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Raza S, Wdowiak M, Paczesny J. An Overview of Diverse Strategies To Inactivate Enterobacteriaceae-Targeting Bacteriophages. EcoSal Plus 2023; 11:eesp00192022. [PMID: 36651738 PMCID: PMC10729933 DOI: 10.1128/ecosalplus.esp-0019-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023]
Abstract
Bacteriophages are viruses that infect bacteria and thus threaten industrial processes relying on the production executed by bacterial cells. Industries bear huge economic losses due to such recurring and resilient infections. Depending on the specificity of the process, there is a need for appropriate methods of bacteriophage inactivation, with an emphasis on being inexpensive and high efficiency. In this review, we summarize the reports on antiphagents, i.e., antibacteriophage agents on inactivation of bacteriophages. We focused on bacteriophages targeting the representatives of the Enterobacteriaceae family, as its representative, Escherichia coli, is most commonly used in the bio-industry. The review is divided into sections dealing with bacteriophage inactivation by physical factors, chemical factors, and nanotechnology-based solutions.
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Affiliation(s)
- Sada Raza
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Mateusz Wdowiak
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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2
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Chan YW, Millard AD, Wheatley PJ, Holmes AB, Mohr R, Whitworth AL, Mann NH, Larkum AWD, Hess WR, Scanlan DJ, Clokie MRJ. Genomic and proteomic characterization of two novel siphovirus infecting the sedentary facultative epibiont cyanobacterium Acaryochloris marina. Environ Microbiol 2015; 17:4239-52. [PMID: 25472545 DOI: 10.1111/1462-2920.12735] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 11/26/2014] [Accepted: 11/27/2003] [Indexed: 11/28/2022]
Abstract
Acaryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far-red light. We report the characterization of the phages A-HIS1 and A-HIS2, capable of infecting Acaryochloris. Morphological characterization of these phages places them in the family Siphoviridae. However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While the phages do show synteny between each other, the nucleotide identity between the phages is low at 45-67%, suggesting they diverged from each other some time ago. The greatest number of genes shared with another phage (a myovirus infecting marine Synechococcus) was four. Unlike most other cyanophages and in common with the Siphoviridae infecting Synechococcus, no photosynthesis-related genes were found in the genome. CRISPR (clustered regularly interspaced short palindromic repeats) spacers from the host Acaryochloris had partial matches to sequences found within the phages, which is the first time CRISPRs have been reported in a cyanobacterial/cyanophage system. The phages also encode a homologue of the proteobacterial RNase T. The potential function of RNase T in the mark-up or digestion of crRNA hints at a novel mechanism for evading the host CRISPR system.
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Affiliation(s)
- Yi-Wah Chan
- Warwick Systems Biology Centre, Coventry, UK
| | | | | | - Antony B Holmes
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Remus Mohr
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Nicholas H Mann
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Anthony W D Larkum
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Wolfgang R Hess
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE19HN, UK
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Han JE, Kim JH, Hwang SY, Choresca CH, Shin SP, Jun JW, Chai JY, Park YH, Park SC. Isolation and characterization of a Myoviridae bacteriophage against Staphylococcus aureus isolated from dairy cows with mastitis. Res Vet Sci 2013; 95:758-63. [PMID: 23790669 DOI: 10.1016/j.rvsc.2013.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 04/29/2013] [Accepted: 06/01/2013] [Indexed: 11/30/2022]
Abstract
A lytic bacteriophage (phage), designated SAH-1, was isolated from sewage effluent near a dairy cow farm in Gwacheon, South Korea to search for biocontrol agents against Staphylococcus aureus infections. The SAH-1 was morphologically classified as Myoviridae and possessed an approximate 144 kb double-stranded genomic DNA. The phage showed broad host ranges within S. aureus strains including methicillin-resistant strains, and its latent period and burst size were approximately 20 min and 100 PFU/cell, respectively. Moreover, morphologic and genomic analysis of SAH-1 revealed that the phage was closely related to other Myoviridae phages infecting Staphylococcus species. The bacteriolytic activity of phage SAH-1 at a multiplicity of infection (MOI) 1 and 100 indicated its efficiency for reducing bacterial growth. Based on these results, phage SAH-1 could be considered a potential therapeutic or prophylactic candidate against S. aureus infections.
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Affiliation(s)
- Jee Eun Han
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Republic of Korea
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Kim JH, Son JS, Choi YJ, Choresca CH, Shin SP, Han JE, Jun JW, Kang DH, Oh C, Heo SJ, Park SC. Isolation and characterization of a lytic Myoviridae bacteriophage PAS-1 with broad infectivity in Aeromonas salmonicida. Curr Microbiol 2012; 64:418-26. [PMID: 22314935 DOI: 10.1007/s00284-012-0091-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 01/18/2012] [Indexed: 10/14/2022]
Abstract
To search for candidate control agents against Aeromonas salmonicida subsp. salmonicida infections in aquaculture, one bacteriophage (phage), designated as PAS-1, was isolated from the sediment samples of the rainbow trout (Oncorhynchus mykiss) culture farm in Korea. The PAS-1 was morphologically classified as Myoviridae and possessed approximately 48 kb of double-strand genomic DNA. The phage showed broad host ranges to other subspecies of A. salmonicida as well as A. salmonicida subsp. salmonicida including antibiotic-resistant strains. Its latent period and burst size were estimated to be approximately 40 min and 116.7 PFU/cell, respectively. Furthermore, genomic and structural proteomic analysis of PAS-1 revealed that the phage was closely related to other Myoviridae phages infecting enterobacteria or Aeromonas species. The bacteriolytic activity of phage PAS-1 was evaluated using three subspecies of A. salmonicida strain at different doses of multiplicity of infection, and the results proved to be efficient for the reduction of bacterial growth. Based on these results, PAS-1 could be considered as a novel Aeromonas phage and might have potentiality to reduce the impacts of A. salmonicida infections in aquaculture.
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Affiliation(s)
- J H Kim
- Laboratory of Aquatic Animal Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea
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Davidson AR, Cardarelli L, Pell LG, Radford DR, Maxwell KL. Long noncontractile tail machines of bacteriophages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:115-42. [PMID: 22297512 DOI: 10.1007/978-1-4614-0980-9_6] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this chapter, we describe the structure, assembly, function, and evolution of the long, noncontractile tail of the siphophages, which comprise ∼60% of the phages on earth. We place -particular emphasis on features that are conserved among all siphophages, and trace evolutionary connections between these phages and myophages, which possess long contractile tails. The large number of high-resolution structures of tail proteins solved recently coupled to studies of tail-related complexes by electron microscopy have provided many new insights in this area. In addition, the availability of thousands of phage and prophage genome sequences has allowed the delineation of several large families of tail proteins that were previously unrecognized. We also summarize current knowledge pertaining to the mechanisms by which siphophage tails recognize the bacterial cell surface and mediate DNA injection through the cell envelope. We show that phages infecting Gram-positive and Gram-negative bacteria possess distinct families of proteins at their tail tips that are involved in this process. Finally, we speculate on the evolutionary advantages provided by long phage tails.
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Affiliation(s)
- Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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Purification of bacteriophages and SDS-PAGE analysis of phage structural proteins from ghost particles. Methods Mol Biol 2009; 502:227-38. [PMID: 19082559 DOI: 10.1007/978-1-60327-565-1_13] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Concentration and purification of infectious particles are prerequisites for structural and functional characterization of bacteriophages. The methods detailed in the first part of this chapter outline the protocols commonly used to obtain purified phages: the concentration of phage particles by precipitation with polyethylene glycol and their purification by centrifugation in CsCl step gradients and subsequently by equilibrium centrifugation. This sequence of procedures, if carried out as a whole, ensures a purification of high quality, which is well suited for most analytical techniques used to characterize bacteriophage particles. The second part of this chapter describes the preparation of "ghosts" or DNA-less bacteriophages. These particles should be preferred to the entire bacteriophages for one-dimensional SDS-PAGE analysis of phage structural proteins, since running of the phage proteins through the gel is not disturbed by the presence of the phage DNA. This allows an optimal resolution, which is necessary for proteomic approaches such as N-terminal protein sequencing or mass spectrometry using proteins isolated from distinct gel bands.
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Clokie MRJ, Thalassinos K, Boulanger P, Slade SE, Stoilova-McPhie S, Cane M, Scrivens JH, Mann NH. A proteomic approach to the identification of the major virion structural proteins of the marine cyanomyovirus S-PM2. MICROBIOLOGY-SGM 2008; 154:1775-1782. [PMID: 18524932 DOI: 10.1099/mic.0.2007/016261-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, an MS-based proteomics approach to characterizing the virion structural proteins of the novel marine 'photosynthetic' phage S-PM2 is presented. The virus infects ecologically important cyanobacteria of the genus Synechococcus that make a substantial contribution to primary production in the oceans. The S-PM2 genome encodes 236 ORFs, some of which exhibit similarity to known phage virion structural proteins, but the majority (54%) show no detectable homology to known proteins from other organisms. Using public and in-house bioinformatics tools the proteome of S-PM2 was predicted and a database compatible with MS-based search engines was constructed. S-PM2 virion proteins were resolved by SDS-PAGE, excised, tryptically digested and analysed by LC-ESI-MS/MS. The resulting MS data were searched against the database. A parallel control study was undertaken on the well-characterized coliphage T4 in order to assess the sensitivity and efficiency of this approach. In total, 11 of the 15 S-PM2 proteins, predicted to be virion proteins by bioinformatics approaches, were confirmed as such, together with the identification of a further 12 novel structural proteins. In the case of T4, 24 of the 39 known virion structural proteins were identified, including the major tail-fibre proteins. This approach has wide-ranging applicability and can be applied to any novel organism whose genome encodes ORFs with few detectable homologies in the public databases.
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Affiliation(s)
- Martha R J Clokie
- Department of Infection, Immunity and Inflammation, Maurice Shock Medical Sciences Building, University of Leicester, Leicester LE1 9HN, UK
| | | | - Pascale Boulanger
- U IBBMC-CNRS UMR 8619, Bât. 430 - Université de Paris-Sud, F-91405 Orsay, Paris, France
| | - Susan E Slade
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Matt Cane
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - James H Scrivens
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Nicholas H Mann
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Heller KJ. Molecular interaction between bacteriophage and the gram-negative cell envelope. Arch Microbiol 1992; 158:235-48. [PMID: 1417416 DOI: 10.1007/bf00245239] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- K J Heller
- Universität Konstanz, Fakultät für Biologie, Federal Republic of Germany
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Roessner CA, Ihler GM. Proteinase sensitivity of bacteriophage lambda tail proteins gpJ and pH in complexes with the lambda receptor. J Bacteriol 1984; 157:165-70. [PMID: 6228546 PMCID: PMC215147 DOI: 10.1128/jb.157.1.165-170.1984] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Previous studies have shown that bacteriophage lambda initially binds to liposomes bearing its receptor protein by the tip of the tail fiber (type 1 complex). It then associates more directly so that the hollow tail tube is in direct contact with the membrane (type 2 complex). DNA can be injected across the lipid bilayer into the liposome from type 2 complexes. We show here that gpJ, the tail fiber protein, becomes more sensitive to proteolytic degradation in type 2 complexes, indicating that the tail fiber does not pass into the liposome and that the tail fiber may undergo a conformational change in type 2 complexes. Another bacteriophage protein, pH, is sensitive to proteolytic degradation in free bacteriophage, type 1 complexes, or type 2 complexes formed with free receptor, but is resistant to proteinases in type 2 complexes formed with liposomes. This finding suggests that pH associates with the membrane. We suggest that this association is part of the mechanism by which a transmembrane hole for DNA entry is formed.
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Roessner CA, Struck DK, Ihler GM. Morphology of complexes formed between bacteriophage lambda and structures containing the lambda receptor. J Bacteriol 1983; 153:1528-34. [PMID: 6219098 PMCID: PMC221805 DOI: 10.1128/jb.153.3.1528-1534.1983] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two types of complexes can be formed between bacteriophage lambda and structures bearing the lambda receptor, either liposomes or rod-shaped particles. Type 1 complexes involve binding between the tip of the lambda tail fiber and the receptor, so that the hollow tail is positioned an average of 17 nm from the surface of the receptor-bearing structures. In type 2 complexes, the hollow tail is in direct contact with the membrane of the liposome or surface of the rod-shaped particle. Type 1 complexes are the precursors for type 2 complexes whose formation is necessary for normal DNA ejection.
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