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Zhang L, Yan Y, Gan Q, She Z, Zhu K, Wang J, Gao Z, Dong Y, Gong Y. Structural and functional characterization of the deep-sea thermophilic bacteriophage GVE2 tailspike protein. Int J Biol Macromol 2020; 164:4415-4422. [PMID: 32926904 DOI: 10.1016/j.ijbiomac.2020.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
The genome of the thermophilic bacteriophage GVE2 encodes a putative tailspike protein (GVE2 TSP). Here we report the crystal structure of the truncated GVE2 TSP at 2.0-Å resolution lacking 204 amino acid residues at its N-terminus (ΔnGVE2 TSP), possessing a "vase" outline similar to other TSP's structures. However, ΔnGVE2 TSP displays structural characteristics distinct from other TSPs. Despite lacking 204 amino acid residues, the head domain forms an asymmetric trimer compared to symmetric in other TSPs, suggesting that its long N-terminus may be unique to the long-tailed bacteriophages. Furthermore, the α-helix of the neck is 5-7 amino acids longer than that of other TSPs. The most striking feature is that its binding domain consists of a β-helix with 10 turns, whereas other TSPs have 13 turns, even including the phage Sf6 TSP, which is the closest homologue of GVE2 TSP. The C-terminal structure is also quite different with those of other TSPs. Furthermore, we observed that ΔnGVE2 TSP can slow down growth of its host, demonstrating that this TSP is essential for the phage GVE2 to infect its host. Overall, the structural characteristics suggest that GVE2 TSP may be more primitive than other phage TSPs.
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Affiliation(s)
- Likui Zhang
- Guangling College, Yangzhou University, China; Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, China
| | - Yuhua Yan
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China; Institute of Physical Science and Information Technology, Anhui University, China
| | - Qi Gan
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, China
| | - Zhun She
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Keli Zhu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China; Institute of Physical Science and Information Technology, Anhui University, China
| | - Jinhui Wang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - Zengqiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China
| | - Yong Gong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, China.
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Ueno T, Niwase K, Tsubokawa D, Kikuchi K, Takai N, Furuta T, Kawano R, Uchihashi T. Dynamic behavior of an artificial protein needle contacting a membrane observed by high-speed atomic force microscopy. NANOSCALE 2020; 12:8166-8173. [PMID: 32239053 DOI: 10.1039/d0nr01121e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacteriophage T4 and other bacteriophages have a protein component known as a molecular needle which is used for the transmembrane reaction in the infection process. In this paper, the transmembrane reaction mechanisms of artificial protein needles (PNs) constructed by protein engineering of the component protein of bacteriophage T4 are elucidated by observation of single-molecules by high-speed atomic force microscopy (HS-AFM) and molecular dynamics (MD) simulations. The HS-AFM images indicate that the tip of the needle structure stabilizes the interaction of the needle with the membrane surface and is involved in controlling the contact angle and angular velocity with respect to the membrane. The MD simulations indicate that the dynamic behavior of PN is governed by hydrogen bonds between the membrane phosphate fragments and the tip. Moreover, quartz crystal microbalance (QCM) and electrophysiological experiments indicate that the tip structure of PN affects its kinetic behavior and membrane potential. These results demonstrate that protein assemblies derived from natural biosupramolecules can be used to create nanomaterials with rationally-designed functionality.
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Affiliation(s)
- Takafumi Ueno
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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Iwasaki T, Yamashita E, Nakagawa A, Enomoto A, Tomihara M, Takeda S. Three-dimensional structures of bacteriophage neck subunits are shared inPodoviridae,SiphoviridaeandMyoviridae. Genes Cells 2018; 23:528-536. [DOI: 10.1111/gtc.12594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/10/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Takuma Iwasaki
- Faculty of Science and Technology; Division of Molecular Science; Gunma University; Kiryu Gunma Japan
| | - Eiki Yamashita
- Institute for Protein Research; Osaka University; Suita Osaka Japan
| | - Atsushi Nakagawa
- Institute for Protein Research; Osaka University; Suita Osaka Japan
| | - Atsushi Enomoto
- Faculty of Science and Technology; Division of Molecular Science; Gunma University; Kiryu Gunma Japan
| | - Masashi Tomihara
- Faculty of Science and Technology; Division of Molecular Science; Gunma University; Kiryu Gunma Japan
| | - Shigeki Takeda
- Faculty of Science and Technology; Division of Molecular Science; Gunma University; Kiryu Gunma Japan
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Inaba H, Ueno T. Artificial bio-nanomachines based on protein needles derived from bacteriophage T4. Biophys Rev 2017; 10:641-658. [PMID: 29147941 DOI: 10.1007/s12551-017-0336-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
Bacteriophage T4 is a natural bio-nanomachine which achieves efficient infection of host cells via cooperative motion of specific three-dimensional protein architectures. The relationships between the protein structures and their dynamic functions have recently been clarified. In this review we summarize the design principles for fabrication of nanomachines using the component proteins of bacteriophage T4 based on these recent advances. We focus on the protein needle known as gp5, which is located at the center of the baseplate at the end of the contractile tail of bacteriophage T4. This protein needle plays a critical role in directly puncturing host cells, and analysis has revealed that it contains a common motif used for cell puncture in other known injection systems, such as T6SS. Our artificial needle based on the β-helical domain of gp5 retains the ability to penetrate cells and can be engineered to deliver various cargos into living cells. Thus, the unique components of bacteriophage T4 and other natural nanomachines have great potential for use as molecular scaffolds in efforts to fabricate new bio-nanomachines.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
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5
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Takeda S. Most of it started with T4 phage and was then taken over. Biophys Rev 2017; 10:141-144. [PMID: 28986776 DOI: 10.1007/s12551-017-0326-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/06/2017] [Indexed: 11/27/2022] Open
Abstract
Professor Fumio Arisaka is one of the famous leaders in bacteriophage research, especially in the areas of protein biophysics and structural biology. Autonomous phage morphogenesis is a self-assembly process controlled by subunit-subunit interaction. Under this principle, Fumio has studied T4 tail assembly and morphology. He has also contributed structural information about T4 phage through a combination of X-ray structural analysis and three-dimensional image reconstruction using cryo-electron microscopy. Most of the development of ultracentrifugation applications for molecular assembly and phage morphogenesis research was also performed in Fumio's laboratory. Fumio is a pioneer of supramolecular protein assembly study, and his science continues in the research work of the approximately 150 people who had attended his final lecture at the Tokyo Institute of Technology.
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Affiliation(s)
- Shigeki Takeda
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan.
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Bacteriophage ϕMAM1, a viunalikevirus, is a broad-host-range, high-efficiency generalized transducer that infects environmental and clinical isolates of the enterobacterial genera Serratia and Kluyvera. Appl Environ Microbiol 2014; 80:6446-57. [PMID: 25107968 DOI: 10.1128/aem.01546-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Members of the enterobacterial genus Serratia are ecologically widespread, and some strains are opportunistic human pathogens. Bacteriophage ϕMAM1 was isolated on Serratia plymuthica A153, a biocontrol rhizosphere strain that produces the potently bioactive antifungal and anticancer haterumalide oocydin A. The ϕMAM1 phage is a generalized transducing phage that infects multiple environmental and clinical isolates of Serratia spp. and a rhizosphere strain of Kluyvera cryocrescens. Electron microscopy allowed classification of ϕMAM1 in the family Myoviridae. Bacteriophage ϕMAM1 is virulent, uses capsular polysaccharides as a receptor, and can transduce chromosomal markers at frequencies of up to 7 × 10(-6) transductants per PFU. We also demonstrated transduction of the complete 77-kb oocydin A gene cluster and heterogeneric transduction of a plasmid carrying a type III toxin-antitoxin system. These results support the notion of the potential ecological importance of transducing phages in the acquisition of genes by horizontal gene transfer. Phylogenetic analyses grouped ϕMAM1 within the ViI-like bacteriophages, and genomic analyses revealed that the major differences between ϕMAM1 and other ViI-like phages arise in a region encoding the host recognition determinants. Our results predict that the wider genus of ViI-like phages could be efficient transducing phages, and this possibility has obvious implications for the ecology of horizontal gene transfer, bacterial functional genomics, and synthetic biology.
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Harada K, Yamashita E, Nakagawa A, Miyafusa T, Tsumoto K, Ueno T, Toyama Y, Takeda S. Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:284-91. [PMID: 22922659 DOI: 10.1016/j.bbapap.2012.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 07/30/2012] [Accepted: 08/16/2012] [Indexed: 11/16/2022]
Abstract
Bacteriophage Mu, which has a contractile tail, is one of the most famous genus of Myoviridae. It has a wide host range and is thought to contribute to horizontal gene transfer. The Myoviridae infection process is initiated by adhesion to the host surface. The phage then penetrates the host cell membrane using its tail to inject its genetic material into the host. In this penetration process, Myoviridae phages are proposed to puncture the membrane of the host cell using a central spike located beneath its baseplate. The central spike of the Mu phage is thought to be composed of gene 45 product (gp45), which has a significant sequence homology with the central spike of P2 phage (gpV). We determined the crystal structure of shortened Mu gp45Δ1-91 (Arg92-Gln197) at 1.5Å resolution and showed that Mu gp45 is a needlelike structure that punctures the membrane. The apex of Mu gp45 and that of P2 gpV contained iron, chloride, and calcium ions. Although the C-terminal domain of Mu gp45 was sufficient for binding to the E. coli membrane, a mutant D188A, in which the Asp amino acid residue that coordinates the calcium ion was replaced by Ala, did not exhibit a propensity to bind to the membrane. Therefore, we concluded that calcium ion played an important role in interaction with the host cell membrane.
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Affiliation(s)
- Kenichi Harada
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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Speight RE, Cooper MA. A Survey of the 2010 Quartz Crystal Microbalance Literature. J Mol Recognit 2012; 25:451-73. [DOI: 10.1002/jmr.2209] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Robert E. Speight
- Institute for Molecular Bioscience; The University of Queensland; St. Lucia; Brisbane; 4072; Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience; The University of Queensland; St. Lucia; Brisbane; 4072; Australia
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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: 88] [Impact Index Per Article: 7.3] [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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