1
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Fortaleza JAG, Ong CJN, De Jesus R. Efficacy and clinical potential of phage therapy in treating methicillin-resistant Staphylococcus aureus (MRSA) infections: A review. Eur J Microbiol Immunol (Bp) 2024; 14:13-25. [PMID: 38305804 PMCID: PMC10895361 DOI: 10.1556/1886.2023.00064] [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: 12/27/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
Staphylococcus aureus infections have already presented a substantial public health challenge, encompassing different clinical manifestations, ranging from bacteremia to sepsis and multi-organ failures. Among these infections, methicillin-resistant S. aureus (MRSA) is particularly alarming due to its well-documented resistance to multiple classes of antibiotics, contributing significantly to global mortality rates. Consequently, the urgent need for effective treatment options has prompted a growing interest in exploring phage therapy as a potential non-antibiotic treatment against MRSA infections. Phages represent a class of highly specific bacterial viruses known for their ability to infect certain bacterial strains. This review paper explores the clinical potential of phages as a treatment for MRSA infections due to their low toxicity and auto-dosing capabilities. The paper also discusses the synergistic effect of phage-antibiotic combination (PAC) and the promising results from in vitro and animal model studies, which could lead to extensive human clinical trials. However, clinicians need to establish and adhere to standard protocols governing phage administration and implementation. Prominent clinical trials are needed to develop and advance phage therapy as a non-antibiotic therapy intervention, meeting regulatory guidelines, logistical requirements, and ethical considerations, potentially revolutionizing the treatment of MRSA infections.
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Affiliation(s)
- Jamil Allen G Fortaleza
- 1Senior High School Department, NU Fairview Incorporated, Quezon City, 1118, Philippines
- 2National University, Philippines, Sampaloc, Manila, 1008, Philippines
| | | | - Rener De Jesus
- 4Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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2
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Xiong W, Liu B, Lu H, Liu X. Two novel bacteriophages isolated from the environment that can help control activated sludge foaming. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01145-4. [PMID: 38363443 DOI: 10.1007/s12223-024-01145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
Nocardia spp., which belongs to one of the Nocardio-form filamentous bacteria, is usually surface hydrophobic and when overproduced attaches to the surface of bubbles under the action of surfactants, allowing the stable presence of foam on the surface of aeration tanks, leading to the occurrence of sludge-foaming events. Two novel phages, P69 and KYD2, were isolated from the environment, and their hosts were Nocardia transvalensis and Nocardia carnea, respectively. These two phages are Siphophages-like with long tails. An aeration tank pilot plant was constructed in the laboratory to simulate sludge foaming, and these two strains of phage were applied. Compared with the reactor not dosed with phage, the application of phage could reduce the host level in the reactor, resulting in the highest decrease in turbidity by more than 68% and sludge volume index by more than 25%. The time for surface foam disappearance was 9 h earlier than that of the control group (the group with the same concentration of Nocardia carnea but no bacteriophage applied), significantly improving water quality. The phage can effectively inhibit the propagation of Nocardia in the actual sludge-foaming event, control the sludge foaming, and improve the effluent quality. It provides a novel and relatively economical solution for controlling sludge foaming in sewage treatment plants in the future, shows that the phages have potential application value in the prevention and control of Nocardia, and provides another way to control the sludge-foaming event caused by the excessive reproduction of Nocardia in the future.
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Affiliation(s)
- Wenbin Xiong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Han Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Binzhou Institute of Technology, Weiqiao-UCAS Science and Technology Park, Binzhou, Shandong Province, 256606, China.
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3
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Subramanian S, Bergland Drarvik SM, Tinney KR, Parent KN. Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins. Structure 2024; 32:24-34.e4. [PMID: 37909043 PMCID: PMC10842012 DOI: 10.1016/j.str.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/02/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
There is a paucity of high-resolution structures of phages infecting Shigella, a human pathogen and a serious threat to global health. HRP29 is a Shigella podophage belonging to the Autographivirinae family, and has very low sequence identity to other known phages. Here, we resolved the structure of the entire HRP29 virion by cryo-EM. Phage HRP29 has a highly unusual tail that is a fusion of a T7-like tail tube and P22-like tailspikes mediated by interactions from a novel tailspike adaptor protein. Understanding phage tail structures is critical as they mediate hosts interactions. Furthermore, we show that the HRP29 capsid is stabilized by two novel, and essential decoration proteins, gp47 and gp48. Only one high resolution structure is currently available for Shigella podophages. The presence of a hybrid tail and an adapter protein suggests that it may be a product of horizontal gene transfer, and may be prevalent in other phages.
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Affiliation(s)
- Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Silje M Bergland Drarvik
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kendal R Tinney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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4
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Jiang YL, Zhou CZ. Multiple masks of a Shigella podophage. Structure 2024; 32:1-2. [PMID: 38181725 DOI: 10.1016/j.str.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024]
Abstract
In this issue of Structure, Subramanian et al. present the cryo-EM structure of Shigella podophage HRP29, which possesses a T7-like tail complex surrounded by six P22/Sf6-like tailspikes and two unique decoration proteins. These colorful masks of HRP29 record the frequent events of horizontal gene transfer during evolution.
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Affiliation(s)
- Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
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5
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Rūmnieks J, Füzik T, Tārs K. Structure of the Borrelia Bacteriophage φBB1 Procapsid. J Mol Biol 2023; 435:168323. [PMID: 37866476 DOI: 10.1016/j.jmb.2023.168323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.
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Affiliation(s)
- Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, 1067 Riga, Latvia.
| | - Tibor Füzik
- Structural Virology, Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, 1067 Riga, Latvia; Faculty of Biology, University of Latvia, Jelgavas 1, 1004 Riga, Latvia
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Podgorski JM, Podgorski J, Abad L, Jacobs-Sera D, Freeman KG, Brown C, Hatfull G, Luque A, White SJ. A novel stabilization mechanism accommodating genome length variation in evolutionarily related viral capsids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565530. [PMID: 37961133 PMCID: PMC10635136 DOI: 10.1101/2023.11.03.565530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Tailed bacteriophages are one of the most numerous and diverse group of viruses. They store their genome at quasi-crystalline densities in capsids built from multiple copies of proteins adopting the HK97-fold. The high density of the genome exerts an internal pressure, requiring a maturation process that reinforces their capsids. However, it is unclear how capsid stabilization strategies have adapted to accommodate the evolution of larger genomes in this virus group. Here we characterized a novel capsid reinforcement mechanism in two evolutionary-related actinobacteriophages that modifies the length of a stabilization protein to accommodate a larger genome while maintaining the same capsid size. We used cryo-EM to reveal that capsids contained split hexamers of HK97-fold proteins with a stabilization protein in the chasm. The observation of split hexamers in mature capsids was unprecedented, so we rationalized this result mathematically, discovering that icosahedral capsids can be formed by all split or skewed hexamers as long as their T-number is not a multiple of three. Our results suggest that analogous stabilization mechanisms can be present in other icosahedral capsids, and they provide a strategy for engineering capsids accommodating larger DNA cargoes as gene delivery systems.
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Affiliation(s)
- Jennifer M. Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA
| | - Joshua Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA
| | - Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Krista G. Freeman
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Colin Brown
- Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
- Department of Physics, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Graham Hatfull
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
- Department of Biology, University of Miami, 1301 Memorial Dr, Coral Gables, FL 33155, USA
| | - Simon J. White
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125. Storrs, CT 06269-3125, USA
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7
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Sonani RR, Esteves NC, Horton AA, Kelly RJ, Sebastian AL, Wang F, Kreutzberger MAB, Leiman PG, Scharf BE, Egelman EH. Neck and capsid architecture of the robust Agrobacterium phage Milano. Commun Biol 2023; 6:921. [PMID: 37684529 PMCID: PMC10491603 DOI: 10.1038/s42003-023-05292-1] [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: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano.
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Affiliation(s)
- Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Nathaniel C Esteves
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Abigail A Horton
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rebecca J Kelly
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA.
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8
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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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9
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d’Acapito A, Roret T, Zarkadas E, Mocaër PY, Lelchat F, Baudoux AC, Schoehn G, Neumann E. Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM. J Virol 2023; 97:e0024823. [PMID: 36943070 PMCID: PMC10134823 DOI: 10.1128/jvi.00248-23] [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: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/23/2023] Open
Abstract
Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely overlooked by the scientific community. By inducing cell lysis on half of the bacterial population daily, their role and influence on the bacterial biomass and evolution, as well as their impact in the global biogeochemical cycles, is undeniable. Cobetia marina virus 1 (Carin-1) is a member of the Podoviridae family infecting the γ-protoabacteria C. marina. Here, we present the almost complete, nearly-atomic resolution structure of Carin-1 comprising capsid, portal, and tail machineries at 3.5 Å, 3.8 Å and 3.9 Å, respectively, determined by cryo-electron microscopy (cryo-EM). Our experimental results, combined with AlphaFold2 (AF), allowed us to obtain the nearly-atomic structure of Carin-1 by fitting and refining the AF atomic models in the high resolution cryo-EM map, skipping the bottleneck of de-novo manual building and speeding up the structure determination process. Our structural results highlighted the T7-like nature of Carin1, as well as several novel structural features like the presence of short spikes on the capsid, reminiscent those described for Rhodobacter capsulatus gene transfer agent (RcGTA). This is, to our knowledge, the first time such assembly is described for a bacteriophage, shedding light into the common evolution and shared mechanisms between gene transfer agents and phages. This first full structure determined for a marine podophage allowed to propose an infection mechanism different than the one proposed for the archetypal podophage T7. IMPORTANCE Oceans play a central role in the carbon cycle on Earth and on the climate regulation (half of the planet's CO2 is absorbed by phytoplankton photosynthesis in the oceans and just as much O2 is liberated). The understanding of the biochemical equilibriums of marine biology represents a major goal for our future. By lysing half of the bacterial population every day, marine bacteriophages are key actors of these equilibriums. Despite their importance, these marine phages have, so far, only been studied a little and, in particular, structural insights are currently lacking, even though they are fundamental for the understanding of the molecular mechanisms of their mode of infection. The structures described in our manuscript allow us to propose an infection mechanism that differs from the one proposed for the terrestrial T7 virus, and might also allow us to, in the future, better understand the way bacteriophages shape the global ecosystem.
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Affiliation(s)
| | - Thomas Roret
- Station Biologique de Roscoff (SBR), CNRS FR2424, Sorbonne Université, Roscoff, France
| | | | - Pierre-Yves Mocaër
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | | | - Anne-Claire Baudoux
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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10
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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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11
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A Capsid Structure of Ralstonia solanacearum podoviridae GP4 with a Triangulation Number T = 9. Viruses 2022; 14:v14112431. [PMID: 36366529 PMCID: PMC9698820 DOI: 10.3390/v14112431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
GP4, a new Ralstonia solanacearum phage, is a short-tailed phage. Few structures of Ralstonia solanacearum phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between Ralstonia solanacearum and corresponding phages.
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12
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Evseev P, Shneider M, Miroshnikov K. Evolution of Phage Tail Sheath Protein. Viruses 2022; 14:v14061148. [PMID: 35746620 PMCID: PMC9230969 DOI: 10.3390/v14061148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 02/06/2023] Open
Abstract
Sheath proteins comprise a part of the contractile molecular machinery present in bacteriophages with myoviral morphology, contractile injection systems, and the type VI secretion system (T6SS) found in many Gram-negative bacteria. Previous research on sheath proteins has demonstrated that they share common structural features, even though they vary in their size and primary sequence. In this study, 112 contractile phage tail sheath proteins (TShP) representing different groups of bacteriophages and archaeal viruses with myoviral morphology have been modelled with the novel machine learning software, AlphaFold 2. The obtained structures have been analysed and conserved and variable protein parts and domains have been identified. The common core domain of all studied sheath proteins, including viral and T6SS proteins, comprised both N-terminal and C-terminal parts, whereas the other parts consisted of one or several moderately conserved domains, presumably added during phage evolution. The conserved core appears to be responsible for interaction with the tail tube protein and assembly of the phage tail. Additional domains may have evolved to maintain the stability of the virion or for adsorption to the host cell. Evolutionary relations between TShPs representing distinct viral groups have been proposed using a phylogenetic analysis based on overall structural similarity and other analyses.
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13
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Boyd CM, Angermeyer A, Hays SG, Barth ZK, Patel KM, Seed KD. Bacteriophage ICP1: A Persistent Predator of Vibrio cholerae. Annu Rev Virol 2021; 8:285-304. [PMID: 34314595 PMCID: PMC9040626 DOI: 10.1146/annurev-virology-091919-072020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteriophages or phages—viruses of bacteria—are abundant and considered to be highly diverse. Interestingly, a particular group of lytic Vibrio cholerae–specific phages (vibriophages) of the International Centre for Diarrheal Disease Research, Bangladesh cholera phage 1 (ICP1) lineage show high levels of genome conservation over large spans of time and geography, despite a constant coevolutionary arms race with their host. From a collection of 67 sequenced ICP1 isolates, mostly from clinical samples, we find these phages have mosaic genomes consisting of large, conserved modules disrupted by variable sequences that likely evolve mostly through mobile endonuclease-mediated recombination during coinfection. Several variable regions have been associated with adaptations against antiphage elements in V. cholerae; notably, this includes ICP1’s CRISPR-Cas system. The ongoing association of ICP1 and V. cholerae in cholera-endemic regions makes this system a rich source for discovery of novel defense and counterdefense strategies in bacteria-phage conflicts in nature.
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Affiliation(s)
- Caroline M Boyd
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Stephanie G Hays
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Kishen M Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; .,Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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