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Potapov S, Krasnopeev A, Tikhonova I, Podlesnaya G, Gorshkova A, Belykh O. The Viral Fraction Metatranscriptomes of Lake Baikal. Microorganisms 2022; 10:1937. [PMID: 36296212 PMCID: PMC9611531 DOI: 10.3390/microorganisms10101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the dominance of transcripts of DNA viruses: bacteriophages and algal viruses. We identified transcripts similar to Pithovirus sibericum, a nucleocytoplasmic large DNA virus (NCLDV) isolated from the permafrost region of Eastern Siberia. Among the families detected were RNA viruses assigned to Retroviridae, Metaviridae, Potyviridae, Astroviridae, and Closteroviridae. Using the PHROG, SEED subsystems databases, and the VOGDB, we indicated that the bulk of transcripts belong to the functional replication of viruses. In a comparative unweighted pair group method with arithmetic mean (UPGMA) analysis, the transcripts from Lake Baikal formed a separate cluster included in the clade with transcripts from other freshwater lakes, as well as marine and oceanic waters, while there was no separation based on the trophic state of the water bodies, the size of the plankton fraction, or salinity.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute SB RAS, 3, Ulan-Batorskaya, 664033 Irkutsk, Russia
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2
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Krylov V, Bourkaltseva M, Pleteneva E, Shaburova O, Krylov S, Karaulov A, Zhavoronok S, Svitich O, Zverev V. Phage phiKZ-The First of Giants. Viruses 2021; 13:149. [PMID: 33498475 PMCID: PMC7909554 DOI: 10.3390/v13020149] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
The paper covers the history of the discovery and description of phiKZ, the first known giant bacteriophage active on Pseudomonas aeruginosa. It also describes its unique features, especially the characteristic manner of DNA packing in the head around a cylinder-shaped structure ("inner body"), which probably governs an ordered and tight packaging of the phage genome. Important properties of phiKZ-like phages include a wide range of lytic activity and the blue opalescence of their negative colonies, and provide a background for the search and discovery of new P. aeruginosa giant phages. The importance of the phiKZ species and of other giant phage species in practical phage therapy is noted given their broad use in commercial phage preparations.
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Affiliation(s)
- Victor Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Maria Bourkaltseva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Elena Pleteneva
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Olga Shaburova
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Sergey Krylov
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
| | - Alexander Karaulov
- Department of Clinical Immunology and Allergy, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia;
| | - Sergey Zhavoronok
- Department of Infectious Diseases, Belarusian State Medical University, 220116 Minsk, Belarus;
| | - Oxana Svitich
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Vitaly Zverev
- I.I. Mechnikov Research Institute of Vaccines & Sera, 105064 Moscow, Russia; (M.B.); (E.P.); (O.S.); (S.K.); (O.S.); (V.Z.)
- Faculty of Preventive Medicine, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
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3
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Abstract
Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.
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Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient. Viruses 2020; 12:v12101138. [PMID: 33049935 PMCID: PMC7600146 DOI: 10.3390/v12101138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023] Open
Abstract
Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
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Evseev P, Sykilinda N, Gorshkova A, Kurochkina L, Ziganshin R, Drucker V, Miroshnikov K. Pseudomonas Phage PaBG-A Jumbo Member of an Old Parasite Family. Viruses 2020; 12:E721. [PMID: 32635178 PMCID: PMC7412058 DOI: 10.3390/v12070721] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteriophage PaBG is a jumbo Myoviridae phage isolated from water of Lake Baikal. This phage has limited diffusion ability and thermal stability and infects a narrow range of Pseudomonas aeruginosa strains. Therefore, it is hardly suitable for phage therapy applications. However, the analysis of the genome of PaBG presents a number of insights into the evolutionary history of this phage and jumbo phages in general. We suggest that PaBG represents an ancient group distantly related to all known classified families of phages.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Nina Sykilinda
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia; (A.G.); (V.D.)
| | - Lidia Kurochkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Rustam Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033 Irkutsk, Russia; (A.G.); (V.D.)
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.E.); (N.S.); (R.Z.)
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Imam M, Alrashid B, Patel F, Dowah ASA, Brown N, Millard A, Clokie MRJ, Galyov EE. vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features. Front Microbiol 2019; 10:2772. [PMID: 31849908 PMCID: PMC6892783 DOI: 10.3389/fmicb.2019.02772] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Phages are the most abundant biological entity on Earth. There are many variants in phage virion sizes, morphology, and genome sizes. Large virion sized phages, with genome sizes greater than 200 kbp have been identified and termed as Jumbo phages. These phages exhibit certain characteristics that have not been reported in phages with smaller genomes. In this work, a jumbo phage named MIJ3 (vB_PaeM_MIJ3) that infects Pseudomonas aeruginosa PAO1 was isolated from an equine livery yard in Leicestershire, United Kingdom. The genome and biological characteristics of this phage have been investigated. MIJ3 is a Myovirus with multiple long tail fibers. Assessment of the host range of MIJ3 revealed that it has the ability to infect many clinical isolates of P. aeruginosa. Bioinformatics analysis of the phage genome indicated that MIJ3 is closely related to the Pseudomonas phage, PA5oct. MIJ3 possesses several unusual features that are either rarely present in other phages or have not yet been reported. In particular, MIJ3 encodes a FtsH-like protein, and a putative lysidine synthase, TilS. These two proteins have not been reported in phages. MIJ3 also possesses a split DNA polymerase B with a novel intein. Of particular interest, unlike other jumbo phages infecting Pseudomonas spp., MIJ3 lacks the genetic elements required for the formation of the phage nucleus, which was believed to be conserved across jumbo Pseudomonas phages.
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Affiliation(s)
- Mohammed Imam
- Department of Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,Laboratory Department, University Medical Center, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Bandar Alrashid
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faizal Patel
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Ahmed S A Dowah
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Nathan Brown
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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7
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Drucker VV, Belykh OI, Gorshkova AS, Bondar AA, Sykilinda NN. Autochthonous Bacteriophages in the Microbial Loop Structure of Different Biotopes of Lake Baikal. CONTEMP PROBL ECOL+ 2019. [DOI: 10.1134/s1995425519020045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Day A, Ahn J, Salmond GPC. Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani. Front Microbiol 2018; 9:2169. [PMID: 30258425 PMCID: PMC6143709 DOI: 10.3389/fmicb.2018.02169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022] Open
Abstract
Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya.
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Affiliation(s)
- Andrew Day
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jiyoon Ahn
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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9
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Buttimer C, Born Y, Lucid A, Loessner MJ, Fieseler L, Coffey A. Erwinia amylovora phage vB_EamM_Y3 represents another lineage of hairy Myoviridae. Res Microbiol 2018; 169:505-514. [PMID: 29777834 DOI: 10.1016/j.resmic.2018.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/23/2018] [Indexed: 10/16/2022]
Abstract
To date, a small number of jumbo myoviruses have been reported to possess atypical whisker-like structures along the surface of their contractile tails. Erwinia amylovora phage vB_EamM_Y3 is another example. It possesses a genome of 261,365 kbp with 333 predicted ORFs. Using a combination of BLASTP, Interproscan and HHpred, about 21% of its putative proteins could be assigned functions involved in nucleotide metabolism, DNA replication, virion structure and cell wall degradation. The phage was found to have a signal-arrest-release (SAR) endolysin (Y3_301) possessing a soluble lytic transglycosylase domain. Like other SAR endolysins, inducible expression of Y3_301 caused Escherichia coli lysis, which is dependent on the presence of an N-terminal signal sequence. Phylogenetic analysis showed that its closest relatives are other jumbo phages including Pseudomonas aeruginosa phage PaBG and P. putida phage Lu11, sharing 105 and 87 homologous proteins respectively. Like these phages, Y3 also shares a distant relationship to Ralstonia solanacearum phage ΦRSL1 (sharing 55 homologous proteins). As these phages are unrelated to the Rak2-like group of hairy phages, Y3 along with Lu11 represent a second lineage of hairy myoviruses.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland.
| | - Yannick Born
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland; Agroscope, Research Division Plant Protection, Wädenswil, Switzerland.
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Martin J Loessner
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland.
| | - Lars Fieseler
- Institute of Food, Nutrition, and Health, ETH Zurich, Zürich, Switzerland.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland; APC Microbiome Institute, University College, Cork, Ireland.
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Kurochkina LP, Semenyuk PI, Sykilinda NN, Miroshnikov KA. The unique two-component tail sheath of giant Pseudomonas phage PaBG. Virology 2017; 515:46-51. [PMID: 29268081 DOI: 10.1016/j.virol.2017.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 11/24/2022]
Abstract
Myoviridae bacteriophages have a special contractile tail machine that facilitates high viral infection efficiency. The major component of this machine is a tail sheath that contracts during infection, allowing delivery of viral DNA into the host cell. Tail sheaths of Myoviridae phages are composed of multiple copies of individual proteins. The giant Pseudomonas aeruginosa phage PaBG is notable in its possession of two tail sheath proteins. These tail sheath proteins are encoded by orf 76 and 204, which were cloned and expressed individually and together in Escherichia coli. We demonstrate that only co-expression of both genes results in efficient assembly of thermostable and proteolytically resistant polysheaths composed of gp76 and gp204 with approximately 1:1 stoichiometry. Both gp76 and gp204 have been identified as structural components of the virion particle. We conclude that during PaBG morphogenesis in vivo two proteins, gp76 and gp204, assemble the tail sheath.
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Affiliation(s)
- Lidia P Kurochkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye gory 1/40, Moscow 119992, Russia.
| | - Pavel I Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye gory 1/40, Moscow 119992, Russia
| | - Nina N Sykilinda
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
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11
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Abstract
Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages, and are rarely isolated by conventional methods. These phages are designated “jumbo” owing to their most notable features of a large phage virion and large genome size. However, in addition to these, jumbo phages also exhibit several novel characteristics that have not been observed for phages with smaller genomes, which differentiate jumbo phages in terms of genome organization, virion structure, progeny propagation, and evolution. In this review, we summarize available reports on jumbo phages and discuss the differences between jumbo phages and small-genome phages. We also discuss data suggesting that jumbo phages might have evolved from phages with smaller genomes by acquiring additional functional genes, and that these additional genes reduce the dependence of the jumbo phages on the host bacteria.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
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12
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Pfreundt U, Spungin D, Hou S, Voß B, Berman-Frank I, Hess WR. Genome of a giant bacteriophage from a decaying Trichodesmium bloom. Mar Genomics 2017; 33:21-25. [PMID: 28237778 DOI: 10.1016/j.margen.2017.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 01/31/2017] [Accepted: 02/04/2017] [Indexed: 10/20/2022]
Abstract
De-novo assembly of a metagenomic dataset obtained from a decaying cyanobacterial Trichodesmium bloom from the New Caledonian lagoon resulted in a complete giant phage genome of 257,908bp, obtained independently with multiple assembly tools. Noteworthy, gammaproteobacteria were an abundant fraction in the sequenced samples. Mapping of the raw reads with 99% accuracy to the giant phage genome resulted in an average coverage of 262X. The closest sequenced relatives, albeit still distant, are the Pseudomonas phages PaBG from Lake Baikal and Lu11 isolated from a soil sample from the Philippines. The phage reported here might belong to the same family within the Myoviridae as PaBG and Lu11 and would thus be its first marine member, indicating a more widespread occurrence of this group. We named this phage NCTB (New Caledonia Trichodesmium Bloom) after its origin.
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Affiliation(s)
- Ulrike Pfreundt
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Dina Spungin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Björn Voß
- Computational Biology, Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
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Khawaja KA, Rauf M, Abbas Z, Rehman SU. A virulent phage JHP against Pseudomonas aeruginosa showed infectivity against multiple genera. J Basic Microbiol 2016; 56:1090-1097. [PMID: 27106788 DOI: 10.1002/jobm.201500764] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/09/2016] [Indexed: 01/08/2023]
Abstract
The resistance to antibiotics in clinically important bacteria is one of the major global health concerns. Phage therapy could be one reliable alternative therapeutic strategy to combat these superbugs. In this study, we assessed host range of a novel bacteriophage, JHP, and characterized for its potential use in phage therapy. The bacteriophage demonstrated infectivity over a broad range of genera including multidrug resistant clinical isolates of Pseudomonas aeruginosa, members of family Enterobacteracae, and other important human pathogens. The antibacterial activity was highest at pH 7, and at temperature of 37 °C. The phage lytic activity gradually decreased till 60 °C and showed no activity when temperature was further raised. The bacteriophage could safely be stored at 4 °C or -20 °C. The latent period of the bacteriophage was 25 min and showed a burst size of 433 virions per cell. The size of JHP genome was approximately 30 kb. Family, Siphoviridae was assigned to JHP based on its icosahedral head with non-contractile tail. The diameter of JHP head and tail length was found 115 and 152 nm, respectively. To sum up, the broad spectrum Siphoviridae phage JHP is an ingenious candidate for phage therapy.
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Affiliation(s)
- Komal Ameer Khawaja
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Mahd Rauf
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Zaigham Abbas
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Shafiq Ur Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan.
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14
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Czajkowski R, Ozymko Z, Siwinska J, Ossowicki A, de Jager V, Narajczyk M, Łojkowska E. The complete genome, structural proteome, comparative genomics and phylogenetic analysis of a broad host lytic bacteriophage ϕD3 infecting pectinolytic Dickeya spp. Stand Genomic Sci 2015; 10:68. [PMID: 26405503 PMCID: PMC4581121 DOI: 10.1186/s40793-015-0068-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 09/17/2015] [Indexed: 11/24/2022] Open
Abstract
Plant necrotrophic Dickeya spp. are among the top ten most devastating bacterial plant pathogens able to infect a number of different plant species worldwide including economically important crops. Little is known of the lytic bacteriophages infecting Dickeya spp. A broad host lytic bacteriophage ϕD3 belonging to the family Myoviridae and order Caudovirales has been isolated in our previous study. This report provides detailed information of its annotated genome, structural proteome and phylogenetic relationships with known lytic bacteriophages infecting species of the Enterobacteriaceae family.
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Affiliation(s)
- Robert Czajkowski
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Zofia Ozymko
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Joanna Siwinska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Adam Ossowicki
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Victor de Jager
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Ewa Łojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
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