1
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Hou CFD, Li F, Iglesias S, Cingolani G. Use of Localized Reconstruction to Visualize the Shigella Phage Sf6 Tail Apparatus. Methods Mol Biol 2024; 2738:215-228. [PMID: 37966602 PMCID: PMC10655839 DOI: 10.1007/978-1-0716-3549-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) single-particle analysis has revolutionized the structural analysis of icosahedral viruses, including tailed bacteriophages. In recent years, localized (or focused) reconstruction has emerged as a powerful data analysis method to capture symmetry mismatches and resolve asymmetric features in icosahedral viruses. Here, we describe the methods used to reconstruct the 2.65-MDa tail apparatus of the Shigella phage Sf6, a representative member of the Podoviridae superfamily.
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Affiliation(s)
- Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Stephano Iglesias
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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2
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Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Bohmer M, Bhullar AS, Weitao T, Zhang L, Lee JH, Guo P. Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand. iScience 2023; 26:106922. [PMID: 37305704 PMCID: PMC10250835 DOI: 10.1016/j.isci.2023.106922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023] Open
Abstract
DsDNA translocation through nanoscale pores is generally accomplished by ATPase biomotors. The discovery of the revolving dsDNA translocation mechanism, as opposed to rotation, in bacteriophage phi29 elucidated how ATPase motors move dsDNA. Revolution-driven, hexameric dsDNA motors have been reported in herpesvirus, bacterial FtsK, Streptomyces TraB, and T7 phage. This review explores the common relationship between their structure and mechanisms. Commonalities include moving along the 5'→3' strand, inchworm sequential action leading to an asymmetrical structure, channel chirality, channel size, and 3-step channel gating for controlling motion direction. The revolving mechanism and contact with one of the dsDNA strands addresses the historic controversy of dsDNA packaging using nicked, gapped, hybrid, or chemically modified DNA. These controversies surrounding dsDNA packaging activity using modified materials can be answered by whether the modification was introduced into the 3'→5' or 5'→3' strand. Perspectives concerning solutions to the controversy of motor structure and stoichiometry are also discussed.
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Affiliation(s)
- Margaret Bohmer
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Abhjeet S. Bhullar
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
| | - Tao Weitao
- Center for the Genetics of Host Defense UT Southwestern Medical Center, Dallas, TX, USA
| | - Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jing-Huei Lee
- Department of Biomedical Engineering, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
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4
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Cao D, Ma B, Cao Z, Zhang X, Xiang Y. Structure of Semliki Forest virus in complex with its receptor VLDLR. Cell 2023; 186:2208-2218.e15. [PMID: 37098345 DOI: 10.1016/j.cell.2023.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/22/2023] [Accepted: 03/28/2023] [Indexed: 04/27/2023]
Abstract
Semliki Forest virus (SFV) is an alphavirus that uses the very-low-density lipoprotein receptor (VLDLR) as a receptor during infection of its vertebrate hosts and insect vectors. Herein, we used cryoelectron microscopy to study the structure of SFV in complex with VLDLR. We found that VLDLR binds multiple E1-DIII sites of SFV through its membrane-distal LDLR class A (LA) repeats. Among the LA repeats of the VLDLR, LA3 has the best binding affinity to SFV. The high-resolution structure shows that LA3 binds SFV E1-DIII through a small surface area of 378 Å2, with the main interactions at the interface involving salt bridges. Compared with the binding of single LA3s, consecutive LA repeats around LA3 promote synergistic binding to SFV, during which the LAs undergo a rotation, allowing simultaneous key interactions at multiple E1-DIII sites on the virion and enabling the binding of VLDLRs from divergent host species to SFV.
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Affiliation(s)
- Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Bingting Ma
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziyi Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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5
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Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
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Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
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6
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Morgan A, Eastlund A, Fischer C, Jardine P. Kinetics of ATP/ADP Binding to the gp16 ATPase. Biophys J 2022; 121:1909-1918. [PMID: 35421388 DOI: 10.1016/j.bpj.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 04/08/2022] [Indexed: 11/02/2022] Open
Abstract
The gp16 ATPase is the constituent subunit of the pentameric dsDNA (Double-stranded Deoxyribonucleic Acid) translocation motor of the B. subtilis Φ29 bacteriophage. Although recent single-molecule studies have provided tantalizing clues about the activity of this motor, the mechanism by which the gp16 subunits couple the energy obtained from the binding and hydrolysis of ATP to the mechanical work of dsDNA translocation remains unknown. To address this need, we have characterized the binding of fluorophore labeled ATP and ADP to monomeric gp16 using a stopped-flow fluorescence assay. These experiments show that the binding of ATP/ADP occurs through a single-step mechanism with corresponding affinities of (523.8 ± 247.3) nM for ATP and a lower limit of 30μM for ADP. When analyzed through the lens of changes in free energy of the system, this difference in binding affinities is reasonable for a cyclical process of binding, hydrolysis, and product release. In addition to answering questions about the activity of monomeric gp16, these results are also a necessary step in constructing a model for inter-subunit communication within the pentameric gp16 motor.
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Affiliation(s)
- Aaron Morgan
- Department of Physics and Astronomy, University of Kansas, Lawrence, KS 66045
| | - Allen Eastlund
- Department of Diagnostic and Biological Sciences, University of Minnesota
| | - Christopher Fischer
- Department of Physics and Astronomy, University of Kansas, Lawrence, KS 66045
| | - Paul Jardine
- Department of Diagnostic and Biological Sciences, University of Minnesota
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7
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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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8
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Woodson M, Pajak J, Mahler BP, Zhao W, Zhang W, Arya G, White MA, Jardine PJ, Morais MC. A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA. SCIENCE ADVANCES 2021; 7:7/19/eabc1955. [PMID: 33962953 PMCID: PMC8104870 DOI: 10.1126/sciadv.abc1955] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible for diverse biological polymer manipulation tasks. Viruses use ASCE segregation motors to package their genomes into their protein capsids and provide accessible experimental systems due to their relative simplicity. We show by cryo-EM-focused image reconstruction that ASCE ATPases in viral double-stranded DNA (dsDNA) packaging motors adopt helical symmetry complementary to their dsDNA substrates. Together with previous data, our results suggest that these motors cycle between helical and planar configurations, providing a possible mechanism for directional translocation of DNA. Similar changes in quaternary structure have been observed for proteasome and helicase motors, suggesting an ancient and common mechanism of force generation that has been adapted for specific tasks over the course of evolution.
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Affiliation(s)
- Michael Woodson
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Bryon P Mahler
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wei Zhao
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Characterization Facility, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Mark A White
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
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9
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Johnson JE, Olson AJ. Icosahedral virus structures and the protein data bank. J Biol Chem 2021; 296:100554. [PMID: 33744290 PMCID: PMC8081926 DOI: 10.1016/j.jbc.2021.100554] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022] Open
Abstract
The structural study of icosahedral viruses has a long and impactful history in both crystallographic methodology and molecular biology. The evolution of the Protein Data Bank has paralleled and supported these studies providing readily accessible formats dealing with novel features associated with viral particle symmetries and subunit interactions. This overview describes the growth in size and complexity of icosahedral viruses from the first early studies of small RNA plant viruses and human picornaviruses up to the larger and more complex bacterial phage, insect, and human disease viruses such as Zika, hepatitis B, Adeno and Polyoma virus. The analysis of icosahedral viral capsid protein domain folds has shown striking similarities, with the beta jelly roll motif observed across multiple evolutionarily divergent species. The icosahedral symmetry of viruses drove the development of noncrystallographic symmetry averaging as a powerful phasing method, and the constraints of maintaining this symmetry resulted in the concept of quasi-equivalence in viral structures. Symmetry also played an important early role in demonstrating the power of cryo-electron microscopy as an alternative to crystallography in generating atomic resolution structures of these viruses. The Protein Data Bank has been a critical resource for assembling and disseminating these structures to a wide community, and the virus particle explorer (VIPER) was developed to enable users to easily generate and view complete viral capsid structures from their asymmetric building blocks. Finally, we share a personal perspective on the early use of computer graphics to communicate the intricacies, interactions, and beauty of these virus structures.
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Affiliation(s)
- John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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10
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Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S. Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor. Biochemistry 2021; 60:886-897. [PMID: 33689296 DOI: 10.1021/acs.biochem.0c00935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage ϕ29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete ϕ29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage ϕ29 and suggested how the individual domains of gp16 work together to power such translocation.
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Affiliation(s)
- Abdullah F U H Saeed
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.,College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China
| | - Chun Chan
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hongxin Guan
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Bing Gong
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535000, China
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.,Center for RNA Nanobiotechnology and Nanomedicine, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiaolin Cheng
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.,Biophysics Graduate Program and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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11
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Reyes-Aldrete E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC. Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28. Viruses 2020; 13:E15. [PMID: 33374840 PMCID: PMC7823558 DOI: 10.3390/v13010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.
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Affiliation(s)
- Emilio Reyes-Aldrete
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Erik A. Dill
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Cecile Bussetta
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Michal R. Szymanski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Geoffrey Diemer
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Priyank Maindola
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
| | - Mark A. White
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Wlodzimierz M. Bujalowski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Kyung H. Choi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Marc C. Morais
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; (E.R.-A.); (E.A.D.); (C.B.); (M.R.S.); (G.D.); (P.M.); (M.A.W.); (W.M.B.); (K.H.C.)
- Sealy Center for Structural Biology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
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12
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Mahler BP, Bujalowski PJ, Mao H, Dill EA, Jardine PJ, Choi K, Morais MC. NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors. Nucleic Acids Res 2020; 48:11737-11749. [PMID: 33089330 PMCID: PMC7672431 DOI: 10.1093/nar/gkaa874] [Citation(s) in RCA: 9] [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: 07/28/2020] [Revised: 09/22/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes oligomerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination. Taken together, these results provide insight into the evolution of functional transitions in viral dsDNA packaging motors.
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Affiliation(s)
- Bryon P Mahler
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Paul J Bujalowski
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Huzhang Mao
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Erik A Dill
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kyung H Choi
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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13
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Reboul CF, Kiesewetter S, Elmlund D, Elmlund H. Point-group symmetry detection in three-dimensional charge density of biomolecules. Bioinformatics 2020; 36:2237-2243. [PMID: 31790146 DOI: 10.1093/bioinformatics/btz904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/31/2019] [Accepted: 11/28/2019] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION No rigorous statistical tests for detecting point-group symmetry in three-dimensional (3D) charge density maps obtained by electron microscopy (EM) and related techniques have been developed. RESULTS We propose a method for determining the point-group symmetry of 3D charge density maps obtained by EM and related techniques. Our ab initio algorithm does not depend on atomic coordinates but utilizes the density map directly. We validate the approach for a range of publicly available single-particle cryo-EM datasets. In straightforward cases, our method enables fully automated single-particle 3D reconstruction without having to input an arbitrarily selected point-group symmetry. When pseudo-symmetry is present, our method provides statistics quantifying the degree to which the 3D density agrees with the different point-groups tested. AVAILABILITY AND IMPLEMENTATION The software is freely available at https://github.com/hael/SIMPLE3.0.
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Affiliation(s)
- Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
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14
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Direct structural evidence supporting a revolving mechanism in DNA packaging motors. BIOPHYSICS REPORTS 2020. [DOI: 10.1007/s41048-020-00115-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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15
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Abrishami V, Ilca SL, Gomez-Blanco J, Rissanen I, de la Rosa-Trevín JM, Reddy VS, Carazo JM, Huiskonen JT. Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:43-52. [PMID: 32470354 DOI: 10.1016/j.pbiomolbio.2020.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 01/10/2023]
Abstract
Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.
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Affiliation(s)
- Vahid Abrishami
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Serban L Ilca
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Josue Gomez-Blanco
- Biocomputing Unit, National Center for Biotechnology (CSIC), Calle Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain; Current address: Department of Anatomy & Cell Biology, McGill University, 3640 University Street, Montreal, Quebec, H3A 0C7, Canada
| | - Ilona Rissanen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland
| | | | - Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, North Torrey Pines Road, La Jolla, 92037, CA, USA
| | - José-Maria Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), Calle Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland; Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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16
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Johnson JE. Michael G. Rossmann (1930–2019): Leadership in structural biology for 60 years. Protein Sci 2019. [DOI: 10.1002/pro.3671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- John E. Johnson
- Department of Integrative Structural and Computational BiologyThe Scripps Research Institute La Jolla California 92037
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17
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Xu J, Wang D, Gui M, Xiang Y. Structural assembly of the tailed bacteriophage ϕ29. Nat Commun 2019; 10:2366. [PMID: 31147544 PMCID: PMC6542822 DOI: 10.1038/s41467-019-10272-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/24/2019] [Indexed: 11/30/2022] Open
Abstract
The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration. Mature particles of bacteriophage ϕ29 consist of a 33-MDa complex formed by over 450 subunits, assembled into a head and a short tail. Here, Xu et al. report the near-atomic structures of the ϕ29 prohead, the mature virion and the genome-emptied virion, providing insights into DNA packaging and release.
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Affiliation(s)
- Jingwei Xu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093, Zürich, Switzerland
| | - Dianhong Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Miao Gui
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
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18
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Abstract
The filamentous bacteriophage IKe is one of many nonenveloped bacterial viruses that encapsulate a circular single-stranded viral genome in the phage capsid shell. The shell of IKe is comprised of about 3,100 copies of the IKe major coat protein. Atomic-resolution structures of filamentous phages are scarce, and the structure of the single-stranded DNA is a matter of debate. Our cryo-electron microscopy structure of the filamentous bacteriophage IKe at a resolution of 3.4 Å provides atomic details on the structure of the major coat protein, the symmetry of the capsid shell, and the key interactions driving its assembly. We propose a model for the conformation of the circular single-stranded DNA core and the interactions between the capsid shell and inner DNA core. The filamentous bacteriophage IKe infects Escherichia coli cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major coat protein [protein 8 (p8)] consists of 47 residues that fold into a ∼68-Å-long helix. An atomic model of the coat protein was built. Five p8 helices in a horizontal layer form a pentamer, and symmetrically neighboring p8 layers form a right-handed helical cylinder having a rise per pentamer of 16.77 Å and a twist of 38.52°. The inner surface of the capsid cylinder is positively charged and has direct interactions with the encapsulated circular single-stranded DNA genome, which has an electron density consistent with an unusual left-handed helix structure. Similar to capsid structures of other filamentous viruses, strong capsid packing in the IKe particle is maintained by hydrophobic residues. Despite having a different length and large sequence differences from other filamentous phages, π–π interactions were found between Tyr9 of one p8 and Trp29 of a neighboring p8 in IKe that are similar to interactions observed in phage M13, suggesting that, despite sequence divergence, overall structural features are maintained.
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19
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Gatsogiannis C, Merino F, Roderer D, Balchin D, Schubert E, Kuhlee A, Hayer-Hartl M, Raunser S. Tc toxin activation requires unfolding and refolding of a β-propeller. Nature 2018; 563:209-213. [DOI: 10.1038/s41586-018-0556-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/23/2018] [Indexed: 12/14/2022]
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20
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Image processing for cryogenic transmission electron microscopy of symmetry-mismatched complexes. Biosci Rep 2018; 38:BSR20170203. [PMID: 29439140 PMCID: PMC5857907 DOI: 10.1042/bsr20170203] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 12/23/2022] Open
Abstract
Cryogenic transmission electron microscopy (cryo-TEM) is a high-resolution biological imaging method, whereby biological samples, such as purified proteins, macromolecular complexes, viral particles, organelles and cells, are embedded in vitreous ice preserving their native structures. Due to sensitivity of biological materials to the electron beam of the microscope, only relatively low electron doses can be applied during imaging. As a result, the signal arising from the structure of interest is overpowered by noise in the images. To increase the signal-to-noise ratio, different image processing-based strategies that aim at coherent averaging of signal have been devised. In such strategies, images are generally assumed to arise from multiple identical copies of the structure. Prior to averaging, the images must be grouped according to the view of the structure they represent and images representing the same view must be simultaneously aligned relatively to each other. For computational reconstruction of the 3D structure, images must contain different views of the original structure. Structures with multiple symmetry-related substructures are advantageous in averaging approaches because each image provides multiple views of the substructures. However, the symmetry assumption may be valid for only parts of the structure, leading to incoherent averaging of the other parts. Several image processing approaches have been adapted to tackle symmetry-mismatched substructures with increasing success. Such structures are ubiquitous in nature and further computational method development is needed to understanding their biological functions.
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21
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Jing P, Burris B, Zhang R. Forces from the Portal Govern the Late-Stage DNA Transport in a Viral DNA Packaging Nanomotor. Biophys J 2017; 111:162-77. [PMID: 27410744 DOI: 10.1016/j.bpj.2016.05.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 01/09/2023] Open
Abstract
In the Phi29 bacteriophage, the DNA packaging nanomotor packs its double-stranded DNA genome into the virus capsid. At the late stage of DNA packaging, the negatively charged genome is increasingly compacted at a higher density in the capsid with a higher internal pressure. During the process, two Donnan effects, osmotic pressure and Donnan equilibrium potentials, are significantly amplified, which, in turn, affect the channel activity of the portal protein, GP10, embedded in the semipermeable capsid shell. In the research, planar lipid bilayer experiments were used to study the channel activities of the viral protein. The Donnan effect on the conformational changes of the viral protein was discovered, indicating GP10 may not be a static channel at the late stage of DNA packaging. Due to the conformational changes, GP10 may generate electrostatic forces that govern the DNA transport. For the section of the genome DNA that remains outside of the connector channel, a strong repulsive force from the viral protein would be generated against the DNA entry; however, for the section of the genome DNA within the channel, the portal protein would become a Brownian motor, which adopts the flash Brownian ratchet mechanism to pump the DNA against the increasingly built-up internal pressure (up to 20 atm) in the capsid. Therefore, the DNA transport in the nanoscale viral channel at the late stage of DNA packaging could be a consequence of Brownian movement of the genomic DNA, which would be rectified and harnessed by the forces from the interior wall of the viral channel under the influence of the Donnan effect.
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Affiliation(s)
- Peng Jing
- Department of Chemistry, College of Arts and Sciences, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana.
| | - Benjamin Burris
- Department of Chemistry, College of Arts and Sciences, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana
| | - Rong Zhang
- Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts
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22
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Liu Z, Zhang J. Exploring the inside details of virions by electron microscopy. BIOPHYSICS REPORTS 2016; 2:21-24. [PMID: 27819027 PMCID: PMC5071365 DOI: 10.1007/s41048-016-0022-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 01/24/2016] [Indexed: 11/03/2022] Open
Affiliation(s)
- Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032 USA
| | - Jingqiang Zhang
- College of Life Science, SunYat-sen University, Guangzhou, 510275 China
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23
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24
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Farley MM, Tu J, Kearns DB, Molineux IJ, Liu J. Ultrastructural analysis of bacteriophage Φ29 during infection of Bacillus subtilis. J Struct Biol 2016; 197:163-171. [PMID: 27480510 DOI: 10.1016/j.jsb.2016.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/13/2022]
Abstract
Recent advances in cryo-electron tomography (cryo-ET) have allowed direct visualization of the initial interactions between bacteriophages and their hosts. Previous studies focused on phage infection in Gram-negative bacteria but it is of particular interest how phages penetrate the thick, highly cross-linked Gram-positive cell wall. Here we detail structural intermediates of phage Φ29 during infection of Bacillus subtilis. Use of a minicell-producing strain facilitated in situ tomographic reconstructions of infecting phage particles. Φ29 initially contacts the cell wall at an angle through a subset of the twelve appendages, which are attached to the collar at the head proximal portion of the tail knob. The appendages are flexible and switch between extended and downward conformations during this stage of reversible adsorption; appendages enzymatically hydrolyze wall teichoic acids to bring the phage closer to the cell. A cell wall-degrading enzyme at the distal tip of the tail knob locally digests peptidoglycan, facilitating penetration of the tail further into the cell wall, and the phage particle reorients so that the tail becomes perpendicular to the cell surface. All twelve appendages attain the same "down" conformation during this stage of adsorption. Once the tail has become totally embedded in the cell wall, the tip can fuse with the cytoplasmic membrane. The membrane bulges out, presumably to facilitate genome ejection into the cytoplasm, and the deformation remains after complete ejection. This study provides the first visualization of the structural changes occurring in a phage particle during adsorption and genome transfer into a Gram-positive bacterium.
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Affiliation(s)
- Madeline M Farley
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Jiagang Tu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
| | - Ian J Molineux
- Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA.
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25
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Hill AC, Bartley LE, Schroeder SJ. Prohead RNA: a noncoding viral RNA of novel structure and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:428-37. [PMID: 26810250 PMCID: PMC5066667 DOI: 10.1002/wrna.1330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/23/2015] [Accepted: 12/02/2015] [Indexed: 12/12/2022]
Abstract
Prohead RNA (pRNA) is an essential component of the powerful Φ29-like bacteriophage DNA packaging motor. However, the specific role of this unique RNA in the Φ29 packaging motor remains unknown. This review examines pRNA as a noncoding RNA of novel structure and function. In order to highlight the reasons for exploring the structure and function of pRNA, we (1) provide an overview of Φ29-like bacteriophage and the Φ29 DNA packaging motor, including putative motor mechanisms and structures of its component parts; (2) discuss pRNA structure and possible roles for pRNA in the Φ29 packaging motor; (3) summarize pRNA self-assembly; and (4) describe the prospective therapeutic applications of pRNA. Many questions remain to be answered in order to connect what is currently known about pRNA structure to its novel function in the Φ29 packaging motor. The knowledge gained from studying the structure, function, and sequence variation in pRNA will help develop tools to better navigate the conformational landscapes of RNA. WIREs RNA 2016, 7:428-437. doi: 10.1002/wrna.1330 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alyssa C Hill
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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26
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Symmetry-mismatch reconstruction of genomes and associated proteins within icosahedral viruses using cryo-EM. BIOPHYSICS REPORTS 2016; 2:25-32. [PMID: 27819028 PMCID: PMC5071370 DOI: 10.1007/s41048-016-0024-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/18/2016] [Indexed: 11/24/2022] Open
Abstract
Although near-atomic resolutions have been routinely achieved for structural determination of many icosahedral viral capsids, structures of genomes and associated proteins within the capsids are still less characterized because the genome information is overlapped by the highly symmetric capsid information in the virus particle images. We recently developed a software package for symmetry-mismatch structural reconstruction and determined the structures of the genome and RNA polymerases within an icosahedral virus for the first time. Here, we describe the protocol used for this structural determination, which may facilitate structural biologists in investigating the structures of viral genome and associated proteins.
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27
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Mao H, Saha M, Reyes-Aldrete E, Sherman MB, Woodson M, Atz R, Grimes S, Jardine PJ, Morais MC. Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor. Cell Rep 2016; 14:2017-2029. [PMID: 26904950 DOI: 10.1016/j.celrep.2016.01.058] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/04/2016] [Accepted: 01/17/2016] [Indexed: 02/02/2023] Open
Abstract
Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.
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Affiliation(s)
- Huzhang Mao
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mitul Saha
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Emilio Reyes-Aldrete
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Michael B Sherman
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Michael Woodson
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Rockney Atz
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shelley Grimes
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, School of Dentistry, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Marc C Morais
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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28
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Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism. Microbiol Mol Biol Rev 2016; 80:161-86. [PMID: 26819321 DOI: 10.1128/mmbr.00056-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. In 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded DNA (dsDNA) bacteriophages. This review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and energy usage rate, in a variety of well-studied motors, including FoF1 ATPase, helicases, viral dsDNA-packaging motors, bacterial chromosome translocases, myosin, kinesin, and dynein. In particular, dsDNA translocases are used to illustrate how these features relate to the motion mechanism and how nature elegantly evolved a revolution mechanism to avoid coiling and tangling during lengthy dsDNA genome transportation in cell division. Motor chirality and channel size are two factors that distinguish rotation motors from revolution motors. Rotation motors use right-handed channels to drive the right-handed dsDNA, similar to the way a nut drives the bolt with threads in same orientation; revolution motors use left-handed motor channels to revolve the right-handed dsDNA. Rotation motors use small channels (<2 nm in diameter) for the close contact of the channel wall with single-stranded DNA (ssDNA) or the 2-nm dsDNA bolt; revolution motors use larger channels (>3 nm) with room for the bolt to revolve. Binding and hydrolysis of ATP are linked to different conformational entropy changes in the motor that lead to altered affinity for the substrate and allow work to be done, for example, helicase unwinding of DNA or translocase directional movement of DNA.
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Ilca SL, Kotecha A, Sun X, Poranen MM, Stuart DI, Huiskonen JT. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun 2015; 6:8843. [PMID: 26534841 PMCID: PMC4667630 DOI: 10.1038/ncomms9843] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022] Open
Abstract
Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems. Electron cryomicroscopy can allow the elucidation of macromolecular structures; however, mismatches in symmetry between different components limit the attainable resolution. Here, the authors set out a computational method for extracting and retaining information from such components.
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Liu H, Cheng L. Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus. Science 2015; 349:1347-50. [PMID: 26383954 DOI: 10.1126/science.aaa4938] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures.
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Affiliation(s)
- Hongrong Liu
- College of Physics and Information Science, Hunan Normal University, Changsha, Hunan 410081, China.
| | - Lingpeng Cheng
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Veesler D, Kearney BM, Johnson JE. Integration of X-ray crystallography and electron cryo-microscopy in the analysis of virus structure and function. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2015.1038530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R. Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data. PLoS Comput Biol 2015; 11:e1004146. [PMID: 25793998 PMCID: PMC4368512 DOI: 10.1371/journal.pcbi.1004146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design.
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Affiliation(s)
- James A Geraets
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
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Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation. Biotechnol Adv 2015; 32:853-72. [PMID: 24913057 DOI: 10.1016/j.biotechadv.2014.01.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 01/24/2014] [Accepted: 01/25/2014] [Indexed: 12/15/2022]
Abstract
Biomotors were once described into two categories: linear motor and rotation motor. Recently, a third type of biomotor with revolution mechanism without rotation has been discovered. By analogy, rotation resembles the Earth rotating on its axis in a complete cycle every 24h, while revolution resembles the Earth revolving around the Sun one circle per 365 days (see animations http://nanobio.uky.edu/movie.html). The action of revolution that enables a motor free of coiling and torque has solved many puzzles and debates that have occurred throughout the history of viral DNA packaging motor studies. It also settles the discrepancies concerning the structure, stoichiometry, and functioning of DNA translocation motors. This review uses bacteriophages Phi29, HK97, SPP1, P22, T4, and T7 as well as bacterial DNA translocase FtsK and SpoIIIE or the large eukaryotic dsDNA viruses such as mimivirus and vaccinia virus as examples to elucidate the puzzles. These motors use ATPase, some of which have been confirmed to be a hexamer, to revolve around the dsDNA sequentially. ATP binding induces conformational change and possibly an entropy alteration in ATPase to a high affinity toward dsDNA; but ATP hydrolysis triggers another entropic and conformational change in ATPase to a low affinity for DNA, by which dsDNA is pushed toward an adjacent ATPase subunit. The rotation and revolution mechanisms can be distinguished by the size of channel: the channels of rotation motors are equal to or smaller than 2 nm, that is the size of dsDNA, whereas channels of revolution motors are larger than 3 nm. Rotation motors use parallel threads to operate with a right-handed channel, while revolution motors use a left-handed channel to drive the right-handed DNA in an anti-chiral arrangement. Coordination of several vector factors in the same direction makes viral DNA-packaging motors unusually powerful and effective. Revolution mechanism that avoids DNA coiling in translocating the lengthy genomic dsDNA helix could be advantageous for cell replication such as bacterial binary fission and cell mitosis without the need for topoisomerase or helicase to consume additional energy.
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34
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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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35
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36
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Dent KC, Thompson R, Barker AM, Hiscox JA, Barr JN, Stockley PG, Ranson NA. The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release. Structure 2014; 21:1225-34. [PMID: 23810697 PMCID: PMC3701328 DOI: 10.1016/j.str.2013.05.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/23/2013] [Accepted: 05/07/2013] [Indexed: 11/23/2022]
Abstract
Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection. The asymmetric structure of a virus receptor complex is described The density for ordered genomic RNA was observed in the structure Viral maturation protein was visualized
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Affiliation(s)
- Kyle C Dent
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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Insights into the structure and assembly of the bacteriophage 29 double-stranded DNA packaging motor. J Virol 2014; 88:3986-96. [PMID: 24403593 DOI: 10.1128/jvi.03203-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The tailed double-stranded DNA (dsDNA) bacteriophage 29 packages its 19.3-kbp genome into a preassembled procapsid structure by using a transiently assembled phage-encoded molecular motor. This process is remarkable considering that compaction of DNA to near-crystalline densities within the confined space of the capsid requires that the packaging motor work against significant entropic, enthalpic, and DNA-bending energies. The motor consists of three phage-encoded components: the dodecameric connector protein gp10, an oligomeric RNA molecule known as the prohead RNA (pRNA), and the homomeric ring ATPase gp16. Although atomic resolution structures of the connector and different pRNA subdomains have been determined, the mechanism of self-assembly and the resulting stoichiometry of the various motor components on the phage capsid have been the subject of considerable controversy. Here a subnanometer asymmetric cryoelectron microscopy (cryo-EM) reconstruction of a connector-pRNA complex at a unique vertex of the procapsid conclusively demonstrates the pentameric symmetry of the pRNA and illuminates the relative arrangement of the connector and the pRNA. Additionally, a combination of biochemical and cryo-EM analyses of motor assembly intermediates suggests a sequence of molecular events that constitute the pathway by which the motor assembles on the head, thereby reconciling conflicting data regarding pRNA assembly and stoichiometry. Taken together, these data provide new insight into the assembly, structure, and mechanism of a complex molecular machine. IMPORTANCE Viruses consist of a protein shell, or capsid, that protects and surrounds their genetic material. Thus, genome encapsidation is a fundamental and essential step in the life cycle of any virus. In dsDNA viruses, powerful molecular motors essentially pump the viral DNA into a preformed protein shell. This article describes how a viral dsDNA packaging motor self-assembles on the viral capsid and provides insight into its mechanism of action.
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Abstract
With fast progresses in instrumentation, image processing algorithms, and computational resources, single particle electron cryo-microscopy (cryo-EM) 3-D reconstruction of icosahedral viruses has now reached near-atomic resolutions (3-4 Å). With comparable resolutions and more predictable outcomes, cryo-EM is now considered a preferred method over X-ray crystallography for determination of atomic structure of icosahedral viruses. At near-atomic resolutions, all-atom models or backbone models can be reliably built that allow residue level understanding of viral assembly and conformational changes among different stages of viral life cycle. With the developments of asymmetric reconstruction, it is now possible to visualize the complete structure of a complex virus with not only its icosahedral shell but also its multiple non-icosahedral structural features. In this chapter, we will describe single particle cryo-EM experimental and computational procedures for both near-atomic resolution reconstruction of icosahedral viruses and asymmetric reconstruction of viruses with both icosahedral and non-icosahedral structure components. Procedures for rigorous validation of the reconstructions and resolution evaluations using truly independent de novo initial models and refinements are also introduced.
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Affiliation(s)
- Fei Guo
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, USA
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Guo P, Schwartz C, Haak J, Zhao Z. Discovery of a new motion mechanism of biomotors similar to the earth revolving around the sun without rotation. Virology 2013; 446:133-43. [PMID: 24074575 PMCID: PMC3941703 DOI: 10.1016/j.virol.2013.07.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/27/2013] [Accepted: 07/21/2013] [Indexed: 12/14/2022]
Abstract
Biomotors have been classified into linear and rotational motors. For 35 years, it has been popularly believed that viral dsDNA-packaging apparatuses are pentameric rotation motors. Recently, a third class of hexameric motor has been found in bacteriophage phi29 that utilizes a mechanism of revolution without rotation, friction, coiling, or torque. This review addresses how packaging motors control dsDNA one-way traffic; how four electropositive layers in the channel interact with the electronegative phosphate backbone to generate four steps in translocating one dsDNA helix; how motors resolve the mismatch between 10.5 bases and 12 connector subunits per cycle of revolution; and how ATP regulates sequential action of motor ATPase. Since motors with all number of subunits can utilize the revolution mechanism, this finding helps resolve puzzles and debates concerning the oligomeric nature of packaging motors in many phage systems. This revolution mechanism helps to solve the undesirable dsDNA supercoiling issue involved in rotation.
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Affiliation(s)
- Peixuan Guo
- Nanobiotechnology Center, and Markey Cancer Center, Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
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Revolution rather than rotation of AAA+ hexameric phi29 nanomotor for viral dsDNA packaging without coiling. Virology 2013; 443:28-39. [PMID: 23763768 PMCID: PMC3850062 DOI: 10.1016/j.virol.2013.04.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/16/2013] [Accepted: 04/20/2013] [Indexed: 01/28/2023]
Abstract
It has long been believed that the DNA-packaging motor of dsDNA viruses
utilizes a rotation mechanism. Here we report a revolution rather than rotation
mechanism for the bacteriophage phi29 DNA packaging motor. The phi29 motor
contains six copies of the ATPase (Schwartz et al., this issue); ATP binding to
one ATPase subunit stimulates the ATPase to adopt a conformation with a high
affinity for dsDNA. ATP hydrolysis induces a new conformation with a lower
affinity, thus transferring the dsDNA to an adjacent subunit by a power stroke.
DNA revolves unidirectionally along the hexameric channel wall of the ATPase,
but neither the dsDNA nor the ATPase itself rotates along its own axis. One ATP
is hydrolyzed in each transitional step, and six ATPs are consumed for one
helical turn of 360°. Transition of the same dsDNA chain along the
channel wall, but at a location 60° different from the last contact,
urges dsDNA to move forward 1.75 base pairs each step (10.5 bp per
turn/6ATP=1.75 bp per ATP). Each connector subunit tilts with a
left-handed orientation at a 30° angle in relation to its vertical axis
that runs anti-parallel to the right-handed dsDNA helix, facilitating the
one-way traffic of dsDNA. The connector channel has been shown to cause four
steps of transition due to four positively charged lysine rings that make direct
contact with the negatively charged DNA phosphate backbone. Translocation of
dsDNA into the procapsid by revolution avoids the difficulties during rotation
that are associated with DNA supercoiling. Since the revolution mechanism can
apply to any stoichiometry, this motor mechanism might reconcile the
stoichiometry discrepancy in many phage systems where the ATPase has been found
as a tetramer, hexamer, or nonamer.
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Zhao Z, Khisamutdinov E, Schwartz C, Guo P. Mechanism of one-way traffic of hexameric phi29 DNA packaging motor with four electropositive relaying layers facilitating antiparallel revolution. ACS NANO 2013; 7:4082-92. [PMID: 23510192 PMCID: PMC3667633 DOI: 10.1021/nn4002775] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/20/2013] [Indexed: 05/21/2023]
Abstract
The importance of nanomotors in nanotechnology is akin to that of mechanical engines to daily life. The AAA+ superfamily is a class of nanomotors performing various functions. Their hexagonal arrangement facilitates bottom-up assembly for stable structures. The bacteriophage phi29 DNA translocation motor contains three coaxial rings: a dodecamer channel, a hexameric ATPase ring, and a hexameric pRNA ring. The viral DNA packaging motor has been believed to be a rotational machine. However, we discovered a revolution mechanism without rotation. By analogy, the earth revolves around the sun while rotating on its own axis. One-way traffic of dsDNA translocation is facilitated by five factors: (1) ATPase changes its conformation to revolve dsDNA within a hexameric channel in one direction; (2) the 30° tilt of the channel subunits causes an antiparallel arrangement between two helices of dsDNA and channel wall to advance one-way translocation; (3) unidirectional flow property of the internal channel loops serves as a ratchet valve to prevent reversal; (4) 5'-3' single-direction movement of one DNA strand along the channel wall ensures single direction; and (5) four electropositive layers interact with one strand of the electronegative dsDNA phosphate backbone, resulting in four relaying transitional pauses during translocation. The discovery of a riding system along one strand provides a motion nanosystem for cargo transportation and a tool for studying force generation without coiling, friction, and torque. The revolution of dsDNA among 12 subunits offers a series of recognition sites on the DNA backbone to provide additional spatial variables for nucleotide discrimination for sensing applications.
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Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7. Proc Natl Acad Sci U S A 2013; 110:6811-6. [PMID: 23580619 DOI: 10.1073/pnas.1215563110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle electron cryomicroscopy to study the multilayer structure of the portal vertex of the bacteriophage T7 procapsid, the recipient of T7 DNA in packaging. A focused asymmetric reconstruction method was developed and applied to selectively resolve neighboring pairs of symmetry-mismatched layers of the portal vertex. However, structural features in all layers of the multilayer portal vertex could not be resolved simultaneously. Our results imply that layers with mismatched symmetries can join together in several different relative orientations, and that orientations at different interfaces assort independently to produce structural isomers, a process that we call combinatorial assembly isomerism. This isomerism explains rotational smearing in previously reported asymmetric reconstructions of the portal vertex of T7 and other bacteriophages. Combinatorial assembly isomerism may represent a new regime of structural biology in which globally varying structures assemble from a common set of components. Our reconstructions collectively validate previously proposed symmetries, compositions, and sequential order of T7 portal vertex layers, resolving in tandem the 5-fold gene product 10 (gp10) shell, 12-fold gp8 portal ring, and an internal core stack consisting of 12-fold gp14 adaptor ring, 8-fold bowl-shaped gp15, and 4-fold gp16 tip. We also found a small tilt of the core stack relative to the icosahedral fivefold axis and propose that this tilt assists DNA spooling without tangling during packaging.
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Guerrero-Ferreira RC, Wright ER. Cryo-electron tomography of bacterial viruses. Virology 2013; 435:179-86. [PMID: 23217626 DOI: 10.1016/j.virol.2012.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/08/2012] [Accepted: 08/19/2012] [Indexed: 01/15/2023]
Abstract
Bacteriophage particles contain both simple and complex macromolecular assemblages and machines that enable them to regulate the infection process under diverse environmental conditions with a broad range of bacterial hosts. Recent developments in cryo-electron tomography (cryo-ET) make it possible to observe the interactions of bacteriophages with their host cells under native-state conditions at unprecedented resolution and in three-dimensions. This review describes the application of cryo-ET to studies of bacteriophage attachment, genome ejection, assembly and egress. Current topics of investigation and future directions in the field are also discussed.
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Affiliation(s)
- Ricardo C Guerrero-Ferreira
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
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Zhang H, Schwartz C, De Donatis GM, Guo P. "Push through one-way valve" mechanism of viral DNA packaging. Adv Virus Res 2012; 83:415-65. [PMID: 22748815 DOI: 10.1016/b978-0-12-394438-2.00009-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Double-stranded (ds)DNA viruses package their genomic DNA into a procapsid using a force-generating nanomotor powered by ATP hydrolysis. Viral DNA packaging motors are mainly composed of the connector channel and two DNA packaging enzymes. In 1998, it was proposed that viral DNA packaging motors exercise a mechanism similar to the action of AAA+ ATPases that assemble into ring-shaped oligomers, often hexamers, with a central channel (Guo et al. Molecular Cell, 2:149). This chapter focuses on the most recent findings in the bacteriophage ϕ29 DNA packaging nanomotor to address this intriguing notion. Almost all dsDNA viruses are composed entirely of protein, but in the unique case of ϕ29, packaging RNA (pRNA) plays an intermediate role in the packaging process. Evidence revealed that DNA packaging is accomplished via a "push through one-way valve" mechanism. The ATPase gp16 pushes dsDNA through the connector channel section by section into the procapsid. The dodecameric connector channel functions as a one-way valve that only allows dsDNA to enter but not exit the procapsid during DNA packaging. Although the roles of the ATPase gp16 and the motor connector channel are separate and independent, pRNA bridges these two components to ensure the coordination of an integrated motor. ATP induces a conformational change in gp16, leading to its stronger binding to dsDNA. Furthermore, ATP hydrolysis led to the departure of dsDNA from the ATPase/dsDNA complex, an action used to push dsDNA through the connector channel. It was found unexpectedly that by mutating the basic lysine rings of the connector channel or by changing the pH did not measurably impair DNA translocation or affect the one-way traffic property of the channel, suggesting that the positive charges in the lysine ring are not essential in gearing the dsDNA. The motor channel exercises three discrete, reversible, and controllable steps of gating, with each step altering the channel size by 31% to control the direction of translocation of dsDNA. Many DNA packaging models have been contingent upon the number of base pairs packaged per ATP relative to helical turns for B-type DNA. Both 2 and 2.5 bp per ATP have been used to argue for four, five, or six discrete steps of DNA translocation. The "push through one-way valve" mechanism renews the perception of dsDNA packaging energy calculations and provides insight into the discrepancy between 2 and 2.5 bp per ATP. Application of the DNA packaging motor in nanotechnology and nanomedicine is also addressed. Comparison with nine other DNA packaging models revealed that the "push through one-way valve" is the most agreeable mechanism to interpret most of the findings that led to historical models. The application of viral DNA packaging motors is also discussed.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY, USA
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45
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A three-helix junction is the interface between two functional domains of prohead RNA in 29 DNA packaging. J Virol 2012; 86:11625-32. [PMID: 22896620 DOI: 10.1128/jvi.01370-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The double-stranded-DNA bacteriophages employ powerful molecular motors to translocate genomic DNA into preformed capsids during the packaging step in phage assembly. Bacillus subtilis bacteriophage 29 has an oligomeric prohead RNA (pRNA) that is an essential component of its packaging motor. The crystal structure of the pRNA-prohead binding domain suggested that a three-helix junction constitutes both a flexible region and part of a rigid RNA superhelix. Here we define the functional role of the three-helix junction in motor assembly and DNA packaging. Deletion mutagenesis showed that a U-rich region comprising two sides of the junction plays a role in the stable assembly of pRNA to the prohead. The retention of at least two bulged residues in this region was essential for pRNA binding and thereby subsequent DNA packaging. Additional deletions resulted in the loss of the ability of pRNA to multimerize in solution, consistent with the hypothesis that this region provides the flexibility required for pRNA oligomerization and prohead binding. The third side of the junction is part of a large RNA superhelix that spans the motor. The insertion of bases into this feature resulted in a loss of DNA packaging and an impairment of initiation complex assembly. Additionally, cryo-electron microscopy (cryoEM) analysis of third-side insertion mutants showed an increased flexibility of the helix that binds the ATPase, suggesting that the rigidity of the RNA superhelix is necessary for efficient motor assembly and function. These results highlight the critical role of the three-way junction in bridging the prohead binding and ATPase assembly functions of pRNA.
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Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Proc Natl Acad Sci U S A 2012; 109:14001-6. [PMID: 22891295 DOI: 10.1073/pnas.1207730109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus were calculated using cryo-electron microscopy. The capsid protein has an HK97 fold arranged into a T = 4 icosahedral lattice. The C1 tail is terminated with a ϕ29-like knob, surrounded by a skirt of twelve long appendages with novel morphology. Several C1 structural proteins have been identified, including a candidate for an appendage. The crystal structure of the knob has an N-terminal domain with a fold observed previously in tube forming proteins of Siphoviridae and Myoviridae phages. The structure of C1 suggests the mechanisms by which the virus digests the cell wall and ejects its genome. Although there is little sequence similarity to other phages, conservation of the structural proteins demonstrates a common origin of the head and tail, but more recent evolution of the appendages.
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Morais MC. The dsDNA Packaging Motor in Bacteriophage ø29. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:511-47. [DOI: 10.1007/978-1-4614-0980-9_23] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Fu X, Walter MH, Paredes A, Morais MC, Liu J. The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography. Virology 2011; 421:141-8. [PMID: 22018785 DOI: 10.1016/j.virol.2011.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/27/2011] [Accepted: 08/30/2011] [Indexed: 10/16/2022]
Abstract
The structure of the Bacillus anthracis spore-binding phage 8a was determined by cryo-electron tomography. The phage capsid forms a T=16 icosahedron attached to a contractile tail via a head-tail connector protein. The tail consists of a six-start helical sheath surrounding a central tail tube, and a structurally novel baseplate at the distal end of the tail that recognizes and attaches to host cells. The parameters of the icosahedral capsid lattice and the helical tail sheath suggest protein folds for the capsid and tail-sheath proteins, respectively, and indicate evolutionary relationships to other dsDNA viruses. Analysis of 2518 intact phage particles show four distinct conformations that likely correspond to four sequential states of the DNA ejection process during infection. Comparison of the four observed conformations suggests a mechanism for DNA ejection, including the molecular basis underlying coordination of tail sheath contraction and genome release from the capsid.
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Affiliation(s)
- Xiaofeng Fu
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, Houston, TX 77030, USA
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Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. Proc Natl Acad Sci U S A 2011; 108:7357-62. [PMID: 21471452 DOI: 10.1073/pnas.1016690108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Prohead RNA (pRNA) is an essential component in the assembly and operation of the powerful bacteriophage 29 DNA packaging motor. The pRNA forms a multimeric ring via intermolecular base-pairing interactions between protomers that serves to guide the assembly of the ring ATPase that drives DNA packaging. Here we report the quaternary structure of this rare multimeric RNA at 3.5 Å resolution, crystallized as tetrameric rings. Strong quaternary interactions and the inherent flexibility helped rationalize how free pRNA is able to adopt multiple oligomerization states in solution. These characteristics also allowed excellent fitting of the crystallographic pRNA protomers into previous prohead/pRNA cryo-EM reconstructions, supporting the presence of a pentameric, but not hexameric, pRNA ring in the context of the DNA packaging motor. The pentameric pRNA ring anchors itself directly to the phage prohead by interacting specifically with the fivefold symmetric capsid structures that surround the head-tail connector portal. From these contacts, five RNA superhelices project from the pRNA ring, where they serve as scaffolds for binding and assembly of the ring ATPase, and possibly mediate communication between motor components. Construction of structure-based designer pRNAs with little sequence similarity to the wild-type pRNA were shown to fully support the packaging of 29 DNA.
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Abstract
A universal goal in studying the structures of macromolecules and macromolecular complexes by means of electron cryo-microscopy (cryo-TEM) and three-dimensional (3D) image reconstruction is the derivation of a reliable atomic or pseudoatomic model. Such a model provides the foundation for exploring in detail the mechanisms by which biomolecules function. Though a variety of highly ordered, symmetric specimens such as 2D crystals, helices, and icosahedral virus capsids have been studied by these methods at near-atomic resolution, until recently, numerous challenges have made it difficult to achieve sub-nanometer resolution with large (≥~500Å), asymmetric molecules such as the tailed bacteriophages. After briefly reviewing some of the history behind the development of asymmetric virus reconstructions, we use recent structural studies of the prolate phage ϕ29 as an example to illustrate the step-by-step procedures used to compute an asymmetric reconstruction at sub-nanometer resolution. In contrast to methods that have been employed to study other asymmetric complexes, we demonstrate how symmetries in the head and tail components of the phage can be exploited to obtain the structure of the entire phage in an expedited, stepwise process. Prospects for future enhancements to the procedures currently employed are noted in the concluding section.
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