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Cingolani G, Iglesias S, Hou CF, Lemire S, Soriaga A, Kyme P. Cryo-EM analysis of Pseudomonas phage Pa193 structural components. RESEARCH SQUARE 2024:rs.3.rs-4189479. [PMID: 38659960 PMCID: PMC11042391 DOI: 10.21203/rs.3.rs-4189479/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
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Cingolani G, Lokareddy R, Hou CF, Forti F, Iglesias S, Li F, Pavlenok M, Niederweis M, Briani F. Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor. RESEARCH SQUARE 2024:rs.3.rs-3941185. [PMID: 38463957 PMCID: PMC10925440 DOI: 10.21203/rs.3.rs-3941185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DEV is an obligatory lytic Pseudomonas phage of the N4-like genus, recently reclassified as Schitoviridae. The DEV genome encodes 91 ORFs, including a 3,398 amino acid virion-associated RNA polymerase. Here, we describe the complete architecture of DEV, determined using a combination of cryo-electron microscopy localized reconstruction, biochemical methods, and genetic knockouts. We built de novo structures of all capsid factors and tail components involved in host attachment. We demonstrate that DEV long tail fibers are essential for infection of Pseudomonas aeruginosa and dispensable for infecting mutants with a truncated lipopolysaccharide devoid of the O-antigen. We identified DEV ejection proteins and, unexpectedly, found that the giant DEV RNA polymerase, the hallmark of the Schitoviridae family, is an ejection protein. We propose that DEV ejection proteins form a genome ejection motor across the host cell envelope and that these structural principles are conserved in all Schitoviridae.
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3
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Liu Z, Tang K, Zhou Y, Liu T, Guo Y, Wu D, Wang X. Active prophages in coral-associated Halomonas capable of lateral transduction. THE ISME JOURNAL 2024; 18:wrae085. [PMID: 38739683 PMCID: PMC11131426 DOI: 10.1093/ismejo/wrae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.
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Affiliation(s)
- Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Yiqing Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
| | - Duoting Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, No.1, Yanqihu East Road, Huairou District, Beijing 101408, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
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4
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Gil J, Paulson J, Zahn H, Brown M, Nguyen MM, Erickson S. Development of a Replication-Deficient Bacteriophage Reporter Lacking an Essential Baseplate Wedge Subunit. Viruses 2023; 16:8. [PMID: 38275943 PMCID: PMC10821221 DOI: 10.3390/v16010008] [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: 11/03/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, the ability of these phages to propagate outside the laboratory was targeted. The phage SEA1 has been previously engineered to facilitate food safety as an accurate and sensitive reporter for Salmonella contamination. In this study, homologous recombination was used to replace the expression of an essential baseplate wedge subunit (gp141) in SEA1 with a luciferase, NanoLuc®. This reporter, referred to as SEA1Δgp141.NL, demonstrated a loss of plaque formation and a failure to increase in titer following infection of Salmonella. SEA1Δgp141.NL was thus incapable of producing infectious progeny in the absence of gp141. In contrast, production of high titer stocks was possible when gp141 was artificially supplied in trans during infection. As a reporter, SEA1Δgp141.NL facilitated rapid, sensitive, and robust detection of Salmonella despite an inability to replicate. These results suggest that replication-deficient reporter phages are an effective method to obtain improved containment without sacrificing significant performance or the ease of production associated with many phage-based diagnostic methods.
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Affiliation(s)
- Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA 90062, USA;
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Henriett Zahn
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC 27215, USA;
| | - Minh M. Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA; (J.P.); (H.Z.); (M.M.N.)
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5
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Chen YL, Bao CJ, Duan JL, Xie Y, Lu WL. Overcoming biological barriers by virus-like drug particles for drug delivery. Adv Drug Deliv Rev 2023; 203:115134. [PMID: 37926218 DOI: 10.1016/j.addr.2023.115134] [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: 09/09/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Virus-like particles (VLPs) have natural structural antigens similar to those found in viruses, making them valuable in vaccine immunization. Furthermore, VLPs have demonstrated significant potential in drug delivery, and emerged as promising vectors for transporting chemical drug, genetic drug, peptide/protein, and even nanoparticle drug. With virus-like permeability and strong retention, they can effectively target specific organs, tissues or cells, facilitating efficient intracellular drug release. Further modifications allow VLPs to transfer across various physiological barriers, thus acting the purpose of efficient drug delivery and accurate therapy. This article provides an overview of VLPs, covering their structural classifications, deliverable drugs, potential physiological barriers in drug delivery, strategies for overcoming these barriers, and future prospects.
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Affiliation(s)
- Yu-Ling Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and Drug Delivery Systems, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chun-Jie Bao
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and Drug Delivery Systems, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia-Lun Duan
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and Drug Delivery Systems, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ying Xie
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and Drug Delivery Systems, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | - Wan-Liang Lu
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and Drug Delivery Systems, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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Wang C, Chen M, Shao Y, Jiang M, Li Q, Chen L, Wu Y, Cen S, Waterfield NR, Yang J, Yang G. Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system. Commun Biol 2023; 6:1195. [PMID: 38001377 PMCID: PMC10673891 DOI: 10.1038/s42003-023-05580-w] [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] [Received: 05/31/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Type VI secretion systems (T6SSs) deliver effectors into target cells. Besides structural and effector proteins, many other proteins, such as adaptors, co-effectors and accessory proteins, are involved in this process. MIX domains can assist in the delivery of T6SS effectors when encoded as a stand-alone gene or fused at the N-terminal of the effector. However, whether there are other conserved domains exhibiting similar encoding forms to MIX in T6SS remains obscure. Here, we scanned publicly available bacterial genomes and established a database which include 130,825 T6SS vgrG loci from 45,041 bacterial genomes. Based on this database, we revealed six domain families encoded within vgrG loci, which are either fused at the C-terminus of VgrG/N-terminus of T6SS toxin or encoded by an independent gene. Among them, DUF2345 was further validated and shown to be indispensable for the T6SS effector delivery and LysM was confirmed to assist the interaction between VgrG and the corresponding effector. Together, our results implied that these widely distributed domain families with similar genetic configurations may be required for the T6SS effector recruitment process.
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Affiliation(s)
- Caihong Wang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Mingxing Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China
| | - Yuhan Shao
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Mengyuan Jiang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China
| | - Yun Wu
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- CAMS Key Laboratory of Antiviral Drug Research, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
| | - Guowei Yang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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7
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Panhwar S, Keerio HA, Ilhan H, Boyacı IH, Tamer U. Principles, Methods, and Real-Time Applications of Bacteriophage-Based Pathogen Detection. Mol Biotechnol 2023:10.1007/s12033-023-00926-5. [PMID: 37914863 DOI: 10.1007/s12033-023-00926-5] [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: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Bacterial pathogens in water, food, and the environment are spreading diseases around the world. According to a World Health Organization (WHO) report, waterborne pathogens pose the most significant global health risks to living organisms, including humans and animals. Conventional bacterial detection approaches such as colony counting, microscopic analysis, biochemical analysis, and molecular analysis are expensive, time-consuming, less sensitive, and require a pre-enrichment step. However, the bacteriophage-based detection of pathogenic bacteria is a robust approach that utilizes bacteriophages, which are viruses that specifically target and infect bacteria, for rapid and accurate detection of targets. This review shed light on cutting-edge technologies about the novel structure of phages and the immobilization process on the surface of electrodes to detect targeted bacterial cells. Similarly, the purpose of this study was to provide a comprehensive assessment of bacteriophage-based biosensors utilized for pathogen detection, as well as their trends, outcomes, and problems. This review article summaries current phage-based pathogen detection strategies for the development of low-cost lab-on-chip (LOC) and point-of-care (POC) devices using electrochemical and optical methods such as surface-enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- Sallahuddin Panhwar
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
- Department of Civil Engineering, National University of Sciences and Technology, Quetta, 24090, Balochistan, Pakistan.
| | - Hareef Ahmed Keerio
- Department of Civil and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
| | - Hasan Ilhan
- Department of Chemistry, Faculty of Science, Ordu University, Altinordu, 52200, Ordu, Turkey
| | - Ismail Hakkı Boyacı
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe, 06800, Ankara, Turkey
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
- Metu MEMS Center, Ankara, Turkey.
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8
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Schamp CN, Dhowlaghar N, Hudson LK, Bryan DW, Zhong Q, Fozo EM, Gaballa A, Wiedmann M, Denes TG. Selection of mutant Listeria phages under food-relevant conditions can enhance application potential. Appl Environ Microbiol 2023; 89:e0100723. [PMID: 37800961 PMCID: PMC10617581 DOI: 10.1128/aem.01007-23] [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] [Received: 06/15/2023] [Accepted: 08/04/2023] [Indexed: 10/07/2023] Open
Abstract
Bacteriophages are viruses that infect and kill bacteria. Currently, phage products are available for the control of the pathogen Listeria monocytogenes in food products in the United States. In this study, we explore whether experimental evolution can be used to generate phages with improved abilities to function under specific food-relevant conditions. Ultra-pasteurized oat and whole milk were chosen as test matrices as they represent different food groups, yet have similar physical traits and macronutrient composition. We showed that (i) wild-type phage LP-125 infection kinetics are different in the two matrices and (ii) LP-125 has a significantly higher burst size in oat milk. From this, we attempted to evolve LP-125 to have improved infection kinetics in whole milk. Ancestral LP-125 was passaged through 10 rounds of amplification in milk conditions. Plaque-purified DNA samples from milk-selected phages were isolated and sequenced, and mutations present in the isolated phages were identified. We found two nonsynonymous substitutions in LP125_108 and LP125_112 genes, which encode putative baseplate-associated glycerophosphoryl diester phosphodiesterase and baseplate protein, respectively. Protein structural modeling showed that the substituted amino acids in the mutant phages are predicted to localize to surface-exposed helices on the corresponding structures, which might affect the surface charge of proteins and their interaction with the bacterial cell. The phage containing the LP125_112 mutation adsorbed significantly faster than the ancestral phage in both oat and whole milk. Follow-up experiments suggest that fat content may be a key factor for the expression of the phenotype of this mutation. IMPORTANCE Bacteriophages are one of the tools available to control the foodborne pathogen, Listeria monocytogenes. Phage products must work under a broad range of food conditions to be an effective control for L. monocytogenes. Here, we show that the experimental evolution of phages can be used to generate new phages with phenotypes useful under specific conditions. We used this approach to select for a mutant phage that more efficiently binds to L. monocytogenes that is grown in whole milk and oat milk. We show that the fat content of these milks is necessary for the expression of this phenotype. Our findings show that experimental evolution can be used to select for improved phages with better performance under specific conditions. This approach has the potential to support the development of condition-specific phage-based biocontrols in the food industry.
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Affiliation(s)
- Claire N. Schamp
- Department of Food Science, The University of Tennessee, Knoxville, Tennessee, USA
| | - Nitin Dhowlaghar
- Department of Food Science, The University of Tennessee, Knoxville, Tennessee, USA
| | - Lauren K. Hudson
- Department of Food Science, The University of Tennessee, Knoxville, Tennessee, USA
| | - Daniel W. Bryan
- Department of Food Science, The University of Tennessee, Knoxville, Tennessee, USA
| | - Qixin Zhong
- Department of Food Science, The University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth M. Fozo
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Thomas G. Denes
- Department of Food Science, The University of Tennessee, Knoxville, Tennessee, USA
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9
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Wang Z, Fokine A, Guo X, Jiang W, Rossmann MG, Kuhn RJ, Luo ZH, Klose T. Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine. Viruses 2023; 15:1673. [PMID: 37632015 PMCID: PMC10457771 DOI: 10.3390/v15081673] [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: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance poses a growing risk to public health, requiring new tools to combat pathogenic bacteria. Contractile injection systems, including bacteriophage tails, pyocins, and bacterial type VI secretion systems, can efficiently penetrate cell envelopes and become potential antibacterial agents. Bacteriophage XM1 is a dsDNA virus belonging to the Myoviridae family and infecting Vibrio bacteria. The XM1 virion, made of 18 different proteins, consists of an icosahedral head and a contractile tail, terminated with a baseplate. Here, we report cryo-EM reconstructions of all components of the XM1 virion and describe the atomic structures of 14 XM1 proteins. The XM1 baseplate is composed of a central hub surrounded by six wedge modules to which twelve spikes are attached. The XM1 tail contains a fewer number of smaller proteins compared to other reported phage baseplates, depicting the minimum requirements for building an effective cell-envelope-penetrating machine. We describe the tail sheath structure in the pre-infection and post-infection states and its conformational changes during infection. In addition, we report, for the first time, the in situ structure of the phage neck region to near-atomic resolution. Based on these structures, we propose mechanisms of virus assembly and infection.
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Affiliation(s)
- Zhiqing Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- National Cryo-EM Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Xinwu Guo
- Sansure Biotech Inc., Changsha 410205, China
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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10
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Li F, Hou CFD, Lokareddy RK, Yang R, Forti F, Briani F, Cingolani G. High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217. Nat Commun 2023; 14:4052. [PMID: 37422479 PMCID: PMC10329688 DOI: 10.1038/s41467-023-39756-z] [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] [Received: 02/05/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023] Open
Abstract
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4.
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Affiliation(s)
- Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.
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11
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Yang F, Wang L, Zhou J, Xiao H, Liu H. In Situ Structures of the Ultra-Long Extended and Contracted Tail of Myoviridae Phage P1. Viruses 2023; 15:1267. [PMID: 37376567 DOI: 10.3390/v15061267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/20/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The Myoviridae phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the Myoviridae tail have been extensively studied, but the dynamic conformational changes before and after contraction and the associated molecular mechanism are still unclear. Here, we present the extended and contracted intact tail-structures of Myoviridae phage P1 by cryo-EM. The ultra-long tail of P1, 2450 Å in length, consists of a neck, a tail terminator, 53 repeated tail sheath rings, 53 repeated tube rings, and a baseplate. The sheath of the contracted tail shrinks by approximately 55%, resulting in the separation of the inner rigid tail tube from the sheath. The extended and contracted tails were further resolved by local reconstruction at 3.3 Å and 3.9 Å resolutions, respectively, allowing us to build the atomic models of the tail terminator protein gp24, the tube protein BplB, and the sheath protein gp22 for the extended tail, and of the sheath protein gp22 for the contracted tail. Our atomic models reveal the complex interaction network in the ultra-long Myoviridae tail and the novel conformational changes of the tail sheath between extended and contracted states. Our structures provide insights into the contraction and stabilization mechanisms of the Myoviridae tail.
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Affiliation(s)
- Fan Yang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
| | - Liwen Wang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
| | - Junquan Zhou
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
| | - Hao Xiao
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Hongrong Liu
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-Dimensional Quantum Structures and Quantum Control, Hunan Normal University, Changsha 410082, China
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12
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Degroux S, Effantin G, Linares R, Schoehn G, Breyton C. Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger. J Virol 2023; 97:e0158422. [PMID: 36779755 PMCID: PMC10062170 DOI: 10.1128/jvi.01584-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/05/2023] [Indexed: 02/14/2023] Open
Abstract
Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of bacteriophages, this host recognition is performed by receptor binding proteins (RBPs) located at the extremity of a tail. Interaction between the RBPs and the host is the trigger for bacteriophage infection, but the molecular details of the mechanisms are unknown for most bacteriophages. Here, we present the electron cryomicroscopy (cryo-EM) structure of bacteriophage T5 RBPpb5 in complex with its Escherichia coli receptor, the iron ferrichrome transporter FhuA. Monomeric RBPpb5 is located at the extremity of T5's long flexible tail, and its irreversible binding to FhuA commits T5 to infection. Analysis of the structure of RBPpb5 within the complex, comparison with its AlphaFold2-predicted structure, and its fit into a previously determined map of the T5 tail tip in complex with FhuA allow us to propose a mechanism of transmission of the RBPpb5 receptor binding to the straight fiber, initiating the cascade of events that commits T5 to DNA ejection. IMPORTANCE Tailed bacteriophages specifically recognize their bacterial host by interaction of their receptor binding protein(s) (RBPs) with saccharides and/or proteins located at the surface of their prey. This crucial interaction commits the virus to infection, but the molecular details of this mechanism are unknown for the majority of bacteriophages. We determined the structure of bacteriophage T5 RBPpb5 in complex with its E. coli receptor, FhuA, by cryo-EM. This first structure of an RBP bound to its protein receptor allowed us to propose a mechanism of transmission of host recognition to the rest of the phage, ultimately opening the capsid and perforating the cell wall and, thus, allowing safe channeling of the DNA into the host cytoplasm.
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Affiliation(s)
| | | | - Romain Linares
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Cécile Breyton
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
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13
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Sun L, You J, Li D, Zhang Z, Qin X, Pang W, Li P, Han Q, Li Y, Huang Z, Zhang X, Gong M, Yang H. Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8. MICROBIOME 2023; 11:18. [PMID: 36721246 PMCID: PMC9887876 DOI: 10.1186/s40168-022-01459-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/31/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Narrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins. RESULTS Here, we report that Pseudomonas phage K8 can evolve broader host range and higher killing efficiency at the cost of virion stability. Phage K8 host range mutant K8-T239A carries a mutant version of the putative baseplate wedge protein GP075, termed GP075m. While phage K8 adsorbs to hosts via the O-specific antigen of bacterial LPS, phage K8-T239A uses GP075m to also bind the bacterial core oligosaccharide, enabling infection of bacterial strains resistant to K8 infection due to modified O-specific antigens. This mutation in GP075 also alters inter-protein interactions among phage proteins, and reduces the stability of phage particles to environmental stressors like heat, acidity, and alkalinity. We find that a variety of mutations in gp075 are widespread in K8 populations, and that the gp075-like genes are widely distributed among the domains of life. CONCLUSION Our data show that a typical life history tradeoff occurs between the stability and the host range in the evolution of phage K8. Reservoirs of viral gene variants may be widely present in phage communities, allowing phages to rapidly adapt to any emerging environmental stressors. Video Abstract.
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Affiliation(s)
- Li Sun
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jiajia You
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xuying Qin
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wenjing Pang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Peize Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qingzhu Han
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yueying Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhiwei Huang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xixi Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | | | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
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14
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Fine structure and assembly pattern of a minimal myophage Pam3. Proc Natl Acad Sci U S A 2023; 120:e2213727120. [PMID: 36656854 PMCID: PMC9942802 DOI: 10.1073/pnas.2213727120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater Myoviridae cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.
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15
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Understanding Bacteriophage Tail Fiber Interaction with Host Surface Receptor: The Key “Blueprint” for Reprogramming Phage Host Range. Int J Mol Sci 2022; 23:ijms232012146. [PMID: 36292999 PMCID: PMC9603124 DOI: 10.3390/ijms232012146] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages (phages), as natural antibacterial agents, are being rediscovered because of the growing threat of multi- and pan-drug-resistant bacterial pathogens globally. However, with an estimated 1031 phages on the planet, finding the right phage to recognize a specific bacterial host is like looking for a needle in a trillion haystacks. The host range of a phage is primarily determined by phage tail fibers (or spikes), which initially mediate reversible and specific recognition and adsorption by susceptible bacteria. Recent significant advances at single-molecule and atomic levels have begun to unravel the structural organization of tail fibers and underlying mechanisms of phage–host interactions. Here, we discuss the molecular mechanisms and models of the tail fibers of the well-characterized T4 phage’s interaction with host surface receptors. Structure–function knowledge of tail fibers will pave the way for reprogramming phage host range and will bring future benefits through more-effective phage therapy in medicine. Furthermore, the design strategies of tail fiber engineering are briefly summarized, including machine-learning-assisted engineering inspired by the increasingly enormous amount of phage genetic information.
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16
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Fang Q, Tang WC, Fokine A, Mahalingam M, Shao Q, Rossmann MG, Rao VB. Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly. Proc Natl Acad Sci U S A 2022; 119:e2203272119. [PMID: 36161892 PMCID: PMC9546572 DOI: 10.1073/pnas.2203272119] [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] [Received: 02/27/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that transforms an immature unexpanded head into a mature genome-packaging head. Bacteriophage T4 is a model virus, well studied genetically and biochemically, but its structure determination has been challenging because of its large size and unusually prolate-shaped, ∼1,200-Å-long and ∼860-Å-wide capsid. Here, we report the cryogenic electron microscopy (cryo-EM) structures of T4 capsid in both of its major conformational states: unexpanded at a resolution of 5.1 Å and expanded at a resolution of 3.4 Å. These are among the largest structures deposited in Protein Data Bank to date and provide insights into virus assembly, head length determination, and shell expansion. First, the structures illustrate major domain movements and ∼70% additional gain in inner capsid volume, an essential transformation to contain the entire viral genome. Second, intricate intracapsomer interactions involving a unique insertion domain dramatically change, allowing the capsid subunits to rotate and twist while the capsomers remain fastened at quasi-threefold axes. Third, high-affinity binding sites emerge for a capsid decoration protein that clamps adjacent capsomers, imparting extraordinary structural stability. Fourth, subtle conformational changes at capsomers' periphery modulate intercapsomer angles between capsomer planes that control capsid length. Finally, conformational changes were observed at the symmetry-mismatched portal vertex, which might be involved in triggering head expansion. These analyses illustrate how small changes in local capsid subunit interactions lead to profound shifts in viral capsid morphology, stability, and volume.
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Affiliation(s)
- Qianglin Fang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wei-Chun Tang
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Marthandan Mahalingam
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064
| | - Qianqian Shao
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064
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17
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Tian F, Li J, Li L, Li F, Tong Y. Molecular dissection of the first Staphylococcus cohnii temperate phage IME1354_01. Virus Res 2022; 318:198812. [DOI: 10.1016/j.virusres.2022.198812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
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18
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Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N). Sci Rep 2022; 12:2061. [PMID: 35136138 PMCID: PMC8825819 DOI: 10.1038/s41598-022-06073-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/24/2022] [Indexed: 11/08/2022] Open
Abstract
Four tailspike proteins (TSP1-4) of Escherichia coli O157:H7 bacteriophage CBA120 enable infection of multiple hosts. They form a branched complex that attaches to the tail baseplate. Each TSP recognizes a different lipopolysaccharide on the membrane of a different bacterial host. The 335 N-terminal residues of TSP4 promote the assembly of the TSP complex and anchor it to the tail baseplate. The crystal structure of TSP4-N335 reveals a trimeric protein comprising four domains. The baseplate anchor domain (AD) contains an intertwined triple-stranded β-helix. The ensuing XD1, XD2 and XD3 β-sheet containing domains mediate the binding of TSP1-3 to TSP4. Each of the XD domains adopts the same fold as the respective XD domains of bacteriophage T4 gp10 baseplate protein, known to engage in protein–protein interactions via its XD2 and XD3 domains. The structural similarity suggests that XD2 and XD3 of TSP4 also function in protein–protein interactions. Analytical ultracentrifugation analyses of TSP4-N335 and of domain deletion proteins showed how TSP4-N335 promotes the formation of the TSP quaternary complex. TSP1 and TSP2 bind directly to TSP4 whereas TSP3 binding requires a pre-formed TSP4-N335:TSP2 complex. A 3-dimensional model of the bacteriophage CBA120 TSP complex has been developed based on the structural and ultracentrifuge information.
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19
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Farquharson EL, Lightbown A, Pulkkinen E, Russell T, Werner B, Nugen SR. Evaluating Phage Tail Fiber Receptor-Binding Proteins Using a Luminescent Flow-Through 96-Well Plate Assay. Front Microbiol 2021; 12:741304. [PMID: 34975779 PMCID: PMC8719110 DOI: 10.3389/fmicb.2021.741304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/25/2021] [Indexed: 12/02/2022] Open
Abstract
Phages have demonstrated significant potential as therapeutics in bacterial disease control and as diagnostics due to their targeted bacterial host range. Host range has typically been defined by plaque assays; an important technique for therapeutic development that relies on the ability of a phage to form a plaque upon a lawn of monoculture bacteria. Plaque assays cannot be used to evaluate a phage's ability to recognize and adsorb to a bacterial strain of interest if the infection process is thwarted post-adsorption or is temporally delayed, and it cannot highlight which phages have the strongest adsorption characteristics. Other techniques, such as classic adsorption assays, are required to define a phage's "adsorptive host range." The issue shared amongst all adsorption assays, however, is that they rely on the use of a complete bacteriophage and thus inherently describe when all adsorption-specific machinery is working together to facilitate bacterial surface adsorption. These techniques cannot be used to examine individual interactions between a singular set of a phage's adsorptive machinery (like long tail fibers, short tail fibers, tail spikes, etc.) and that protein's targeted bacterial surface receptor. To address this gap in knowledge we have developed a high-throughput, filtration-based, bacterial binding assay that can evaluate the adsorptive capability of an individual set of a phage's adsorption machinery. In this manuscript, we used a fusion protein comprised of an N-terminal bioluminescent tag translationally fused to T4's long tail fiber binding tip (gp37) to evaluate and quantify gp37's relative adsorptive strength against the Escherichia coli reference collection (ECOR) panel of 72 Escherichia coli isolates. Gp37 could adsorb to 61 of the 72 ECOR strains (85%) but coliphage T4 only formed plaques on 8 of the 72 strains (11%). Overlaying these two datasets, we were able to identify ECOR strains incompatible with T4 due to failed adsorption, and strains T4 can adsorb to but is thwarted in replication at a step post-adsorption. While this manuscript only demonstrates our assay's ability to characterize adsorptive capabilities of phage tail fibers, our assay could feasibly be modified to evaluate other adsorption-specific phage proteins.
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Affiliation(s)
| | | | | | | | | | - Sam R. Nugen
- Nugen Research Laboratory, Department of Food Science, Cornell University, Ithaca, NY, United States
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20
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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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21
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Investigating the process of sheath maturation in Anti-feeding prophage- a phage tail-like protein translocation structure. J Bacteriol 2021; 203:e0010421. [PMID: 34370558 DOI: 10.1128/jb.00104-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Anti-feeding prophage (Afp) produced by the bacterium Serratia entomophila is the archetype, external contractile injection system (eCIS). Afp and its orthologues are characterized by three sheath proteins while contractile bacteriophages and pyocins encode only one. Using targeted mutagenesis, transmission electron microscopy (TEM) and pull-down studies, we interrogated the roles of the three sheath proteins (Afp2, Afp3 and Afp4) in Afp assembly, in particular, the interaction between the two sequence-related helical-sheath forming proteins Afp2 and Afp3 and their cross-talks with the tail termination sheath capping protein (Trp) Afp16 in the sheath maturation process. The expressed assemblies for afp2- mutant were mostly a mixture of isolated tail fibres, detached baseplates without tail fibres and sheath-less, inner tube baseplate complexes (TBC) of length similar to that in mature Afp, which were surrounded in many cases by fibrillar polymerized material. In the afp3- mutant, variable length TBC with similar but shorter length fibrillar polymerized material, largely bereft of tail-fibres, were observed; while, only detached baseplate assemblies were seen for the afp4- mutant. Further, we found that a) only trans complementation of afp2 with its mutated counterpart restored mature Afp particles with full biological activity, b) purified Afp3 pulled down Afp2 by forming a SDS-resistant complex but not vice versa, c) Afp16 had a greater affinity for binding Afp2 or Afp3 than Afp4 and d) Afp4 is required for the association of the polymerized sheath on the baseplate via Afp2. A proposed model for sheath maturation and assembly in Afp is presented. Importance Members of the contractile bacteriophage related but evolutionarily divergent, eCIS contain not one but three sheath proteins - two of which, namely Afp2 and Afp3 in the Afp, arranged as alternate hexameric stacks constitute the helical sheath. We revealed that Afp2 and Afp3 even though they are highly similar, possess markedly distinct, crucial roles in Afp assembly. We find that Afp3, by virtue of its interaction with the tail terminating protein Afp16, regulates tube and sheath length while Afp2 is critical to proper sheath polymerisation and assembly of the baseplate. The resulting model for the Afp assembly will further guide in the manipulation of Afp and its related eCISs as nano delivery vehicles for pest control and phage therapy.
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22
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Component Parts of Bacteriophage Virions Accurately Defined by a Machine-Learning Approach Built on Evolutionary Features. mSystems 2021; 6:e0024221. [PMID: 34042467 PMCID: PMC8269216 DOI: 10.1128/msystems.00242-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) continues to evolve as a major threat to human health, and new strategies are required for the treatment of AMR infections. Bacteriophages (phages) that kill bacterial pathogens are being identified for use in phage therapies, with the intention to apply these bactericidal viruses directly into the infection sites in bespoke phage cocktails. Despite the great unsampled phage diversity for this purpose, an issue hampering the roll out of phage therapy is the poor quality annotation of many of the phage genomes, particularly for those from infrequently sampled environmental sources. We developed a computational tool called STEP3 to use the “evolutionary features” that can be recognized in genome sequences of diverse phages. These features, when integrated into an ensemble framework, achieved a stable and robust prediction performance when benchmarked against other prediction tools using phages from diverse sources. Validation of the prediction accuracy of STEP3 was conducted with high-resolution mass spectrometry analysis of two novel phages, isolated from a watercourse in the Southern Hemisphere. STEP3 provides a robust computational approach to distinguish specific and universal features in phages to improve the quality of phage cocktails and is available for use at http://step3.erc.monash.edu/. IMPORTANCE In response to the global problem of antimicrobial resistance, there are moves to use bacteriophages (phages) as therapeutic agents. Selecting which phages will be effective therapeutics relies on interpreting features contributing to shelf-life and applicability to diagnosed infections. However, the protein components of the phage virions that dictate these properties vary so much in sequence that best estimates suggest failure to recognize up to 90% of them. We have utilized this diversity in evolutionary features as an advantage, to apply machine learning for prediction accuracy for diverse components in phage virions. We benchmark this new tool showing the accurate recognition and evaluation of phage component parts using genome sequence data of phages from undersampled environments, where the richest diversity of phage still lies.
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23
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Park SK, Diao Y. Martensitic transition in molecular crystals for dynamic functional materials. Chem Soc Rev 2020; 49:8287-8314. [PMID: 33021272 DOI: 10.1039/d0cs00638f] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular martensitic materials are an emerging class of smart materials with enormous tunability in physicochemical properties, attributed to the tailored molecular and crystal structures through molecular design. This class of materials exhibits ultrafast and reversible structural transitions in response to thermal and mechanical stimuli, which underlies fascinating properties such as thermoelasticity, superelasticity, ferroelasticity, and shape memory effect. These dynamic properties are not widely explored in molecular crystals and therefore molecular martensitic materials represent a new frontier in the field of solid-state chemistry. In martensitic transitions, the materials not only exhibit substantial shape changes but also remember the functions in the associated polymorphic phases. This suggests promising applicability towards light-weight actuators, lifts, dampers, sensors, shape-/function-memory and ultraflexible optoelectronic devices. In this article, we review characteristics, detailed transition mechanisms, and potential applications of molecular martensitic materials. In particular, we aim to describe transition characteristics by collecting cases with similar transition principles in order to glean insights into further advancement of molecular martensitic materials. Overall, we believe that molecular martensitic materials are emerging as the next generation smart materials that have shown promise in advancing a wide range of domains of applications.
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Affiliation(s)
- Sang Kyu Park
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, USA.
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24
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Vonshak O, Divon Y, Förste S, Garenne D, Noireaux V, Lipowsky R, Rudorf S, Daube SS, Bar-Ziv RH. Programming multi-protein assembly by gene-brush patterns and two-dimensional compartment geometry. NATURE NANOTECHNOLOGY 2020; 15:783-791. [PMID: 32690886 DOI: 10.1038/s41565-020-0720-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
The assembly of protein machines in cells is precise, rapid, and coupled to protein synthesis with regulation in space and time. The assembly of natural and synthetic nanomachines could be similarly controlled by genetic programming outside the cell. Here, we present quasi-two-dimensional (2D) silicon compartments that enable programming of protein assembly lines by local synthesis from surface-immobilized DNA brushes. Using this platform, we studied the autonomous synthesis and assembly of a structural complex from a bacteriophage and a bacterial RNA-synthesizing machine. Local synthesis and surface capture of complexes provided high assembly yield and sensitive detection of spatially resolved assembly intermediates, with the 3D geometry of the compartment and the 2D pattern of brushes dictating the yield and mode of assembly steps. Localized synthesis of proteins in a single gene brush enhances their interactions, and displacement of their genes in separated brushes leads to step-by-step surface assembly. This methodology enables spatial regulation of protein synthesis, and deciphering, reconstruction and design of biological machine assembly lines.
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Affiliation(s)
- Ohad Vonshak
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yiftach Divon
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, Israel
| | - Stefanie Förste
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - David Garenne
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | | | - Sophia Rudorf
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Shirley S Daube
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, Israel.
| | - Roy H Bar-Ziv
- Department of Chemical and Biological Physics, The Weizmann Institute of Science, Rehovot, Israel.
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25
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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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Abstract
SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes. The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.
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Pham JY, Ogbunugafor CB, Nguyen Ba AN, Hartl DL. Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes. Microbiologyopen 2020; 9:e968. [PMID: 31778298 PMCID: PMC7002106 DOI: 10.1002/mbo3.968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
Ecologists have long studied the evolution of niche breadth, including how variability in environments can drive the evolution of specialism and generalism. This concept is of particular interest in viruses, where niche breadth evolution may explain viral disease emergence, or underlie the potential for therapeutic measures like phage therapy. Despite the significance and potential applications of virus-host interactions, the genetic determinants of niche breadth evolution remain underexplored in many bacteriophages. In this study, we present the results of an evolution experiment with a model bacteriophage system, Escherichia virus T4, in several host environments: exposure to Escherichia coli C, exposure to E. coli K-12, and exposure to both E. coli C and E. coli K-12. This experimental framework allowed us to investigate the phenotypic and molecular manifestations of niche breadth evolution. First, we show that selection on different hosts led to measurable changes in phage productivity in all experimental populations. Second, whole-genome sequencing of experimental populations revealed signatures of selection. Finally, clear and consistent patterns emerged across the host environments, especially the presence of new mutations in phage structural genes-genes encoding proteins that provide morphological and biophysical integrity to a virus. A comparison of mutations found across functional gene categories revealed that structural genes acquired significantly more mutations than other categories. Our findings suggest that structural genes are central determinants in bacteriophage niche breadth.
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Affiliation(s)
- Jenny Y. Pham
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | | | - Alex N. Nguyen Ba
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
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Islam MZ, Fokine A, Mahalingam M, Zhang Z, Garcia-Doval C, van Raaij MJ, Rossmann MG, Rao VB. Molecular anatomy of the receptor binding module of a bacteriophage long tail fiber. PLoS Pathog 2019; 15:e1008193. [PMID: 31856258 PMCID: PMC6957217 DOI: 10.1371/journal.ppat.1008193] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/13/2020] [Accepted: 11/05/2019] [Indexed: 12/26/2022] Open
Abstract
Tailed bacteriophages (phages) are one of the most abundant life forms on Earth. They encode highly efficient molecular machines to infect bacteria, but the initial interactions between a phage and a bacterium that then lead to irreversible virus attachment and infection are poorly understood. This information is critically needed to engineer machines with novel host specificities in order to combat antibiotic resistance, a major threat to global health today. The tailed phage T4 encodes a specialized device for this purpose, the long tail fiber (LTF), which allows the virus to move on the bacterial surface and find a suitable site for infection. Consequently, the infection efficiency of phage T4 is one of the highest, reaching the theoretical value of 1. Although the atomic structure of the tip of the LTF has been determined, its functional architecture and how interactions with two structurally very different Escherichia coli receptor molecules, lipopolysaccharide (LPS) and outer membrane protein C (OmpC), contribute to virus movement remained unknown. Here, by developing direct receptor binding assays, extensive mutational and biochemical analyses, and structural modeling, we discovered that the ball-shaped tip of the LTF, a trimer of gene product 37, consists of three sets of symmetrically alternating binding sites for LPS and/or OmpC. Our studies implicate reversible and dynamic interactions between these sites and the receptors. We speculate that the LTF might function as a “molecular pivot” allowing the virus to “walk” on the bacterium by adjusting the angle or position of interaction of the six LTFs attached to the six-fold symmetric baseplate. Bacteriophage (phage) T4 belongs to myoviridae, a widely distributed family of viruses on Earth. They contain a head (capsid), a contractile tail, and a baseplate to which six long tail fibers (LTFs) are attached. During infection, the genome packed inside the capsid is injected into its host, Escherichia coli bacterium, to initiate virus replication. The first step of infection is recognition of receptor molecules, lipopolysaccharide (LPS) and/or outer membrane protein C (OmpC), present on bacterial surface by the tips of LTFs. This allows phage to attach to bacterium, move on the surface, and find a suitable site for infection. However, the interactions that govern this critical process are poorly understood. Here, we provide the first molecular description of a tail fiber tip. Extensive mutational, structural, and biochemical analyses show that the ball-shaped tip contains patches of binding sites that allow dynamic interactions with LPS and/or OmpC. We speculate that each LTF might act as a molecular pivot, able to change its position and angle and allow phage to move on the bacterium. Our studies uncover the basic architecture of a phage molecular device used for gaining entry into bacteria and provide insights into engineering novel phages to curtail multidrug-resistance bacteria.
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Affiliation(s)
- Mohammad Z. Islam
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Marthandan Mahalingam
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
| | - Zhihong Zhang
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
| | - Carmela Garcia-Doval
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Mark J. van Raaij
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Venigalla B. Rao
- Department of Biology, The Catholic University of America, Washington, DC, United States of America
- * E-mail:
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How the phage T4 injection machinery works including energetics, forces, and dynamic pathway. Proc Natl Acad Sci U S A 2019; 116:25097-25105. [PMID: 31767752 DOI: 10.1073/pnas.1909298116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The virus bacteriophage T4, from the family Myoviridae, employs an intriguing contractile injection machine to inject its genome into the bacterium Escherichia coli Although the atomic structure of phage T4 is largely understood, the dynamics of its injection machinery remains unknown. This study contributes a system-level model describing the nonlinear dynamics of the phage T4 injection machinery interacting with a host cell. The model employs a continuum representation of the contractile sheath using elastic constants inferred from atomistic molecular-dynamics (MD) simulations. Importantly, the sheath model is coupled to component models representing the remaining structures of the virus and the host cell. The resulting system-level model captures virus-cell interactions as well as competing energetic mechanisms that release and dissipate energy during the injection process. Simulations reveal the dynamical pathway of the injection process as a "contraction wave" that propagates along the sheath, the energy that powers the injection machinery, the forces responsible for piercing the host cell membrane, and the energy dissipation that controls the timescale of the injection process. These results from the model compare favorably with the available (but limited) experimental measurements.
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Broeker NK, Roske Y, Valleriani A, Stephan MS, Andres D, Koetz J, Heinemann U, Barbirz S. Time-resolved DNA release from an O-antigen-specific Salmonella bacteriophage with a contractile tail. J Biol Chem 2019; 294:11751-11761. [PMID: 31189652 PMCID: PMC6682738 DOI: 10.1074/jbc.ra119.008133] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/11/2019] [Indexed: 12/20/2022] Open
Abstract
Myoviruses, bacteriophages with T4-like architecture, must contract their tails prior to DNA release. However, quantitative kinetic data on myovirus particle opening are lacking, although they are promising tools in bacteriophage-based antimicrobial strategies directed against Gram-negative hosts. For the first time, we show time-resolved DNA ejection from a bacteriophage with a contractile tail, the multi-O-antigen-specific Salmonella myovirus Det7. DNA release from Det7 was triggered by lipopolysaccharide (LPS) O-antigen receptors and notably slower than in noncontractile-tailed siphoviruses. Det7 showed two individual kinetic steps for tail contraction and particle opening. Our in vitro studies showed that highly specialized tailspike proteins (TSPs) are necessary to attach the particle to LPS. A P22-like TSP confers specificity for the Salmonella Typhimurium O-antigen. Moreover, crystal structure analysis at 1.63 Å resolution confirmed that Det7 recognized the Salmonella Anatum O-antigen via an ϵ15-like TSP, DettilonTSP. DNA ejection triggered by LPS from either host showed similar velocities, so particle opening is thus a process independent of O-antigen composition and the recognizing TSP. In Det7, at permissive temperatures TSPs mediate O-antigen cleavage and couple cell surface binding with DNA ejection, but no irreversible adsorption occurred at low temperatures. This finding was in contrast to short-tailed Salmonella podoviruses, illustrating that tailed phages use common particle-opening mechanisms but have specialized into different infection niches.
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Affiliation(s)
- Nina K Broeker
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mareike S Stephan
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Dorothee Andres
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Joachim Koetz
- Kolloidchemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustrasse 6, 14195 Berlin, Germany
| | - Stefanie Barbirz
- Department of Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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Kolomeisky AB. How Viruses Enter Cells: A Story behind Bacteriophage T4. Biophys J 2019; 113:4-5. [PMID: 28700923 DOI: 10.1016/j.bpj.2017.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022] Open
Affiliation(s)
- Anatoly B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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33
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McNulty R, Cardone G, Gilcrease EB, Baker TS, Casjens SR, Johnson JE. Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release. Biophys J 2019; 114:1295-1301. [PMID: 29590587 DOI: 10.1016/j.bpj.2018.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/24/2017] [Accepted: 01/17/2018] [Indexed: 11/19/2022] Open
Abstract
Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the mature virion upon DNA release are not fully understood. We used cryogenic electron microscopy to obtain what is, to our knowledge, the first asymmetric reconstruction of mature bacteriophage P22 after double-stranded DNA has been extruded from the capsid-a state representative of one step during viral infection. Results of icosahedral and asymmetric reconstructions at estimated resolutions of 7.8 and 12.5 Å resolutions, respectively, are presented. The reconstruction shows tube-like protein density extending from the center of the tail assembly. The portal protein does not revert to the more contracted, procapsid state, but instead maintains an extended and splayed barrel structure. These structural details contribute to our understanding of the molecular mechanism of P22 phage infection and also set the foundation for future exploitation serving engineering purposes.
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Affiliation(s)
- Reginald McNulty
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California.
| | - Giovanni Cardone
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Timothy S Baker
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California; Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.
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Jiang F, Li N, Wang X, Cheng J, Huang Y, Yang Y, Yang J, Cai B, Wang YP, Jin Q, Gao N. Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Cell 2019; 177:370-383.e15. [PMID: 30905475 DOI: 10.1016/j.cell.2019.02.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. Here, we report the cryo-EM structure of an intact PVC from P. asymbiotica. This over 10-MDa device resembles a simplified T4 phage tail, containing a hexagonal baseplate complex with six fibers and a capped 117-nanometer sheath-tube trunk. One distinct feature of the PVC is the presence of three variants for both tube and sheath proteins, indicating a functional specialization of them during evolution. The terminal hexameric cap docks onto the topmost layer of the inner tube and locks the outer sheath in pre-contraction state with six stretching arms. Our results on the PVC provide a framework for understanding the general mechanism of widespread CISs and pave the way for using them as delivery tools in biological or therapeutic applications.
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Affiliation(s)
- Feng Jiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC
| | - Xia Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC
| | - Jiaxuan Cheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, PRC
| | - Yaoguang Huang
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PRC
| | - Yun Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Bin Cai
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC.
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Park YJ, Lacourse KD, Cambillau C, DiMaio F, Mougous JD, Veesler D. Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy. Nat Commun 2018; 9:5385. [PMID: 30568167 PMCID: PMC6300606 DOI: 10.1038/s41467-018-07796-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/22/2018] [Indexed: 11/13/2022] Open
Abstract
Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Kaitlyn D Lacourse
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Christian Cambillau
- Architecture et Fonction des Macromolecules Biologiques, Aix-Marseille Universite, CNRS, Campus de Luminy, Case 932, 13288, Marseille, Cedex 09, France
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
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36
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Jamal M, Bukhari SMAUS, Andleeb S, Ali M, Raza S, Nawaz MA, Hussain T, Rahman SU, Shah SSA. Bacteriophages: an overview of the control strategies against multiple bacterial infections in different fields. J Basic Microbiol 2018; 59:123-133. [PMID: 30485461 DOI: 10.1002/jobm.201800412] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/24/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022]
Abstract
Bacteriophages (phages/viruses) need host bacteria to replicate and propagate. Primarily, a bacteriophage contains a head/capsid to encapsidate the genetic material. Some phages contain tails. Phages encode endolysins to hydrolyze bacterial cell wall. The two main classes of phages are lytic or virulent and lysogenic or temperate. In comparison with antibiotics, to deal with bacterial infections, phage therapy is thought to be more effective. In 1921, the use of phages against bacterial infections was first demonstrated. Later on, in humans, phage therapy was used to treat skin infections caused by Pseudomonas species. Furthermore, phages were successfully employed against infections in animals - calves, lambs, and pigs infected with Escherichia coli. In agriculture, for instance, phages have successfully been used e.g., Apple blossom infection, caused by Erwinia amylovora, was effectively catered with the use of bacteriophages. Bacteriophages were also used to control E. coli, Salmonella, Listeria, and Campylobacter contamination in food. Comparatively, phage display is a recently discovered technology, whereby, bacteriophages play a significant role. This review is an effort to collect almost recent and relevant information regarding applications and complications associated with the use of bacteriophages.
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Affiliation(s)
- Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan, Pakistan
| | - Sayed M A U S Bukhari
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Ali
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Sana Raza
- Institute of Health Sciences, Mardan, Pakistan
| | - Muhammad A Nawaz
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Dir (Upper), Pakistan
| | - Tahir Hussain
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan, Pakistan
| | - Sadeeq U Rahman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Garden Campus, Mardan, Pakistan
| | - Syed S A Shah
- Department of Zoology, Abdul Wali Khan University, Garden Campus, Mardan, Pakistan
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Enav H, Kirzner S, Lindell D, Mandel-Gutfreund Y, Béjà O. Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nat Commun 2018; 9:4698. [PMID: 30409965 PMCID: PMC6224464 DOI: 10.1038/s41467-018-07164-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022] Open
Abstract
Cyanophages of the Myoviridae family include generalist viruses capable of infecting a wide range of hosts including those from different cyanobacterial genera. While the influence of phages on host evolution has been studied previously, it is not known how the infection of distinct hosts influences the evolution of cyanophage populations. Here, using an experimental evolution approach, we investigated the adaptation of multiple cyanophage populations to distinct cyanobacterial hosts. We show that when infecting an "optimal" host, whose infection is the most efficient, phage populations accumulated only a few mutations. However, when infecting "sub-optimal" hosts, different mutations spread in the phage populations, leading to rapid diversification into distinct subpopulations. Based on our results, we propose a model demonstrating how shifts in microbial abundance, which lead to infection of "sub-optimal" hosts, act as a driver for rapid diversification of viral populations.
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Affiliation(s)
- Hagay Enav
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel. .,Department of Microbiome Science, Max-Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| | - Shay Kirzner
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.,Department of Computer Sciences, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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Aiewsakun P, Adriaenssens EM, Lavigne R, Kropinski AM, Simmonds P. Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy. J Gen Virol 2018; 99:1331-1343. [PMID: 30016225 PMCID: PMC6230767 DOI: 10.1099/jgv.0.001110] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/13/2018] [Indexed: 01/01/2023] Open
Abstract
Genome Relationship Applied to Virus Taxonomy (GRAViTy) is a genetics-based tool that computes sequence relatedness between viruses. Composite generalized Jaccard (CGJ) distances combine measures of homology between encoded viral genes and similarities in genome organizational features (gene orders and orientations). This scoring framework effectively recapitulates the current, largely morphology and phenotypic-based, family-level classification of eukaryotic viruses. Eukaryotic virus families typically formed monophyletic groups with consistent CGJ distance cut-off dividing between and within family divergence ranges. In the current study, a parallel analysis of prokaryotic virus families revealed quite different sequence relationships, particularly those of tailed phage families (Siphoviridae, Myoviridae and Podoviridae), where members of the same family were generally far more divergent and often not detectably homologous to each other. Analysis of the 20 currently classified prokaryotic virus families indeed split them into 70 separate clusters of tailed phages genetically equivalent to family-level assignments of eukaryotic viruses. It further divided several bacterial (Sphaerolipoviridae, Tectiviridae) and archaeal (Lipothrixviridae) families. We also found that the subfamily-level groupings of tailed phages were generally more consistent with the family assignments of eukaryotic viruses, and this supports ongoing reclassifications, including Spounavirinae and Vi1virus taxa as new virus families. The current study applied a common benchmark with which to compare taxonomies of eukaryotic and prokaryotic viruses. The findings support the planned shift away from traditional morphology-based classifications of prokaryotic viruses towards a genome-based taxonomy. They demonstrate the feasibility of a unified taxonomy of viruses into which the vast body of metagenomic viral sequences may be consistently assigned.
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Affiliation(s)
- Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks, Oxford, OX1 3SY, UK
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Evelien M. Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB Liverpool, UK
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven. Kasteelpark Arenberg 21, Box 2462, 3001 Leuven, Belgium
| | - Andrew M. Kropinski
- Departments of Food Science, and Pathobiology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks, Oxford, OX1 3SY, UK
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Azam AH, Hoshiga F, Takeuchi I, Miyanaga K, Tanji Y. Analysis of phage resistance in Staphylococcus aureus SA003 reveals different binding mechanisms for the closely related Twort-like phages ɸSA012 and ɸSA039. Appl Microbiol Biotechnol 2018; 102:8963-8977. [DOI: 10.1007/s00253-018-9269-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 02/01/2023]
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Hall D, Takagi J, Nakamura H. Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday. Biophys Rev 2018; 10:105-129. [PMID: 29500796 PMCID: PMC5899743 DOI: 10.1007/s12551-018-0401-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.
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Affiliation(s)
- Damien Hall
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
- Research School of Chemistry, Australian National University, Acton, ACT 2601 Australia
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871 Japan
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Arisaka F. Forty years of research on the assembly and infection process of bacteriophage. Biophys Rev 2018; 10:131-136. [PMID: 29411257 DOI: 10.1007/s12551-018-0396-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/07/2018] [Indexed: 11/28/2022] Open
Abstract
This short biographical note was written as part of the lead-in material for a festschrift kindly organized for me on the occasion of my 70th birthday. The collection of articles assembled in this issue range within the spectrum of the topics covered in the special issue 'Multiscale structural biology-biophysical principles and practice ranging from biomolecules to bionanomachines.' Here I describe some of the high points of my 40 years of research science conducted in the USA, Switzerland and Japan. I also use this opportunity to express my sincerest thanks to my former colleagues and the very many contributors who so kindly contributed to this special issue.
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My happy years of collaboration with Fumio Arisaka. Biophys Rev 2017; 10:139-140. [PMID: 29235082 DOI: 10.1007/s12551-017-0359-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 10/18/2022] Open
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Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 2017; 114:13708-13713. [PMID: 29229840 DOI: 10.1073/pnas.1716614114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Unlike tailed bacteriophages, which use a preformed tail for transporting their genomes into a host bacterium, the ssDNA bacteriophage ΦX174 is tailless. Using cryo-electron microscopy and time-resolved small-angle X-ray scattering, we show that lipopolysaccharides (LPS) form bilayers that interact with ΦX174 at an icosahedral fivefold vertex and induce single-stranded (ss) DNA genome ejection. The structures of ΦX174 complexed with LPS have been determined for the pre- and post-ssDNA ejection states. The ejection is initiated by the loss of the G protein spike that encounters the LPS, followed by conformational changes of two polypeptide loops on the major capsid F proteins. One of these loops mediates viral attachment, and the other participates in making the fivefold channel at the vertex contacting the LPS.
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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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Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses. Proc Natl Acad Sci U S A 2017; 114:E8184-E8193. [PMID: 28893988 DOI: 10.1073/pnas.1708483114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) Tend = 13 for end caps and Tmid = 20 for midsection. A mutation in the major capsid protein, gp23, produced T=13 icosahedral capsids. The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. The occupancies of Soc molecules are proportional to the size of the angle between the planes of adjacent hexameric capsomers. The angle between adjacent hexameric capsomers is greatest around the fivefold vertices, where there is the largest deviation from a planar hexagonal array. Thus, the Soc molecules reinforce the structure where there is the greatest strain in the gp23 hexagonal lattice. Mutations that change the angles between adjacent capsomers affect the positions of the pentameric vertices, resulting in different triangulation numbers in bacteriophage T4. The analysis of the T4 mutant head assembly gives guidance to how other icosahedral viruses reproducibly assemble into capsids with a predetermined T number, although the influence of scaffolding proteins is also important.
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Brackmann M, Nazarov S, Wang J, Basler M. Using Force to Punch Holes: Mechanics of Contractile Nanomachines. Trends Cell Biol 2017; 27:623-632. [DOI: 10.1016/j.tcb.2017.05.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/25/2022]
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Dynamic Model Exposes the Energetics and Dynamics of the Injection Machinery for Bacteriophage T4. Biophys J 2017; 113:195-205. [PMID: 28700918 DOI: 10.1016/j.bpj.2017.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/07/2017] [Accepted: 05/04/2017] [Indexed: 11/24/2022] Open
Abstract
Bacteriophage T4 infects the bacterial host (Escherichia coli) using an efficient genomic delivery machine that is driven by elastic energy stored in a contractile tail sheath. Although the atomic structure of T4 is largely known, the dynamics of its fascinating injection machinery is not understood. This article contributes, to our knowledge, the first predictions of the energetics and dynamics of the T4 injection machinery using a novel dynamic model. The model employs an atomistic (molecular dynamics) representation of a fraction of the sheath structure to generate a continuum model of the entire sheath that also couples to a model of the viral capsid and tail tube. The resulting model of the entire injection machine reveals estimates for the energetics, timescale, and pathway of the T4 injection process as well as the force available for cell rupture. It also reveals the large and highly nonlinear conformational changes of the sheath whose elastic energy drives the injection process.
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48
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Vincent AT, Paquet VE, Bernatchez A, Tremblay DM, Moineau S, Charette SJ. Characterization and diversity of phages infecting Aeromonas salmonicida subsp. salmonicida. Sci Rep 2017; 7:7054. [PMID: 28765570 PMCID: PMC5539321 DOI: 10.1038/s41598-017-07401-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/27/2017] [Indexed: 01/21/2023] Open
Abstract
Phages infecting Aeromonas salmonicida subsp. salmonicida, the causative agent of the fish disease furunculosis, have been isolated for decades but very few of them have been characterized. Here, the host range of 12 virulent phages, including three isolated in the present study, was evaluated against a panel of 65 A. salmonicida isolates, including representatives of the psychrophilic subspecies salmonicida, smithia, masoucida, and the mesophilic subspecies pectinolytica. This bacterial set also included three isolates from India suspected of being members of a new subspecies. Our results allowed to elucidate a lytic dichotomy based on the lifestyle of A. salmonicida (mesophilic or psychrophilic) and more generally, on phage types (lysotypes) for the subspecies salmonicida. The genomic analyses of the 12 phages from this study with those available in GenBank led us to propose an A. salmonicida phage pan-virome. Our comparative genomic analyses also suggest that some phage genes were under positive selection and A. salmonicida phage genomes having a discrepancy in GC% compared to the host genome encode tRNA genes to likely overpass the bias in codon usage. Finally, we propose a new classification scheme for A. salmonicida phages.
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Affiliation(s)
- Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Valérie E Paquet
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Alex Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Denise M Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada.
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Arisaka F, Yap ML, Kanamaru S, Rossmann MG. Molecular assembly and structure of the bacteriophage T4 tail. Biophys Rev 2016; 8:385-396. [PMID: 28510021 DOI: 10.1007/s12551-016-0230-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022] Open
Abstract
The tail of bacteriophage T4 undergoes large structural changes upon infection while delivering the phage genome into the host cell. The baseplate is located at the distal end of the contractile tail and plays a central role in transmitting the signal to the tail sheath that the tailfibers have been adsorbed by a host bacterium. This then triggers the sheath contraction. In order to understand the mechanism of assembly and conformational changes of the baseplate upon infection, we have determined the structure of an in vitro assembled baseplate through the three-dimensional reconstruction of cryo-electron microscopy images to a resolution of 3.8 Å from electron micrographs. The atomic structure was fitted to the baseplate structure before and after sheath contraction in order to elucidate the conformational changes that occur after bacteriophage T4 has attached itself to a cell surface. The structure was also used to investigate the protease digestion of the assembly intermediates and the mutation sites of the tail genes, resulting in a number of phenotypes.
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Affiliation(s)
- Fumio Arisaka
- Life Science Research Center, School of Bioresource Science, Nihon University, 1866 Kameino, Fujisawa, 252-0880, Japan.
| | - Moh Lan Yap
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Shuji Kanamaru
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259, Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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50
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Fokine A, Rossmann MG. Common Evolutionary Origin of Procapsid Proteases, Phage Tail Tubes, and Tubes of Bacterial Type VI Secretion Systems. Structure 2016; 24:1928-1935. [PMID: 27667692 PMCID: PMC5093050 DOI: 10.1016/j.str.2016.08.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/27/2016] [Accepted: 08/20/2016] [Indexed: 01/07/2023]
Abstract
Many large viruses, including tailed dsDNA bacteriophages and herpesviruses, assemble their capsids via formation of precursors, called procapsids or proheads. The prohead has an internal core, made of scaffolding proteins, and an outer shell, formed by the major capsid protein. The prohead usually contains a protease, which is activated during capsid maturation to destroy the inner core and liberate space for the genome. Here, we report a 2.0 Å resolution structure of the pentameric procapsid protease of bacteriophage T4, gene product (gp)21. The structure corresponds to the enzyme's pre-active state in which its N-terminal region blocks the catalytic center, demonstrating that the activation mechanism involves self-cleavage of nine N-terminal residues. We describe similarities and differences between T4 gp21 and related herpesvirus proteases. We found that gp21 and the herpesvirus proteases have similarity with proteins forming the tubes of phage tails and bacterial type VI secretion systems, suggesting their common evolutionary origin.
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Affiliation(s)
- Andrei Fokine
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA,Correspondence: (A. F); (M. G. R)
| | - Michael G. Rossmann
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, Purdue University, West Lafayette, IN 47907, USA,Correspondence: (A. F); (M. G. R)
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