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Sae-Ueng U, Bunsuwansakul C, Showpanish K, Phironrit N, Thadajarassiri J, Nehls C. Nanomechanical resilience and thermal stability of RSJ2 phage. Sci Rep 2024; 14:19389. [PMID: 39169068 PMCID: PMC11339380 DOI: 10.1038/s41598-024-70056-8] [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: 02/23/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
As the world moves toward a green economy and sustainable agriculture, bacterial viruses or bacteriophages (phages) become attractive biocontrol agents for controlling crop diseases. Effective utilization of phages in farms requires integrated knowledge of crops, pathogens, phages, and surroundings. Phages must encounter environmental fluctuations, including temperature, and must remain infectious for successful bacteria lysis. This work studied a soilborne RSJ2 phage discovered in Thailand, which can eliminate Ralstonia solanacearum, causing bacterial wilt disease in chili. We investigated how phage infectivity and nanomechanics responded to thermal changes. The plaque-based assay showed that the infectivity of the RSJ2 phage was stable within 24-40 °C, an average temperature fluctuation in tropical regions. The structural examination also showed that the phage remained intact. The nanomechanical property of the phage was inspected by the atomic force microscopy-based nanoindentation. The result revealed that the phage stiffness within 24-40 °C was statistically similar (0.05-0.06 N/m). Upon heating at 40 °C for 1, 5, and 10 h and resting at 25 °C, the stiffness of the phage particles increased to 0.09-0.11 N/m (54-83% increase). The stiffness results suggest structural adaptation of the protein subunits as a response to thermal alteration. The study exhibits that the phage structure is highly dynamic and can nanomechanically respond to varying temperatures. The phage stiffness may reveal insight into phage adaptation to environmental factors. Equipped with the knowledge of phage infectivity, structure, and nanomechanics, we can design practical guidelines for effective phage usage in farming and propelling green and safe agriculture.
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Affiliation(s)
- Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Chooseel Bunsuwansakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kittiya Showpanish
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Namthip Phironrit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Jidapa Thadajarassiri
- Department of Mathematics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Christians Nehls
- Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
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2
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Sattar S, Bailie M, Yaqoob A, Khanum S, Fatima K, Altaf AURB, Ahmed I, Shah STA, Munawar J, Zehra QA, Daud S, Arshad A, Imdad K, Javed S, Tariq A, Bostan N, Altermann E. Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential. Sci Rep 2023; 13:10043. [PMID: 37340022 DOI: 10.1038/s41598-023-37176-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.
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Affiliation(s)
- Sadia Sattar
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan.
| | - Marc Bailie
- AgResearch, Palmerston North, 4410, New Zealand
| | - Akasha Yaqoob
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | | | - Kaniz Fatima
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Anees Ur Rehman Bin Altaf
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, 45710, Pakistan
| | - Syed Tahir Abbas Shah
- Functional Genomics Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Javeria Munawar
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Quaratul Ain Zehra
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Sajeela Daud
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Ayesha Arshad
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Kaleem Imdad
- Microbiology and Immunology Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Sundus Javed
- Microbiology and Immunology Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Amira Tariq
- Microbiology and Immunology Lab, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Nazish Bostan
- Molecular Virology Labs, Department of Biosciences, Comsats University Islamabad, Islamabad, 45550, Pakistan
| | - Eric Altermann
- School of Veterinary Science Massey University Centre for Bioparticle Applications, Massey University, Palmerston North, 4472, New Zealand
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3
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Application of a novel phage vB_SalS-LPSTLL for the biological control of Salmonella in foods. Food Res Int 2021; 147:110492. [PMID: 34399488 DOI: 10.1016/j.foodres.2021.110492] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 02/01/2023]
Abstract
Salmonella is one of the most common foodborne pathogens around the world. Phages are envisioned as a new strategy to control foodborne pathogenic bacteria and food safety. A Salmonella specific lytic phage vB_SalS-LPSTLL (LPSTLL) was selected for food applications on the basis of lytic range, lytic efficiency, functional stability and characteristics. Phage LPSTLL was able to lyse 11 Salmonella serotypes, which represents the broadest range reported Salmonella phages, and was able to suppress the growth of Salmonella enterica in liquid culture over nine hours. LPSTLL exhibited rapid reproductive activity with a short latent period and a large burst size in one-step growth experiment. LPSTLL remained active over a pH range of 3.0 to 12.0, and at incubation temperatures up to 60 °C for 60 min, indicating wide applicability for food processing and storage. Significant reductions of viable Salmonella were observed in diverse foods (milk, apple juice, chicken and lettuce) with reductions up to 2.8 log CFU/mL recorded for milk. Sensory evaluation indicated that treatment with phage LPSTLL did not alter the visual or tactile quality of food matrices. Genome analysis of LPSTLL indicated the absence of any virulence or antimicrobial resistance genes. Genomic comparisons suggest phage LPSTLL constitutes a novel member of a new genus, the LPSTLLvirus with the potential for Salmonella biocontrol in the food industry.
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Analysis of a Novel Bacteriophage vB_AchrS_AchV4 Highlights the Diversity of Achromobacter Viruses. Viruses 2021; 13:v13030374. [PMID: 33673419 PMCID: PMC7996906 DOI: 10.3390/v13030374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
Achromobacter spp. are ubiquitous in nature and are increasingly being recognized as emerging nosocomial pathogens. Nevertheless, to date, only 30 complete genome sequences of Achromobacter phages are available in GenBank, and nearly all of those phages were isolated on Achromobacter xylosoxidans. Here, we report the isolation and characterization of bacteriophage vB_AchrS_AchV4. To the best of our knowledge, vB_AchrS_AchV4 is the first virus isolated from Achromobacter spanius. Both vB_AchrS_AchV4 and its host, Achromobacter spanius RL_4, were isolated in Lithuania. VB_AchrS_AchV4 is a siphovirus, since it has an isometric head (64 ± 3.2 nm in diameter) and a non-contractile flexible tail (232 ± 5.4). The genome of vB_AchrS_AchV4 is a linear dsDNA molecule of 59,489 bp with a G+C content of 62.8%. It contains no tRNA genes, yet it includes 82 protein-coding genes, of which 27 have no homologues in phages. Using bioinformatics approaches, 36 vB_AchrS_AchV4 genes were given a putative function. A further four were annotated based on the results of LC-MS/MS. Comparative analyses revealed that vB_AchrS_AchV4 is a singleton siphovirus with no close relatives among known tailed phages. In summary, this work not only describes a novel and unique phage, but also advances our knowledge of genetic diversity and evolution of Achromobacter bacteriophages.
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Isolation and characterization of the novel Pseudomonas stutzeri bacteriophage 8P. Arch Virol 2021; 166:601-606. [PMID: 33392816 DOI: 10.1007/s00705-020-04912-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/23/2020] [Indexed: 10/22/2022]
Abstract
Bacteriophage 8P was isolated with a Pseudomonas stutzeri strain isolated from an oil reservoir as its host bacterium. The phage genome comprises 63,753 base pairs with a G+C content of 64.35. The phage encodes 63 predicted proteins, and 27 of them were functionally assigned. No tRNA genes were found. Comparative genomics analysis showed that 8P displayed some relatedness to F116-like phages (78% identity, 20% query coverage). The genome has very low sequence similarity to the other phage genomes in the GenBank database and Viral Sequence Database. Based on whole-genome analysis and transmission electron microscopy imaging, 8P is proposed to be a member of a new species in the genus Hollowayvirus, family Podoviridae.
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6
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Korf IHE, Kittler S, Bierbrodt A, Mengden R, Rohde C, Rohde M, Kroj A, Lehnherr T, Fruth A, Flieger A, Lehnherr H, Wittmann J. In Vitro Evaluation of a Phage Cocktail Controlling Infections with Escherichia coli. Viruses 2020; 12:v12121470. [PMID: 33352791 PMCID: PMC7768485 DOI: 10.3390/v12121470] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Worldwide, poultry industry suffers from infections caused by avian pathogenic Escherichia coli. Therapeutic failure due to resistant bacteria is of increasing concern and poses a threat to human and animal health. This causes a high demand to find alternatives to fight bacterial infections in animal farming. Bacteriophages are being especially considered for the control of multi-drug resistant bacteria due to their high specificity and lack of serious side effects. Therefore, the study aimed on characterizing phages and composing a phage cocktail suitable for the prevention of infections with E. coli. Six phages were isolated or selected from our collections and characterized individually and in combination with regard to host range, stability, reproduction, and efficacy in vitro. The cocktail consisting of six phages was able to inhibit formation of biofilms by some E. coli strains but not by all. Phage-resistant variants arose when bacterial cells were challenged with a single phage but not when challenged by a combination of four or six phages. Resistant variants arising showed changes in carbon metabolism and/or motility. Genomic comparison of wild type and phage-resistant mutant E28.G28R3 revealed a deletion of several genes putatively involved in phage adsorption and infection.
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Affiliation(s)
- Imke H. E. Korf
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
- Correspondence:
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany;
| | | | - Ruth Mengden
- Food Inspection, Animal Welfare and Veterinary Service of the Land of Bremen, Border Control Post Bremerhaven, Senator-Borttscheller-Straße 8, 27568 Bremerhaven, Germany;
| | - Christine Rohde
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
| | - Andrea Kroj
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Tatiana Lehnherr
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Angelika Fruth
- Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (A.F.); (A.F.)
| | - Antje Flieger
- Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (A.F.); (A.F.)
| | - Hansjörg Lehnherr
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
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7
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Noreika A, Meškys R, Lazutka J, Kaliniene L. Complete genome sequence of Buttiauxella phage vB_ButM_GuL6. Arch Virol 2020; 165:2685-2687. [DOI: 10.1007/s00705-020-04780-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
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8
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Šimoliūnienė M, Truncaitė L, Petrauskaitė E, Zajančkauskaitė A, Meškys R, Skapas M, Kaupinis A, Valius M, Šimoliūnas E. Pantoeaagglomerans-Infecting Bacteriophage vB_PagS_AAS21: A Cold-Adapted Virus Representing a Novel Genus within the Family Siphoviridae. Viruses 2020; 12:E479. [PMID: 32340233 PMCID: PMC7232348 DOI: 10.3390/v12040479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
A novel cold-adapted siphovirus, vB_PagS_AAS21 (AAS21), was isolated in Lithuania using Pantoea agglomerans as the host for phage propagation. AAS21 has an isometric head (~85 nm in diameter) and a non-contractile flexible tail (~174 × 10 nm). With a genome size of 116,649 bp, bacteriophage AAS21 is the largest Pantoea-infecting siphovirus sequenced to date. The genome of AAS21 has a G+C content of 39.0% and contains 213 putative protein-encoding genes and 29 genes for tRNAs. A comparative sequence analysis revealed that 89 AAS21 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 63 AAS21 ORFs were functionally annotated, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. Proteomic analysis led to the experimental identification of 19 virion proteins, including 11 that were predicted by bioinformatics approaches. Based on comparative phylogenetic analysis, AAS21 cannot be assigned to any genus currently recognized by ICTV and may represents a new branch of viruses within the family Siphoviridae.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Emilija Petrauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.P.); (A.Z.); (R.M.)
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9
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Špakova A, Šimoliūnas E, Batiuškaitė R, Pajeda S, Meškys R, Petraitytė-Burneikienė R. Self-Assembly of Tail Tube Protein of Bacteriophage vB_EcoS_NBD2 into Extremely Long Polytubes in E. coli and S. cerevisiae. Viruses 2019; 11:E208. [PMID: 30832262 PMCID: PMC6466441 DOI: 10.3390/v11030208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 01/01/2023] Open
Abstract
Nucleotides, peptides and proteins serve as a scaffold material for self-assembling nanostructures. In this study, the production of siphovirus vB_EcoS_NBD2 (NBD2) recombinant tail tube protein gp39 reached approximately 33% and 27% of the total cell protein level in Escherichia coli and Saccharomyces cerevisiae expression systems, respectively. A simple purification protocol allowed us to produce a recombinant gp39 protein with 85%⁻90% purity. The yield of gp39 was 2.9 ± 0.36 mg/g of wet E. coli cells and 0.85 ± 0.33 mg/g for S. cerevisiae cells. The recombinant gp39 self-assembled into well-ordered tubular structures (polytubes) in vivo in the absence of other phage proteins. The diameter of these structures was the same as the diameter of the tail of phage NBD2 (~12 nm). The length of these structures varied from 0.1 µm to >3.95 µm, which is 23-fold the normal NBD2 tail length. Stability analysis demonstrated that the polytubes could withstand various chemical and physical conditions. These polytubes show the potential to be used as a nanomaterial in various fields of science.
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Affiliation(s)
- Aliona Špakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Eugenijus Šimoliūnas
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Raminta Batiuškaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Simonas Pajeda
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Rolandas Meškys
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Rasa Petraitytė-Burneikienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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Characterization of the Escherichia coli Virulent Myophage ST32. Viruses 2018; 10:v10110616. [PMID: 30405057 PMCID: PMC6266442 DOI: 10.3390/v10110616] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 12/15/2022] Open
Abstract
The virulent phage ST32 that infects the Escherichiacoli strain ST130 was isolated from a wastewater sample in China and analyzed. Morphological observations showed that phage ST32 belongs to the Myoviridae family, as it has an icosahedral capsid and long contractile tail. Host range analysis showed that it exhibits a broad range of hosts including non-pathogenic and pathogenic E. coli strains. Interestingly, phage ST32 had a much larger burst size when amplified at 20 °C as compared to 30 °C or 37 °C. Its double-stranded DNA genome was sequenced and found to contain 53,092 bp with a GC content of 44.14%. Seventy-nine open reading frames (ORFs) were identified and annotated as well as a tRNA-Arg. Only nineteen ORFs were assigned putative functions. A phylogenetic tree using the large terminase subunit revealed a close relatedness with four unclassified Myoviridae phages. A comparative genomic analysis of these phages showed that the Enterobacteria phage phiEcoM-GJ1 is the closest relative to ST32 and shares the same new branch in the phylogenetic tree. Still, these two phages share only 47 of 79 ORFs with more than 90% identity. Phage ST32 has unique characteristics that make it a potential biological control agent under specific conditions.
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11
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Šimoliūnas E, Šimoliūnienė M, Kaliniene L, Zajančkauskaitė A, Skapas M, Meškys R, Kaupinis A, Valius M, Truncaitė L. Pantoea Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine. Viruses 2018; 10:v10110583. [PMID: 30366363 PMCID: PMC6266253 DOI: 10.3390/v10110583] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/12/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
A novel low-temperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using Pantoea agglomerans isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G–C content of 48.8% and contains 99 probable protein encoding genes and one gene for tRNASer. A comparative sequence analysis revealed that 46 out of 99 Vid5 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 33 Vid5 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a cluster of genes possibly involved in the biosynthesis of 7-deazaguanine derivatives was identified. Notably, one of these genes encodes a putative preQ0/preQ1 transporter, which has never been detected in bacteriophages to date. A proteomic analysis led to the experimental identification of 11 virion proteins, including nine that were predicted by bioinformatics approaches. Based on the phylogenetic analysis, Vid5 cannot be assigned to any genus currently recognized by ICTV, and may represent a new one within the family of Siphoviridae.
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Affiliation(s)
- Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
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