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Choe J, Kim B, Park MK, Roh E. Biological and Genetic Characterizations of a Novel Lytic ΦFifi106 against Indigenous Erwinia amylovora and Evaluation of the Control of Fire Blight in Apple Plants. BIOLOGY 2023; 12:1060. [PMID: 37626946 PMCID: PMC10452218 DOI: 10.3390/biology12081060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023]
Abstract
Erwinia amylovora is a devastating phytobacterium causing fire blight in the Rosaceae family. In this study, ΦFifi106, isolated from pear orchard soil, was further purified and characterized, and its efficacy for the control of fire blight in apple plants was evaluated. Its genomic analysis revealed that it consisted of 84,405 bp and forty-six functional ORFs, without any genes encoding antibiotic resistance, virulence, and lysogenicity. The phage was classified into the genus Kolesnikvirus of the subfamily Ounavirinae. ΦFifi106 specifically infected indigenous E. amylovora and E. pyrifoliae. The lytic activity of ΦFifi106 was stable under temperature and pH ranges of 4-50 °C and 4-10, as well as the exposure to ultraviolet irradiation for 6 h. ΦFifi106 had a latent period of 20 min and a burst size of 310 ± 30 PFU/infected cell. ΦFifi106 efficiently inhibited E. amylovora YKB 14808 at a multiplicity of infection (MOI) of 0.1 for 16 h. Finally, the pretreatment of ΦFifi106 at an MOI of 1000 efficiently reduced disease incidence to 37.0% and disease severity to 0.4 in M9 apple plants. This study addressed the use of ΦFifi106 as a novel, safe, efficient, and effective alternative to control fire blight in apple plants.
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Affiliation(s)
- Jaein Choe
- School of Food Science and Biotechnology, Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Byeori Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea;
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea;
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2
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Hou Y, Wu Z, Ren L, Chen Y, Zhang YA, Zhou Y. Characterization and application of a lytic jumbo phage ZPAH34 against multidrug-resistant Aeromonas hydrophila. Front Microbiol 2023; 14:1178876. [PMID: 37415809 PMCID: PMC10321303 DOI: 10.3389/fmicb.2023.1178876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/18/2023] [Indexed: 07/08/2023] Open
Abstract
Aeromonas hydrophila is an emerging foodborne pathogen causing human gastroenteritis. Aeromonas species isolated from food such as seafood presented multidrug-resistance (MDR), raising serious concerns regarding food safety and public health. The use of phages to infect bacteria is a defense against drug-resistant pathogens. In this study, phage ZPAH34 isolated from the lake sample exerted lytic activity against MDR A. hydrophila strain ZYAH75 and inhibited the biofilm on different food-contacting surfaces. ZPAH34 has a large dsDNA genome of 234 kb which belongs to a novel jumbo phage. However, its particle size is the smallest of known jumbo phages so far. Based on phylogenetic analysis, ZPAH34 was used to establish a new genus Chaoshanvirus. Biological characterization revealed that ZPAH34 exhibited wide environmental tolerance, and a high rapid adsorb and reproductive capacity. Food biocontrol experiments demonstrated that ZPAH34 reduces the viable count of A. hydrophila on fish fillets (2.31 log) and lettuce (3.28 log) with potential bactericidal effects. This study isolated and characterized jumbo phage ZPAH34 not only enriched the understanding of phage biological entity diversity and evolution because of its minimal virion size with large genome but also was the first usage of jumbo phage in food safety to eliminate A. hydrophila.
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Affiliation(s)
- Yuting Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhihao Wu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Li Ren
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yuan Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yong-An Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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3
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep 2023; 42:112432. [PMID: 37120812 PMCID: PMC10299810 DOI: 10.1016/j.celrep.2023.112432] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023] Open
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas G Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kyle P Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika E Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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4
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy A, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett K, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529968. [PMID: 36865095 PMCID: PMC9980170 DOI: 10.1101/2023.02.24.529968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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5
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Besarab NV, Letarov AV, Kulikov EE, Babenko VV, Belalov IS, Lagonenko AL, Golomidova AK, Evtushenkov AN. Two novel Erwinia amylovora bacteriophages, Loshitsa2 and Micant, isolated in Belarus. Arch Virol 2022; 167:2633-2642. [PMID: 36207555 DOI: 10.1007/s00705-022-05601-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Abstract
The complete genomes of the new Erwinia amylovora bacteriophages Loshitsa2 and Micant are 43,092 bp and 43,028 bp long, respectively, encode 51 putative proteins, and have two tRNA genes. Comparative analysis with representatives of the class Caudoviricetes suggests that bacteriophages Loshitsa2 and Micant are related to LIMElight bacteriophage belonging to the family Autographiviridae and could be proposed to be members of a novel subfamily.
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Affiliation(s)
- Natalya V Besarab
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, Nezavisimisty Ave., 4, 220030, Minsk, Belarus.
| | - Andrey V Letarov
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of microbiology, pr. 60-letiya Oktyabrya 7 bld. 2, 117312, Moscow, Russia
| | - Eugene E Kulikov
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of microbiology, pr. 60-letiya Oktyabrya 7 bld. 2, 117312, Moscow, Russia
| | - Vladislav V Babenko
- GENOMIC Research and Computational Biology Lab, FSCC of Physico-Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Ilya S Belalov
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of microbiology, pr. 60-letiya Oktyabrya 7 bld. 2, 117312, Moscow, Russia
| | - Alexander L Lagonenko
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, Nezavisimisty Ave., 4, 220030, Minsk, Belarus
| | - Alla K Golomidova
- Research Center of Biotechnology of Russian Academy of Sciences, Winogradsky Institute of microbiology, pr. 60-letiya Oktyabrya 7 bld. 2, 117312, Moscow, Russia
| | - Anatoly N Evtushenkov
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, Nezavisimisty Ave., 4, 220030, Minsk, Belarus
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6
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Šimoliūnienė M, Žukauskienė E, Truncaitė L, Cui L, Hutinet G, Kazlauskas D, Kaupinis A, Skapas M, de Crécy-Lagard V, Dedon PC, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA. Int J Mol Sci 2021; 22:7333. [PMID: 34298953 PMCID: PMC8306585 DOI: 10.3390/ijms22147333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 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 gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Emilija Žukauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, 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; (A.K.); (M.V.)
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
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7
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Kim SG, Roh E, Park J, Giri SS, Kwon J, Kim SW, Kang JW, Lee SB, Jung WJ, Lee YM, Cho K, Park SC. The Bacteriophage pEp_SNUABM_08 Is a Novel Singleton Siphovirus with High Host Specificity for Erwinia pyrifoliae. Viruses 2021; 13:1231. [PMID: 34202208 PMCID: PMC8310351 DOI: 10.3390/v13071231] [Citation(s) in RCA: 8] [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: 04/30/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 01/16/2023] Open
Abstract
Species belonging to the genus Erwinia are predominantly plant pathogens. A number of bacteriophages capable of infecting Erwinia have been used for the control of plant diseases such as fire blight. Public repositories provide the complete genome information for such phages, which includes genomes ranging from 30 kb to 350 kb in size. However, limited information is available regarding bacteriophages belonging to the family Siphoviridae. A novel lytic siphophage, pEp_SNUABM_08, which specifically infects Erwinia pyrifoliae, was isolated from the soil of an affected apple orchard in South Korea. A comprehensive genome analysis was performed using the Erwinia-infecting siphophage. The whole genome of pEp_SNUABM_08 comprised 62,784 bp (GC content, 57.24%) with 79 open reading frames. The genomic characteristics confirmed that pEp_SNUABM_08 is a singleton lytic bacteriophage belonging to the family Siphoviridae, and no closely related phages have been reported thus far. Our study not only characterized a unique phage, but also provides insight into the genetic diversity of Erwinia bacteriophages.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (E.R.); (J.P.)
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (E.R.); (J.P.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Jeong Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Young Min Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Kevin Cho
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.S.G.); (J.K.); (S.W.K.); (J.W.K.); (S.B.L.); (W.J.J.); (Y.M.L.); (K.C.)
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Žukauskienė E, Šimoliūnienė M, Truncaitė L, Skapas M, Kaupinis A, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus. Microorganisms 2021; 9:668. [PMID: 33807116 PMCID: PMC8004638 DOI: 10.3390/microorganisms9030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.
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Affiliation(s)
- Emilija Žukauskienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Monika Šimoliūnienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Lidija Truncaitė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (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 Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Eugenijus Šimoliūnas
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
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9
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Kim SG, Lee SB, Giri SS, Kim HJ, Kim SW, Kwon J, Park J, Roh E, Park SC. Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus. Viruses 2020; 12:E1373. [PMID: 33266226 PMCID: PMC7760394 DOI: 10.3390/v12121373] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Hyoun Joong Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
| | - Jungkum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (J.P.); (E.R.)
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea; (J.P.); (E.R.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (S.G.K.); (S.B.L.); (S.S.G.); (H.J.K.); (S.W.K.); (J.K.)
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10
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Whitley KV, Tueller JA, Weber KS. Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations. Int J Mol Sci 2020; 21:ijms21030768. [PMID: 31991576 PMCID: PMC7037382 DOI: 10.3390/ijms21030768] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 12/23/2022] Open
Abstract
Since the completion of the Human Genome Project in 2003, genomic sequencing has become a prominent tool used by diverse disciplines in modern science. In the past 20 years, the cost of genomic sequencing has decreased exponentially, making it affordable and accessible. Bioinformatic and biological studies have produced significant scientific breakthroughs using the wealth of genomic information now available. Alongside the scientific benefit of genomics, companies offer direct-to-consumer genetic testing which provide health, trait, and ancestry information to the public. A key area that must be addressed is education about what conclusions can be made from this genomic information and integrating genomic education with foundational genetic principles already taught in academic settings. The promise of personal genomics providing disease treatment is exciting, but many challenges remain to validate genomic predictions and diagnostic correlations. Ethical and societal concerns must also be addressed regarding how personal genomic information is used. This genomics revolution provides a powerful opportunity to educate students, clinicians, and the public on scientific and ethical issues in a personal way to increase learning. In this review, we discuss the influence of personal genomics in society and focus on the importance and benefits of genomics education in the classroom, clinics, and the public and explore the potential consequences of personal genomic education.
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Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
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Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A. Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A. Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B. Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A. Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L. Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A. Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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Thompson DW, Casjens SR, Sharma R, Grose JH. Genomic comparison of 60 completely sequenced bacteriophages that infect Erwinia and/or Pantoea bacteria. Virology 2019; 535:59-73. [PMID: 31276862 DOI: 10.1016/j.virol.2019.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
Abstract
Erwinia and Pantoea are closely related bacterial plant pathogens in the Gram negative Enterobacteriales order. Sixty tailed bacteriophages capable of infecting these pathogens have been completely sequenced by investigators around the world and are in the current databases, 30 of which were sequenced by our lab. These 60 were compared to 991 other Enterobacteriales bacteriophage genomes and found to be, on average, just over twice the overall average length. These Erwinia and Pantoea phages comprise 20 clusters based on nucleotide and protein sequences. Five clusters contain only phages that infect the Erwinia and Pantoea genera, the other 15 clusters are closely related to bacteriophages that infect other Enterobacteriales; however, within these clusters the Erwinia and Pantoea phages tend to be distinct, suggesting ecological niche may play a diversification role. The failure of many of their encoded proteins to have predicted functions highlights the need for further study of these phages.
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Affiliation(s)
- Daniel W Thompson
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, University of Utah, Salt Lake City, UT, 84112, USA; School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Utah, USA.
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Genome Sequences of Nine Erwinia amylovora Bacteriophages. Microbiol Resour Announc 2018; 7:MRA00944-18. [PMID: 30533701 PMCID: PMC6256631 DOI: 10.1128/mra.00944-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
Erwinia amylovora is a plant pathogen belonging to the Enterobacteriaceae family, a family containing many plant and animal pathogens. Herein, we announce nine genome sequences of E. amylovora bacteriophages isolated from infected apple trees along the Wasatch Front in Utah.
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