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Zlatohurska M, Gorb T, Romaniuk L, Shenderovska N, Faidiuk Y, Zhuminska G, Hubar Y, Hubar O, Kropinski AM, Kushkina A, Tovkach F. Broad-host-range lytic Erwinia phage Key with exopolysaccharide degrading activity. Virus Res 2023; 329:199088. [PMID: 36907559 DOI: 10.1016/j.virusres.2023.199088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/18/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
In this study, the genome of the lytic broad-host-range phage Key infecting Erwinia amylovora, Erwinia horticola, and Pantoea agglomerans strains was characterized. Key phage has a 115,651 bp long double-stranded DNA genome with the G + C ratio of 39.03%, encoding 182 proteins and 27 tRNA genes. The majority (69%) of predicted coding sequences (CDSs) encode proteins with unknown functions. The protein products of 57 annotated genes were found to have probable functions in nucleotide metabolism, DNA replication, recombination, repair, and packaging, virion morphogenesis, phage-host interaction and lysis. Furthermore, the product of gene 141 shared amino acid sequence similarity and conserved domain architecture with the exopolysaccharide (EPS) degrading proteins of Erwinia and Pantoea infecting phages as well as bacterial EPS biosynthesis proteins. Due to the genome synteny and similarity to the proteins of T5-related phages, phage Key, together with its closest relative, Pantoea phage AAS21, was suggested to represent a novel genus within the Demerecviridae family, for which we tentatively propose the name "Keyvirus".
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Affiliation(s)
- Maryna Zlatohurska
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Tetiana Gorb
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Liudmyla Romaniuk
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Natalia Shenderovska
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine; Biotechnology products development lab, Scientific Center, Pharmaceutical Corporation YURiA-PHARM, Kyiv 03151, Ukraine
| | - Yuliia Faidiuk
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine; Educational and Scientific Center "Institute of Biology and Medicine", Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine; Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw 53-114, Poland
| | - Ganna Zhuminska
- Department of Microbiology, Virology and Biotechnology, Biological Faculty, Odesa National Mechnykov University, Odesa 65058, Ukraine
| | - Yuliia Hubar
- Preclinical and Clinical Trials Department, Pharmaceutical Corporation YURiA-PHARM, Kyiv 03151, Ukraine
| | - Oleksandr Hubar
- Biotechnology products development lab, Scientific Center, Pharmaceutical Corporation YURiA-PHARM, Kyiv 03151, Ukraine
| | - Andrew M Kropinski
- Departments of Food Science; and, Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alla Kushkina
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
| | - Fedor Tovkach
- Department of Bacteriophage Molecular Genetics, D. K. Zabolotny Institute of Microbiology and Virology, the National Academy of Sciences (NAS) of Ukraine, Kyiv 03143, Ukraine
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Abstract
During the course of evolution, viruses have learned to take advantage of the natural resources of their hosts for their own benefit. Due to their small dimension and limited size of genomes, bacteriophages have optimized the exploitation of bacterial host factors to increase the efficiency of DNA replication and hence to produce vast progeny. The Bacillus subtilis phage φ29 genome consists of a linear double-stranded DNA molecule that is duplicated by means of a protein-primed mode of DNA replication. Its genome has been shown to be topologically constrained at the size of the bacterial nucleoid and, as to avoid generation of positive supercoiling ahead of the replication forks, the bacterial DNA gyrase is used by the phage. In addition, the B. subtilis actin-like MreB cytoskeleton plays a crucial role in the organization of φ29 DNA replication machinery in peripheral helix-like structures. Thus, in the absence of an intact MreB cytoskeleton, φ29 DNA replication is severely impaired. Importantly, MreB interacts directly with the phage membrane protein p16.7, responsible for attaching φ29 DNA at the cell membrane. Moreover, the φ29-encoded protein p56 inhibits host uracil-DNA glycosylase activity and has been proposed to be a defense mechanism developed by the phage to prevent the action of the base excision repair pathway if uracil residues arise in replicative intermediates. All of them constitute incoming examples on how viruses have profited from the cellular machinery of their hosts.
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Serrano-Heras G, Bravo A, Salas M. Phage phi29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase. Proc Natl Acad Sci U S A 2008; 105:19044-9. [PMID: 18845683 PMCID: PMC2565649 DOI: 10.1073/pnas.0808797105] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Indexed: 01/08/2023] Open
Abstract
Protein p56 encoded by the Bacillus subtilis phage phi29 inhibits host uracil-DNA glycosylase (UDG) activity. In previous studies, we suggested that this inhibition is likely a defense mechanism developed by phage phi29 to prevent the action of UDG if uracilation occurs in DNA either from deamination of cytosine or the incorporation of dUMP during viral DNA replication. In this work, we analyzed the ability of phi29 DNA polymerase to insert dUMP into DNA. Primer extension analysis showed that viral DNA polymerase incorporates dU opposite dA with a catalytic efficiency only 2-fold lower than that for dT. Using the phi29 DNA amplification system, we found that phi29 DNA polymerase is also able to carry out the extension of the dA:dUMP pair and replicate past uracil. Additionally, UDG and apurinic-apyrimidinic endonuclease treatment of viral DNA isolated from phi29-infected cells revealed that uracil residues arise in phi29 DNA during replication, probably as a result of misincorporation of dUMP by the phi29 DNA polymerase. On the other hand, the action of UDG on uracil-containing phi29 DNA impaired in vitro viral DNA replication, which was prevented by the presence of protein p56. Furthermore, transfection activity of uracil-containing phi29 DNA was significantly higher in cells that constitutively synthesized p56 than in cells lacking this protein. Thus, our data support a model in which protein p56 ensures an efficient viral DNA replication, preventing the deleterious effect caused by UDG when it eliminates uracil residues present in the phi29 genome.
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Affiliation(s)
- Gemma Serrano-Heras
- Instituto de Biología Molecular “Eladio Viñuela,” Centro de Biología Molecular “Severo Ochoa,” Consejo Superior de Investigaciones Científicas-Universidad Autónoma, Nicolás Cabrera 1, Canto Blanco, 28049 Madrid, Spain; and
| | - Alicia Bravo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Margarita Salas
- Instituto de Biología Molecular “Eladio Viñuela,” Centro de Biología Molecular “Severo Ochoa,” Consejo Superior de Investigaciones Científicas-Universidad Autónoma, Nicolás Cabrera 1, Canto Blanco, 28049 Madrid, Spain; and
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Wang J, Jiang Y, Vincent M, Sun Y, Yu H, Wang J, Bao Q, Kong H, Hu S. Complete genome sequence of bacteriophage T5. Virology 2005; 332:45-65. [PMID: 15661140 DOI: 10.1016/j.virol.2004.10.049] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Revised: 09/07/2004] [Accepted: 10/25/2004] [Indexed: 11/22/2022]
Abstract
The 121,752-bp genome sequence of bacteriophage T5 was determined; the linear, double-stranded DNA is nicked in one of the strands and has large direct terminal repeats of 10,139 bp (8.3%) at both ends. The genome structure is consistently arranged according to its lytic life cycle. Of the 168 potential open reading frames (ORFs), 61 were annotated; these annotated ORFs are mainly enzymes involved in phage DNA replication, repair, and nucleotide metabolism. At least five endonucleases that believed to help inducing nicks in T5 genomic DNA, and a DNA ligase gene was found to be split into two separate ORFs. Analysis of T5 early promoters suggests a probable motif AAA{3, 4 T}nTTGCTT{17, 18 n}TATAATA{12, 13 W}{10 R} for strong promoters that may strengthen the step modification of host RNA polymerase, and thus control transcription of phage DNA. The distinct protein domain profile and a mosaic genome structure suggest an origin from the common genetic pool.
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Affiliation(s)
- Jianbin Wang
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China
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Kaliman AV. Identification of the bacteriophage T5 dUTPase by protein sequence comparisons. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1996; 6:347-50. [PMID: 8988373 DOI: 10.3109/10425179609047573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
It is shown by protein sequence comparisons that a 148 amino acid open reading frame (ORF 148) located at 67% of the bacteriophage T5 genome encodes a protein with strong similarity to known dUTPases. This protein contains five characteristic amino acid sequence motifs that are common to the dUTPase gene family. A similarity in size and high degree of sequence identity strongly suggest that the protein encoded by the ORF 148 of bacteriophage T5 is dUTPase.
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Affiliation(s)
- A V Kaliman
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia.
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