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Williams J, Burton N, Dhanoa G, Sagona AP. Host-phage interactions and modeling for therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:127-158. [PMID: 37739552 DOI: 10.1016/bs.pmbts.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Phage are drivers of numerous ecological processes on the planet and have the potential to be developed into a therapy alternative to antibiotics. Phage at all points of their life cycle, from initiation of infection to their release, interact with their host in some manner. More importantly, to harness their antimicrobial potential it is vital to understand how phage interact with the eukaryotic environment in the context of applying phage for therapy. In this chapter, the various mechanisms of phage interplay with their hosts as part of their natural life cycle are discussed in depth for Gram-positive and negative bacteria. Further, the literature surrounding the various models utilized to develop phage as a therapeutic are examined, and how these models may improve our understanding of phage-host interactions and current progress in utilizing phage for therapy in the clinical environment.
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Affiliation(s)
- Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Nathan Burton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gurneet Dhanoa
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Antonia P Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.
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2
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Danis-Wlodarczyk KM, Cai A, Chen A, Gittrich MR, Sullivan MB, Wozniak DJ, Abedon ST. Friends or Foes? Rapid Determination of Dissimilar Colistin and Ciprofloxacin Antagonism of Pseudomonas aeruginosa Phages. Pharmaceuticals (Basel) 2021; 14:1162. [PMID: 34832944 PMCID: PMC8624478 DOI: 10.3390/ph14111162] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022] Open
Abstract
Phage therapy is a century-old technique employing viruses (phages) to treat bacterial infections, and in the clinic it is often used in combination with antibiotics. Antibiotics, however, interfere with critical bacterial metabolic activities that can be required by phages. Explicit testing of antibiotic antagonism of phage infection activities, though, is not a common feature of phage therapy studies. Here we use optical density-based 'lysis-profile' assays to assess the impact of two antibiotics, colistin and ciprofloxacin, on the bactericidal, bacteriolytic, and new-virion-production activities of three Pseudomonas aeruginosa phages. Though phages and antibiotics in combination are more potent in killing P. aeruginosa than either acting alone, colistin nevertheless substantially interferes with phage bacteriolytic and virion-production activities even at its minimum inhibitory concentration (1× MIC). Ciprofloxacin, by contrast, has little anti-phage impact at 1× or 3× MIC. We corroborate these results with more traditional measures, particularly colony-forming units, plaque-forming units, and one-step growth experiments. Our results suggest that ciprofloxacin could be useful as a concurrent phage therapy co-treatment especially when phage replication is required for treatment success. Lysis-profile assays also appear to be useful, fast, and high-throughput means of assessing antibiotic antagonism of phage infection activities.
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Affiliation(s)
| | - Alice Cai
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Anna Chen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Marissa R. Gittrich
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
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Hylling O, Carstens AB, Kot W, Hansen M, Neve H, Franz CMAP, Johansen A, Ellegaard-Jensen L, Hansen LH. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci Rep 2020; 10:11879. [PMID: 32681144 PMCID: PMC7368026 DOI: 10.1038/s41598-020-68389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/12/2020] [Indexed: 11/09/2022] Open
Abstract
Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.
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Affiliation(s)
- Ole Hylling
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Alexander B Carstens
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Witold Kot
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark.,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Lars H Hansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark. .,Department of Plant- and Environmental Sciences, Section for Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark.
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A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing. Appl Environ Microbiol 2020; 86:AEM.00073-20. [PMID: 32357999 DOI: 10.1128/aem.00073-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Providencia stuartii is emerging as a significant drug-resistant nosocomial pathogen, which encourages the search for alternative therapies. Here, we have isolated Providencia stuartii phage Stuart, a novel podovirus infecting multidrug-resistant hospital isolates of this bacterium. Phage Stuart is a proposed member of a new Autographivirinae subfamily genus, with a 41,218-bp genome, direct 345-bp repeats at virion DNA ends, and limited sequence similarity of proteins to proteins in databases. Twelve out of the 52 predicted Stuart proteins are virion components. We found one to be a tailspike with depolymerase activity. The tailspike could form a highly thermostable oligomeric β-structure migrating close to the expected trimer in a nondenaturing gel. It appeared to be essential for the infection of three out of four P. stuartii hosts infected by phage Stuart. Moreover, it degraded the exopolysaccharide of relevant phage Stuart hosts, making the bacteria susceptible to serum killing. Prolonged exposure of a sensitive host to the tailspike did not cause the emergence of bacteria resistant to the phage or to serum killing, opposite to the prolonged exposure to the phage. This indicates that phage tail-associated depolymerases are attractive antivirulence agents that could complement the immune system in the fight with P. stuartii IMPORTANCE The pace at which multidrug-resistant strains emerge has been alarming. P. stuartii is an infrequent but relevant drug-resistant nosocomial pathogen causing local to systemic life-threatening infections. We propose an alternative approach to fight this bacterium based on the properties of phage tailspikes with depolymerase activity that degrade the surface bacterial polymers, making the bacteria susceptible to the immune system. Unlike antibiotics, phage tailspikes have narrow and specific substrate spectra, and by acting as antivirulent but not bactericidal agents they do not cause the selection of resistant bacteria.
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González B, Monroe L, Li K, Yan R, Wright E, Walter T, Kihara D, Weintraub ST, Thomas JA, Serwer P, Jiang W. Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus. J Mol Biol 2020; 432:4139-4153. [PMID: 32454153 DOI: 10.1016/j.jmb.2020.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Å resolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.
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Affiliation(s)
- Brenda González
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA
| | - Lyman Monroe
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA
| | - Kunpeng Li
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA
| | - Rui Yan
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA
| | - Elena Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Thomas Walter
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA; Department of Computer Science, Purdue University, 305 North University Street, West Lafayette, IN 47907-2107, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Julie A Thomas
- Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USA
| | - Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Wen Jiang
- Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA; Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA; Purdue Cryo-EM Facility, Purdue University, Hockmeyer Hall of Structural Biology, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA; Purdue Center for Cancer Research, Purdue University, 201 South University Street, West Lafayette, IN 47907, USA; Purdue Institute for Infectious, Immunology and Inflammatory Diseases, Purdue University, 207 South Martin Jischke Drive, West Lafayette, IN 47907, USA; Purdue Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47097, USA.
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6
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Jagdale S, Ahiwale S, Gajbhiye M, Kapadnis B. Green approach to phytopathogen: Characterization of lytic bacteriophages of Pseudomonas sp., an etiology of the bacterial blight of pomegranate. Microbiol Res 2019; 228:126300. [PMID: 31422230 DOI: 10.1016/j.micres.2019.126300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/07/2019] [Accepted: 07/12/2019] [Indexed: 11/17/2022]
Abstract
Two morphologically different bacteriophages were isolated from the river and soil samples from various locations of Maharashtra, India against the phytopathogen Pseudomonas sp. that was recently reported to cause a new bacterial blight of pomegranate. Both the phages belonged to the order Caudovirales representing the families Siphoviridae (vB_Psp.S_PRɸL2) and Myoviridae (vB_Psp.M_SSɸL8). The multiplicity of infection ranged from 0.01 to 0.1, phage adsorption rate from 39% to 66%, latent period from 10 to 20 min with a burst size of 24-85 phage particles per infected host cell. The genome size of phages PRɸL2 and SSɸL8 was approximately 25.403 kb and 29.877 kb respectively. Restriction digestion pattern of phage genomic DNA was carried out for phage PRɸL2, Eco RI resulted in two bands and Hind III resulted in three bands while for phage SSɸL8, both Eco RI and Hind III each resulted in three bands. SDS-PAGE protein profile showed six bands for PRɸL2 and nine bands for SSɸL8 of different proteins. Phages showed high pH stability over a range of 4-9, temperature stability over a range of 4-50 °C and UV radiation showed a reduction up to 89.36% for PRɸL2 and 96% for SSɸL8. In short, the present research work discusses for the first time in-detailed characterization of phages of a phytopathogen Pseudomonas sp. from Maharashtra, India, which can be further efficiently used for biological control of the causative agent of a new bacterial blight disease of pomegranate.
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Affiliation(s)
- Smita Jagdale
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India
| | - Sangeeta Ahiwale
- Department of Microbiology, Mahatma Phule Mahavidyalaya, Pimpri, 411017, Pune, Maharashtra, India
| | - Milind Gajbhiye
- Department of Microbiology, Tuljaram Chaturchand College of Arts, Science and Commerce, Baramati, 413102, Maharashtra, India
| | - Balu Kapadnis
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, Maharashtra, India.
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Wang Y, Zhao J, Wang D, Liu Y, Wang Q, Ni BJ, Chen F, Yang Q, Li X, Zeng G, Yuan Z. Free nitrous acid promotes hydrogen production from dark fermentation of waste activated sludge. WATER RESEARCH 2018; 145:113-124. [PMID: 30121432 DOI: 10.1016/j.watres.2018.08.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/10/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Simultaneous sludge fermentation and nitrite removal is an effective approach to enhance nutrient removal from low carbon-wastewater. It was found in this work that the presence of nitrite largely promoted hydrogen production from acidic fermentation of waste activated sludge (WAS). The results showed that with an increase of nitrite from 0 to 250 mg/L, the maximal hydrogen yield increased from 8.5 to 15.0 mL/g VSS at pH 5.5 fermentation and 8.1-13.0 mL/g VSS at pH 6 fermentation. However, the maximal hydrogen yield from WAS fermentation at pH 8 remained almost constant (2.9-3.7 mL/g VSS) when nitrite was in the range of 0-250 mg/L. Further analyses revealed that free nitrous acid (FNA) rather than nitrite was the major contributor to the promotion of hydrogen yield. The mechanism investigations showed that FNA not only accelerated the disruption of sludge cells but also promoted the biodegradability of organics released, thereby provided more biodegradable substrates for subsequent hydrogen production. Although FNA inhibited activities of all microbes involved in the anaerobic fermentation, its inhibitions to hydrogen consumers were much severer than those to hydrolytic microorganisms and hydrogen producers. Further investigations with microbial community showed that FNA increased the abundances of hydrogen producers (e.g., Citrobacter sp.) and denitrifiers (e.g., Dechloromonas sp.), but reduced the abundances of hydrogen consumers (e.g., Clostridium_aceticum). This work demonstrated for the first time that FNA in WAS fermentation systems enhanced hydrogen production. The findings obtained expand the application field of FNA and may provide supports for sustainable operation of wastewater treatment plants.
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Affiliation(s)
- Yali Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China.
| | - Jianwei Zhao
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China.
| | - Yiwen Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Qilin Wang
- Griffith School of Engineering & Centre for Clean Environment and Energy, Griffith University, QLD, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Fei Chen
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Qi Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Xiaoming Li
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, PR China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
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Urban-Chmiel R, Wernicki A, Wawrzykowski J, Puchalski A, Nowaczek A, Dec M, Stęgierska D, Alomari MMM. Protein profiles of bacteriophages of the family Myoviridae-like induced on M. haemolytica. AMB Express 2018; 8:102. [PMID: 29923151 PMCID: PMC6008273 DOI: 10.1186/s13568-018-0630-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/14/2018] [Indexed: 01/03/2023] Open
Abstract
The aim of study was to isolate, characterize and analyse the protein profiles of Myoviridae-like bacteriophages obtained from M. haemolytica using MALDI TOF mass spectrometry. The material consisted of the M. haemolytica reference strain ATCC® BAA410, reference serotypes A1, A2, A5, A6, A7, A9, and A11, and wild-type isolates of serotype A1. Bacteriophage morphology was examined with a transmission electron microscope. The proteins were separated in SDS-PAGE and two-dimensional electrophoresis and characterized by MALDI-TOF. Among the phages obtained, seven were specific for strains A1, A2, A5, A6, A7 and 25, and PHL-1 was specific for the BAA410 strain. The protein profiles for the phages were very similar to one another, but differed from the reference phage in that they lacked protein fractions with molecular weights of 22.9, 56.3 and 73.1 kDa. 2D electrophoresis revealed significant differences in the size of proteins and their localization in the pH gradient. The most similar profiles were observed in phages specific for strains BAA-410 and A6. In all profiles two main spots were observed in the molecular weight range from 44 to 70 kDa at pH < 4. The results indicate that 2D electrophoresis is a very useful tool for characterization of phage protein profiles. An important objective was to determine the molecular differences between morphologically similar phages belonging to one family and to find similarities to phages specific for other pathogens. The study also assessed the suitability of the methods used to characterize phages.
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Phage-Derived Peptidoglycan Degrading Enzymes: Challenges and Future Prospects for In Vivo Therapy. Viruses 2018; 10:v10060292. [PMID: 29844287 PMCID: PMC6024856 DOI: 10.3390/v10060292] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/17/2023] Open
Abstract
Peptidoglycan degrading enzymes are of increasing interest as antibacterial agents, especially against multi-drug resistant pathogens. Herein we present a review about the biological features of virion-associated lysins and endolysins, phage-derived enzymes that have naturally evolved to compromise the bacterial peptidoglycan from without and from within, respectively. These natural features may determine the adaptability of the enzymes to kill bacteria in different environments. Endolysins are by far the most studied group of peptidoglycan-degrading enzymes, with several studies showing that they can exhibit potent antibacterial activity under specific conditions. However, the lytic activity of most endolysins seems to be significantly reduced when tested against actively growing bacteria, something that may be related to fact that these enzymes are naturally designed to degrade the peptidoglycan from within dead cells. This may negatively impact the efficacy of the endolysin in treating some infections in vivo. Here, we present a critical view of the methods commonly used to evaluate in vitro and in vivo the antibacterial performance of PG-degrading enzymes, focusing on the major hurdles concerning in vitro-to-in vivo translation.
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10
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Zhang F, Huang K, Yang X, Sun L, You J, Pan X, Cui X, Yang H. Characterization of a novel lytic podovirus O4 of Pseudomonas aeruginosa. Arch Virol 2018; 163:2377-2383. [PMID: 29749589 DOI: 10.1007/s00705-018-3866-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/13/2018] [Indexed: 12/18/2022]
Abstract
Phage O4 of Pseudomonas aeruginosa was previously visualized as a short-tailed virus using a transmission electron microscope. In this work, the O4 genome was characterized to be a linear dsDNA molecule comprising 50509 bp with 76 predicted genes located in five clusters. Mass spectrometry showed that the O4 virion contains 6 putative structural proteins, 2 putative enzymes, and 7 hypothetical proteins. By analyzing a Tn5G transposon mutation library, eight genes, wbpR, wbpV, wbpO, wbpT, wbpS, wbpL, galU, and wzy, were identified and confirmed responsible for the phage-resistant phenotype; all of them are related to the synthesis of O-specific antigen (OSA) of lipopolysaccharide (LPS), indicating that OSA is the receptor for the adsorption of phage O4. Comparative genomic analysis revealed that the phage O4 genome shares little similarity to any known podovirus, indicating that phage O4 is classifiable as a novel member of the Podoviridae family.
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Affiliation(s)
- Fenjiao Zhang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Kechong Huang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xiaojing Yang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Li Sun
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jiajia You
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xuewei Pan
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xiaoli Cui
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
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11
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Kankeu C, Clarke K, Van Haver D, Gevaert K, Impens F, Dittrich A, Roderick HL, Passante E, Huber HJ. Quantitative proteomics and systems analysis of cultured H9C2 cardiomyoblasts during differentiation over time supports a 'function follows form' model of differentiation. Mol Omics 2018; 14:181-196. [PMID: 29770421 DOI: 10.1039/c8mo00036k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis. These changes in the proteome were followed later in the differentiation time-course by alterations in the expression of proteins involved in cation transport and beta-oxidation. Studying the temporal profile of the H9C2 proteome during differentiation in further detail revealed eight clusters of co-regulated proteins that can be associated with early, late, continuous and transient up- and downregulation. Subsequent reactome pathway analysis based on these eight clusters further corroborated and detailed the results of the GO analysis. Specifically, this analysis confirmed that proteins related to pathways in muscle contraction are upregulated early and transiently, and proteins relevant to extracellular matrix organization are downregulated early. In contrast, upregulation of proteins related to cardiac metabolism occurs at later time points. Finally, independent validation of the proteomics results by immunoblotting confirmed hereto unknown regulators of cardiac structure and ionic metabolism. Our results are consistent with a 'function follows form' model of differentiation, whereby early and transient alterations of structural proteins enable subsequent changes that are relevant to the characteristic physiology of cardiomyocytes.
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Affiliation(s)
- Cynthia Kankeu
- Department of Cardiovascular Sciences, KU Leuven, 3000 Leuven, Belgium
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12
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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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13
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A Lytic Providencia rettgeri Virus of Potential Therapeutic Value Is a Deep-Branching Member of the T5virus Genus. Appl Environ Microbiol 2017; 83:AEM.01567-17. [PMID: 28939601 DOI: 10.1128/aem.01567-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 11/20/2022] Open
Abstract
Providencia rettgeri is emerging as a new opportunistic pathogen with high antibiotic resistance. The need to find alternative methods to control antibiotic-resistant bacteria and the recent advances in phage therapy motivate the search for new phages able to infect Providencia spp. This study describes the isolation and characterization of an obligatory lytic phage, vB_PreS_PR1 (PR1), with therapeutic potential against drug-resistant P. rettgeri PR1 is a siphovirus. Its virion DNA size (118,537 bp), transcriptional organization, terminal repeats (10,461 bp), and nicks in the 3'-to-5' strand are similar to those of phage T5. However, sequence similarities of PR1 to phages of the T5virus genus at the DNA and protein levels are limited, suggesting that it belongs to a new species within the Siphoviridae family. PR1 exhibits the ability to kill P. rettgeri antibiotic-resistant strains, is highly specific to the species, and did not present known genomic markers indicating a temperate lifestyle. The lack of homologies between its proteins and proteins of the only other sequenced Providencia prophage, Redjac, suggests that these two phages evolved separately and may target different host proteins.IMPORTANCE The alarming increase in the number of bacteria resistant to antibiotics has been observed worldwide. This is particularly true for Gram-negative bacteria. For certain of their strains, no effective antibiotics are available. Providencia sp. has been a neglected pathogen but is emerging as a multidrug-resistant bacterium. This has revived interest in bacteriophages as alternative therapeutic agents against this bacterium. We describe the morphological, physiological, and genomic characterization of a novel lytic virus, PR1, which is able to kill drug-resistant P. rettgeri clinical isolates. Genomic and phylogenetic analyses indicate that PR1 is a distant relative of T5virus genus representatives. The lack of known virulence- or temperate lifestyle-associated genes in the genome of PR1 makes this phage a potential candidate for therapeutic use. Analysis of its genome also improves our knowledge of the ecology and diversity of T5-like siphoviruses, providing a new link for evolutionary studies of this phage group.
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14
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Yu X, Xu Y, Gu Y, Zhu Y, Liu X. Characterization and genomic study of "phiKMV-Like" phage PAXYB1 infecting Pseudomonas aeruginosa. Sci Rep 2017; 7:13068. [PMID: 29026171 PMCID: PMC5638911 DOI: 10.1038/s41598-017-13363-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022] Open
Abstract
Bacteriophage PAXYB1 was recently isolated from wastewater samples. This phage was chosen based on its lytic properties against clinical isolates of Pseudomonas aeruginosa (P. aeruginosa). In the present study, characterized PAXYB1, clarified its morphological and lytic properties, and analyzed its complete genome sequence. Based on the morphology of PAXYB1, it is a Podoviridae. The linear GC-rich (62.29%) double-stranded DNA genome of PAXYB1 is 43,337 bp including direct terminal repeats (DTRs) of 468 bp. It contains 60 open reading frames (ORFs) that are all encoded within the same strand. We also showed that PAXYB1 is a virulent phage and a new member of the phiKMV-like phages genus. Twenty-eight out of sixty predicted gene products (gps) showed significant homology to proteins of known function, which were confirmed by analyzing the structural proteome. Altogether, our work identified a novel lytic bacteriophage that lyses P. aeruginosa PAO1 and efficiently infects and kills several clinical isolates of P. aeruginosa. This phage has potential for development as a biological disinfectant to control P. aeruginosa infections.
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Affiliation(s)
- Xinyan Yu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Xu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yu Gu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yefei Zhu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China.
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15
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Oliveira H, Pinto G, Oliveira A, Noben JP, Hendrix H, Lavigne R, Łobocka M, Kropinski AM, Azeredo J. Characterization and genomic analyses of two newly isolated Morganella phages define distant members among Tevenvirinae and Autographivirinae subfamilies. Sci Rep 2017; 7:46157. [PMID: 28387353 PMCID: PMC5384007 DOI: 10.1038/srep46157] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/09/2017] [Indexed: 11/09/2022] Open
Abstract
Morganella morganii is a common but frequent neglected environmental opportunistic pathogen which can cause deadly nosocomial infections. The increased number of multidrug-resistant M. morganii isolates motivates the search for alternative and effective antibacterials. We have isolated two novel obligatorily lytic M. morganii bacteriophages (vB_MmoM_MP1, vB_MmoP_MP2) and characterized them with respect to specificity, morphology, genome organization and phylogenetic relationships. MP1's dsDNA genome consists of 163,095 bp and encodes 271 proteins, exhibiting low DNA (<40%) and protein (<70%) homology to other members of the Tevenvirinae. Its unique property is a >10 kb chromosomal inversion that encompass the baseplate assembly and head outer capsid synthesis genes when compared to other T-even bacteriophages. MP2 has a dsDNA molecule with 39,394 bp and encodes 55 proteins, presenting significant genomic (70%) and proteomic identity (86%) but only to Morganella bacteriophage MmP1. MP1 and MP2 are then novel members of Tevenvirinae and Autographivirinae, respectively, but differ significantly from other tailed bacteriophages of these subfamilies to warrant proposing new genera. Both bacteriophages together could propagate in 23 of 27 M. morganii clinical isolates of different origin and antibiotic resistance profiles, making them suitable for further studies on a development of bacteriophage cocktail for potential therapeutic applications.
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Affiliation(s)
- Hugo Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Graça Pinto
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Ana Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Diepenbeek 3590, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
| | - Małgorzata Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland.,Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Andrew M Kropinski
- Departments of Food Science; Molecular and Cellular Biology; and, Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - 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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16
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Parmar KM, Gaikwad SL, Dhakephalkar PK, Kothari R, Singh RP. Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol 2017; 8:559. [PMID: 28439260 PMCID: PMC5383658 DOI: 10.3389/fmicb.2017.00559] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through “omics” approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial “omics” data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.
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Affiliation(s)
| | | | | | - Ramesh Kothari
- Department of Biosciences, Saurashtra UniversityRajkot, India
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17
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Krylov V, Shaburova O, Pleteneva E, Bourkaltseva M, Krylov S, Kaplan A, Chesnokova E, Kulakov L, Magill D, Polygach O. Modular Approach to Select Bacteriophages Targeting Pseudomonas aeruginosa for Their Application to Children Suffering With Cystic Fibrosis. Front Microbiol 2016; 7:1631. [PMID: 27790211 PMCID: PMC5062033 DOI: 10.3389/fmicb.2016.01631] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/30/2016] [Indexed: 01/21/2023] Open
Abstract
This review discusses the potential application of bacterial viruses (phage therapy) toward the eradication of antibiotic resistant Pseudomonas aeruginosa in children with cystic fibrosis (CF). In this regard, several potential relationships between bacteria and their bacteriophages are considered. The most important aspect that must be addressed with respect to phage therapy of bacterial infections in the lungs of CF patients is in ensuring the continuity of treatment in light of the continual occurrence of resistant bacteria. This depends on the ability to rapidly select phages exhibiting an enhanced spectrum of lytic activity among several well-studied phage groups of proven safety. We propose a modular based approach, utilizing both mono-species and hetero-species phage mixtures. With an approach involving the visual recognition of characteristics exhibited by phages of well-studied phage groups on lawns of the standard P. aeruginosa PAO1 strain, the simple and rapid enhancement of the lytic spectrum of cocktails is permitted, allowing the development of tailored preparations for patients capable of circumventing problems associated with phage resistant bacterial mutants.
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Affiliation(s)
- Victor Krylov
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Olga Shaburova
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Elena Pleteneva
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Maria Bourkaltseva
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Sergey Krylov
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Alla Kaplan
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Elena Chesnokova
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
| | - Leonid Kulakov
- Medical Biology Centre, School of Biological Sciences, Queen's University Belfast Belfast, UK
| | - Damian Magill
- Medical Biology Centre, School of Biological Sciences, Queen's University Belfast Belfast, UK
| | - Olga Polygach
- Laboratory for Genetics of Bacteriophages, Department of Microbiology, I.I. Mechnikov Research Institute for Vaccines and Sera Moscow, Russia
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18
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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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19
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Yuan Y, Gao M. Proteomic Analysis of a Novel Bacillus Jumbo Phage Revealing Glycoside Hydrolase As Structural Component. Front Microbiol 2016; 7:745. [PMID: 27242758 PMCID: PMC4870245 DOI: 10.3389/fmicb.2016.00745] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/03/2016] [Indexed: 12/31/2022] Open
Abstract
Tailed phages with genomes of larger than 200 kbp are classified as Jumbo phages and exhibited extremely high uncharted diversity. The genomic annotation of Jumbo phage is often disappointing because most of the predicted proteins, including structural proteins, failed to make good hits to the sequences in the databases. In this study, 23 proteins of a novel Bacillus Jumbo phage, vB_BpuM_BpSp, were identified as phage structural proteins by the structural proteome analysis, including 14 proteins of unknown function, 5 proteins with predicted function as structural proteins, a glycoside hydrolase, a Holliday junction resolvase, a RNA-polymerase β-subunit, and a host-coding portal protein, which might be hijacked from the host strain during phage virion assembly. The glycoside hydrolase (Gp255) was identified as phage virion component and was found to interact with the phage baseplate protein. Gp255 shows specific lytic activity against the phage host strain GR8 and has high temperature tolerance. In situ peptidoglycan-hydrolyzing activities analysis revealed that the expressed Gp255 and phage structural proteome exhibited glycoside hydrolysis activity against the tested GR8 cell extracts. This study identified the first functional individual structural glycoside hydrolase in phage virion. The presence of activated glycoside hydrolase in phage virions might facilitate the injection of the phage genome during infection by forming pores on the bacterial cell wall.
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Affiliation(s)
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
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20
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Hardies SC, Thomas JA, Black L, Weintraub ST, Hwang CY, Cho BC. Identification of structural and morphogenesis genes of Pseudoalteromonas phage φRIO-1 and placement within the evolutionary history of Podoviridae. Virology 2015; 489:116-27. [PMID: 26748333 PMCID: PMC4819975 DOI: 10.1016/j.virol.2015.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/12/2015] [Accepted: 12/13/2015] [Indexed: 10/27/2022]
Abstract
The virion proteins of Pseudoalteromonas phage φRIO-1 were identified and quantitated by mass spectrometry and gel densitometry. Bioinformatic methods customized to deal with extreme divergence defined a φRIO-1 tail structure homology group of phages, which was further related to T7 tail and internal virion proteins (IVPs). Similarly, homologs of tubular tail components and internal virion proteins were identified in essentially all completely sequenced podoviruses other than those in the subfamily Picovirinae. The podoviruses were subdivided into several tail structure homology groups, in addition to the RIO-1 and T7 groups. Molecular phylogeny indicated that these groups all arose about the same ancient time as the φRIO-1/T7 split. Hence, the T7-like infection mechanism involving the IVPs was an ancestral property of most podoviruses. The IVPs were found to variably host both tail lysozyme domains and domains destined for the cytoplasm, including the N4 virion RNA polymerase embedded within an IVP-D homolog.
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Affiliation(s)
- Stephen C Hardies
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, TX 78229-3900, USA.
| | - Julie A Thomas
- Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Lindsay Black
- Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD, USA
| | - Susan T Weintraub
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, TX 78229-3900, USA
| | - Chung Y Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Byung C Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography (RIO), Seoul National University, Seoul 08826, South Korea.
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21
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Incomplete LPS Core-Specific Felix01-Like Virus vB_EcoM_VpaE1. Viruses 2015; 7:6163-81. [PMID: 26633460 PMCID: PMC4690856 DOI: 10.3390/v7122932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/10/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Bacteriophages represent a valuable source for studying the mechanisms underlying virus-host interactions. A better understanding of the host-specificity of viruses at the molecular level can promote various phage applications, including bacterial diagnostics, antimicrobial therapeutics, and improve methods in molecular biology. In this study, we describe the isolation and characterization of a novel coliphage, vB_EcoM_VpaE1, which has different host specificity than its relatives. Morphology studies, coupled with the results of genomic and proteomic analyses, indicate that vB_EcoM_VpaE1 belongs to the newly proposed genus Felix01likevirus in the family Myoviridae. The genus Felix01likevirus comprises a group of highly similar phages that infect O-antigen-expressing Salmonella and Escherichia coli (E. coli) strains. Phage vB_EcoM_VpaE1 differs from the rest of Felix01-like viruses, since it infects O-antigen-deficient E. coli strains with an incomplete core lipopolysaccharide (LPS). We show that vB_EcoM_VpaE1 can infect mutants of E. coli that contain various truncations in their LPS, and can even recognize LPS that is truncated down to the inner-core oligosaccharide, showing potential for the control of rough E. coli strains, which usually emerge as resistant mutants upon infection by O-Ag-specific phages. Furthermore, VpaE1 can replicate in a wide temperature range from 9 to 49 °C, suggesting that this virus is well adapted to harsh environmental conditions. Since the structural proteins of such phages tend to be rather robust, the receptor-recognizing proteins of VpaE1 are an attractive tool for application in glycan analysis, bacterial diagnostics and antimicrobial therapeutics.
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22
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Complete Genome Sequence of Caulobacter crescentus Podophage Percy. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01373-15. [PMID: 26607888 PMCID: PMC4661307 DOI: 10.1128/genomea.01373-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Podophage Percy infects Caulobacter crescentus, a Gram-negative bacterium that divides asymmetrically and is a commonly used model organism to study the cell cycle, asymmetric cell division, and cell differentiation. Here, we announce the sequence and annotated complete genome of the phiKMV-like podophage Percy and note its prominent features.
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23
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Henry M, Bobay LM, Chevallereau A, Saussereau E, Ceyssens PJ, Debarbieux L. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS One 2015; 10:e0117163. [PMID: 25629728 PMCID: PMC4309531 DOI: 10.1371/journal.pone.0117163] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/19/2014] [Indexed: 11/18/2022] Open
Abstract
In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.
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Affiliation(s)
- Marine Henry
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
| | - Louis-Marie Bobay
- Institut Pasteur, Microbial Evolutionary Genomics Unit, Department of Genomes and Genetics, Paris, France
- CNRS, UMR3525, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Anne Chevallereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Emilie Saussereau
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Division of Gene Technology, Katholieke Universiteit Leuven, Heverlee, B-3001, Belgium
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Laurent Debarbieux
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, Paris, France
- * E-mail:
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24
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Yuan Y, Peng Q, Wu D, Kou Z, Wu Y, Liu P, Gao M. Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis. Appl Environ Microbiol 2015; 81:339-50. [PMID: 25344242 PMCID: PMC4272706 DOI: 10.1128/aem.02889-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/20/2014] [Indexed: 12/16/2022] Open
Abstract
We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen Bacillus pumilus GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Qin Peng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Dandan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zheng Kou
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Pengming Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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Wagemans J, Blasdel BG, Van den Bossche A, Uytterhoeven B, De Smet J, Paeshuyse J, Cenens W, Aertsen A, Uetz P, Delattre AS, Ceyssens PJ, Lavigne R. Functional elucidation of antibacterial phage ORFans targetingPseudomonas aeruginosa. Cell Microbiol 2014; 16:1822-35. [DOI: 10.1111/cmi.12330] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Jeroen Wagemans
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Bob G. Blasdel
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - An Van den Bossche
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Birgit Uytterhoeven
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Jeroen De Smet
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Jan Paeshuyse
- Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Minderbroedersstraat 10 - box 1030 3000 Leuven Belgium
| | - William Cenens
- Department of Microbial and Molecular Systems; Katholieke Universiteit Leuven; Kasteelpark Arenberg 22 - box 2457 3001 Leuven Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems; Katholieke Universiteit Leuven; Kasteelpark Arenberg 22 - box 2457 3001 Leuven Belgium
| | - Peter Uetz
- Centre for the Study of Biological Complexity; Virginia Commonwealth University; 1000 West Cary Street - room 333 Richmond VA 23284 USA
| | - Anne-Sophie Delattre
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Pieter-Jan Ceyssens
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
- Bacterial Diseases Division; Scientific Institute of Public Health (WIV-ISP); J. Wytsmanstraat 14 1050 Brussels Belgium
| | - Rob Lavigne
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
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Merabishvili M, Vandenheuvel D, Kropinski AM, Mast J, De Vos D, Verbeken G, Noben JP, Lavigne R, Vaneechoutte M, Pirnay JP. Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii. PLoS One 2014; 9:e104853. [PMID: 25111143 PMCID: PMC4128745 DOI: 10.1371/journal.pone.0104853] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/18/2014] [Indexed: 12/24/2022] Open
Abstract
Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections.
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Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
- Laboratory for Bacteriology Research (LBR), Faculty Medicine & Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Dieter Vandenheuvel
- Laboratory of Gene Technology, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Noben
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research (LBR), Faculty Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology (LabMCT), Queen Astrid Military Hospital, Brussels, Belgium
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Abbasifar R, Griffiths MW, Sabour PM, Ackermann HW, Vandersteegen K, Lavigne R, Noben JP, Alanis Villa A, Abbasifar A, Nash JHE, Kropinski AM. Supersize me: Cronobacter sakazakii phage GAP32. Virology 2014; 460-461:138-46. [PMID: 25010279 DOI: 10.1016/j.virol.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/05/2014] [Accepted: 05/03/2014] [Indexed: 01/27/2023]
Abstract
Cronobacter sakazakii is a Gram-negative pathogen found in milk-based formulae that causes infant meningitis. Bacteriophages have been proposed to control bacterial pathogens; however, comprehensive knowledge about a phage is required to ensure its safety before clinical application. We have characterized C. sakazakii phage vB_CsaM_GAP32 (GAP32), which possesses the second largest sequenced phage genome (358,663bp). A total of 571 genes including 545 protein coding sequences and 26 tRNAs were identified, thus more genes than in the smallest bacterium, Mycoplasma genitalium G37. BLASTP and HHpred searches, together with proteomic analyses reveal that only 23.9% of the putative proteins have defined functions. Some of the unique features of this phage include: a chromosome condensation protein, two copies of the large subunit terminase, a predicted signal-arrest-release lysin; and an RpoD-like protein, which is possibly involved in the switch from immediate early to delayed early transcription. Its closest relatives are all extremely large myoviruses, namely coliphage PBECO4 and Klebsiella phage vB_KleM-RaK2, with whom it shares approximately 44% homologous proteins. Since the homologs are not evenly distributed, we propose that these three phages belong to a new subfamily.
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Affiliation(s)
- Reza Abbasifar
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Mansel W Griffiths
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Parviz M Sabour
- Agriculture and Agri-Food Canada, Guelph Food Research Centre, Guelph, ON, Canada N1G 5C9
| | - Hans-Wolfgang Ackermann
- Department of Microbiology-Infectiology and Immunology, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | | | - Rob Lavigne
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Argentina Alanis Villa
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Arash Abbasifar
- Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - John H E Nash
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, Canada N1G 3W4
| | - Andrew M Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, ON, Canada N1G 3W4; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1.
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28
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Mahony J, van Sinderen D. Current taxonomy of phages infecting lactic acid bacteria. Front Microbiol 2014; 5:7. [PMID: 24478767 PMCID: PMC3900856 DOI: 10.3389/fmicb.2014.00007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/07/2014] [Indexed: 01/29/2023] Open
Abstract
Phages infecting lactic acid bacteria have been the focus of significant research attention over the past three decades. Through the isolation and characterization of hundreds of phage isolates, it has been possible to classify phages of the dairy starter and adjunct bacteria Lactococus lactis, Streptococcus thermophilus, Leuconostoc spp., and Lactobacillus spp. Among these, phages of L. lactis have been most thoroughly scrutinized and serve as an excellent model system to address issues that arise when attempting taxonomic classification of phages infecting other LAB species. Here, we present an overview of the current taxonomy of phages infecting LAB genera of industrial significance, the methods employed in these taxonomic efforts and how these may be employed for the taxonomy of phages of currently underrepresented and emerging phage species.
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Affiliation(s)
- Jennifer Mahony
- Department of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology, University College Cork Cork, Ireland ; Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland
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29
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Moran D, Cross T, Brown LM, Colligan RM, Dunbar D. Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome. J Virol Methods 2013; 195:9-17. [PMID: 24129072 DOI: 10.1016/j.jviromet.2013.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/25/2013] [Accepted: 10/01/2013] [Indexed: 01/10/2023]
Abstract
In this work, a method was developed to study the structural proteome of mycobacteriophage Marvin, a recent isolate from soil with 107 predicted coding sequences. This prototype method was applied for semi-quantitative analysis of the composition of this mycobacteriophage virion using ion mobility spectrometry and data-independent acquisition (MS(E)-IMS). MS(E)-IMS was compared to a more conventional proteomics technique employing mass spectrometry with a data-dependent acquisition strategy. MS(E)-IMS provided broad coverage of the virion proteome and high sequence coverage for individual proteins. This shotgun method does not depend on the limited sensitivity of visualization of protein bands by staining reagents inherent in gel-based methods. The method is comprehensive, provides high sequence coverage and is proposed as a particularly efficient method for the study of bacteriophage proteomes.
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Affiliation(s)
- Deborah Moran
- Cabrini College, Department of Science, 610 King of Prussia Road, Radnor, PA 19087, United States
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Lynch KH, Abdu AH, Schobert M, Dennis JJ. Genomic characterization of JG068, a novel virulent podovirus active against Burkholderia cenocepacia. BMC Genomics 2013; 14:574. [PMID: 23978260 PMCID: PMC3765740 DOI: 10.1186/1471-2164-14-574] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/09/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND As is true for many other antibiotic-resistant Gram-negative pathogens, members of the Burkholderia cepacia complex (BCC) are currently being assessed for their susceptibility to phage therapy as an antimicrobial treatment. The objective of this study was to perform genomic and limited functional characterization of the novel BCC phage JG068 (vB_BceP_JG068). RESULTS JG068 is a podovirus that forms large, clear plaques on Burkholderia cenocepacia K56-2. Host range analysis indicates that this phage can infect environmental, clinical, and epidemic isolates of Burkholderia multivorans, B. cenocepacia, Burkholderia stabilis, and Burkholderia dolosa, likely through interaction with the host lipopolysaccharide as a receptor. The JG068 chromosome is 41,604 base pairs (bp) in length and is flanked by 216 bp short direct terminal repeats. Gene expression originates from both host and phage promoters and is in the forward direction for all 49 open reading frames. The genome sequence shows similarity to Ralstonia phage ϕRSB1, Caulobacter phage Cd1, and uncharacterized genetic loci of blood disease bacterium R229 and Burkholderia pseudomallei 1710b. CoreGenesUniqueGenes analysis indicates that JG068 belongs to the Autographivirinae subfamily and ϕKMV-like phages genus. Modules within the genome encode proteins involved in DNA-binding, morphogenesis, and lysis, but none associated with pathogenicity or lysogeny. Similar to the signal-arrest-release (SAR) endolysin of ϕKMV, inducible expression of the JG068 SAR endolysin causes lysis of Escherichia coli that is dependent on the presence of an N-terminal signal sequence. In an in vivo assay using the Galleria mellonella infection model, treatment of B. cenocepacia K56-2-infected larvae with JG068 results in a significant increase in larval survival. CONCLUSIONS As JG068 has a broad host range, does not encode virulence factors, is obligately lytic, and has activity against an epidemic B. cenocepacia strain in vivo, this phage is a highly promising candidate for BCC phage therapy development.
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Affiliation(s)
- Karlene H Lynch
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
| | - Ashraf H Abdu
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
| | - Max Schobert
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jonathan J Dennis
- Department of Biological Sciences, 6–008 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB T6G 2E9 Canada
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Vandersteegen K, Kropinski AM, Nash JHE, Noben JP, Hermans K, Lavigne R. Romulus and Remus, two phage isolates representing a distinct clade within the Twortlikevirus genus, display suitable properties for phage therapy applications. J Virol 2013; 87:3237-47. [PMID: 23302893 PMCID: PMC3592175 DOI: 10.1128/jvi.02763-12] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/07/2012] [Indexed: 11/20/2022] Open
Abstract
The renewed interest in controlling Staphylococcus aureus infections using their natural enemies, bacteriophages, has led to the isolation of a limited number of virulent phages so far. These phages are all members of the Twortlikevirus, displaying little variance. We present two novel closely related (95.9% DNA homology) lytic myoviruses, Romulus and Remus, with double-stranded DNA (dsDNA) genomes of 131,333 bp and 134,643 bp, respectively. Despite their relatedness to Staphylococcus phages K, G1, ISP, and Twort and Listeria phages A511 and P100, Romulus and Remus can be proposed as isolates of a new species within the Twortlikevirus genus. A distinguishing feature for these phage genomes is the unique distribution of group I introns compared to that in other staphylococcal myoviruses. In addition, a hedgehog/intein domain was found within their DNA polymerase genes, and an insertion sequence-encoded transposase exhibits splicing behavior and produces a functional portal protein. From a phage therapy application perspective, Romulus and Remus infected approximately 70% of the tested S. aureus isolates and displayed promising lytic activity against these isolates. Furthermore, both phages showed a rapid initial adsorption and demonstrated biofilm-degrading capacity in a proof-of-concept experiment.
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Affiliation(s)
- Katrien Vandersteegen
- Laboratory of Gene Technology, Division of Gene Technology, University of Leuven, Heverlee, Belgium
| | - Andrew M. Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - John H. E. Nash
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Katleen Hermans
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Division of Gene Technology, University of Leuven, Heverlee, Belgium
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Complete genome sequence of IME15, the first T7-like bacteriophage lytic to pan-antibiotic-resistant Stenotrophomonas maltophilia. J Virol 2013; 86:13839-40. [PMID: 23166248 DOI: 10.1128/jvi.02661-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
T7-like bacteriophages are a class of virulent bacteriophages which have a clearer genetic background and smaller genomes than other phages. In addition, it grows faster and is easier to culture than other phages. At present, the numbers of available T7-like bacteriophage genomes and Stenotrophomonas maltophilia genomes are small, and IME15 is the first T7-like virulent Stenotrophomonas phage whose sequence has been reported. It shows effective lysis of S. maltophilia. Here we announce its complete genome, and major findings from its annotation are described.
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33
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Gu J, Liu X, Yang M, Li Y, Sun C, Lu R, Song J, Zhang Q, Lei L, Feng X, Du C, Yu H, Yang Y, Han W. Genomic characterization of lytic Staphylococcus aureus phage GH15: providing new clues to intron shift in phages. J Gen Virol 2012; 94:906-915. [PMID: 23255621 DOI: 10.1099/vir.0.049197-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phage GH15 is a polyvalent phage that shows activity against a wide range of Staphylcoccus aureus strains. This study analysed the genome of GH15. The genome size of GH15 (139 806 bp) was found to be larger than that of the known staphylococcal phages, and the G+C content (30.23 mol%) of GH15 was lower than that of any other staphylococcal myovirus phages. By mass spectrometry, ten structural proteins were identified. Analysis revealed that GH15 was closely related to phages G1, ISP, A5W, Sb-1 and K, and was moderately related to Twort. In light of the variability in identity, coverage, G+C content and genome size, coupled with the large number of mosaicisms, there certainly were close evolutionary relationships from K to Sb-1, A5W, ISP, G1 and finally GH15. Interestingly, all the introns and inteins present in the above phages were absent in GH15 and there appeared to be intron loss in GH15 compared with the intron gain seen in other phages. A comparison of the intron- and intein-related genes demonstrated a clear distinction in the location of the insertion site between intron-containing and intron-free alleles, and this might lead to the establishment of a consensus sequence associated with the presence of an intron or intein. The comparative analysis of the GH15 genome sequence with other phages not only provides compelling evidence for the diversity of staphylococcal myovirus phages but also offers new clues to intron shift in phages.
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Affiliation(s)
- Jingmin Gu
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Xiaohe Liu
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Mei Yang
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Yue Li
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Changjiang Sun
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Rong Lu
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Jun Song
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Qingming Zhang
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Liancheng Lei
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Xin Feng
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Chongtao Du
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Hao Yu
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Yongjun Yang
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
| | - Wenyu Han
- College of Animal Science and Veterinary Medicine, Jilin University, Changchun, PR China
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Abstract
The complete genome sequence of the Escherichia coli O157:H7 typing phage V7 was determined. Its double-stranded DNA genome is 166,452 bp long, encoding 273 proteins and including 11 tRNAs. This virus belongs to the genus T4-like viruses within the subfamily Tevenvirinae, family Myoviridae.
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35
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Expression and functional characterization of the first bacteriophage-encoded chaperonin. J Virol 2012; 86:10103-11. [PMID: 22787217 DOI: 10.1128/jvi.00940-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chaperonins promote protein folding in vivo and are ubiquitously found in bacteria, archaea, and eukaryotes. The first viral chaperonin GroEL ortholog, gene product 146 (gp146), whose gene was earlier identified in the genome of bacteriophage EL, has been shown to be synthesized during phage propagation in Pseudomonas aeruginosa cells. The recombinant gp146 has been expressed in Escherichia coli and characterized by different physicochemical methods for the first time. Using serum against the recombinant protein, gp146's native substrate, the phage endolysin gp188, has been immunoprecipitated from the lysate of EL-infected bacteria and identified by mass spectrometry. In vitro experiments have shown that gp146 has a protective effect against endolysin thermal inactivation and aggregation, providing evidence of its chaperonin function. The phage chaperonin has been found to have the architecture and some properties similar to those of GroEL but not to require cochaperonin for its functional activity.
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36
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Kropinski AM, Van den Bossche A, Lavigne R, Noben JP, Babinger P, Schmitt R. Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. Virol J 2012; 9:102. [PMID: 22650361 PMCID: PMC3517404 DOI: 10.1186/1743-422x-9-102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 05/04/2012] [Indexed: 11/16/2022] Open
Abstract
Background The flagellotropic phage 7-7-1 infects motile cells of Agrobacterium sp H13-3 by attaching to and traveling along the rotating flagellar filament to the secondary receptor at the base, where it injects its DNA into the host cell. Here we describe the complete genomic sequence of 69,391 base pairs of this unusual bacteriophage. Methods The sequence of the 7-7-1 genome was determined by pyro(454)sequencing to a coverage of 378-fold. It was annotated using MyRAST and a variety of internet resources. The structural proteome was analyzed by SDS-PAGE coupled electrospray ionization-tandem mass spectrometry (MS/MS). Results Sequence annotation and a structural proteome analysis revealed 127 open reading frames, 84 of which are unique. In six cases 7-7-1 proteins showed sequence similarity to proteins from the virulent Burkholderia myovirus BcepB1A. Unique features of the 7-7-1 genome are the physical separation of the genes encoding the small (orf100) and large (orf112) subunits of the DNA packaging complex and the apparent lack of a holin-lysin cassette. Proteomic analysis revealed the presence of 24 structural proteins, five of which were identified as baseplate (orf7), putative tail fibre (orf102), portal (orf113), major capsid (orf115) and tail sheath (orf126) proteins. In the latter case, the N-terminus was removed during capsid maturation, probably by a putative prohead protease (orf114).
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Affiliation(s)
- Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, NIG 3W4, Canada.
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BVPaP-3, a T7-Like Lytic Phage of Pseudomonas aeruginosa: Its Isolation and Characterisation. Curr Microbiol 2012; 64:305-11. [DOI: 10.1007/s00284-011-0071-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/14/2011] [Indexed: 10/14/2022]
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Fogg PC, Hynes AP, Digby E, Lang AS, Beatty JT. Characterization of a newly discovered Mu-like bacteriophage, RcapMu, in Rhodobacter capsulatus strain SB1003. Virology 2011; 421:211-21. [DOI: 10.1016/j.virol.2011.09.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 08/25/2011] [Accepted: 09/28/2011] [Indexed: 10/16/2022]
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Vandersteegen K, Mattheus W, Ceyssens PJ, Bilocq F, De Vos D, Pirnay JP, Noben JP, Merabishvili M, Lipinska U, Hermans K, Lavigne R. Microbiological and molecular assessment of bacteriophage ISP for the control of Staphylococcus aureus. PLoS One 2011; 6:e24418. [PMID: 21931710 PMCID: PMC3170307 DOI: 10.1371/journal.pone.0024418] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/09/2011] [Indexed: 01/03/2023] Open
Abstract
The increasing antibiotic resistance in bacterial populations requires alternatives for classical treatment of infectious diseases and therefore drives the renewed interest in phage therapy. Methicillin resistant Staphylococcus aureus (MRSA) is a major problem in health care settings and live-stock breeding across the world. This research aims at a thorough microbiological, genomic, and proteomic characterization of S. aureus phage ISP, required for therapeutic applications. Host range screening of a large batch of S. aureus isolates and subsequent fingerprint and DNA microarray analysis of the isolates revealed a substantial activity of ISP against 86% of the isolates, including relevant MRSA strains. From a phage therapy perspective, the infection parameters and the frequency of bacterial mutations conferring ISP resistance were determined. Further, ISP was proven to be stable in relevant in vivo conditions and subcutaneous as well as nasal and oral ISP administration to rabbits appeared to cause no adverse effects. ISP encodes 215 gene products on its 138,339 bp genome, 22 of which were confirmed as structural proteins using tandem electrospray ionization-mass spectrometry (ESI-MS/MS), and shares strong sequence homology with the ‘Twort-like viruses’. No toxic or virulence-associated proteins were observed. The microbiological and molecular characterization of ISP supports its application in a phage cocktail for therapeutic purposes.
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Affiliation(s)
| | - Wesley Mattheus
- Division of Gene Technology, Katholieke Universiteit Leuven, Heverlee, Belgium
| | - Pieter-Jan Ceyssens
- Division of Gene Technology, Katholieke Universiteit Leuven, Heverlee, Belgium
| | - Florence Bilocq
- Laboratory for Molecular and Cellular Technology, Burn Centre, Queen Astrid Military Hospital, Brussels, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Burn Centre, Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Burn Centre, Queen Astrid Military Hospital, Brussels, Belgium
| | - Jean-Paul Noben
- Hasselt University, Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Diepenbeek, Belgium
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Burn Centre, Queen Astrid Military Hospital, Brussels, Belgium
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
| | - Urszula Lipinska
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Katleen Hermans
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Rob Lavigne
- Division of Gene Technology, Katholieke Universiteit Leuven, Heverlee, Belgium
- * E-mail:
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Genomic and proteomic characterization of the broad-host-range Salmonella phage PVP-SE1: creation of a new phage genus. J Virol 2011; 85:11265-73. [PMID: 21865376 DOI: 10.1128/jvi.01769-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
(Bacterio)phage PVP-SE1, isolated from a German wastewater plant, presents a high potential value as a biocontrol agent and as a diagnostic tool, even compared to the well-studied typing phage Felix 01, due to its broad lytic spectrum against different Salmonella strains. Sequence analysis of its genome (145,964 bp) shows it to be terminally redundant and circularly permuted. Its G+C content, 45.6 mol%, is lower than that of its hosts (50 to 54 mol%). We found a total of 244 open reading frames (ORFs), representing 91.6% of the coding capacity of the genome. Approximately 46% of encoded proteins are unique to this phage, and 22.1% of the proteins could be functionally assigned. This myovirus encodes a large number of tRNAs (n=24), reflecting its lytic capacity and evolution through different hosts. Tandem mass spectrometric analysis using electron spray ionization revealed 25 structural proteins as part of the mature phage particle. The genome sequence was found to share homology with 140 proteins of the Escherichia coli bacteriophage rV5. Both phages are unrelated to any other known virus, which suggests that an "rV5-like virus" genus should be created within the Myoviridae to contain these two phages.
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Isolation and characterisation of KP34--a novel φKMV-like bacteriophage for Klebsiella pneumoniae. Appl Microbiol Biotechnol 2011; 90:1333-45. [PMID: 21327407 PMCID: PMC3082699 DOI: 10.1007/s00253-011-3149-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 10/28/2022]
Abstract
Bacteriophage KP34 is a novel virus belonging to the subfamily Autographivirinae lytic for extended-spectrum β-lactamase-producing Klebsiella pneumoniae strains. Its biological features, morphology, susceptibility to chemical and physical agents, burst size, host specificity and activity spectrum were determined. As a potential antibacterial agent used in therapy, KP34 molecular features including genome sequence and protein composition were examined. Phylogenetic analyses and clustering of KP34 phage genome sequences revealed its clear relationships with "phiKMV-like viruses". Simultaneously, whole-genome analyses permitted clustering and classification of all phages, with completely sequenced genomes, belonging to the Podoviridae.
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42
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Chang KC, Lin NT, Hu A, Lin YS, Chen LK, Lai MJ. Genomic analysis of bacteriophage ϕAB1, a ϕKMV-like virus infecting multidrug-resistant Acinetobacter baumannii. Genomics 2011; 97:249-55. [PMID: 21241792 DOI: 10.1016/j.ygeno.2011.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 12/29/2010] [Accepted: 01/04/2011] [Indexed: 10/18/2022]
Abstract
We present the complete genomic sequence of a lytic bacteriophage ϕAB1 which can infect many clinical isolates of multidrug-resistant Acinetobacter baumannii. The recently isolated bacteriophage displays morphology resembling Podoviridae family. The ϕAB1 genome is a linear double-stranded DNA of 41,526 bp containing 46 possible open reading frames (ORFs). The majority of the predicted structural proteins were identified as part of the phage particle by mass spectrometry analysis. According to the virion morphology, overall genomic structure, and the phylogenetic tree of RNA polymerase, we propose that ϕAB1 is a new member of the ϕKMV-like phages. Additionally, we identified four ORFs encoding putative HNH endonucleases, one of which is presumed to integrate and create a genes-in-pieces DNA polymerase. Also, a potential lysis cassette was identified in the late genome. The lytic power of this bacteriophage combined with its specificity for A. baumannii makes ϕAB1 an attractive agent for therapeutic or disinfection applications.
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Affiliation(s)
- Kai-Chih Chang
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien 970, Taiwan
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43
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Ceyssens PJ, Brabban A, Rogge L, Lewis MS, Pickard D, Goulding D, Dougan G, Noben JP, Kropinski A, Kutter E, Lavigne R. Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the "N4-like viruses". Virology 2010; 405:26-30. [PMID: 20619867 PMCID: PMC3715699 DOI: 10.1016/j.virol.2010.06.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/31/2010] [Accepted: 06/03/2010] [Indexed: 11/28/2022]
Abstract
We present a detailed analysis of the genome architecture, structural proteome and infection-related properties of three Pseudomonas phages, designated LUZ7, LIT1 and PEV2. These podoviruses encapsulate 72.5 to 74.9 kb genomes and lyse their host after 25 min aerobic infection. PEV2 can successfully infect under anaerobic conditions, but its latent period is tripled, the lysis proceeds far slower and the burst size decreases significantly. While the overall genome structure of these phages resembles the well-studied coliphage N4, these Pseudomonas phages encode a cluster of tail genes which displays significant similarity to a Pseudomonasaeruginosa (cryptic) prophage region. Using ESI-MS/MS, these tail proteins were shown to be part of the phage particle, as well as ten other proteins including a giant 370 kDa virion RNA polymerase. These phages are the first described representatives of a novel kind of obligatory lytic P. aeruginosa-infecting phages, belonging to the widespread "N4-like viruses" genus.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Leuven, B-3001, Belgium
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Whichard JM, Weigt LA, Borris DJ, Li LL, Zhang Q, Kapur V, Pierson FW, Lingohr EJ, She YM, Kropinski AM, Sriranganathan N. Complete genomic sequence of bacteriophage felix o1. Viruses 2010; 2:710-730. [PMID: 21994654 PMCID: PMC3185647 DOI: 10.3390/v2030710] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Revised: 02/25/2010] [Accepted: 03/08/2010] [Indexed: 11/16/2022] Open
Abstract
Bacteriophage O1 is a Myoviridae A1 group member used historically for identifying Salmonella. Sequencing revealed a single, linear, 86,155-base-pair genome with 39% average G+C content, 131 open reading frames, and 22 tRNAs. Closest protein homologs occur in Erwinia amylovora phage φEa21-4 and Escherichia coli phage wV8. Proteomic analysis indentified structural proteins: Gp23, Gp36 (major tail protein), Gp49, Gp53, Gp54, Gp55, Gp57, Gp58 (major capsid protein), Gp59, Gp63, Gp64, Gp67, Gp68, Gp69, Gp73, Gp74 and Gp77 (tail fiber). Based on phage-host codon differences, 7 tRNAs could affect translation rate during infection. Introns, holin-lysin cassettes, bacterial toxin homologs and host RNA polymerase-modifying genes were absent.
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Affiliation(s)
- Jean M. Whichard
- Mailstop G29, Centers for Disease Control and Prevention; 1600 Clifton Road, Atlanta, GA 30329, USA; E-Mail: (J.M.W.)
| | - Lee A. Weigt
- Smithsonian National Institution, National Museum in Natural History, MRC 534, Washington, DC 20560, USA; E-Mail: (L.A.W.)
| | - Douglas J. Borris
- Abbot Point of Care, 185 Corkstown Road, Ottawa, ON, K2H 8V4, Canada
| | - Ling Ling Li
- Pennsylvania State University, Department of Veterinary and Biomedical Sciences, 204 Wartick Laboratory, University Park, PA 16802, USA; E-Mail: (L.L.L.)
| | - Qing Zhang
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA; E-Mail: (Q.Z.)
| | - Vivek Kapur
- Pennsylvania State University, 115 Henning Bldg., University Park, PA 16802, USA; E-Mail: (V.K.)
| | - F. William Pierson
- VA-MD Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Duck Pond Drive (0442), Blacksburg, Virginia 24061, USA, E-Mail: (F.W.P.)
| | - Erika J. Lingohr
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario N1G 3W4, Canada; E-Mails: (E.J.L.); (A.M.K.)
| | - Yi-Min She
- Centre for Biologics Research, Health Canada, Room D159, Frederick G. Banting Building 251 Sir Frederick Banting Driveway, Tunney’s Pasture, Ottawa, ON K1A 0K9, Canada; E-Mail: (Y.-M.S.)
| | - Andrew M. Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario N1G 3W4, Canada; E-Mails: (E.J.L.); (A.M.K.)
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, Ontario N1G 2W1, Canada
| | - Nammalwar Sriranganathan
- Center for Molecular Medicine and Infectious Disease; 1410 Prices Fork Road; Blacksburg, VA 24061-0342, USA
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Ceyssens PJ, Miroshnikov K, Mattheus W, Krylov V, Robben J, Noben JP, Vanderschraeghe S, Sykilinda N, Kropinski AM, Volckaert G, Mesyanzhinov V, Lavigne R. Comparative analysis of the widespread and conserved PB1-like viruses infectingPseudomonas aeruginosa. Environ Microbiol 2009; 11:2874-83. [DOI: 10.1111/j.1462-2920.2009.02030.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Lecoutere E, Ceyssens PJ, Miroshnikov KA, Mesyanzhinov VV, Krylov VN, Noben JP, Robben J, Hertveldt K, Volckaert G, Lavigne R. Identification and comparative analysis of the structural proteomes of ϕKZ and EL, two giant Pseudomonas aeruginosa
bacteriophages. Proteomics 2009; 9:3215-9. [DOI: 10.1002/pmic.200800727] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Ceyssens PJ, Noben JP, Ackermann HW, Verhaegen J, De Vos D, Pirnay JP, Merabishvili M, Vaneechoutte M, Chibeu A, Volckaert G, Lavigne R. Survey ofPseudomonas aeruginosaand its phages:de novopeptide sequencing as a novel tool to assess the diversity of worldwide collected viruses. Environ Microbiol 2009; 11:1303-13. [DOI: 10.1111/j.1462-2920.2008.01862.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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48
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Roucourt B, Lecoutere E, Chibeu A, Hertveldt K, Volckaert G, Lavigne R. A procedure for systematic identification of bacteriophage-host interactions of P. aeruginosa phages. Virology 2009; 387:50-8. [PMID: 19261318 DOI: 10.1016/j.virol.2009.01.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/24/2008] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
Immediately after bacteriophage infection, phage early proteins establish optimal conditions for phage infection, often through a direct interaction with host-cell proteins. We implemented a yeast two-hybrid approach for Pseudomonas aeruginosa phages as a first step in the analysis of these - often uncharacterized - proteins. A 24-fold redundant prey library of P. aeruginosa PAO1 (7.32x10(6) independent clones), was screened against early proteins (gp1 to 9) of phiKMV, a P. aeruginosa-infecting member of the Podoviridae; interactions were verified using an independent in vitro assay. None resembles previously known bacteriophage-host interactions, as the three identified target malate synthase G, a regulator of a secretion system and a regulator of nitrogen assimilation. Although at least two-bacteriophage infections are non-essential to phiKMV infection, their disruption has an influence on infection efficiency. This methodology allows systematic analysis of phage proteins and is applicable as an interaction analysis tool for P. aeruginosa.
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Affiliation(s)
- Bart Roucourt
- Division of Gene Technology, Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21 box 2462, Leuven, B-3001, Belgium.
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Abstract
Current techniques in mass spectrometry (MS) allow sensitive and accurate identification of proteins thanks to the in silico availability of these protein sequences within databases. This chapter provides a short overview of MS techniques used in the identification of phage structural proteins and focuses on an electron spray peptide ionization (ESI-MS/MS) approach to identify the phage structural proteome in a comprehensive and systematic ways. Such analyses provide an experimental examination of structural proteins and confirm genome-based gene predictions.
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Affiliation(s)
- Rob Lavigne
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Leuven, Belgium
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Serwer P, Wright ET, Hakala KW, Weintraub ST. Evidence for bacteriophage T7 tail extension during DNA injection. BMC Res Notes 2008; 1:36. [PMID: 18710489 PMCID: PMC2525648 DOI: 10.1186/1756-0500-1-36] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 06/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Electron micrographs of bacteriophage T7 reveal a tail shorter than needed to reach host cytoplasm during infection-initiating injection of a T7 DNA molecule through the tail and cell envelope. However, recent data indicate that internal T7 proteins are injected before the DNA molecule is injected. Thus, bacteriophage/host adsorption potentially causes internal proteins to become external and lengthen the tail for DNA injection. But, the proposed adsorption-induced tail lengthening has never been visualized. FINDINGS In the present study, electron microscopy of particles in T7 lysates reveals a needle-like capsid extension that attaches partially emptied bacteriophage T7 capsids to non-capsid vesicles and sometimes enters an attached vesicle. This extension is 40-55 nm long, 1.7-2.4x longer than the T7 tail and likely to be the proposed lengthened tail. The extension is 8-11 nm in diameter, thinner than most of the tail, with an axial hole 3-4 nm in diameter. Though the bound vesicles are not identified by microscopy, these vesicles resemble the major vesicles in T7 lysates, found to be E. coli outer membrane vesicles by non-denaturing agarose gel electrophoresis, followed by mass spectrometry. CONCLUSION The observed lengthened tail is long enough to reach host cytoplasm during DNA injection. Its channel is wide enough to be a conduit for DNA injection and narrow enough to clamp DNA during a previously observed stalling/re-starting of injection. However, its outer diameter is too large to explain formation by passing of an intact assembly through any known capsid hole unless the hole is widened.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA.
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