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Huang Y, Sun H, Wei S, Cai L, Liu L, Jiang Y, Xin J, Chen Z, Que Y, Kong Z, Li T, Yu H, Zhang J, Gu Y, Zheng Q, Li S, Zhang R, Xia N. Structure and proposed DNA delivery mechanism of a marine roseophage. Nat Commun 2023; 14:3609. [PMID: 37330604 PMCID: PMC10276861 DOI: 10.1038/s41467-023-39220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/02/2023] [Indexed: 06/19/2023] Open
Abstract
Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
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Affiliation(s)
- Yang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hui Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Liqin Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yanan Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jiabao Xin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhenqin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yuqiong Que
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhibo Kong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, 361102, China.
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Major tail proteins of bacteriophages of the order Caudovirales. J Biol Chem 2021; 298:101472. [PMID: 34890646 PMCID: PMC8718954 DOI: 10.1016/j.jbc.2021.101472] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/18/2022] Open
Abstract
Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form or when packed within a crystal lattice. These hollow elongated protein structures, present in most bacteriophages of the order Caudovirales, connect the DNA-containing capsid with a receptor function at the distal end of the tail and consist of helical and polymerized major tail proteins. However, the resolution of cryo-EM data for these systems differs enormously between different tail tube types, partly inhibiting the building of high-fidelity models and barring a combination with further structural biology methods. Here, we review the structural biology efforts within this field and highlight the role of integrative structural biology approaches that have proved successful for some of these systems. Finally, we summarize the structural elements of major tail proteins and conceptualize how different amounts of tail tube flexibility confer heterogeneity within cryo-EM maps and, thus, limit high-resolution reconstructions.
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3
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Structural Studies of the Phage G Tail Demonstrate an Atypical Tail Contraction. Viruses 2021; 13:v13102094. [PMID: 34696524 PMCID: PMC8570332 DOI: 10.3390/v13102094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/07/2021] [Accepted: 10/14/2021] [Indexed: 01/28/2023] Open
Abstract
Phage G is recognized as having a remarkably large genome and capsid size among isolated, propagated phages. Negative stain electron microscopy of the host–phage G interaction reveals tail sheaths that are contracted towards the distal tip and decoupled from the head–neck region. This is different from the typical myophage tail contraction, where the sheath contracts upward, while being linked to the head–neck region. Our cryo-EM structures of the non-contracted and contracted tail sheath show that: (1) The protein fold of the sheath protein is very similar to its counterpart in smaller, contractile phages such as T4 and phi812; (2) Phage G’s sheath structure in the non-contracted and contracted states are similar to phage T4’s sheath structure. Similarity to other myophages is confirmed by a comparison-based study of the tail sheath’s helical symmetry, the sheath protein’s evolutionary timetree, and the organization of genes involved in tail morphogenesis. Atypical phase G tail contraction could be due to a missing anchor point at the upper end of the tail sheath that allows the decoupling of the sheath from the head–neck region. Explaining the atypical tail contraction requires further investigation of the phage G sheath anchor points.
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Santin YG, Doan T, Journet L, Cascales E. Cell Width Dictates Type VI Secretion Tail Length. Curr Biol 2019; 29:3707-3713.e3. [DOI: 10.1016/j.cub.2019.08.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/25/2019] [Accepted: 08/21/2019] [Indexed: 01/22/2023]
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Taylor NMI, van Raaij MJ, Leiman PG. Contractile injection systems of bacteriophages and related systems. Mol Microbiol 2018; 108:6-15. [PMID: 29405518 DOI: 10.1111/mmi.13921] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2018] [Indexed: 12/31/2022]
Abstract
Contractile tail bacteriophages, or myobacteriophages, use a sophisticated biomolecular structure to inject their genome into the bacterial host cell. This structure consists of a contractile sheath enveloping a rigid tube that is sharpened by a spike-shaped protein complex at its tip. The spike complex forms the centerpiece of a baseplate complex that terminates the sheath and the tube. The baseplate anchors the tail to the target cell membrane with the help of fibrous proteins emanating from it and triggers contraction of the sheath. The contracting sheath drives the tube with its spiky tip through the target cell membrane. Subsequently, the bacteriophage genome is injected through the tube. The structural transformation of the bacteriophage T4 baseplate upon binding to the host cell has been recently described in near-atomic detail. In this review we discuss structural elements and features of this mechanism that are likely to be conserved in all contractile injection systems (systems evolutionary and structurally related to contractile bacteriophage tails). These include the type VI secretion system (T6SS), which is used by bacteria to transfer effectors into other bacteria and into eukaryotic cells, and tailocins, a large family of contractile bacteriophage tail-like compounds that includes the P. aeruginosa R-type pyocins.
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Affiliation(s)
- Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Calle Darwin 3, E-28049 Madrid, Spain
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, 301 University Blvd, University of Texas Medical Branch, Galveston, TX 77555-0647, USA
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6
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Abstract
Many icosahedral viruses use a specialized portal vertex for genome encapsidation in the viral capsid (or head). This structure then controls release of the viral genetic information to the host cell at the beginning of infection. In tailed bacteriophages, the portal system is connected to a tail device that delivers their genome to the bacterial cytoplasm. The head-to-tail interface is a multiprotein complex that locks the viral DNA inside the phage capsid correctly positioned for egress and that controls its ejection when the viral particle interacts with the host cell receptor. Here we review the molecular mechanisms how this interface is assembled and how it carries out those two critical steps in the life cycle of tailed phages.
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Affiliation(s)
- Paulo Tavares
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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7
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Structural remodeling of bacteriophage T4 and host membranes during infection initiation. Proc Natl Acad Sci U S A 2015; 112:E4919-28. [PMID: 26283379 DOI: 10.1073/pnas.1501064112] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The first stages of productive bacteriophage infections of bacterial host cells require efficient adsorption to the cell surface followed by ejection of phage DNA into the host cytoplasm. To achieve this goal, a phage virion must undergo significant structural remodeling. For phage T4, the most obvious change is the contraction of its tail. Here, we use skinny E. coli minicells as a host, along with cryo-electron tomography and mutant phage virions, to visualize key structural intermediates during initiation of T4 infection. We show for the first time that most long tail fibers are folded back against the tail sheath until irreversible adsorption, a feature compatible with the virion randomly walking across the cell surface to find an optimal site for infection. Our data confirm that tail contraction is triggered by structural changes in the baseplate, as intermediates were found with remodeled baseplates and extended tails. After contraction, the tail tube penetrates the host cell periplasm, pausing while it degrades the peptidoglycan layer. Penetration into the host cytoplasm is accompanied by a dramatic local outward curvature of the cytoplasmic membrane as it fuses with the phage tail tip. The baseplate hub protein gp27 and/or the ejected tape measure protein gp29 likely form the transmembrane channel for viral DNA passage into the cell cytoplasm. Building on the wealth of prior biochemical and structural information, this work provides new molecular insights into the mechanistic pathway of T4 phage infection.
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8
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Rybakova D, Schramm P, Mitra AK, Hurst MRH. Afp14 is involved in regulating the length of Anti-feeding prophage (Afp). Mol Microbiol 2015; 96:815-26. [DOI: 10.1111/mmi.12974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Daria Rybakova
- Innovative Farm Systems; AgResearch; Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
| | - Peter Schramm
- Academy of Life Science, Engineering, and Design; Saxion University of Applied Science; Enschede M.H. Tromplaan 28 7513 AB Enschede The Netherlands
| | - Alok K. Mitra
- School of Biological Sciences; University of Auckland; Thomas Building 3A Symonds Street Auckland New Zealand
| | - Mark R. H. Hurst
- Innovative Farm Systems; AgResearch; Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
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9
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Auzat I, Petitpas I, Lurz R, Weise F, Tavares P. A touch of glue to complete bacteriophage assembly: the tail-to-head joining protein (THJP) family. Mol Microbiol 2014; 91:1164-78. [DOI: 10.1111/mmi.12526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Isabelle Auzat
- Laboratoire de Virologie Moléculaire et Structurale; Centre de Recherche de Gif; CNRS UPR 3296 and IFR115; 91198 Gif-sur-Yvette France
| | - Isabelle Petitpas
- Laboratoire de Virologie Moléculaire et Structurale; Centre de Recherche de Gif; CNRS UPR 3296 and IFR115; 91198 Gif-sur-Yvette France
| | - Rudi Lurz
- Max Planck Institute for Molecular Genetics; Ihnestraße 63-73 D-14195 Berlin Germany
| | - Frank Weise
- Max Planck Institute for Molecular Genetics; Ihnestraße 63-73 D-14195 Berlin Germany
| | - Paulo Tavares
- Laboratoire de Virologie Moléculaire et Structurale; Centre de Recherche de Gif; CNRS UPR 3296 and IFR115; 91198 Gif-sur-Yvette France
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10
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Heymann JB, Bartho JD, Rybakova D, Venugopal HP, Winkler DC, Sen A, Hurst MRH, Mitra AK. Three-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. J Biol Chem 2013; 288:25276-25284. [PMID: 23857636 DOI: 10.1074/jbc.m113.456145] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Serratia entomophila antifeeding prophage (Afp) is a bullet-shaped toxin-delivery apparatus similar to the R-pyocins of Pseudomonas aeruginosa. Morphologically it resembles the sheathed tail of bacteriophages such as T4, including a baseplate at one end. It also shares features with the type VI secretion systems. Cryo-electron micrographs of tilted Afp specimens (up to 60 degrees) were analyzed to determine the correct cyclic symmetry to overcome the limitation imposed by exclusively side views in nominally untilted specimens. An asymmetric reconstruction shows clear 6-fold cyclic symmetry contrary to a previous conclusion of 4-fold symmetry based on analysis of only the preferred side views (Sen, A., Rybakova, D., Hurst, M. R., and Mitra, A. K. (2010) J. Bacteriol. 192, 4522-4525). Electron tomography of negatively stained Afp revealed right-handed helical striations in many of the particles, establishing the correct hand. Higher quality micrographs of untilted specimens were processed to produce a reconstruction at 2.0-nm resolution with imposed 6-fold symmetry. The helical parameters of the sheath were determined to be 8.14 nm for the subunit rise along and 40.5° for the rotation angle around the helix. The sheath is similar to that of the T4 phage tail but with a different arrangement of the subdomain of the polymerizing sheath protein(s). The central tube is similar to the diameter and axial width of the Hcp1 hexamer of P. aeruginosa type VI secretion system. The tube extends through the baseplate into a needle resembling the "puncture device" of the T4 tail. The tube contains density that may be the toxin and/or a length-determining protein.
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Affiliation(s)
- J Bernard Heymann
- From the NIAMS, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph D Bartho
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and
| | - Daria Rybakova
- Innovative Farm Systems, Agresearch, Lincoln, Christchurch 8140, New Zealand
| | - Hari P Venugopal
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and
| | - Dennis C Winkler
- From the NIAMS, National Institutes of Health, Bethesda, Maryland 20892
| | - Anindito Sen
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and
| | - Mark R H Hurst
- Innovative Farm Systems, Agresearch, Lincoln, Christchurch 8140, New Zealand
| | - Alok K Mitra
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and.
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11
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Rybakova D, Radjainia M, Turner A, Sen A, Mitra AK, Hurst MRH. Role of antifeeding prophage (Afp) protein Afp16 in terminating the length of the Afp tailocin and stabilizing its sheath. Mol Microbiol 2013; 89:702-14. [DOI: 10.1111/mmi.12305] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Mazdak Radjainia
- School of Biological Sciences; University of Auckland; Thomas Building, 3A Symonds Street; Auckland; New Zealand
| | - Adrian Turner
- School of Biological Sciences; University of Auckland; Thomas Building, 3A Symonds Street; Auckland; New Zealand
| | | | - Alok K. Mitra
- School of Biological Sciences; University of Auckland; Thomas Building, 3A Symonds Street; Auckland; New Zealand
| | - Mark R. H. Hurst
- Innovative Farm Systems; AgResearch; Lincoln Research Centre; Private Bag 4749; Christchurch; 8140; New Zealand
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12
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Fokine A, Zhang Z, Kanamaru S, Bowman VD, Aksyuk AA, Arisaka F, Rao VB, Rossmann MG. The molecular architecture of the bacteriophage T4 neck. J Mol Biol 2013; 425:1731-44. [PMID: 23434847 PMCID: PMC3746776 DOI: 10.1016/j.jmb.2013.02.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 01/07/2023]
Abstract
A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently assembled head. Here we report the crystal structure of the gp15 hexamer, describe its interactions in T4 virions that have either an extended tail or a contracted tail, and discuss its structural relationship to other phage proteins. The neck of T4 virions is decorated by the "collar" and "whiskers", made of fibritin molecules. Fibritin acts as a chaperone helping to attach the long tail fibers to the virus during the assembly process. The collar and whiskers are environment-sensing devices, regulating the retraction of the long tail fibers under unfavorable conditions, thus preventing infection. Cryo-electron microscopy analysis suggests that twelve fibritin molecules attach to the phage neck with six molecules forming the collar and six molecules forming the whiskers.
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Affiliation(s)
- Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Zhihong Zhang
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Shuji Kanamaru
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA,Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-9 4259 Nagatsuta, Midori-ku, Yokohama 226–8501, Japan
| | - Valorie D. Bowman
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Anastasia A. Aksyuk
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Fumio Arisaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-9 4259 Nagatsuta, Midori-ku, Yokohama 226–8501, Japan
| | - Venigalla B. Rao
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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13
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Davidson AR, Cardarelli L, Pell LG, Radford DR, Maxwell KL. Long noncontractile tail machines of bacteriophages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:115-42. [PMID: 22297512 DOI: 10.1007/978-1-4614-0980-9_6] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this chapter, we describe the structure, assembly, function, and evolution of the long, noncontractile tail of the siphophages, which comprise ∼60% of the phages on earth. We place -particular emphasis on features that are conserved among all siphophages, and trace evolutionary connections between these phages and myophages, which possess long contractile tails. The large number of high-resolution structures of tail proteins solved recently coupled to studies of tail-related complexes by electron microscopy have provided many new insights in this area. In addition, the availability of thousands of phage and prophage genome sequences has allowed the delineation of several large families of tail proteins that were previously unrecognized. We also summarize current knowledge pertaining to the mechanisms by which siphophage tails recognize the bacterial cell surface and mediate DNA injection through the cell envelope. We show that phages infecting Gram-positive and Gram-negative bacteria possess distinct families of proteins at their tail tips that are involved in this process. Finally, we speculate on the evolutionary advantages provided by long phage tails.
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Affiliation(s)
- Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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14
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Abstract
Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.
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15
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Pell LG, Liu A, Edmonds L, Donaldson LW, Howell PL, Davidson AR. The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages. J Mol Biol 2009; 389:938-51. [PMID: 19426744 DOI: 10.1016/j.jmb.2009.04.072] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 04/23/2009] [Accepted: 04/28/2009] [Indexed: 01/28/2023]
Abstract
The tail terminator protein (TrP) plays an essential role in phage tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for phage heads. Here, we present the 2.7-A crystal structure of a hexameric ring of gpU, the TrP of phage lambda. Using sequence alignment analysis and site-directed mutagenesis, we have shown that this multimeric structure is biologically relevant and we have delineated its functional surfaces. Comparison of the hexameric crystal structure with the solution structure of gpU that we previously solved using NMR spectroscopy shows large structural changes occurring upon multimerization and suggests a mechanism that allows gpU to remain monomeric at high concentrations on its own, yet polymerize readily upon contact with an assembled tail tube. The gpU hexamer displays several flexible loops that play key roles in head and tail binding, implying a role for disorder-to-order transitions in controlling assembly as has been observed with other lambda morphogenetic proteins. Finally, we have found that the hexameric structure of gpU is very similar to the structure of a putative TrP from a contractile phage tail even though it displays no detectable sequence similarity. This finding coupled with further bioinformatic investigations has led us to conclude that the TrPs of non-contractile-tailed phages, such as lambda, are evolutionarily related to those of contractile-tailed phages, such as P2 and Mu, and that all long-tailed phages may utilize a conserved mechanism for tail termination.
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Affiliation(s)
- Lisa G Pell
- Department of Biochemistry, University of Toronto, ON, Canada
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16
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Akhter T, Zhao L, Kohda A, Mio K, Kanamaru S, Arisaka F. The neck of bacteriophage T4 is a ring-like structure formed by a hetero-oligomer of gp13 and gp14. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1036-43. [PMID: 17602902 DOI: 10.1016/j.bbapap.2007.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 05/01/2007] [Accepted: 05/10/2007] [Indexed: 11/26/2022]
Abstract
After packaging of DNA into the head of bacteriophage T4 is completed, a neck is formed at the portal vertex of the head to be ready for the tail attachment. The main components of the neck are gp13 and gp14 (gp: gene product), which consist of 309 and 256 amino acid residues, respectively. In order to elucidate the structure and subunit arrangement in the neck, overexpression systems of gene 13 and gene 14 were constructed and purified to homogeneity. Far-UV circular dichroism (CD) spectra of gp13 and gp14 indicated that gp13 is rich in alpha-helices whereas gp14 is rich in beta-sheets. Sedimentation velocity analysis of gp13 and gp14 revealed that both proteins are present as monomers in solution. The frictional ratios (f/f(0)) of the two proteins indicated that gp14 has a more elongated shape than gp13. Although isolated gp13 and gp14 do not interact with each other when mixed under physiological conditions, they form a hetero-oligomer complex with the stoichiometry of 10:5 after treatment with ammonium sulfate. Electron microscopy of this complex has shown that it forms a ring-like structure of 15 nm in diameter.
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Affiliation(s)
- Tahmina Akhter
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4359-B39 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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17
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Fiebig A, Keren K, Theriot JA. Fine-scale time-lapse analysis of the biphasic, dynamic behaviour of the two Vibrio cholerae chromosomes. Mol Microbiol 2007; 60:1164-78. [PMID: 16689793 PMCID: PMC2779472 DOI: 10.1111/j.1365-2958.2006.05175.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Using fluorescent repressor-operator systems in live cells, we investigated the dynamic behaviour of chromosomal origins in Vibrio cholerae, whose genome is divided between two chromosomes. We have developed a method of analysing fine-scale motion in the curved co-ordinate system of vibrioid bacteria. Using this method, we characterized two different modes of chromosome behaviour corresponding to periods between segregation events and periods of segregation. Between segregation events, the origin positions are not fixed but rather maintained within ellipsoidal caged domains, similar to eukaryotic interphase chromosome territories. These domains are approximately 0.4 µm wide and 0.6 µm long, reflecting greater restriction in the short axis of the cell. During segregation, movement is directionally biased, speed is comparable between origins, and cell growth can account for nearly 20% of the motion observed. Furthermore, the home domain of each origin is positioned by a different mechanism. Specifically, the oriCI domain is maintained at a constant actual distance from the pole regardless of cell length, while the oriCII domain is maintained at a constant relative position. Thus the actual position of oriCII varies with cell length. While the gross behaviours of the two origins are distinct, their fine-scale dynamics are remarkably similar, indicating that both experience similar microenvironments.
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Affiliation(s)
| | | | - Julie A Theriot
- *For correspondence. E-mail ; Tel. (+1) 650 725 7968; Fax (+1) 650 725 6044
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18
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Edmonds L, Liu A, Kwan JJ, Avanessy A, Caracoglia M, Yang I, Maxwell KL, Rubenstein J, Davidson AR, Donaldson LW. The NMR structure of the gpU tail-terminator protein from bacteriophage lambda: identification of sites contributing to Mg(II)-mediated oligomerization and biological function. J Mol Biol 2006; 365:175-86. [PMID: 17056065 DOI: 10.1016/j.jmb.2006.09.068] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 09/20/2006] [Accepted: 09/25/2006] [Indexed: 11/29/2022]
Abstract
During the late stages of lambda bacteriophage assembly, the protein gpU terminates tail polymerization and participates at the interface between the mature capsid and tail components. When it engages the lambda tail, gpU undergoes a monomer-hexamer transition to achieve its biologically active form. Towards understanding how gpU participates in multiple protein-protein interactions, we have solved the structure of gpU in its monomeric state using NMR methods. The structure reveals a mixed alpha/beta motif with several dynamic loops at the periphery. Addition of 20 mM MgCl(2) is known to oligomerize gpU in the absence of its protein partners. Multiple image analysis of electron micrographs revealed ring-like structures of magnesium ion saturated gpU with a 30 A pore, consistent with its function as a portal for the passage of viral DNA into the host bacterium. The ability of magnesium ions to promote oligomerization was lost when substitutions were made at a cluster of acidic amino acids in the vicinity of helix alpha2 and the beta1-beta2 loop. Furthermore, substitutions at these sites abolished the biological activity of gpU.
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Affiliation(s)
- Lizbeth Edmonds
- Department of Biology, York University, 4700 Keele Street, Canada M3J 1P3
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19
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Rossmann MG, Mesyanzhinov VV, Arisaka F, Leiman PG. The bacteriophage T4 DNA injection machine. Curr Opin Struct Biol 2005; 14:171-80. [PMID: 15093831 DOI: 10.1016/j.sbi.2004.02.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The tail of bacteriophage T4 consists of a contractile sheath surrounding a rigid tube and terminating in a multiprotein baseplate, to which the long and short tail fibers of the phage are attached. Upon binding of the fibers to their cell receptors, the baseplate undergoes a large conformational switch, which initiates sheath contraction and culminates in transfer of the phage DNA from the capsid into the host cell through the tail tube. The baseplate has a dome-shaped sixfold-symmetric structure, which is stabilized by a garland of six short tail fibers, running around the periphery of the dome. In the center of the dome, there is a membrane-puncturing device, containing three lysozyme domains, which disrupts the intermembrane peptidoglycan layer during infection.
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Affiliation(s)
- Michael G Rossmann
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, USA.
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20
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Abstract
The problem of organelle size control can be addressed most simply by considering cellular structures that are linear, so that their size can be defined by a single parameter: length. We compare existing studies on several linear biological structures including prokaryotic flagella and flagellar hooks, eukaryotic flagella, sarcomere thin filaments, and microvilli. In some cases, existing evidence strongly supports the idea that length control involves a molecular ruler, in which the size of the overall structure is compared with the size of an individual molecule. In other cases, length control is likely to involve a steady-state balance of assembly and disassembly, in which one or the other rate is inherently length dependent. The lessons learned from size control in linear structures should be applicable to organelles with more complex three-dimensional structures.
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, CA 94143, USA.
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21
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Leiman PG, Chipman PR, Kostyuchenko VA, Mesyanzhinov VV, Rossmann MG. Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host. Cell 2004; 118:419-29. [PMID: 15315755 DOI: 10.1016/j.cell.2004.07.022] [Citation(s) in RCA: 207] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2004] [Revised: 06/23/2004] [Accepted: 06/28/2004] [Indexed: 11/16/2022]
Abstract
The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal to a star shape. This causes the sheath around the tail tube to contract and the tail tube to protrude from the baseplate and pierce the outer cell membrane and the cell wall before reaching the inner cell membrane for subsequent viral DNA injection. Analogously, the T4 tail can be contracted by treatment with 3 M urea. The structure of the T4 contracted tail, including the head-tail joining region, has been determined by cryo-electron microscopy to 17 A resolution. This 1200 A-long, 20 MDa structure has been interpreted in terms of multiple copies of its approximately 20 component proteins. A comparison with the metastable hexagonal baseplate of the mature virus shows that the baseplate proteins move as rigid bodies relative to each other during the structural change.
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Affiliation(s)
- Petr G Leiman
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
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Mesyanzhinov VV. Bacteriophage T4: Structure, Assembly, and Initiation Infection Studied in Three Dimensions. Adv Virus Res 2004; 63:287-352. [PMID: 15530564 DOI: 10.1016/s0065-3527(04)63005-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Vadim V Mesyanzhinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya S., 117997 Moscow, Russia
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23
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Leiman PG, Shneider MM, Kostyuchenko VA, Chipman PR, Mesyanzhinov VV, Rossmann MG. Structure and location of gene product 8 in the bacteriophage T4 baseplate. J Mol Biol 2003; 328:821-33. [PMID: 12729757 DOI: 10.1016/s0022-2836(03)00366-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Many bacteriophages, such as T4, T7, RB49, and phi29, have complex, sometimes multilayered, tails that facilitate an almost 100% success rate for the viral particles to infect host cells. In bacteriophage T4, there is a baseplate, which is a multiprotein assembly, at the distal end of the contractile tail. The baseplate communicates to the tail that the phage fibers have attached to the host cell, thereby initiating the infection process. Gene product 8 (gp8), whose amino acid sequence consists of 334 residues, is one of at least 16 different structural proteins that constitute the T4 baseplate and is the sixth baseplate protein whose structure has been determined. A 2.0A resolution X-ray structure of gp8 shows that the two-domain protein forms a dimer, in which each monomer consists of a three-layered beta-sandwich with two loops, each containing an alpha-helix at the opposite sides of the sandwich. The crystals of gp8 were produced in the presence of concentrated chloride and bromide ions, resulting in at least 11 halide-binding sites per monomer. Five halide sites, situated at the N termini of alpha-helices, have a protein environment observed in other halide-containing protein crystal structures. The computer programs EMfit and SITUS were used to determine the positions of six gp8 dimers within the 12A resolution cryo-electron microscopy image reconstruction of the baseplate-tail tube complex. The gp8 dimers were found to be located in the upper part of the baseplate outer rim. About 20% of the gp8 surface is involved in contacts with other baseplate proteins, presumed to be gp6, gp7, and gp10. With the structure determination of gp8, a total of 53% of the volume of the baseplate has now been interpreted in terms of its atomic structure.
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Affiliation(s)
- Petr G Leiman
- Department of Biological Sciences, Purdue University, Lilly Hall of Life Sciences, West Lafayette, IN 47907-2054, USA
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24
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Zhao L, Kanamaru S, Chaidirek C, Arisaka F. P15 and P3, the tail completion proteins of bacteriophage T4, both form hexameric rings. J Bacteriol 2003; 185:1693-700. [PMID: 12591887 PMCID: PMC148078 DOI: 10.1128/jb.185.5.1693-1700.2003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two proteins, gp15 and gp3 (gp for gene product), are required to complete the assembly of the T4 tail. gp15 forms the connector which enables the tail to bind to the head, whereas gp3 is involved in terminating the elongation of the tail tube. In this work, genes 15 and 3 were cloned and overexpressed, and the purified gene products were studied by analytical ultracentrifugation, electron microscopy, and circular dichroism. Determination of oligomerization state by sedimentation equilibrium revealed that both gp15 and gp3 are hexamers of the respective polypeptide chains. Electron microscopy of the negatively stained P15 and P3 (P denotes the oligomeric state of the gene product) revealed that both proteins form hexameric rings, the diameter of which is close to that of the tail tube. The differential roles between gp15 and gp3 upon completion of the tail are discussed.
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Affiliation(s)
- Li Zhao
- Department of Molecular and Cellular Assembly, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
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25
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003; 67:86-156, table of contents. [PMID: 12626685 PMCID: PMC150520 DOI: 10.1128/mmbr.67.1.86-156.2003] [Citation(s) in RCA: 551] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
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Affiliation(s)
- Eric S Miller
- Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA.
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Tétart F, Desplats C, Kutateladze M, Monod C, Ackermann HW, Krisch HM. Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J Bacteriol 2001; 183:358-66. [PMID: 11114936 PMCID: PMC94885 DOI: 10.1128/jb.183.1.358-366.2001] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined a number of bacteriophages with T4-type morphology that propagate in different genera of enterobacteria, Aeromonas, Burkholderia, and Vibrio. Most of these phages had a prolate icosahedral head, a contractile tail, and a genome size that was similar to that of T4. A few of them had more elongated heads and larger genomes. All these phages are phylogenetically related, since they each had sequences homologous to the capsid gene (gene 23), tail sheath gene (gene 18), and tail tube gene (gene 19) of T4. On the basis of the sequence comparison of their virion genes, the T4-type phages can be classified into three subgroups with increasing divergence from T4: the T-evens, pseudoT-evens, and schizoT-evens. In general, the phages that infect closely related host species have virion genes that are phylogenetically closer to each other than those of phages that infect distantly related hosts. However, some of the phages appear to be chimeras, indicating that, at least occasionally, some genetic shuffling has occurred between the different T4-type subgroups. The compilation of a number of gene 23 sequences reveals a pattern of conserved motifs separated by sequences that differ in the T4-type subgroups. Such variable patches in the gene 23 sequences may determine the size of the virion head and consequently the viral genome length. This sequence analysis provides molecular evidence that phages related to T4 are widespread in the biosphere and diverged from a common ancestor in acquiring the ability to infect different host bacteria and to occupy new ecological niches.
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Affiliation(s)
- F Tétart
- Laboratoire de Microbiologie et Génétique Moléculaire du CNRS, Toulouse, France
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