1
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Zheng J, Chen W, Xiao H, Yang F, Song J, Cheng L, Liu H. Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers. J Mol Biol 2023; 435:168258. [PMID: 37660940 DOI: 10.1016/j.jmb.2023.168258] [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: 06/15/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments.
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Affiliation(s)
- Jing Zheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Wenyuan Chen
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, 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, School of Physics and Electronics, 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
| | - 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, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Jingdong Song
- 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
| | - Lingpeng Cheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, 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, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China.
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2
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Geng H, Song L, Yang X, Xing S, Wang R, Xu Y, Jia X, Luan G. Resistance of Klebsiella pneumoniae to Phage hvKpP3 Due to High-Molecular Weight Lipopolysaccharide Synthesis Failure. Microbiol Spectr 2023; 11:e0438422. [PMID: 37022197 PMCID: PMC10269817 DOI: 10.1128/spectrum.04384-22] [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: 10/27/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
The spread of multidrug resistant and hypervirulent Klebsiella pneumoniae has recently increased. Phages have been considered alternatives for treating infections caused by tenacious pathogens. Our study describes a novel lytic Klebsiella phage, hvKpP3, and we obtained spontaneous mutants, hvKpP3R and hvKpP3R15, of hvKpLS8 strain that showing strong resistance to the lytic phage hvKpP3. Sequencing analysis showed that nucleotide-deletion mutations of the glycosyltransferase gene (GT) and wcaJ genes, located in the lipopolysaccharide (LPS) gene cluster and the capsular polysaccharide (CPS) gene cluster, respectively, led to phage resistance. The wcaJ mutation confers the inhibition of phage adsorption by affecting the synthesis of hvKpP3R15 capsular polysaccharide, indicating that the capsule is the main adsorption receptor for bacteriophage hvKpP3. Interestingly, the phage-resistant mutant hvKpP3R has a loss-of-function mutation in GT, which is responsible for lipopolysaccharide biosynthesis. This results in the loss of high-molecular weight lipopolysaccharide (HMW-LPS), and alteration of the lipopolysaccharide structure of the bacterial cell wall confers resistance to phages. In conclusion, our study provides a detailed description of phage hvKpP3 and provides new insights into phage resistance in K. pneumoniae. IMPORTANCE Multidrug-resistant (MDR) Klebsiella pneumoniae strains pose a particular threat to human health. Therefore, it is very important for us to isolate phage and overcome phage resistance. In this study, we isolated a novel phage belonging to the Myoviridae family, hvKpP3, that exhibited high lytic activity against K2 hypervirulent K. pneumoniae. We demonstrated the excellent stability of phage hvKpP3 through in vitro and in vivo experiments, indicating its potential as a candidate for future clinical phage therapy. Furthermore, we identified that loss of function in the glycotransferase gene (GT) caused the failure of HMW-LPS synthesis, leading to phage resistance, which provides new insights into phage resistance in K. pneumoniae.
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Affiliation(s)
- Huaixin Geng
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Lingjie Song
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xianggui Yang
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Siyu Xing
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Rui Wang
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ying Xu
- Department of Laboratory Medicine, Clinical Medical College and the First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
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3
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Noreika A, Rutkiene R, Dumalakienė I, Vilienė R, Laurynėnas A, Povilonienė S, Skapas M, Meškys R, Kaliniene L. Insights into the Alcyoneusvirus Adsorption Complex. Int J Mol Sci 2023; 24:ijms24119320. [PMID: 37298271 DOI: 10.3390/ijms24119320] [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: 05/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The structures of the Caudovirales phage tails are key factors in determining the host specificity of these viruses. However, because of the enormous structural diversity, the molecular anatomy of the host recognition apparatus has been elucidated in only a number of phages. Klebsiella viruses vB_KleM_RaK2 (RaK2) and phiK64-1, which form a new genus Alcyoneusvirus according to the ICTV, have perhaps one of the most structurally sophisticated adsorption complexes of all tailed viruses described to date. Here, to gain insight into the early steps of the alcyoneusvirus infection process, the adsorption apparatus of bacteriophage RaK2 is studied in silico and in vitro. We experimentally demonstrate that ten proteins, gp098 and gp526-gp534, previously designated as putative structural/tail fiber proteins (TFPs), are present in the adsorption complex of RaK2. We show that two of these proteins, gp098 and gp531, are essential for attaching to Klebsiella pneumoniae KV-3 cells: gp531 is an active depolymerase that recognizes and degrades the capsule of this particular host, while gp098 is a secondary receptor-binding protein that requires the coordinated action of gp531. Finally, we demonstrate that RaK2 long tail fibers consist of nine TFPs, seven of which are depolymerases, and propose a model for their assembly.
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Affiliation(s)
- Algirdas Noreika
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Rasa Rutkiene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Irena Dumalakienė
- Department of Immunology, State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08410 Vilnius, Lithuania
| | - Rita Vilienė
- Department of Immunology, State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08410 Vilnius, Lithuania
| | - Audrius Laurynėnas
- Department of Bioanalysis, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Simona Povilonienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
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4
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Klumpp J, Dunne M, Loessner MJ. A perfect fit: Bacteriophage receptor-binding proteins for diagnostic and therapeutic applications. Curr Opin Microbiol 2023; 71:102240. [PMID: 36446275 DOI: 10.1016/j.mib.2022.102240] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022]
Abstract
Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to specifically infect and kill bacteria, phages and their encoded endolysins and receptor-binding proteins (RBPs) have enormous potential for development into precision antimicrobials for treatment of bacterial infections and microbial disbalances; or as biocontrol agents to tackle bacterial contaminations during various biotechnological processes. The extraordinary binding specificity of phages and RBPs can be exploited in various areas of bacterial diagnostics and monitoring, from food production to health care. We review and describe the distinctive features of phage RBPs, explain why they are attractive candidates for use as therapeutics and in diagnostics, discuss recent applications using RBPs, and finally provide our perspective on how synthetic technology and artificial intelligence-driven approaches will revolutionize how we use these tools in the future.
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Affiliation(s)
- Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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5
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Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins. Viruses 2023; 15:v15020286. [PMID: 36851500 PMCID: PMC9965104 DOI: 10.3390/v15020286] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/10/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
Host range is a major determinant in the industrial utility of a bacteriophage. A model host range permits broad recognition across serovars of a target bacterium while avoiding cross-reactivity with commensal microbiota. Searching for a naturally occurring bacteriophage with ideal host ranges is challenging, time-consuming, and restrictive. To address this, SPTD1.NL, a previously published luciferase reporter bacteriophage for Salmonella, was used to investigate manipulation of host range through receptor-binding protein engineering. Similar to related members of the Ackermannviridae bacteriophage family, SPTD1.NL possessed a receptor-binding protein gene cluster encoding four tailspike proteins, TSP1-4. Investigation of the native gene cluster through chimeric proteins identified TSP3 as the tailspike protein responsible for Salmonella detection. Further analysis of chimeric phages revealed that TSP2 contributed off-target Citrobacter recognition, whereas TSP1 and TSP4 were not essential for activity against any known host. To improve the host range of SPTD1.NL, TSP1 and TSP2 were sequentially replaced with chimeric receptor-binding proteins targeting Salmonella. This engineered construct, called RBP-SPTD1-3, was a superior diagnostic reporter, sensitively detecting additional Salmonella serovars while also demonstrating improved specificity. For industrial applications, bacteriophages of the Ackermannviridae family are thus uniquely versatile and may be engineered with multiple chimeric receptor-binding proteins to achieve a custom-tailored host range.
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6
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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7
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Ruiz‐Cruz S, Erazo Garzon A, Kelleher P, Bottacini F, Breum SØ, Neve H, Heller KJ, Vogensen FK, Palussière S, Courtin P, Chapot‐Chartier M, Vinogradov E, Sadovskaya I, Mahony J, van Sinderen D. Host genetic requirements for DNA release of lactococcal phage TP901-1. Microb Biotechnol 2022; 15:2875-2889. [PMID: 36259418 PMCID: PMC9733650 DOI: 10.1111/1751-7915.14156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/29/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
The first step in phage infection is the recognition of, and adsorption to, a receptor located on the host cell surface. This reversible host adsorption step is commonly followed by an irreversible event, which involves phage DNA delivery or release into the bacterial cytoplasm. The molecular components that trigger this latter event are unknown for most phages of Gram-positive bacteria. In the current study, we present a comparative genome analysis of three mutants of Lactococcus cremoris 3107, which are resistant to the P335 group phage TP901-1 due to mutations that affect TP901-1 DNA release. Through genetic complementation and phage infection assays, a predicted lactococcal three-component glycosylation system (TGS) was shown to be required for TP901-1 infection. Major cell wall saccharidic components were analysed, but no differences were found. However, heterologous gene expression experiments indicate that this TGS is involved in the glucosylation of a cell envelope-associated component that triggers TP901-1 DNA release. To date, a saccharide modification has not been implicated in the DNA delivery process of a Gram-positive infecting phage.
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Affiliation(s)
- Sofía Ruiz‐Cruz
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Andrea Erazo Garzon
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Francesca Bottacini
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland,Department of Biological SciencesMunster Technological UniversityCorkIreland
| | - Solvej Østergaard Breum
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark,Present address:
Department of Virus & Microbiological Special Diagnostics, Division of Infectious Disease Preparedness, Statens Serum InstitutCopenhagenDenmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner‐InstitutFederal Research Institute of Nutrition and FoodKielGermany
| | - Knut J. Heller
- Department of Microbiology and Biotechnology, Max Rubner‐InstitutFederal Research Institute of Nutrition and FoodKielGermany
| | - Finn K. Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Simon Palussière
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
| | - Pascal Courtin
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis InstituteJouy‐en‐JosasFrance
| | | | - Evgeny Vinogradov
- National Research Council CanadaInstitute for Biological SciencesOttawaOntarioCanada
| | - Irina Sadovskaya
- Equipe BPA, Université du Littoral‐Côte d'Opale, Institut Charles Violette EA 7394 USC AnsesBoulogne‐sur‐merFrance
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
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8
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Abstract
The first critical step in a virus’s infection cycle is attachment to its host. This interaction is precise enough to ensure the virus will be able to productively infect the cell, but some flexibility can be beneficial to enable coevolution and host range switching or expansion. Bacteriophage Sf6 utilizes a two-step process to recognize and attach to its host Shigella flexneri. Sf6 first recognizes the lipopolysaccharide (LPS) of S. flexneri and then binds outer membrane protein (Omp) A or OmpC. This phage infects serotype Y strains but can also form small, turbid plaques on serotype 2a2; turbid plaques appear translucent rather than transparent, indicating greater survival of bacteria. Reduced plating efficiency further suggested inefficient infection. To examine the interactions between Sf6 and this alternate host, phages were experimentally evolved using mixed populations of S. flexneri serotypes Y and 2a2. The recovered mutants could infect serotype 2a2 with greater efficiency than the ancestral Sf6, forming clear plaques on both serotypes. All mutations mapped to two distinct regions of the receptor-binding tailspike protein: (i) adjacent to the LPS binding site near the N terminus; and (ii) at the distal, C-terminal tip of the protein. Although we anticipated interactions between the Sf6 tailspike and 2a2 O-antigen to be weak, LPS of this serotype appears to inhibit infection through strong binding of particles, effectively removing them from the environment. The mutations of the evolved strains reduce the inhibitory effect by either reducing electrostatic interactions with the O-antigen or increasing reliance on the Omp secondary receptors. IMPORTANCE Viruses depend on host cells to propagate themselves. In mixed populations and communities of host cells, finding these susceptible host cells may have to be balanced with avoiding nonhost cells. Alternatively, being able to infect new cell types can increase the fitness of the virus. Many bacterial viruses use a two-step process to identify their hosts, binding first to an LPS receptor and then to a host protein. For Shigella virus Sf6, the tailspike protein was previously known to bind the LPS receptor. Genetic data from this work imply the tailspike also binds to the protein receptor. By experimentally evolving Sf6, we also show that point mutations in this protein can dramatically affect the binding of one or both receptors. This may provide Sf6 flexibility in identifying host cells and the ability to rapidly alter its host range under selective pressure.
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9
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Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Stefanie Barbirz
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia
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10
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Ye J, Guo J, Li T, Tian J, Yu M, Wang X, Majeed U, Song W, Xiao J, Luo Y, Yue T. Phage-based technologies for highly sensitive luminescent detection of foodborne pathogens and microbial toxins: A review. Compr Rev Food Sci Food Saf 2022; 21:1843-1867. [PMID: 35142431 DOI: 10.1111/1541-4337.12908] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023]
Abstract
Foodborne pathogens and microbial toxins are the main causes of foodborne illness. However, trace pathogens and toxins in foods are difficult to detect. Thus, techniques for their rapid and sensitive identification and quantification are urgently needed. Phages can specifically recognize and adhere to certain species of microbes or toxins due to molecular complementation between capsid proteins of phages and receptors on the host cell wall or toxins, and thus they have been successfully developed into a detection platform for pathogens and toxins. This review presents an update on phage-based luminescent detection technologies as well as their working principles and characteristics. Based on phage display techniques of temperate phages, reporter gene detection assays have been designed to sensitively detect trace pathogens by luminous intensity. By the host-specific lytic effects of virulent phages, enzyme-catalyzed chemiluminescent detection technologies for pathogens have been exploited. Notably, these phage-based luminescent detection technologies can discriminate viable versus dead microbes. Further, highly selective and sensitive immune-based assays have been developed to detect trace toxins qualitatively and quantitatively via antibody analogs displayed by phages, such as phage-ELISA (enzyme-linked immunosorbent assay) and phage-IPCR (immuno-polymerase chain reaction). This literature research may lead to novel and innocuous phage-based rapid detection technologies to ensure food safety.
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Affiliation(s)
- Jianming Ye
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jiaqing Guo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Tairan Li
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jiaxin Tian
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Mengxi Yu
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiaochen Wang
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Usman Majeed
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Wei Song
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo-Ourense Campus, Ourense, Spain
| | - Yane Luo
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China.,Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an, Shaanxi, China.,Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, China
| | - Tianli Yue
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi, China.,Laboratory of Nutritional and Healthy Food-Individuation Manufacturing Engineering, Xi'an, Shaanxi, China.,Research Center of Food Safety Risk Assessment and Control, Xi'an, Shaanxi, China
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11
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Sørensen AN, Woudstra C, Sørensen MCH, Brøndsted L. Subtypes of tail spike proteins predicts the host range of Ackermannviridae phages. Comput Struct Biotechnol J 2021; 19:4854-4867. [PMID: 34527194 PMCID: PMC8432352 DOI: 10.1016/j.csbj.2021.08.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 12/01/2022] Open
Abstract
Phages belonging to the Ackermannviridae family encode up to four tail spike proteins (TSPs), each recognizing a specific receptor of their bacterial hosts. Here, we determined the TSPs diversity of 99 Ackermannviridae phages by performing a comprehensive in silico analysis. Based on sequence diversity, we assigned all TSPs into distinctive subtypes of TSP1, TSP2, TSP3 and TSP4, and found each TSP subtype to be specifically associated with the genera (Kuttervirus, Agtrevirus, Limestonevirus, Taipeivirus) of the Ackermannviridae family. Further analysis showed that the N-terminal XD1 and XD2 domains in TSP2 and TSP4, hinging the four TSPs together, are preserved. In contrast, the C-terminal receptor binding modules were only conserved within TSP subtypes, except for some Kuttervirus TSP1s and TSP3s that were similar to specific TSP4s. A conserved motif in TSP1, TSP3 and TSP4 of Kuttervirus phages may allow recombination between receptor binding modules, thus altering host recognition. The receptors for numerous uncharacterized phages expressing TSPs in the same subtypes were predicted using previous host range data. To validate our predictions, we experimentally determined the host recognition of three of the four TSPs expressed by kuttervirus S117. We confirmed that S117 TSP1 and TSP2 bind to their predicted host receptors, and identified the receptor for TSP3, which is shared by 51 other Kuttervirus phages. Kuttervirus phages were thus shown encode a vast genetic diversity of potentially exchangeable TSPs influencing host recognition. Overall, our study demonstrates that comprehensive in silico and host range analysis of TSPs can predict host recognition of Ackermannviridae phages.
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Key Words
- ANI, Average nucleotide identity
- Ackermannviridae family
- Bacteriophage
- CPS, Capsular polysaccharide
- EOP, Efficiency of plating
- Escherichia coli O:157
- Host range
- LB, Luria-Bertani
- LPS, Lipopolysaccharide
- NCBI, National Center for Biotechnology Information
- O-antigen
- ORF, Open reading frame
- PFU, Plaque formation unit
- RBP, Receptor binding protein
- Receptor-binding proteins
- Salmonella
- TSP, Tail spike protein
- Tail spike proteins
- VriC, Virulence-associated protein
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Affiliation(s)
- Anders Nørgaard Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Cedric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Martine C Holst Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
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12
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Witte S, Zinsli LV, Gonzalez-Serrano R, Matter CI, Loessner MJ, van Mierlo JT, Dunne M. Structural and functional characterization of the receptor binding proteins of Escherichia coli O157 phages EP75 and EP335. Comput Struct Biotechnol J 2021; 19:3416-3426. [PMID: 34194667 PMCID: PMC8217332 DOI: 10.1016/j.csbj.2021.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteriophages (phages) are widely used as biocontrol agents in food and as antibacterial agents for treatment of food production plant surfaces. An important feature of such phages is broad infectivity towards a given pathogenic species. Phages attach to the surfaces of bacterial cells using receptor binding proteins (RBPs), namely tail fibers or tailspikes (TSPs). The binding range of RBPs is the primary determinant of phage host range and infectivity, and therefore dictates a phage's suitability as an antibacterial agent. Phages EP75 and EP335 broadly infect strains of E. coli serotype O157. To better understand host recognition by both phages, here we focused on characterizing the structures and functions of their RBPs. We identified two distinct tail fibers in the genome of the podovirus EP335: gp12 and gp13. Using fluorescence microscopy, we reveal how gp13 recognizes strains of E. coli serotypes O157 and O26. Phage EP75 belongs to the Kuttervirus genus within the Ackermannviridae family and features a four TSP complex (TSPs 1-4) that is universal among such phages. We demonstrate enzymatic activity of TSP1 (gp167) and TSP2 (gp168) toward the O18A and O157 O-antigens of E. coli, respectively, as well as TSP3 activity (gp169.1) against O4, O7, and O9 Salmonella O-antigens. TSPs of EP75 present high similarity to TSPs from E. coli phages CBA120 (TSP2) and HK620 (TSP1) and Salmonella myovirus Det7 (TSP3), which helps explain the cross-genus infectivity observed for EP75.
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Affiliation(s)
- Sander Witte
- Micreos Food Safety B.V., Wageningen, Nieuwe Kanaal 7P, 6709PA, The Netherlands
| | - Léa V. Zinsli
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | | | - Cassandra I. Matter
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Martin J. Loessner
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Joël T. van Mierlo
- Micreos Food Safety B.V., Wageningen, Nieuwe Kanaal 7P, 6709PA, The Netherlands
| | - Matthew Dunne
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
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13
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Dunne M, Prokhorov NS, Loessner MJ, Leiman PG. Reprogramming bacteriophage host range: design principles and strategies for engineering receptor binding proteins. Curr Opin Biotechnol 2021; 68:272-281. [PMID: 33744824 PMCID: PMC10163921 DOI: 10.1016/j.copbio.2021.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 01/09/2023]
Abstract
Bacteriophages (phages) use specialized tail machinery to deliver proteins and genetic material into a bacterial cell during infection. Attached at the distal ends of their tails are receptor binding proteins (RBPs) that recognize specific molecules exposed on host bacteria surfaces. Since the therapeutic capacity of naturally occurring phages is often limited by narrow host ranges, there is significant interest in expanding their host range via directed evolution or structure-guided engineering of their RBPs. Here, we describe the design principles of different RBP engineering platforms and draw attention to the mechanisms linking RBP binding and the correct spatial and temporal attachment of the phage to the bacterial surface. A deeper understanding of these mechanisms will directly benefit future engineering of more effective phage-based therapeutics.
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Affiliation(s)
- Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Nikolai S Prokhorov
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA
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14
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Bacteriophage-based advanced bacterial detection: Concept, mechanisms, and applications. Biosens Bioelectron 2021; 177:112973. [DOI: 10.1016/j.bios.2021.112973] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022]
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15
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Irmscher T, Roske Y, Gayk I, Dunsing V, Chiantia S, Heinemann U, Barbirz S. Pantoea stewartii WceF is a glycan biofilm-modifying enzyme with a bacteriophage tailspike-like fold. J Biol Chem 2021; 296:100286. [PMID: 33450228 PMCID: PMC7949094 DOI: 10.1016/j.jbc.2021.100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 11/19/2022] Open
Abstract
Pathogenic microorganisms often reside in glycan-based biofilms. Concentration and chain length distribution of these mostly anionic exopolysaccharides (EPS) determine the overall biophysical properties of a biofilm and result in a highly viscous environment. Bacterial communities regulate this biofilm state via intracellular small-molecule signaling to initiate EPS synthesis. Reorganization or degradation of this glycan matrix, however, requires the action of extracellular glycosidases. So far, these were mainly described for bacteriophages that must degrade biofilms for gaining access to host bacteria. The plant pathogen Pantoea stewartii (P. stewartii) encodes the protein WceF within its EPS synthesis cluster. WceF has homologs in various biofilm forming plant pathogens of the Erwinia family. In this work, we show that WceF is a glycosidase active on stewartan, the main P. stewartii EPS biofilm component. WceF has remarkable structural similarity with bacteriophage tailspike proteins (TSPs). Crystal structure analysis showed a native trimer of right-handed parallel β-helices. Despite its similar fold, WceF lacks the high stability found in bacteriophage TSPs. WceF is a stewartan hydrolase and produces oligosaccharides, corresponding to single stewartan repeat units. However, compared with a stewartan-specific glycan hydrolase of bacteriophage origin, WceF showed lectin-like autoagglutination with stewartan, resulting in notably slower EPS cleavage velocities. This emphasizes that the bacterial enzyme WceF has a role in P. stewartii biofilm glycan matrix reorganization clearly different from that of a bacteriophage exopolysaccharide depolymerase.
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Affiliation(s)
- Tobias Irmscher
- Physikalische Biochemie, Universität Potsdam, Potsdam, Germany; Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Yvette Roske
- Crystallography, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Igor Gayk
- Physikalische Biochemie, Universität Potsdam, Potsdam, Germany
| | - Valentin Dunsing
- Physikalische Zellbiochemie, Universität Potsdam, Potsdam, Germany
| | | | - Udo Heinemann
- Crystallography, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany; Institut für Chemie und Biochemie, Freie Universität, Berlin, Germany.
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16
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Stephan MS, Broeker NK, Saragliadis A, Roos N, Linke D, Barbirz S. In vitro Analysis of O-Antigen-Specific Bacteriophage P22 Inactivation by Salmonella Outer Membrane Vesicles. Front Microbiol 2020; 11:510638. [PMID: 33072001 PMCID: PMC7541932 DOI: 10.3389/fmicb.2020.510638] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/26/2020] [Indexed: 11/23/2022] Open
Abstract
Bacteriophages use a large number of different bacterial cell envelope structures as receptors for surface attachment. As a consequence, bacterial surfaces represent a major control point for the defense against phage attack. One strategy for phage population control is the production of outer membrane vesicles (OMVs). In Gram-negative host bacteria, O-antigen-specific bacteriophages address lipopolysaccharide (LPS) to initiate infection, thus relying on an essential outer membrane glycan building block as receptor that is constantly present also in OMVs. In this work, we have analyzed interactions of Salmonella (S.) bacteriophage P22 with OMVs. For this, we isolated OMVs that were formed in large amounts during mechanical cell lysis of the P22 S. Typhimurium host. In vitro, these OMVs could efficiently reduce the number of infective phage particles. Fluorescence spectroscopy showed that upon interaction with OMVs, bacteriophage P22 released its DNA into the vesicle lumen. However, only about one third of the phage P22 particles actively ejected their genome. For the larger part, no genome release was observed, albeit the majority of phages in the system had lost infectivity towards their host. With OMVs, P22 ejected its DNA more rapidly and could release more DNA against elevated osmotic pressures compared to DNA release triggered with protein-free LPS aggregates. This emphasizes that OMV composition is a key feature for the regulation of infective bacteriophage particles in the system.
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Affiliation(s)
- Mareike S Stephan
- Physical Biochemistry, Department for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nina K Broeker
- Physical Biochemistry, Department for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Norbert Roos
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Stefanie Barbirz
- Physical Biochemistry, Department for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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17
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Kunstmann S, Engström O, Wehle M, Widmalm G, Santer M, Barbirz S. Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein. Chemistry 2020; 26:7263-7273. [PMID: 32189378 PMCID: PMC7463171 DOI: 10.1002/chem.202000495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D 1 H,1 H-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.
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Affiliation(s)
- Sonja Kunstmann
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Current address: Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads2800 Kgs.LyngbyDenmark
| | - Olof Engström
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Marko Wehle
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Göran Widmalm
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Mark Santer
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Stefanie Barbirz
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
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18
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Abstract
Numerous bacteriophages-viruses of bacteria, also known as phages-have been described for hundreds of bacterial species. The Gram-negative Shigella species are close relatives of Escherichia coli, yet relatively few previously described phages appear to exclusively infect this genus. Recent efforts to isolate Shigella phages have indicated these viruses are surprisingly abundant in the environment and have distinct genomic and structural properties. In addition, at least one model system used for experimental evolution studies has revealed a unique mechanism for developing faster infection cycles. Differences between these bacteriophages and other well-described model systems may mirror differences between their hosts' ecology and defense mechanisms. In this review, we discuss the history of Shigella phages and recent developments in their isolation and characterization and the structural information available for three model systems, Sf6, Sf14, and HRP29; we also provide an overview of potential selective pressures guiding both Shigella phage and host evolution.
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Affiliation(s)
- Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Sarah M Doore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan 48824, USA;
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19
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Structural and Functional Studies of a Klebsiella Phage Capsule Depolymerase Tailspike: Mechanistic Insights into Capsular Degradation. Structure 2020; 28:613-624.e4. [PMID: 32386574 DOI: 10.1016/j.str.2020.04.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/09/2020] [Accepted: 04/17/2020] [Indexed: 01/01/2023]
Abstract
Capsule polysaccharide is a major virulence factor of Klebsiella pneumoniae, a nosocomial pathogen associated with a wide range of infections. It protects bacteria from harsh environmental conditions, immune system response, and phage infection. To access cell wall-located receptors, some phages possess tailspike depolymerases that degrade the capsular polysaccharide. Here, we present the crystal structure of a tailspike against Klebsiella, KP32gp38, whose primary sequence shares no similarity to other proteins of known structure. In the trimeric structure of KP32gp38, each chain contains a flexible N-terminal domain, a right-handed parallel β helix domain and two β sandwiches with carbohydrate binding features. The crystal structure and activity assays allowed us to locate the catalytic site. Also, our data provide experimental evidence of a branching architecture of depolymerases in KP32 Klebsiella viruses, as KP32gp38 displays nanomolar affinity to another depolymerase from the same phage, KP32gp37. Results provide a structural framework for enzyme engineering to produce serotype-broad-active enzyme complexes against K. pneumoniae.
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20
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Laumay F, Chaïb A, Linares R, Breyton C. "French Phage Network" Annual Conference-Fifth Meeting Report. Viruses 2020; 12:v12040446. [PMID: 32295276 PMCID: PMC7232257 DOI: 10.3390/v12040446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 04/09/2020] [Indexed: 12/04/2022] Open
Abstract
Attracting about 100 participants, the fifth edition of our French Phages.fr annual conference was once more a success. This year’s conference took place at the Institute for Structural Biology on the European Electron and Photon Campus in Grenoble, 8–9 October 2019. Similar to previous years, our meeting gathered scientists mainly working in France, from academic labs and hospitals as well as from industry. We also had the pleasure of welcoming attendees from different European countries and even beyond. The conference was divided into four sessions: Ecology and Evolution, Phage Therapy and Biotechnology, Structure and Assembly and Phage–Host Interaction, each opened by a keynote lecture. The talks, selected from abstracts, gave the opportunity for young scientists (especially students and post-docs) to present their project and results in a friendly atmosphere. Poster sessions also favoured interactions and discussions between young researchers and more senior scientists. Here, we provide a summary of the topics developed during the conference.
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Affiliation(s)
- Floriane Laumay
- Genomic Research Laboratory, Geneva University Hospitals, CH-1211 Geneva, Switzerland;
| | - Amel Chaïb
- ISVV, EA4577 Œnologie, University of Bordeaux, Villenave d’Ornon, 33140 Bordeaux, France;
| | - Romain Linares
- CNRS, CEA, IBS, University Grenoble Alpes, F-38000 Grenoble, France;
| | - Cécile Breyton
- CNRS, CEA, IBS, University Grenoble Alpes, F-38000 Grenoble, France;
- Correspondence:
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21
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Dunsing V, Irmscher T, Barbirz S, Chiantia S. Purely Polysaccharide-Based Biofilm Matrix Provides Size-Selective Diffusion Barriers for Nanoparticles and Bacteriophages. Biomacromolecules 2019; 20:3842-3854. [DOI: 10.1021/acs.biomac.9b00938] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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