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Asgharzadeh Kangachar S, Logel DY, Trofimova E, Zhu HX, Zaugg J, Schembri MA, Weynberg KD, Jaschke PR. Discovery and characterisation of new phage targeting uropathogenic Escherichia coli. Virology 2024; 597:110148. [PMID: 38941748 DOI: 10.1016/j.virol.2024.110148] [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: 01/31/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Antimicrobial resistance is an escalating threat with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are prone to becoming recurrent and antibiotic resistant. We discovered and characterized six novel Autographiviridae and Guernseyvirinae bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), a leading cause of UTIs. The phage genomes were between 39,471 bp - 45,233 bp, with 45.0%-51.0% GC%, and 57-84 predicted coding sequences per genome. We show that tail fiber domain structure, predicted host capsule type, and host antiphage repertoire correlate with phage host range. In vitro characterisation of phage cocktails showed synergistic improvement against a mixed UPEC strain population and when sequentially dosed. Together, these phage are a new set extending available treatments for UTI from UPEC, and phage vM_EcoM_SHAK9454 represents a promising candidate for further improvement through engineering.
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Affiliation(s)
- Shahla Asgharzadeh Kangachar
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Ellina Trofimova
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Queensland, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Karen D Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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2
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Evseev PV, Shneider MM, Kolupaeva LV, Kasimova AA, Timoshina OY, Perepelov AV, Shpirt AM, Shelenkov AA, Mikhailova YV, Suzina NE, Knirel YA, Miroshnikov KA, Popova AV. New Obolenskvirus Phages Brutus and Scipio: Biology, Evolution, and Phage-Host Interaction. Int J Mol Sci 2024; 25:2074. [PMID: 38396752 PMCID: PMC10888812 DOI: 10.3390/ijms25042074] [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: 12/29/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Two novel virulent phages of the genus Obolenskvirus infecting Acinetobacter baumannii, a significant nosocomial pathogen, have been isolated and studied. Phages Brutus and Scipio were able to infect A. baumannii strains belonging to the K116 and K82 capsular types, respectively. The biological properties and genomic organization of the phages were characterized. Comparative genomic, phylogenetic, and pangenomic analyses were performed to investigate the relationship of Brutus and Scipio to other bacterial viruses and to trace the possible origin and evolutionary history of these phages and other representatives of the genus Obolenskvirus. The investigation of enzymatic activity of the tailspike depolymerase encoded in the genome of phage Scipio, the first reported virus infecting A. baumannii of the K82 capsular type, was performed. The study of new representatives of the genus Obolenskvirus and mechanisms of action of depolymerases encoded in their genomes expands knowledge about the diversity of viruses within this taxonomic group and strategies of Obolenskvirus-host bacteria interaction.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Mikhail M. Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
| | - Lyubov V. Kolupaeva
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
| | - Anastasia A. Kasimova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Olga Y. Timoshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
| | - Andrey V. Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Anna M. Shpirt
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Andrey A. Shelenkov
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia (Y.V.M.)
| | - Yulia V. Mikhailova
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia (Y.V.M.)
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, Moscow Region, 142290 Pushchino, Russia;
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Konstantin A. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
| | - Anastasia V. Popova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
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3
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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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Pas C, Latka A, Fieseler L, Briers Y. Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups. Virol J 2023; 20:174. [PMID: 37550759 PMCID: PMC10408124 DOI: 10.1186/s12985-023-02138-4] [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: 04/24/2023] [Accepted: 07/23/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups. METHODS Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution. RESULTS We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages. CONCLUSION The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.
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Affiliation(s)
- Célia Pas
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Agnieszka Latka
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63, 51-148, Wrocław, Poland
| | - Lars Fieseler
- Centre for Food Safety and Quality Management, ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Yves Briers
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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Tang M, Huang Z, Zhang X, Kong J, Zhou B, Han Y, Zhang Y, Chen L, Zhou T. Phage resistance formation and fitness costs of hypervirulent Klebsiella pneumoniae mediated by K2 capsule-specific phage and the corresponding mechanisms. Front Microbiol 2023; 14:1156292. [PMID: 37538841 PMCID: PMC10394836 DOI: 10.3389/fmicb.2023.1156292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Introduction Phage is promising for the treatment of hypervirulent Klebsiella pneumoniae (hvKP) infections. Although phage resistance seems inevitable, we found that there still was optimization space in phage therapy for hvKP infection. Methods The clinical isolate K. pneumoniae FK1979 was used to recover the lysis phage ΦFK1979 from hospital sewage. Phage-resistant bacteria were obtained on LB agar and used to isolate phages from sewage. The plaque assay, transmission electron microscopy (TEM), multiplicity of infection test, one-step growth curve assay, and genome analysis were performed to characterize the phages. Colony morphology, precipitation test and scanning electron microscope were used to characterize the bacteria. The absorption test, spot test and efficiency of plating (EOP) assay were used to identify the sensitivity of bacteria to phages. Whole genome sequencing (WGS) was used to identify gene mutations of phage-resistant bacteria. The gene expression levels were detected by RT-qPCR. Genes knockout and complementation of the mutant genes were performed. The change of capsules was detected by capsule quantification and TEM. The growth kinetics, serum resistance, biofilm formation, adhesion and invasion to A549 and RAW 264.7 cells, as well as G. mellonella and mice infection models, were used to evaluate the fitness and virulence of bacteria. Results and discussion Here, we demonstrated that K2 capsule type sequence type 86 hvKP FK1979, one of the main pandemic lineages of hvKP with thick capsule, rapidly developed resistance to a K2-specific lysis phage ΦFK1979 which was well-studied in this work to possess polysaccharide depolymerase. The phage-resistant mutants showed a marked decrease in capsule expression. WGS revealed single nucleotide polymorphism (SNP) in genes encoding RfaH, galU, sugar glycosyltransferase, and polysaccharide deacetylase family protein in the mutants. RfaH and galU were further identified as being required for capsule production and phage sensitivity. Expressions of genes involved in the biosynthesis or regulation of capsule and/or lipopolysaccharide significantly decreased in the mutants. Despite the rapid and frequent development of phage resistance being a disadvantage, the attenuation of virulence and fitness in vitro and in vivo indicated that phage-resistant mutants of hvKP were more susceptible to the immunity system. Interestingly, the newly isolated phages targeting mutants changed significantly in their plaque and virus particle morphology. Their genomes were much larger than and significantly different from that of ΦFK1979. They possessed much more functional proteins and strikingly broader host spectrums than ΦFK1979. Our study suggests that K2-specific phage has the potential to function as an antivirulence agent, or a part of phage cocktails combined with phages targeting phage-resistant bacteria, against hvKP-relevant infections.
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Affiliation(s)
- Miran Tang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University and Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zeyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University and Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaodong Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University and Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jingchun Kong
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Beibei Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University and Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yijia Han
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Zhang
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University and Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University and Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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Teklemariam AD, Al-Hindi RR, Qadri I, Alharbi MG, Ramadan WS, Ayubu J, Al-Hejin AM, Hakim RF, Hakim FF, Hakim RF, Alseraihi LI, Alamri T, Harakeh S. The Battle between Bacteria and Bacteriophages: A Conundrum to Their Immune System. Antibiotics (Basel) 2023; 12:381. [PMID: 36830292 PMCID: PMC9952470 DOI: 10.3390/antibiotics12020381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Bacteria and their predators, bacteriophages, or phages are continuously engaged in an arms race for their survival using various defense strategies. Several studies indicated that the bacterial immune arsenal towards phage is quite diverse and uses different components of the host machinery. Most studied antiphage systems are associated with phages, whose genomic matter is double-stranded-DNA. These defense mechanisms are mainly related to either the host or phage-derived proteins and other associated structures and biomolecules. Some of these strategies include DNA restriction-modification (R-M), spontaneous mutations, blocking of phage receptors, production of competitive inhibitors and extracellular matrix which prevent the entry of phage DNA into the host cytoplasm, assembly interference, abortive infection, toxin-antitoxin systems, bacterial retrons, and secondary metabolite-based replication interference. On the contrary, phages develop anti-phage resistance defense mechanisms in consortium with each of these bacterial phage resistance strategies with small fitness cost. These mechanisms allow phages to undergo their replication safely inside their bacterial host's cytoplasm and be able to produce viable, competent, and immunologically endured progeny virions for the next generation. In this review, we highlight the major bacterial defense systems developed against their predators and some of the phage counterstrategies and suggest potential research directions.
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Affiliation(s)
- Addisu D. Teklemariam
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rashad R. Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mona G. Alharbi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Wafaa S. Ramadan
- Department of Anatomy, Faculty of Medicine (FM), King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Anatomy, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Jumaa Ayubu
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M. Al-Hejin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Microbiology Level 2 Laboratory, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | | | - Fanar F. Hakim
- Department of Internal Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rahad F. Hakim
- Ibn Sina National College for Medical Studies, Jeddah 21418, Saudi Arabia
| | | | - Turki Alamri
- Family and Community Medicine Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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7
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Sanchez BC, Heckmann ER, Green SI, Clark JR, Kaplan HB, Ramig RF, Muldrew KL, Hines-Munson C, Skelton F, Trautner BW, Maresso AW. Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms. Front Microbiol 2022; 13:796132. [PMID: 35620093 PMCID: PMC9127763 DOI: 10.3389/fmicb.2022.796132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
High rates of antimicrobial resistance and formation of biofilms makes treatment of Escherichia coli catheter-associated urinary tract infections (CAUTI) particularly challenging. CAUTI affect 1 million patients per year in the United States and are associated with morbidity and mortality, particularly as an etiology for sepsis. Phage have been proposed as a potential therapeutic option. Here, we report the development of phage cocktails that lyse contemporary E. coli strains isolated from the urine of patients with spinal cord injury (SCI) and display strong biofilm-forming properties. We characterized E. coli phage against biofilms in two in vitro CAUTI models. Biofilm viability was measured by an MTT assay that determines cell metabolic activity and by quantification of colony forming units. Nine phage decreased cell viability by >80% when added individually to biofilms of two E. coli strains in human urine. A phage cocktail comprising six phage lyses 82% of the strains in our E. coli library and is highly effective against young and old biofilms and against biofilms on silicon catheter materials. Using antibiotics together with our phage cocktail prevented or decreased emergence of E. coli resistant to phage in human urine. We created an anti-biofilm phage cocktail with broad host range against E. coli strains isolated from urine. These phage cocktails may have therapeutic potential against CAUTI.
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Affiliation(s)
- Belkys C. Sanchez
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Emmaline R. Heckmann
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sabrina I. Green
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Justin R. Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth Houston, Houston, TX, United States
| | - Robert F. Ramig
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Kenneth L. Muldrew
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Pathology and Laboratory Medicine, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Casey Hines-Munson
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Felicia Skelton
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, United States
| | - Barbara W. Trautner
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, United States,Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Anthony W. Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Anthony W. Maresso,
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8
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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: 29] [Impact Index Per Article: 9.7] [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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9
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Zhang Y, Liao YT, Salvador A, Lavenburg VM, Wu VCH. Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm. Microorganisms 2021; 9:microorganisms9071527. [PMID: 34361962 PMCID: PMC8303462 DOI: 10.3390/microorganisms9071527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 01/21/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103.
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10
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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11
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Engineering the Modular Receptor-Binding Proteins of Klebsiella Phages Switches Their Capsule Serotype Specificity. mBio 2021; 12:mBio.00455-21. [PMID: 33947754 PMCID: PMC8262889 DOI: 10.1128/mbio.00455-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The high specificity of bacteriophages is driven by their receptor-binding proteins (RBPs). Many Klebsiella bacteriophages target the capsular exopolysaccharide as the receptor and encode RBPs with depolymerase activity. The modular structure of these RBPs with an N-terminal structural module to attach the RBP to the phage tail, and a C-terminal specificity module for exopolysaccharide degradation, supports horizontal transfer as a major evolutionary driver for Klebsiella phage RBPs. We mimicked this natural evolutionary process by the construction of modular RBP chimeras, exchanging N-terminal structural modules and C-terminal specificity modules. All chimeras strictly follow the capsular serotype specificity of the C-terminal module. Transplanting chimeras with a K11 N-terminal structural RBP module in a Klebsiella phage K11 scaffold results in a capsular serotype switch and corresponding host range modification of the synthetic phages, demonstrating that horizontal transfer of C-terminal specificity modules offers Klebsiella phages an evolutionary highway for rapid adaptation to new capsular serotypes.
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12
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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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13
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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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14
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Mangalea MR, Duerkop BA. Fitness Trade-Offs Resulting from Bacteriophage Resistance Potentiate Synergistic Antibacterial Strategies. Infect Immun 2020; 88:e00926-19. [PMID: 32094257 PMCID: PMC7309606 DOI: 10.1128/iai.00926-19] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacteria that cause life-threatening infections in humans are becoming increasingly difficult to treat. In some instances, this is due to intrinsic and acquired antibiotic resistance, indicating that new therapeutic approaches are needed to combat bacterial pathogens. There is renewed interest in utilizing viruses of bacteria known as bacteriophages (phages) as potential antibacterial therapeutics. However, critics suggest that similar to antibiotics, the development of phage-resistant bacteria will halt clinical phage therapy. Although the emergence of phage-resistant bacteria is likely inevitable, there is a growing body of literature showing that phage selective pressure promotes mutations in bacteria that allow them to subvert phage infection, but with a cost to their fitness. Such fitness trade-offs include reduced virulence, resensitization to antibiotics, and colonization defects. Resistance to phage nucleic acid entry, primarily via cell surface modifications, compromises bacterial fitness during antibiotic and host immune system pressure. In this minireview, we explore the mechanisms behind phage resistance in bacterial pathogens and the physiological consequences of acquiring phage resistance phenotypes. With this knowledge, it may be possible to use phages to alter bacterial populations, making them more tractable to current therapeutic strategies.
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Affiliation(s)
- Mihnea R Mangalea
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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15
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Knecht LE, Veljkovic M, Fieseler L. Diversity and Function of Phage Encoded Depolymerases. Front Microbiol 2020; 10:2949. [PMID: 31998258 PMCID: PMC6966330 DOI: 10.3389/fmicb.2019.02949] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages of the Podoviridae family often exhibit so-called depolymerases as structural components of the virion. These enzymes appear as tail spike proteins (TSPs). After specific binding to capsular polysaccharides (CPS), exopolysaccharides (EPS) or lipopolysaccharide (LPS) of the host bacteria, polysaccharide-repeating units are specifically cleaved. Finally, the phage reaches the last barrier, the cell wall, injects its DNA, and infects the cell. Recently, similar enzymes from bacteriophages of the Ackermannviridae, Myoviridae, and Siphoviridae families were also described. In this mini-review the diversity and function of phage encoded CPS-, EPS-, and LPS-degrading depolymerases is summarized. The function of the enzymes is described in terms of substrate specificity and applications in biotechnology.
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Affiliation(s)
- Leandra E Knecht
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Marjan Veljkovic
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
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16
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Latka A, Leiman PG, Drulis-Kawa Z, Briers Y. Modeling the Architecture of Depolymerase-Containing Receptor Binding Proteins in Klebsiella Phages. Front Microbiol 2019; 10:2649. [PMID: 31803168 PMCID: PMC6872550 DOI: 10.3389/fmicb.2019.02649] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/30/2019] [Indexed: 11/30/2022] Open
Abstract
Klebsiella pneumoniae carries a thick polysaccharide capsule. This highly variable chemical structure plays an important role in its virulence. Many Klebsiella bacteriophages recognize this capsule with a receptor binding protein (RBP) that contains a depolymerase domain. This domain degrades the capsule to initiate phage infection. RBPs are highly specific and thus largely determine the host spectrum of the phage. A majority of known Klebsiella phages have only one or two RBPs, but phages with up to 11 RBPs with depolymerase activity and a broad host spectrum have been identified. A detailed bioinformatic analysis shows that similar RBP domains repeatedly occur in K. pneumoniae phages with structural RBP domains for attachment of an RBP to the phage tail (anchor domain) or for branching of RBPs (T4gp10-like domain). Structural domains determining the RBP architecture are located at the N-terminus, while the depolymerase is located in the center of protein. Occasionally, the RBP is complemented with an autocleavable chaperone domain at the distal end serving for folding and multimerization. The enzymatic domain is subjected to an intense horizontal transfer to rapidly shift the phage host spectrum without affecting the RBP architecture. These analyses allowed to model a set of conserved RBP architectures, indicating evolutionary linkages.
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Affiliation(s)
- Agnieszka Latka
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.,Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Petr G Leiman
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
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17
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Complete Genome Sequence of Enterotoxigenic Escherichia coli Podophage LL11. Microbiol Resour Announc 2019; 8:8/32/e00693-19. [PMID: 31395642 PMCID: PMC6687929 DOI: 10.1128/mra.00693-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is an opportunistic pathogen that commonly causes foodborne illness. Study of bacteriophages against this pathogen could be useful to develop alternative treatment approaches. Here, we present the complete genome sequence of LL11, a T7-like podophage that infects ETEC. Enterotoxigenic Escherichia coli (ETEC) is an opportunistic pathogen that commonly causes foodborne illness. Study of bacteriophages against this pathogen could be useful to develop alternative treatment approaches. Here, we present the complete genome sequence of LL11, a T7-like podophage that infects ETEC.
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18
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Plattner M, Shneider MM, Arbatsky NP, Shashkov AS, Chizhov AO, Nazarov S, Prokhorov NS, Taylor NMI, Buth SA, Gambino M, Gencay YE, Brøndsted L, Kutter EM, Knirel YA, Leiman PG. Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. J Mol Biol 2019; 431:3718-3739. [PMID: 31325442 DOI: 10.1016/j.jmb.2019.07.022] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages recognize their host cells with the help of tail fiber and tailspike proteins that bind, cleave, or modify certain structures on the cell surface. The spectrum of ligands to which the tail fibers and tailspikes can bind is the primary determinant of the host range. Bacteriophages with multiple tailspike/tail fibers are thought to have a wider host range than their less endowed relatives but the function of these proteins remains poorly understood. Here, we describe the structure, function, and substrate specificity of three tailspike proteins of bacteriophage CBA120-TSP2, TSP3 and TSP4 (orf211 through orf213, respectively). We show that tailspikes TSP2, TSP3 and TSP4 are hydrolases that digest the O157, O77, and O78 Escherichia coli O-antigens, respectively. We demonstrate that recognition of the E. coli O157:H7 host by CBA120 involves binding to and digesting the O157 O-antigen by TSP2. We report the crystal structure of TSP2 in complex with a repeating unit of the O157 O-antigen. We demonstrate that according to the specificity of its tailspikes TSP2, TSP3, and TSP4, CBA120 can infect E. coli O157, O77, and O78, respectively. We also show that CBA120 infects Salmonella enterica serovar Minnesota, and this host range expansion is likely due to the function of TSP1. Finally, we describe the assembly pathway and the architecture of the TSP1-TSP2-TSP3-TSP4 branched complex in CBA120 and its related ViI-like phages.
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Affiliation(s)
- Michel Plattner
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA; École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Mikhail M Shneider
- Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
| | - Nikolay P Arbatsky
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander O Chizhov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Nazarov
- École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, 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 Blvd, Galveston, TX 77555-0647, USA
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Sergey A Buth
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Yilmaz Emre Gencay
- 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
| | | | - Yuriy A Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0647, USA.
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19
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Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, van Raaij MJ, Wittmann J. Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy. Viruses 2019; 11:E454. [PMID: 31109012 PMCID: PMC6563267 DOI: 10.3390/v11050454] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against E. coli isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against E. coli are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of E. coli phages.
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Affiliation(s)
- Imke H E Korf
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
| | | | - Andrew M Kropinski
- Departments of Food Science and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Manfred Nimtz
- Protein Analytics Platform, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig,Germany.
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), 38124 Braunschweig,Germany.
| | - Mark J van Raaij
- Department of Macromolecular Structure, Centro Nacional de Biotecnologia CNB-CSIC, 28049 Madrid,Spain.
| | - Johannes Wittmann
- Leibniz Institute DSMZ⁻German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig,Germany.
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20
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Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ. Adaptive Evolution within Gut Microbiomes of Healthy People. Cell Host Microbe 2019; 25:656-667.e8. [PMID: 31028005 PMCID: PMC6749991 DOI: 10.1016/j.chom.2019.03.007] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/23/2019] [Accepted: 03/15/2019] [Indexed: 02/06/2023]
Abstract
Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.
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Affiliation(s)
- Shijie Zhao
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tami D Lieberman
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn M Kauffman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute for Systems Biology, Seattle, WA 98109, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA
| | - Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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21
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Pan Y, Lin T, Chen Y, Lai P, Tsai Y, Hsu C, Hsieh P, Lin Y, Wang J. Identification of three podoviruses infecting Klebsiella encoding capsule depolymerases that digest specific capsular types. Microb Biotechnol 2019; 12:472-486. [PMID: 30706654 PMCID: PMC6465236 DOI: 10.1111/1751-7915.13370] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/13/2018] [Accepted: 12/21/2018] [Indexed: 12/11/2022] Open
Abstract
Klebsiella pneumoniae is an important human pathogen causing opportunistic nosocomial and community-acquired infections. A major public health concern regarding K. pneumoniae is the increasing incidence of multidrug-resistant strains. Here, we isolated three novel Klebsiella bacteriophages, KN1-1, KN3-1 and KN4-1, which infect KN1, KN3 and K56, and KN4 types respectively. We determined their genome sequences and conducted a comparative analysis that revealed a variable region containing capsule depolymerase-encoding genes. Recombinant depolymerase proteins were produced, and their enzymatic activity and specificity were evaluated. We identified four capsule depolymerases in these phages that could only digest the capsule types of their respective hosts. Our results demonstrate that the activities of these capsule depolymerases were correlated with the host range of each phage; thus, the capsule depolymerases are host specificity determinants. By generating a capsule mutant, we demonstrate that capsule was essential for phage adsorption and infection. Further, capsule depolymerases can enhance bacterial susceptibility to serum killing. The discovery of these phages and depolymerases lays the foundation for the typing of KN1, KN3, KN4 and K56 Klebsiella and could be useful alternative therapeutics for the treatment of K. pneumoniae infections.
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Affiliation(s)
- Yi‐Jiun Pan
- Department of Microbiology and ImmunologySchool of MedicineChina Medical UniversityTaichungTaiwan
| | - Tzu‐Lung Lin
- Department of Medical Biotechnology and Laboratory scienceCollege of MedicineChang Gung UniversityTaoyuanTaiwan
| | - Yi‐Yin Chen
- Department of PediatricsCollege of MedicineChang Gung Children's HospitalChang Gung Memorial HospitalChang Gung UniversityTaoyuanTaiwan
| | - Peng‐Hsuan Lai
- Department of Microbiology and ImmunologySchool of MedicineChina Medical UniversityTaichungTaiwan
| | - Yun‐Ting Tsai
- Department of Microbiology and ImmunologySchool of MedicineChina Medical UniversityTaichungTaiwan
| | - Chun‐Ru Hsu
- Department of Medical ResearchE‐Da HospitalKaohsiungTaiwan
| | - Pei‐Fang Hsieh
- Department of MicrobiologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Yi‐Tsung Lin
- Division of Infectious DiseasesDepartment of MedicineTaipei Veterans General HospitalTaipeiTaiwan
| | - Jin‐Town Wang
- Department of MicrobiologyNational Taiwan University College of MedicineTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University HospitalTaipeiTaiwan
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22
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Cai R, Wu M, Zhang H, Zhang Y, Cheng M, Guo Z, Ji Y, Xi H, Wang X, Xue Y, Sun C, Feng X, Lei L, Tong Y, Liu X, Han W, Gu J. A Smooth-Type, Phage-Resistant Klebsiella pneumoniae Mutant Strain Reveals that OmpC Is Indispensable for Infection by Phage GH-K3. Appl Environ Microbiol 2018; 84:e01585-18. [PMID: 30171001 PMCID: PMC6193389 DOI: 10.1128/aem.01585-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/22/2018] [Indexed: 01/06/2023] Open
Abstract
Bacteriophage can be used as an alternative or complementary therapy to antibiotics for treating multidrug-resistant bacterial infections. However, the rapid emergence of resistant host variants during phage treatment has limited its therapeutic applications. In this study, a potential phage-resistant mechanism of Klebsiella pneumoniae was revealed. After phage GH-K3 treatment, a smooth-type colony, named K7RB, was obtained from the K. pneumoniae K7 culture. Treatment with IO4- and/or proteinase K indicated that polysaccharides of K7 played an important role in phage recruitment, and protein receptors on K7 were essential for effective infection by GH-K3. Differences in protein expression between K7 and K7RB were quantitatively analyzed by liquid chromatography-tandem mass spectrometry. Among differentially expressed proteins, OmpC, OmpN, KPN_02430, and OmpF were downregulated significantly in K7RBtrans-Complementation of OmpC in K7RB conferred rapid adsorption and sensitivity to GH-K3. In contrast, a single-base deletion mutation of ompC in K7, which resulted in OmpC silencing, led to lower adsorption efficiency and resistance to GH-K3. These assays proved that OmpC is the key receptor-binding protein for GH-K3. In addition, the native K. pneumoniae strains KPP14, KPP27, and KPP36 showed low or no sensitivity to GH-K3. However, these strains became more sensitive to GH-K3 after their native receptors were replaced by OmpC of K7, suggesting that OmpCK7 was the most suitable receptor for GH-K3. This study revealed that K7RB became resistant to GH-K3 due to gene mutation of ompC and that OmpC of K7 is essential for effective infection by GH-K3.IMPORTANCE With increased incidence of multidrug-resistant (MDR) bacterial strains, phages have regained attention as promising potential antibacterial agents. However, the rapid emergence of resistant variants during phage treatment has limited the therapeutic applications of phage. According to our trans-complementation, ompC mutation, and phage adsorption efficiency assays, we identified OmpC as the key receptor-binding protein (RBP) for phage GH-K3, which is essential for effective infection. This study revealed that the phage secondary receptor of K. pneumoniae, OmpC, is the essential RBP not only for phage infecting Gram-negative bacteria, such as Escherichia coli and Salmonella, but also for K. pneumoniae.
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Affiliation(s)
- Ruopeng Cai
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Mei Wu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hao Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Yufeng Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Mengjun Cheng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Yalu Ji
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Hengyu Xi
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Xinwu Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Yibing Xue
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Changjiang Sun
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Xin Feng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Liancheng Lei
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wenyu Han
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jingmin Gu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, People's Republic of China
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23
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Enzymes and Mechanisms Employed by Tailed Bacteriophages to Breach the Bacterial Cell Barriers. Viruses 2018; 10:v10080396. [PMID: 30060520 PMCID: PMC6116005 DOI: 10.3390/v10080396] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023] Open
Abstract
Monoderm bacteria possess a cell envelope made of a cytoplasmic membrane and a cell wall, whereas diderm bacteria have and extra lipid layer, the outer membrane, covering the cell wall. Both cell types can also produce extracellular protective coats composed of polymeric substances like, for example, polysaccharidic capsules. Many of these structures form a tight physical barrier impenetrable by phage virus particles. Tailed phages evolved strategies/functions to overcome the different layers of the bacterial cell envelope, first to deliver the genetic material to the host cell cytoplasm for virus multiplication, and then to release the virion offspring at the end of the reproductive cycle. There is however a major difference between these two crucial steps of the phage infection cycle: virus entry cannot compromise cell viability, whereas effective virion progeny release requires host cell lysis. Here we present an overview of the viral structures, key protein players and mechanisms underlying phage DNA entry to bacteria, and then escape of the newly-formed virus particles from infected hosts. Understanding the biological context and mode of action of the phage-derived enzymes that compromise the bacterial cell envelope may provide valuable information for their application as antimicrobials.
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24
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Chen L, Yuan S, Liu Q, Mai G, Yang J, Deng D, Zhang B, Liu C, Ma Y. In Vitro Design and Evaluation of Phage Cocktails Against Aeromonas salmonicida. Front Microbiol 2018; 9:1476. [PMID: 30034378 PMCID: PMC6043867 DOI: 10.3389/fmicb.2018.01476] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/13/2018] [Indexed: 01/21/2023] Open
Abstract
As an alternative approach against multidrug-resistant bacterial infections, phages are now being increasingly investigated as effective therapeutic agents. Here, aiming to design an efficient phage cocktail against Aeromonas salmonicida infections, we isolated and characterized five lytic A. salmonicida phages, AS-szw, AS-yj, AS-zj, AS-sw, and AS-gz. The results of morphological and genomic analysis suggested that all these phages are affiliated to the T4virus genus of the Caudovirales order. Their heterogeneous lytic capacities against A. salmonicida strains were demonstrated by experiments. A series of phage cocktails were prepared and investigated in vitro. We observed that the cocktail combining AS-gz and AS-yj showed significantly higher antimicrobial activity than other cocktails and individual phages. Given the divergent genomes between the phages AS-yj and AS-gz, our results highlight that the heterogeneous mechanisms that phages use to infect their hosts likely lead to phage synergy in killing the host. Conclusively, our study described a strategy to develop an effective and promising phage cocktail as a therapeutic agent to combat A. salmonicida infections, and thereby to control the outbreak of relevant fish diseases. Our study suggests that in vitro investigations into phages are prerequisite to obtain satisfying phage cocktails prior to application in practice.
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Affiliation(s)
- Ling Chen
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shengjian Yuan
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Quan Liu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Guoqin Mai
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jinfang Yang
- R&D Center, Shenzhen Alpha Feed Co., Ltd., Shenzhen, China
| | - Deng Deng
- R&D Center, Shenzhen Alpha Feed Co., Ltd., Shenzhen, China
| | - Bingzhao Zhang
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chenli Liu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingfei Ma
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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25
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Hernandez-Morales AC, Lessor LL, Wood TL, Migl D, Mijalis EM, Cahill J, Russell WK, Young RF, Gill JJ. Genomic and Biochemical Characterization of Acinetobacter Podophage Petty Reveals a Novel Lysis Mechanism and Tail-Associated Depolymerase Activity. J Virol 2018; 92:e01064-17. [PMID: 29298884 PMCID: PMC5827379 DOI: 10.1128/jvi.01064-17] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/06/2017] [Indexed: 01/08/2023] Open
Abstract
The increased prevalence of drug-resistant, nosocomial Acinetobacter infections, particularly from pathogenic members of the Acinetobacter calcoaceticus-baumannii complex, necessitates the exploration of novel treatments such as phage therapy. In the present study, we characterized phage Petty, a novel podophage that infects multidrug-resistant Acinetobacter nosocomialis and Acinetobacter baumannii Genome analysis reveals that phage Petty is a 40,431-bp ϕKMV-like phage, with a coding density of 92.2% and a G+C content of 42.3%. Interestingly, the lysis cassette encodes a class I holin and a single-subunit endolysin, but it lacks canonical spanins to disrupt the outer membrane. Analysis of other ϕKMV-like genomes revealed that spaninless lysis cassettes are a feature of phages infecting Acinetobacter within this subfamily of bacteriophages. The observed halo surrounding Petty's large clear plaques indicated the presence of a phage-encoded depolymerase capable of degrading capsular exopolysaccharides (EPS). The product of gene 39, a putative tail fiber, was hypothesized to possess depolymerase activity based on weak homology to previously reported phage tail fibers. The 101.4-kDa protein gene product 39 (gp39) was cloned and expressed, and its activity against Acinetobacter EPS in solution was determined. The enzyme degraded purified EPS from its host strain A. nosocomialis AU0783, reducing its viscosity, and generated reducing ends in solution, indicative of hydrolase activity. Given that the accessibility to cells within a biofilm is enhanced by degradation of EPS, phages with depolymerases may have enhanced diagnostic and therapeutic potential against drug-resistant Acinetobacter strains.IMPORTANCE Bacteriophage therapy is being revisited as a treatment for difficult-to-treat infections. This is especially true for Acinetobacter infections, which are notorious for being resistant to antimicrobials. Thus, sufficient data need to be generated with regard to phages with therapeutic potential, if they are to be successfully employed clinically. In this report, we describe the isolation and characterization of phage Petty, a novel lytic podophage, and its depolymerase. To our knowledge, it is the first phage reported to be able to infect both A. baumannii and A. nosocomialis The lytic phage has potential as an alternative therapeutic agent, and the depolymerase could be used for modulating EPS both during infections and in biofilms on medical equipment, as well as for capsular typing. We also highlight the lack of predicted canonical spanins in the phage genome and confirm that, unlike the rounding of lambda lysogens lacking functional spanin genes, A. nosocomialis cells infected with phage Petty lyse by bursting. This suggests that phages like Petty employ a different mechanism to disrupt the outer membrane of Acinetobacter hosts during lysis.
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Affiliation(s)
- A C Hernandez-Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - L L Lessor
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - T L Wood
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - D Migl
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - E M Mijalis
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - J Cahill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - W K Russell
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - R F Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - J J Gill
- Center for Phage Technology, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
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26
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Taylor NMI, van Raaij MJ, Leiman PG. Contractile injection systems of bacteriophages and related systems. Mol Microbiol 2018; 108:6-15. [PMID: 29405518 DOI: 10.1111/mmi.13921] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2018] [Indexed: 12/31/2022]
Abstract
Contractile tail bacteriophages, or myobacteriophages, use a sophisticated biomolecular structure to inject their genome into the bacterial host cell. This structure consists of a contractile sheath enveloping a rigid tube that is sharpened by a spike-shaped protein complex at its tip. The spike complex forms the centerpiece of a baseplate complex that terminates the sheath and the tube. The baseplate anchors the tail to the target cell membrane with the help of fibrous proteins emanating from it and triggers contraction of the sheath. The contracting sheath drives the tube with its spiky tip through the target cell membrane. Subsequently, the bacteriophage genome is injected through the tube. The structural transformation of the bacteriophage T4 baseplate upon binding to the host cell has been recently described in near-atomic detail. In this review we discuss structural elements and features of this mechanism that are likely to be conserved in all contractile injection systems (systems evolutionary and structurally related to contractile bacteriophage tails). These include the type VI secretion system (T6SS), which is used by bacteria to transfer effectors into other bacteria and into eukaryotic cells, and tailocins, a large family of contractile bacteriophage tail-like compounds that includes the P. aeruginosa R-type pyocins.
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Affiliation(s)
- Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Calle Darwin 3, E-28049 Madrid, Spain
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, 301 University Blvd, University of Texas Medical Branch, Galveston, TX 77555-0647, USA
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27
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Letarov AV, Kulikov EE. Adsorption of bacteriophages on bacterial cells. BIOCHEMISTRY (MOSCOW) 2018. [DOI: 10.1134/s0006297917130053] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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28
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Turner D, Ackermann HW, Kropinski AM, Lavigne R, Sutton JM, Reynolds DM. Comparative Analysis of 37 Acinetobacter Bacteriophages. Viruses 2017; 10:E5. [PMID: 29295549 PMCID: PMC5795418 DOI: 10.3390/v10010005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 02/07/2023] Open
Abstract
Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK.
| | - Hans-Wolfgang Ackermann
- Faculty of Medicine, Department of Microbiology, Immunology and Infectiology, Université Laval, Quebec, QC G1X 46, Canada
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology; and Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, box 2462, 3001 Leuven, Belgium.
| | - J Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK.
| | - Darren M Reynolds
- Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK.
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29
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Bando SY, Iamashita P, Guth BE, dos Santos LF, Fujita A, Abe CM, Ferreira LR, Moreira-Filho CA. A hemolytic-uremic syndrome-associated strain O113:H21 Shiga toxin-producing Escherichia coli specifically expresses a transcriptional module containing dicA and is related to gene network dysregulation in Caco-2 cells. PLoS One 2017; 12:e0189613. [PMID: 29253906 PMCID: PMC5734773 DOI: 10.1371/journal.pone.0189613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/29/2017] [Indexed: 01/22/2023] Open
Abstract
Shiga toxin-producing (Stx) Escherichia coli (STEC) O113:H21 strains are associated with human diarrhea and some of these strains may cause hemolytic uremic syndrome (HUS). The molecular mechanism underlying this capacity and the differential host cell response to HUS-causing strains are not yet completely understood. In Brazil O113:H21 strains are commonly found in cattle but, so far, were not isolated from HUS patients. Here we conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from HUS patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. Conversely, global gene expression comparison of both strains cultured in conditioned medium revealed a gene set exclusively expressed in EH41, which includes the dicA putative virulence factor regulator. Network analysis showed that this set of genes constitutes an EH41 specific transcriptional module. PCR analysis in Ec472/01 and in other 10 Brazilian cattle-isolated STEC strains revealed absence of dicA in all these strains. The GCNs of Caco-2 cells exposed to EH41 or to Ec472/01 presented a major transcriptional module containing many hubs related to inflammatory response that was not found in the GCN of control cells. Moreover, EH41 seems to cause gene network dysregulation in Caco-2 as evidenced by the large number of genes with high positive and negative covariance interactions. EH41 grows slowly than Ec472/01 when cultured in Caco-2 conditioned medium and fitness-related genes are hypoexpressed in that strain. Therefore, EH41 virulence may be derived from its capacity for dysregulating enterocyte genome functioning and its enhanced enteric survival due to slow growth.
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Affiliation(s)
- Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Beatriz E. Guth
- Departament of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, SP, Brazil
| | - Luis F. dos Santos
- Departament of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, SP, Brazil
| | - André Fujita
- Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cecilia M. Abe
- Laboratory of Bacteriology, Butantan Institute, São Paulo, SP, Brazil
| | - Leandro R. Ferreira
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
- * E-mail:
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30
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Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells. Nat Commun 2017; 8:1915. [PMID: 29203765 PMCID: PMC5715158 DOI: 10.1038/s41467-017-02057-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 11/03/2017] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic organisms are continuously exposed to bacteriophages, which are efficient gene transfer agents in bacteria. However, bacteriophages are considered not to pass the eukaryotic cell membrane and enter nonphagocytic cells. Here we report the binding and penetration of Escherichia coli PK1A2 bacteriophage into live eukaryotic neuroblastoma cells in vitro. The phage interacts with cell surface polysialic acid, which shares structural similarity with the bacterial phage receptor. Using fluorescence and electron microscopy, we show that phages are internalized via the endolysosomal route and persist inside the human cells up to one day without affecting cell viability. Phage capsid integrity is lost in lysosomes, and the phage DNA is eventually degraded. We did not detect the entry of phage DNA into the nucleus; however, we speculate that this might occur as a rare event, and propose that this potential mechanism could explain prokaryote–eukaryote gene flow. Eukaryotic organisms are continuously exposed to bacteriophages, but these are not thought to enter non-phagocytic cells. Here, Lehti et al. show that a bacteriophage can bind to a specific receptor on the surface of human neuroblastoma cells in vitro, and be internalized via the endolysosomal route.
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31
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Oliveira H, Costa AR, Konstantinides N, Ferreira A, Akturk E, Sillankorva S, Nemec A, Shneider M, Dötsch A, Azeredo J. Ability of phages to infectAcinetobacter calcoaceticus-Acinetobacter baumanniicomplex species through acquisition of different pectate lyase depolymerase domains. Environ Microbiol 2017; 19:5060-5077. [DOI: 10.1111/1462-2920.13970] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/22/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Hugo Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
| | - Ana R. Costa
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
| | - Nico Konstantinides
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
- Laboratory of Microbiology; Wageningen University; Stippeneng 6708 WE Wageningen The Netherlands
| | - Alice Ferreira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
| | - Ergun Akturk
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
| | - Sanna Sillankorva
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics; National Institute of Public Health, Šrobárova 48; 100 42 Prague Czech Republic
| | - Mikhail Shneider
- Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry; 117997 Moscow Russia
| | - Andreas Dötsch
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT); Eggenstein-Leopoldshafen Germany
- Max Rubner-Institute, Institute for Physiologie and Biochemistry of Nutrition, Haid-und-Neu-Str. 9; 76131 Karlsruhe Germany
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira; University of Minho; 4710-057 Braga Portugal
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32
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Johnson MC, Sena-Velez M, Washburn BK, Platt GN, Lu S, Brewer TE, Lynn JS, Stroupe ME, Jones KM. Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome. J Struct Biol 2017; 200:343-359. [DOI: 10.1016/j.jsb.2017.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/24/2017] [Accepted: 08/21/2017] [Indexed: 11/26/2022]
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Lin H, Paff ML, Molineux IJ, Bull JJ. Therapeutic Application of Phage Capsule Depolymerases against K1, K5, and K30 Capsulated E. coli in Mice. Front Microbiol 2017; 8:2257. [PMID: 29201019 PMCID: PMC5696595 DOI: 10.3389/fmicb.2017.02257] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022] Open
Abstract
Capsule depolymerase enzymes offer a promising class of new antibiotics. In vivo studies are encouraging but it is unclear how well this type of phage product will generalize in therapeutics, or whether different depolymerases against the same capsule function similarly. Here, in vivo efficacy was tested using cloned bacteriophage depolymerases against Escherichia coli strains with three different capsule types: K1, K5, and K30. When treating infections with the cognate capsule type in a mouse thigh model, the previously studied K1E depolymerase rescued poorly, whereas K1F, K1H, K5, and K30 depolymerases rescued well. K30 gp41 was identified as the catalytically active protein. In contrast to the in vivo studies, K1E enzyme actively degraded K1 capsule polysaccharide in vitro and sensitized K1 bacteria to serum killing. The only in vitro correlate of poor K1E performance in vivo was that the purified enzyme did not form the expected trimer. K1E appeared as an 18-mer which might limit its in vivo distribution. Overall, depolymerases were easily identified, cloned from phage genomes, and as purified proteins they proved generally effective.
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Affiliation(s)
- Han Lin
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
| | - Matthew L Paff
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Ian J Molineux
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - James J Bull
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, United States
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Abstract
The human intestine harbors a dense microbial ecosystem (microbiota) that is different between individuals, dynamic over time, and critical for aspects of health and disease. Dietary polysaccharides directly shape the microbiota because of a gap in human digestive physiology, which is equipped to assimilate only proteins, lipids, simple sugars, and starch, leaving nonstarch polysaccharides as major nutrients reaching the microbiota. A mutualistic role of gut microbes is to digest dietary complex carbohydrates, liberating host-absorbable energy via fermentation products. Emerging data indicate that polysaccharides play extensive roles in host-gut microbiota symbiosis beyond dietary polysaccharide digestion, including microbial interactions with endogenous host glycans and the importance of microbial polysaccharides. In this review, we consider multiple mechanisms through which polysaccharides mediate aspects of host-microbe symbiosis in the gut, including some affecting health. As host and microbial metabolic pathways are intimately connected with diet, we highlight the potential to manipulate this system for health.
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Affiliation(s)
- Nathan T Porter
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109;
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109;
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35
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Genome Sequence of a Podovirus (AAPEc6) Isolated from Wastewater in New Zealand That Infects Escherichia coli O45:H10. GENOME ANNOUNCEMENTS 2017; 5:5/31/e00462-17. [PMID: 28774967 PMCID: PMC5543629 DOI: 10.1128/genomea.00462-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteriophages are ideal candidates for pathogen biocontrol to mitigate outbreaks of prevalent foodborne pathogens, such as Escherichia coli. We identified a bacteriophage (AAPEc6) from wastewater that infects E. coli O45:H10. The AAPEc6 genome sequence shares 93% identity (with 92% coverage) to enterobacterial phage K1E (Sp6likevirus) in the Autographivirinae subfamily (Podoviridae).
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36
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Tu J, Park T, Morado DR, Hughes KT, Molineux IJ, Liu J. Dual host specificity of phage SP6 is facilitated by tailspike rotation. Virology 2017; 507:206-215. [PMID: 28456019 DOI: 10.1016/j.virol.2017.04.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/13/2017] [Accepted: 04/17/2017] [Indexed: 01/08/2023]
Abstract
Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37. SP6 infection of Salmonella enterica serovars Typhimurium and Newport results in distinguishable changes in tailspike orientation, providing the first direct demonstration how tailspikes can confer dual host adsorption specificity. SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection.
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Affiliation(s)
- Jiagang Tu
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Taehyun Park
- Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Dustin R Morado
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ian J Molineux
- Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030, USA.
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37
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Novel therapeutics for bacterial infections. Emerg Top Life Sci 2017; 1:85-92. [PMID: 33525811 DOI: 10.1042/etls20160017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 01/28/2023]
Abstract
The relentless increase in antibiotic resistance among all major groups of bacterial pathogens shows no sign of abating. The situation is exacerbated by a marked decline in the number of new antibiotics entering the marketplace. It is essential that new ways to treat severe bacterial infections are investigated before the antibiotic well runs dry. This review covers many promising approaches, some novel and some based on old ideas that were not considered viable when clinicians were able to exploit a wide palette of cheap and effective antibacterial chemotherapeutics. These approaches include the use of photosensitive dyes, bacteriophage and phage-encoded proteins, and agents that compromise virulence and antibiotic-resistance machineries. I also make a case for continuing in some form with tried and trusted platforms for drug discovery that served society well in the past.
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38
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Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol 2017; 101:3103-3119. [PMID: 28337580 PMCID: PMC5380687 DOI: 10.1007/s00253-017-8224-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/23/2017] [Accepted: 03/04/2017] [Indexed: 11/24/2022]
Abstract
Bacteriophages are bacterial viruses that infect the host after successful receptor recognition and adsorption to the cell surface. The irreversible adherence followed by genome material ejection into host cell cytoplasm must be preceded by the passage of diverse carbohydrate barriers such as capsule polysaccharides (CPSs), O-polysaccharide chains of lipopolysaccharide (LPS) molecules, extracellular polysaccharides (EPSs) forming biofilm matrix, and peptidoglycan (PG) layers. For that purpose, bacteriophages are equipped with various virion-associated carbohydrate active enzymes, termed polysaccharide depolymerases and lysins, that recognize, bind, and degrade the polysaccharide compounds. We discuss the existing diversity in structural locations, variable architectures, enzymatic specificities, and evolutionary aspects of polysaccharide depolymerases and virion-associated lysins (VALs) and illustrate how these aspects can correlate with the host spectrum. In addition, we present methods that can be used for activity determination and the application potential of these enzymes as antibacterials, antivirulence agents, and diagnostic tools.
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Affiliation(s)
- Agnieszka Latka
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.,Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Grazyna Majkowska-Skrobek
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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Gebhart D, Williams SR, Scholl D. Bacteriophage SP6 encodes a second tailspike protein that recognizes Salmonella enterica serogroups C 2 and C 3. Virology 2017; 507:263-266. [PMID: 28285722 DOI: 10.1016/j.virol.2017.02.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 10/20/2022]
Abstract
SP6 is a salmonella phage closely related to coliphage K1-5. K1-5 is notable in that it encodes two polysaccharide-degrading tailspike proteins, an endosialidase that allows it to infect E. coli K1, and a lyase that enables it to infect K5 strains. SP6 is similar to K1-5 except that it encodes a P22-like endorhamnosidase tailspike, gp46, allowing it to infect group B Salmonella. We show here that SP6 can also infect Salmonella serogroups C2 and C3 and that a mutation in a putative second tailspike, gp47, eliminates this specificity. Gene 47 was fused to the coding region of the N-terminal portion of the Pseudomonas aeruginosa R2 pyocin tail fiber and expressed in trans such that the fusion protein becomes incorporated into pyocin particles. These pyocins, termed AvR2-SP47, killed serogroups C2 and C3Salmonella. We conclude that SP6 encodes two tail proteins providing it a broad host range among Salmonella enterica.
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Affiliation(s)
- Dana Gebhart
- AvidBiotics Corporation, 100 Kimball Way, S., San Francisco, CA 94080, USA
| | - Steven R Williams
- AvidBiotics Corporation, 100 Kimball Way, S., San Francisco, CA 94080, USA
| | - Dean Scholl
- AvidBiotics Corporation, 100 Kimball Way, S., San Francisco, CA 94080, USA.
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40
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Klebsiella Phage ΦK64-1 Encodes Multiple Depolymerases for Multiple Host Capsular Types. J Virol 2017; 91:JVI.02457-16. [PMID: 28077636 DOI: 10.1128/jvi.02457-16] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/20/2022] Open
Abstract
The genome of the multihost bacteriophage ΦK64-1, capable of infecting Klebsiella capsular types K1, K11, K21, K25, K30, K35, K64, and K69, as well as new capsular types KN4 and KN5, was analyzed and revealed that 11 genes (S1-1, S1-2, S1-3, S2-1, S2-2, S2-3, S2-4, S2-5, S2-6, S2-7, and S2-8) encode proteins with amino acid sequence similarity to tail fibers/spikes or lyases. S2-5 previously was shown to encode a K64 capsule depolymerase (K64dep). Specific capsule-degrading activities of an additional eight putative capsule depolymerases (S2-4 against K1, S1-1 against K11, S1-3 against K21, S2-2 against K25, S2-6 against K30/K69, S2-3 against K35, S1-2 against KN4, and S2-1 against KN5) was demonstrated by expression and purification of the recombinant proteins. Consistent with the capsular type-specific depolymerization activity of these gene products, phage mutants of S1-2, S2-2, S2-3, or S2-6 lost infectivity for KN4, K25, K35, or K30/K69, respectively, indicating that capsule depolymerase is crucial for infecting specific hosts. In conclusion, we identified nine functional capsule depolymerase-encoding genes in a bacteriophage and correlated activities of the gene products to all ten hosts of this phage, providing an example of type-specific host infection mechanisms in a multihost bacteriophage.IMPORTANCE We currently identified eight novel capsule depolymerases in a multihost Klebsiella bacteriophage and correlated the activities of the gene products to all hosts of this phage, providing an example of carriage of multiple depolymerases in a phage with a wide capsular type host spectrum. Moreover, we also established a recombineering system for modification of Klebsiella bacteriophage genomes and demonstrated the importance of capsule depolymerase for infecting specific hosts. Based on the powerful tool for modification of phage genome, further studies can be conducted to improve the understanding of mechanistic details of Klebsiella phage infection. Furthermore, the newly identified capsule depolymerases will be of great value for applications in capsular typing.
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41
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Identification of a capsular variant and characterization of capsular acetylation in Klebsiella pneumoniae PLA-associated type K57. Sci Rep 2016; 6:31946. [PMID: 27550826 PMCID: PMC4994043 DOI: 10.1038/srep31946] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023] Open
Abstract
Klebsiella pneumoniae can cause community-acquired pyogenic liver abscess (PLA). Capsular polysaccharide (CPS) is important for its virulence. Among 79 capsular (K) types discovered thus far, K57 is often associated with PLA. Here, we report the identification of a K57 variant. Cps gene locus sequencing revealed differences between the K57 reference strain 4425/51 (Ref-K57) and a variant, the PLA isolate A1142. While Ref-K57 cps contained orf13 encoding a putative acetyltransferase, the insertion of a putative transposase-encoding gene at this position was detected in A1142. This variation was detected in other K57 clinical strains. Biochemical analyses indicated that A1142 was deficient in CPS acetylation. Genetic replacement and complementation verified that orf13 was responsible for CPS acetylation. Acetylation increased CPS immunoreactivity to antiserum and enhanced K. pneumoniae induction of pro-inflammatory cytokines through JNK and MAPK signaling. While acetylation diminished the serum resistance of bacteria, it promoted adhesion to intestinal epithelial cells possibly via increasing production of type I fimbriae. In conclusion, acetylation-mediated capsular variation in K57 was observed. Capsular acetylation contributed to the variety and antigenic diversity of CPS, influenced its biological activities, and was involved in K. pneumoniae-host interactions. These findings have implications for vaccine design and pathogenicity of K. pneumoniae.
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42
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Cornelissen A, Sadovskaya I, Vinogradov E, Blangy S, Spinelli S, Casey E, Mahony J, Noben JP, Dal Bello F, Cambillau C, van Sinderen D. The Baseplate of Lactobacillus delbrueckii Bacteriophage Ld17 Harbors a Glycerophosphodiesterase. J Biol Chem 2016; 291:16816-27. [PMID: 27268053 PMCID: PMC4974393 DOI: 10.1074/jbc.m116.728279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/25/2016] [Indexed: 11/06/2022] Open
Abstract
Glycerophosphodiester phosphodiesterases (GDPDs; EC 3.1.4.46) typically hydrolyze glycerophosphodiesters to sn-glycerol 3-phosphate (Gro3P) and their corresponding alcohol during patho/physiological processes in bacteria and eukaryotes. GDPD(-like) domains were identified in the structural particle of bacterial viruses (bacteriophages) specifically infecting Gram-positive bacteria. The GDPD of phage 17 (Ld17; GDPDLd17), representative of the group b Lactobacillus delbrueckii subsp. bulgaricus (Ldb)-infecting bacteriophages, was shown to hydrolyze, besides the simple glycerophosphodiester, two complex surface-associated carbohydrates of the Ldb17 cell envelope: the Gro3P decoration of the major surface polysaccharide d-galactan and the oligo(glycerol phosphate) backbone of the partially glycosylated cell wall teichoic acid, a minor Ldb17 cell envelope component. Degradation of cell wall teichoic acid occurs according to an exolytic mechanism, and Gro3P substitution is presumed to be inhibitory for GDPDLd17 activity. The presence of the GDPDLd17 homotrimer in the viral baseplate structure involved in phage-host interaction together with the dependence of native GDPD activity, adsorption, and efficiency of plating of Ca(2+) ions supports a role for GDPDLd17 activity during phage adsorption and/or phage genome injection. In contrast to GDPDLd17, we could not identify any enzymatic activity for the GDPD-like domain in the neck passage structure of phage 340, a 936-type Lactococcus lactis subsp. lactis bacteriophage.
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Affiliation(s)
| | - Irina Sadovskaya
- Equipe Biochimie des Produits Aquatiques, Université du Littoral-Côte d'Opale, Boulevard du Bassin Napoléon, BP 120, 62327 Boulogne-sur-mer, France
| | | | - Stéphanie Blangy
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, 13288 Marseille Cedex 09, France, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Silvia Spinelli
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, 13288 Marseille Cedex 09, France, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, 13288 Marseille Cedex 09, France
| | | | | | - Jean-Paul Noben
- Biomedical Research Institute (Biomed) and School of Life Sciences, Transnationale Universiteit Limburg, Hasselt University, Agoralaan-Building C, BE-3590 Diepenbeek, Belgium, and
| | | | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, 13288 Marseille Cedex 09, France, CNRS, Architecture et Fonction des Macromolécules Biologiques, UMR 6098, Campus de Luminy, 13288 Marseille Cedex 09, France
| | - Douwe van Sinderen
- From the School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland,
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43
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Drulis-Kawa Z, Majkowska-Skrobek G, Maciejewska B. Bacteriophages and phage-derived proteins--application approaches. Curr Med Chem 2016; 22:1757-73. [PMID: 25666799 PMCID: PMC4468916 DOI: 10.2174/0929867322666150209152851] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/29/2014] [Accepted: 02/02/2015] [Indexed: 12/17/2022]
Abstract
Currently, the bacterial resistance, especially to most commonly used antibiotics has proved to be a severe therapeutic problem. Nosocomial and community-acquired infections are usually caused by multidrug resistant strains. Therefore, we are forced to develop an alternative or supportive treatment for successful cure of life-threatening infections. The idea of using natural bacterial pathogens such as bacteriophages is already well known. Many papers have been published proving the high antibacterial efficacy of lytic phages tested in animal models as well as in the clinic. Researchers have also investigated the application of non-lytic phages and temperate phages, with promising results. Moreover, the development of molecular biology and novel generation methods of sequencing has opened up new possibilities in the design of engineered phages and recombinant phage-derived proteins. Encouraging performances were noted especially for phage enzymes involved in the first step of viral infection responsible for bacterial envelope degradation, named depolymerases. There are at least five major groups of such enzymes – peptidoglycan hydrolases, endosialidases, endorhamnosidases, alginate lyases and hyaluronate lyases – that have application potential. There is also much interest in proteins encoded by lysis cassette genes (holins, endolysins, spanins) responsible for progeny release during the phage lytic cycle. In this review, we discuss several issues of phage and phage-derived protein application approaches in therapy, diagnostics and biotechnology in general.
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Affiliation(s)
- Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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44
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Speck P, Smithyman A. Safety and efficacy of phage therapy via the intravenous route. FEMS Microbiol Lett 2015; 363:fnv242. [PMID: 26691737 DOI: 10.1093/femsle/fnv242] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 12/16/2022] Open
Abstract
Increasing development of antimicrobial resistance is driving a resurgence in interest in phage therapy: the use of bacteriophages to treat bacterial infections. As the lytic action of bacteriophages is unaffected by the antibiotic resistance status of their bacterial target, it is thought that phage therapy may have considerable potential in the treatment of a wide range of topical and localized infections. As yet this interest has not extended to intravenous (IV) use, which is surprising given that the historical record shows that phages are likely to be safe and effective when delivered by this route. Starting almost 100 years ago, phages were administered intravenously in treatment of systemic infections including typhoid, and Staphylococcal bacteremia. There was extensive IV use of phages in the 1940s to treat typhoid, reportedly with outstanding efficacy and safety. The safety of IV phage administration is also underpinned by the detailed work of Ochs and colleagues in Seattle who have over four decades' experience with IV injection into human subjects of large doses of highly purified coliphage PhiX174. Though these subjects included a large number of immune-deficient children, no serious side effects were observed over this extended time period. The large and continuing global health problems of typhoid and Staphylococcus aureus are exacerbated by the increasing antibiotic resistance of these pathogens. We contend that these infections are excellent candidates for use of IV phage therapy.
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Affiliation(s)
- Peter Speck
- School of Biological Sciences, Flinders University, Bedford Park, SA, Australia
| | - Anthony Smithyman
- School of Biological Sciences, Flinders University, Bedford Park, SA, Australia
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45
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Lee JS, Jang HB, Kim KS, Kim TH, Im SP, Kim SW, Lazarte JMS, Kim JS, Jung TS. Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC). PLoS One 2015; 10:e0142504. [PMID: 26555076 PMCID: PMC4640515 DOI: 10.1371/journal.pone.0142504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/22/2015] [Indexed: 11/18/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. Here, bacteriophage KBNP1315, infecting APEC strain KBP1315, was genomically and functionally characterized. The evolutionary relationships of KBNP1315 were analyzed at the genomic level using gene (protein)-sharing networks, the Markov clustering (MCL) algorithm, and comparative genomics. Our network analysis showed that KBNP1315 was connected to 30 members of the Autographivirinae subfamily, which comprises the SP6-, T7-, P60-, phiKMV-, GAP227- and KP34-related groups. Network decomposition suggested that KBNP1315 belongs to the SP6-like phages, but our comparison of putative encoded proteins revealed that key proteins of KBNP1315, including the tail spike protein and endolysin, had relative low levels of amino acid sequence similarity with other members of the SP6-like phages. Thus KBNP1315 may only be distantly related to the SP6-like phages, and (based on the difference in endolysin) its lysis mechanism may differ from theirs. To characterize the lytic functions of the holin and endolysin proteins from KBNP1315, we expressed these proteins individually or simultaneously in E. coli BL21 (DE3) competent cell. Interestingly, the expressed endolysin was secreted into the periplasm and caused a high degree of host cell lysis that was dose-dependently delayed/blocked by NaN3-mediated inhibition of the SecA pathway. The expressed holin triggered only a moderate inhibition of cell growth, whereas coexpression of holin and endolysin enhanced the lytic effect of endolysin. Together, these results revealed that KBNP1315 appears to use a pin-holin/signal-arrest-release (SAR) endolysin pathway to trigger host cell lysis.
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Affiliation(s)
- Jung Seok Lee
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Ho Bin Jang
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001, Leuven, Belgium
| | - Ki Sei Kim
- KBNP Technology Institute, KBNP, Inc., Yesan, Choongcheongnam-do, South Korea
| | - Tae Hwan Kim
- KBNP Technology Institute, KBNP, Inc., Yesan, Choongcheongnam-do, South Korea
| | - Se Pyeong Im
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Si Won Kim
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Jassy Mary S. Lazarte
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Jae Sung Kim
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, South Korea
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 660-701, South Korea
- * E-mail:
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Archaeal viruses multiply: temporal screening in a solar saltern. Viruses 2015; 7:1902-26. [PMID: 25866903 PMCID: PMC4411682 DOI: 10.3390/v7041902] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/16/2015] [Accepted: 03/31/2015] [Indexed: 11/16/2022] Open
Abstract
Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment.
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Grose JH, Casjens SR. Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 2015; 468-470:421-443. [PMID: 25240328 DOI: 10.1016/j.virol.2014.08.024] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/18/2014] [Accepted: 08/22/2014] [Indexed: 02/03/2023]
Abstract
Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships.
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Affiliation(s)
- Julianne H Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT 84602, USA.
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Parent KN, Tang J, Cardone G, Gilcrease EB, Janssen ME, Olson NH, Casjens SR, Baker TS. Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain. Virology 2014; 464-465:55-66. [PMID: 25043589 DOI: 10.1016/j.virol.2014.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 01/21/2023]
Abstract
CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the "HK97-fold" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain ("I-domain"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently.
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Affiliation(s)
- Kristin N Parent
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States.
| | - Jinghua Tang
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Giovanni Cardone
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Eddie B Gilcrease
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112, United States
| | - Mandy E Janssen
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Norman H Olson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States
| | - Sherwood R Casjens
- University of Utah School of Medicine, Division of Microbiology and Immunology, Department of Pathology, Salt Lake City, UT 84112, United States.
| | - Timothy S Baker
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, United States; University of California, San Diego, Division of Biological Sciences, La Jolla, CA, 92093, United States.
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Liu W, Lin YR, Lu MW, Sung PJ, Wang WH, Lin CS. Genome sequences characterizing five mutations in RNA polymerase and major capsid of phages ϕA318 and ϕAs51 of Vibrio alginolyticus with different burst efficiencies. BMC Genomics 2014; 15:505. [PMID: 24952762 PMCID: PMC4099482 DOI: 10.1186/1471-2164-15-505] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 05/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background The burst size of a phage is important prior to phage therapy and probiotic usage. The efficiency for a phage to burst its host bacterium can result from molecular domino effects of the phage gene expressions which dominate to control host machinery after infection. We found two Podoviridae phages, ϕA318 and ϕAs51, burst a common host V. alginolyticus with different efficiencies of 72 and 10 PFU/bacterium, respectively. Presumably, the genome sequences can be compared to explain their differences in burst sizes. Results Among genes in 42.5 kb genomes with a GC content of 43.5%, 16 out of 47 open-reading frames (ORFs) were annotated to known functions, including RNA polymerase (RNAP) and phage structure proteins. 11 strong phage promoters and three terminators were found. The consensus sequence for the new vibriophage promoters is AATAAAGTTGCCCTATA, where the AGTTG bases of −8 through −12 are important for the vibriophage specificity, especially a consensus T at −9 position eliminating RNAP of K1E, T7 and SP6 phages to transcribe the genes. ϕA318 and ϕAs51 RNAP shared their own specific promoters. In comparing ϕAs51 with ϕA318 genomes, only two nucleotides were deleted in the RNAP gene and three mutating nucleotides were found in the major capsid genes. Conclusion Subtle analyses on the residue alterations uncovered the effects of five nucleotide mutations on the functions of the RNAP and capsid proteins, which account for the host-bursting efficiency. The deletion of two nucleotides in RNAP gene truncates the primary translation due to early stop codon, while a second translational peptide starting from GTG just at deletion point can remediate the polymerase activity. Out of three nucleotide mutations in major capsid gene, H53N mutation weakens the subunit assembly between capsomeres for the phage head; E313K reduces the fold binding between β-sheet and Spine Helix inside the peptide. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-505) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Chan-Shing Lin
- Department of Marine Biotechnology and Resources, Asia-Pacific Ocean Research Center, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.
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Drilling A, Morales S, Jardeleza C, Vreugde S, Speck P, Wormald PJ. Bacteriophage Reduces Biofilm of Staphylococcus Aureus Ex Vivo Isolates from Chronic Rhinosinusitis Patients. Am J Rhinol Allergy 2014; 28:3-11. [DOI: 10.2500/ajra.2014.28.4001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background Staphylococcus aureus is the most common organism in recalcitrant chronic rhinosinusitis (CRS) and is often resistant to traditional antibiotic therapy. Bacteriophages (“phages”) are a potential candidate for a new, effective therapy. For phages to be useful in setting CRS, two minimum requirements must be presented: (1) phages must be effective against S. aureus biofilms and (2) phages must have a broad spectrum of activity. This study aimed to assess the in vitro activity of a phage cocktail (CockTail of Staphylococcus aureus specific bacteriophage [CT-SA]) against S. aureus biofilms and a broad panel of strains isolated from patients with CRS. Methods The study examined 66 clinical isolates (CIs) of S. aureus. All isolates were tested for the susceptibility to phage lysis by spotting CT-SA onto bacterial lawns. To measure its effect on S. aureus biofilms, a minimum biofilm eradication concentration assay was used, using five S. aureus isolates. Biofilms of these isolates were grown, treated with CT-SA for 48 hours, fluorescently stained, and viewed using confocal scanning laser microscopy. Results CT-SA lysed 62 of 66 (94%) CIs of S. aureus. CT-SA treatment yielded significant reductions in biofilm mass for 4/5 CIs tested and for ATCC 25923. Challenge of S. aureus with a single phage resulted in the emergence of bacteriophage-insensitive mutants (BIM) with a frequency of 10−7, and challenge with CT-SA completely prevented their development. Conclusion This study indicates that phage cocktail CT-SA can effectively eliminate S. aureus, in planktonic and biofilm forms, from the great majority of CIs from this hospital setting. In addition, its potential effect in preventing the emergence BIMs was a established. Thus, CT-SA has the potential to treat S. aureus infection and biofilm in CRS patients.
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Affiliation(s)
- Amanda Drilling
- Department of Surgery–Otolaryngology Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia, and the University of Adelaide, Adelaide, South Australia, Australia
| | - Sandra Morales
- Special Phage Services Pty, Ltd., New South Wales, Australia
| | - Camille Jardeleza
- Department of Surgery–Otolaryngology Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia, and the University of Adelaide, Adelaide, South Australia, Australia
| | - Sarah Vreugde
- Department of Surgery–Otolaryngology Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia, and the University of Adelaide, Adelaide, South Australia, Australia
| | - Peter Speck
- School of Biological Sciences, Flinders University, Bedford Park, South Australia, Australia
| | - Peter-John Wormald
- Department of Surgery–Otolaryngology Head and Neck Surgery, The Queen Elizabeth Hospital, Woodville South, South Australia, Australia, and the University of Adelaide, Adelaide, South Australia, Australia
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