectures and use a hand-over-hand mechanism. By challenging the dsDNA packaging motor of bacteriophage ϕ29 with hybrid and dsRNA, the authors propose that the motor cycles between planar and lock-washer structures.
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10
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Pajak J, Atz R, Hilbert BJ, Morais MC, Kelch BA, Jardine PJ, Arya G. Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation. Proc Natl Acad Sci U S A 2021; 118:e2024928118. [PMID: 33888587 PMCID: PMC8092589 DOI: 10.1073/pnas.2024928118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors.
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Affiliation(s)
- Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708
| | - Rockney Atz
- Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455
| | - Brendan J Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708;
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11
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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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12
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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13
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Cruz B, Zhu Z, Calderer C, Arsuaga J, Vazquez M. Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor. Biophys J 2020; 118:2103-2116. [PMID: 32353255 PMCID: PMC7203069 DOI: 10.1016/j.bpj.2020.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/04/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.
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Affiliation(s)
- Brian Cruz
- Department of Mathematics, University of California, Berkeley, California
| | - Zihao Zhu
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California
| | - Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California at Davis, Davis, California; Department of Molecular and Cellular Biology, University of California at Davis, Davis, California.
| | - Mariel Vazquez
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California; Department of Mathematics, University of California at Davis, Davis, California.
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14
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Bayfield OW, Steven AC, Antson AA. Cryo-EM structure in situ reveals a molecular switch that safeguards virus against genome loss. eLife 2020; 9:e55517. [PMID: 32286226 PMCID: PMC7234808 DOI: 10.7554/elife.55517] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/13/2020] [Indexed: 01/01/2023] Open
Abstract
The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid, and how these processes are controlled. A cryo-EM structure of the portal protein of thermostable virus P23-45, determined in situ in its procapsid-bound state, indicates a mechanism that naturally safeguards the virus against genome loss. This occurs via an inversion of the conformation of the loops that define the constriction in the central tunnel, accompanied by a hydrophilic-hydrophobic switch. The structure also shows how translocation of DNA into the capsid could be modulated by a changing mode of protein-protein interactions between portal and capsid, across a symmetry-mismatched interface.
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Affiliation(s)
- Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of YorkYorkUnited Kingdom
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of HealthBethesdaUnited States
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of HealthBethesdaUnited States
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of YorkYorkUnited Kingdom
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15
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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16
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Dedeo CL, Cingolani G, Teschke CM. Portal Protein: The Orchestrator of Capsid Assembly for the dsDNA Tailed Bacteriophages and Herpesviruses. Annu Rev Virol 2019; 6:141-160. [PMID: 31337287 PMCID: PMC6947915 DOI: 10.1146/annurev-virology-092818-015819] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tailed, double-stranded DNA bacteriophages provide a well-characterized model system for the study of viral assembly, especially for herpesviruses and adenoviruses. A wealth of genetic, structural, and biochemical work has allowed for the development of assembly models and an understanding of the DNA packaging process. The portal complex is an essential player in all aspects of bacteriophage and herpesvirus assembly. Despite having low sequence similarity, portal structures across bacteriophages share the portal fold and maintain a conserved function. Due to their dynamic role, portal proteins are surprisingly plastic, and their conformations change for each stage of assembly. Because the maturation process is dependent on the portal protein, researchers have been working to validate this protein as a potential antiviral drug target. Here we review recent work on the role of portal complexes in capsid assembly, including DNA packaging, as well as portal ring assembly and incorporation and analysis of portal structures.
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Affiliation(s)
- Corynne L Dedeo
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA;
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA;
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA
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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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