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Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
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Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
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2
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da Silva JD, Melo LDR, Santos SB, Kropinski AM, Xisto MF, Dias RS, da Silva Paes I, Vieira MS, Soares JJF, Porcellato D, da Silva Duarte V, de Paula SO. Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage. Appl Microbiol Biotechnol 2023; 107:7231-7250. [PMID: 37741937 PMCID: PMC10638138 DOI: 10.1007/s00253-023-12743-6] [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: 04/03/2023] [Revised: 04/03/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.
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Affiliation(s)
- Jéssica Duarte da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luís D R Melo
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mariana Fonseca Xisto
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Isabela da Silva Paes
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marcella Silva Vieira
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - José Júnior Ferreira Soares
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Vinícius da Silva Duarte
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
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3
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Kallies R, Hu D, Abdulkadir N, Schloter M, Rocha U. Identification of Huge Phages from Wastewater Metagenomes. Viruses 2023; 15:2330. [PMID: 38140571 PMCID: PMC10747093 DOI: 10.3390/v15122330] [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: 10/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.
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Affiliation(s)
- René Kallies
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Die Hu
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Nafi’u Abdulkadir
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Michael Schloter
- Department of Environmental Health, Helmholtz Munich, Ingolstaedter Landstr. 1, D-85758 Neuherberg, Germany;
| | - Ulisses Rocha
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
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4
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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: 0] [Impact Index Per Article: 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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5
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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: 0] [Impact Index Per Article: 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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6
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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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7
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Chen M, Guo HM, Di SS, Zhao Y, Zhou DD, Cao YW, Tian P, Yang ZH, Zhao HY. Stereoselective behaviors and enantiomeric effects of paclobutrazol on microorganisms during Chinese cabbage pickling process. Chirality 2023; 35:376-386. [PMID: 36924145 DOI: 10.1002/chir.23549] [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: 01/06/2023] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Studies on the differences between chiral pesticide enantiomers have caused widespread concern in the last decade. In the current work, the selective behaviors and different biological activities of paclobutrazol enantiomers during Chinese cabbage pickling process were evaluated. Results of degradation kinetics indicated that when paclobutrazol reside in raw material (Chinese cabbage) and was introduced into the pickling process, the degradation rates of the two paclobutrazol enantiomers were significantly different, the half-lives of (2R, 3R)-paclobutrazol (R-paclobutrazol) and (2S, 3S)-paclobutrazol (S-paclobutrazol) were 18.24 and 6.19 d, respectively. Besides, the conversion between the two enantiomers could also be observed, and the conversion rate of R-paclobutrazol to S-paclobutrazol was slower than that of reverse process. In addition, from the analysis of 16S rRNA and ITS sequencing, we inferred that the degradation of paclobutrazol was probably due to the presence of Pseudomonas and Serratia. Moreover, there has a significant difference in biological activity between R-paclobutrazol and S-paclobutrazol and shown an obviously enantiomeric effects on microbial community composition of pickling system. Besides, the analysis of microbial community displayed R-paclobutrazol might inhibit the growth of Erwinia (a sort of plant pathogens). Results from this study served to enhance our understanding of chiral pesticide residues on food safety and the potential risks to human health.
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Affiliation(s)
- Min Chen
- College of Plant Science and Technology, Department of Plant Protection, Huazhong Agriculture University, Wuhan, China
| | - Hao-Ming Guo
- College of Plant Science and Technology, Department of Plant Protection, Huazhong Agriculture University, Wuhan, China
| | - Shan-Shan Di
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.,Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou, P. R. China
| | - Yue Zhao
- College of Plant Science and Technology, Department of Plant Protection, Huazhong Agriculture University, Wuhan, China
| | - Dong-Dong Zhou
- College of Plant Science and Technology, Department of Plant Protection, Huazhong Agriculture University, Wuhan, China
| | - Yi-Wen Cao
- College of Plant Science and Technology, Department of Plant Protection, Huazhong Agriculture University, Wuhan, China
| | - Pei Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.,Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou, P. R. China
| | - Zhong-Hua Yang
- College of Plant Science and Technology, Department of Plant Protection, Huazhong Agriculture University, Wuhan, China
| | - Hui-Yu Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/Key Laboratory of Detection for Pesticide Residues and Control of Zhejiang, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.,Agricultural Ministry Key Laboratory for Pesticide Residue Detection, Hangzhou, P. R. China
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8
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Aylward FO, Moniruzzaman M. Viral Complexity. Biomolecules 2022; 12:biom12081061. [PMID: 36008955 PMCID: PMC9405923 DOI: 10.3390/biom12081061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/18/2022] Open
Abstract
Although traditionally viewed as streamlined and simple, discoveries over the last century have revealed that viruses can exhibit surprisingly complex physical structures, genomic organization, ecological interactions, and evolutionary histories. Viruses can have physical dimensions and genome lengths that exceed many cellular lineages, and their infection strategies can involve a remarkable level of physiological remodeling of their host cells. Virus–virus communication and widespread forms of hyperparasitism have been shown to be common in the virosphere, demonstrating that dynamic ecological interactions often shape their success. And the evolutionary histories of viruses are often fraught with complexities, with chimeric genomes including genes derived from numerous distinct sources or evolved de novo. Here we will discuss many aspects of this viral complexity, with particular emphasis on large DNA viruses, and provide an outlook for future research.
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Affiliation(s)
- Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
- Correspondence:
| | - Mohammad Moniruzzaman
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Coral Gables, FL 33149, USA;
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9
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Park J, Kim B, Song S, Lee YW, Roh E. Isolation of Nine Bacteriophages Shown Effective against Erwinia amylovora in Korea. THE PLANT PATHOLOGY JOURNAL 2022; 38:248-253. [PMID: 35678058 PMCID: PMC9343912 DOI: 10.5423/ppj.nt.11.2021.0172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Erwinia amylovora is a devastating bacterial plant pathogen that infects Rosaceae including apple and pear and causes fire blight. Bacteriophages have been considered as a biological control agent for preventing bacterial infections of plants. In this study, nine bacteriophages (ΦFifi011, ΦFifi044, ΦFifi051, ΦFifi067, ΦFifi106, ΦFifi287, ΦFifi318, ΦFifi450, and ΦFifi451) were isolated from soil and water samples in seven orchards with fire blight in Korea. The genetic diversity of bacteriophage isolates was confirmed through restriction fragment length polymorphism pattern analysis. Host range of the nine phages was tested against 45 E. amylovora strains and 14 E. pyrifoliae strains and nine other bacterial strains. Among the nine phages, ΦFifi044 and ΦFifi451 infected and lysed E. amylovora only. And the remaining seven phages infected both E. amylovora and E. pyrifoliae. The results suggest that the isolated phages were different from each other and effective to control E. amylovora, providing a basis to develop biological agents and utilizing phage cocktails.
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Affiliation(s)
| | | | | | | | - Eunjung Roh
- Corresponding author. Phone) +82-63-238-3284, FAX) +82-63-238-3838, E-mail)
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10
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Zhang B, Sun H, Zhao F, Wang Q, Pan Q, Tong Y, Ren H. Characterization and Genomic Analysis of a Novel Jumbo Bacteriophage vB_StaM_SA1 Infecting Staphylococcus aureus With Two Lysins. Front Microbiol 2022; 13:856473. [PMID: 35572667 PMCID: PMC9096886 DOI: 10.3389/fmicb.2022.856473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The development of new antimicrobial agents is critically needed due to the alarming increase in antibiotic resistance in bacterial pathogens. Phages have been widely considered as effective alternatives to antibiotics. A novel phage vB_StaM_SA1 (hereinafter as SA1) that can infect multiple Staphylococcus strains was isolated from untreated sewage of a pig farm, which belonged to Myoviridae family. At MOI of 0.1, the latent period of phage SA1 was 55 min, and the final titer reached about 109 PFU/mL. The genome of phage SA1 was 260,727 bp, indicating that it can be classified as a jumbo phage. The genome of SA1 had 258 ORFs and a serine tRNA, while only 53 ORFs were annotated with functions. Phage SA1 contained a group of core genes that was characterized by multiple RNA polymerase subunits and also found in phiKZ-related jumbo phages. The phylogenetic tree showed that phage SA1 was a phiKZ-related phage and was closer to jumbo phages compared with Staphylococcus phages with small genome. Three proteins (lys4, lys210, and lys211) were predicted to be associated with lysins, and two proteins with lytic function were verified by recombinant expression and bacterial survival test. Both lys210 and lys211 possessed efficient bactericidal ability, and lys210 could lyse all test strains. The results show that phage SA1 and lys210/lys211 could be potentially used as antibiotic agents to treat Staphylococcus infection.
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Affiliation(s)
- Bingyan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co., Ltd., Qingdao, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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11
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Trifonova TS, Moiseenko AV, Bourkaltseva MV, Shaburova OV, Shaytan AK, Krylov VN, Sokolova OS. [DNA mapping in the capsid of giant bacteriophage phiEL (Caudovirales: Myoviridae: Elvirus) by analytical electron microscopy]. Vopr Virusol 2022; 66:434-441. [PMID: 35019250 DOI: 10.36233/0507-4088-80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Giant phiKZ-like bacteriophages have a unique protein formation inside the capsid, an inner body (IB) with supercoiled DNA molecule wrapped around it. Standard cryo-electron microscopy (cryo-EM) approaches do not allow to distinguish this structure from the surrounding nucleic acid of the phage. We previously developed an analytical approach to visualize protein-DNA complexes on Escherichia coli bacterial cell slices using the chemical element phosphorus as a marker. In the study presented, we adapted this technique for much smaller objects, namely the capsids of phiKZ-like bacteriophages. MATERIAL AND METHODS Following electron microscopy techniques were used in the study: analytical (AEM) (electron energy loss spectroscopy, EELS), and cryo-EM (images of samples subjected to low and high dose of electron irradiation were compared). RESULTS We studied DNA packaging inside the capsids of giant bacteriophages phiEL from the Myoviridae family that infect Pseudomonas aeruginosa. Phosphorus distribution maps were obtained, showing an asymmetrical arrangement of DNA inside the capsid. DISCUSSION We developed and applied an IB imaging technique using a high angle dark-field detector (HAADF) and the STEM-EELS analytical approach. Phosphorus mapping by EELS and cryo-electron microscopy revealed a protein formation as IB within the phage phiEL capsid. The size of IB was estimated using theoretical calculations. CONCLUSION The developed technique can be applied to study the distribution of phosphorus in other DNA- or RNA-containing viruses at relatively low concentrations of the element sought.
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Affiliation(s)
- T S Trifonova
- FSAEI HE «People's Friendship University of Russia», Physical, Mathematical, and Natural Sciences Department; FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - A V Moiseenko
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty; FSBIS «N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences»
| | | | - O V Shaburova
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - A K Shaytan
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
| | - V N Krylov
- FSBRI «I.I. Mechnikov Research Institute of Vaccines and Sera»
| | - O S Sokolova
- FSBEI HE «Lomonosov Moscow State University», Bioengineering Department, Biological Faculty
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12
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Kumar P, Meghvansi MK, Kamboj DV. Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage. Sci Rep 2021; 11:22197. [PMID: 34772986 PMCID: PMC8590004 DOI: 10.1038/s41598-021-01419-8] [Citation(s) in RCA: 3] [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: 01/07/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
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Affiliation(s)
- Prince Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Mukesh K Meghvansi
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - D V Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
- Defence Research Laboratory, Tezpur, Assam, 784001, India.
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13
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The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting Pseudomonas aeruginosa. Microorganisms 2021; 9:microorganisms9102040. [PMID: 34683360 PMCID: PMC8541153 DOI: 10.3390/microorganisms9102040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022] Open
Abstract
The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Many alternatives to antibiotics have been studied, with bacteriophages emerging as the most promising alternatives. Here, we isolated and characterized a novel phage, pPa_SNUABM_DT01, by investigating its morphology, growth, lysis kinetics, and genomic characteristics. Phages have a vigorous capacity to eliminate bacterial cells through bacterial lysis. This capacity is dependent on the multiplicity of infection (MOI), but even at low MOIs, the phage successfully inhibited bacterial regrowth. The phage genome was 265,520 bp in size and comprised 312 putative open reading frames (ORFs). Comparative genome analysis demonstrated that the phage is a novel species in Myoviridae. The nucleotide similarity was moderately high compared with the Pseudomonas virus, Noxifer. However, a phylogenetic analysis and a dot plot indicated that pPa_SNUABM_DT01 is not closely related to the Phikzvirus or Noxifervirus genus but, instead, belongs to a novel one. The genome comparisons also indicate that the phage, pPa_SNUABM_DT01, could be a novel genus.
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14
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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: 1] [Impact Index Per Article: 0.3] [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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15
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Besarab NV, Akhremchuk AE, Zlatohurska MA, Romaniuk LV, Valentovich LN, Tovkach FI, Lagonenko AL, Evtushenkov AN. Isolation and characterization of Hena1 - a novel Erwinia amylovora bacteriophage. FEMS Microbiol Lett 2021; 367:5823740. [PMID: 32319510 DOI: 10.1093/femsle/fnaa070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/20/2020] [Indexed: 01/04/2023] Open
Abstract
Fire blight, caused by plant pathogenic bacterium Erwinia amylovora, is one of the most important diseases of Rosaceae plants. Due to the lack of effective control measures, fire blight infections pose a recurrent threat on agricultural production worldwide. Recently, bacterial viruses, or bacteriophages, have been proposed as environmentally friendly natural antimicrobial agents for fire blight control. Here, we isolated a novel bacteriophage Hena1 with activity against E. amylovora. Further analysis revealed that Hena1 is a narrow-host-range lytic phage belonging to Myoviridae family. Its genome consists of a linear 148,842 bp dsDNA (48.42% GC content) encoding 240 ORFs and 23 tRNA genes. Based on virion structure and genomic composition, Hena1 was classified as a new species of bacteriophage subfamily Vequintavirinae. The comprehensive analysis of Hena1 genome may provide further insights into evolution of bacteriophages infecting plant pathogenic bacteria.
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Affiliation(s)
- Natalya V Besarab
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Artur E Akhremchuk
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Maryna A Zlatohurska
- Zabolotny Institute of Microbiology and Virology of NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Liudmyla V Romaniuk
- Zabolotny Institute of Microbiology and Virology of NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Leonid N Valentovich
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus.,Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Fedor I Tovkach
- Zabolotny Institute of Microbiology and Virology of NAS of Ukraine, D03680 Kyiv, Ukraine
| | - Alexander L Lagonenko
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Anatoly N Evtushenkov
- Department of Molecular Biology, Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
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16
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Chaudhari HV, Inamdar MM, Kondabagil K. Scaling relation between genome length and particle size of viruses provides insights into viral life history. iScience 2021; 24:102452. [PMID: 34113814 PMCID: PMC8169800 DOI: 10.1016/j.isci.2021.102452] [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: 01/18/2021] [Revised: 03/23/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
In terms of genome and particle sizes, viruses exhibit great diversity. With the discovery of several nucleocytoplasmic large DNA viruses (NCLDVs) and jumbo phages, the relationship between particle and genome sizes has emerged as an important criterion for understanding virus evolution. We use allometric scaling of capsid volume with the genome length of different groups of viruses to shed light on its relationship with virus life history. The allometric exponents for icosahedral dsDNA bacteriophages and NCDLVs were found to be 1 and 2, respectively, indicating that with increasing capsid size DNA packaging density remains the same in bacteriophages but decreases for NCLDVs. We argue that the exponents are largely shaped by their entry mechanism and capsid mechanical stability. We further show that these allometric size parameters are also intricately linked to the relative energy costs of translation and replication in viruses and can have further implications on viral life history. Capsid and genome size allometric exponent gives insights into viral life history The allometric exponent of NCLDVs is almost twice that of bacteriophages The exponent is largely shaped by the viral entry mechanism and capsid stability The relaxed genome size constraint allows large viruses to evolve greater autonomy
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Affiliation(s)
- Harshali V Chaudhari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mandar M Inamdar
- Department of Civil Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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17
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Sasaki R, Miyashita S, Ando S, Ito K, Fukuhara T, Takahashi H. Isolation and Characterization of a Novel Jumbo Phage from Leaf Litter Compost and Its Suppressive Effect on Rice Seedling Rot Diseases. Viruses 2021; 13:v13040591. [PMID: 33807245 PMCID: PMC8066314 DOI: 10.3390/v13040591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 11/16/2022] Open
Abstract
Jumbo phages have DNA genomes larger than 200 kbp in large virions composed of an icosahedral head, tail, and other adsorption structures, and they are known to be abundant biological substances in nature. In this study, phages in leaf litter compost were screened for their potential to suppress rice seedling rot disease caused by the bacterium Burkholderia glumae, and a novel phage was identified in a filtrate-enriched suspension of leaf litter compost. The phage particles consisted of a rigid tailed icosahedral head and contained a DNA genome of 227,105 bp. The phage could lyse five strains of B. glumae and six strains of Burkholderia plantarii. The phage was named jumbo Burkholderia phage FLC6. Proteomic tree analysis revealed that phage FLC6 belongs to the same clade as two jumbo Ralstonia phages, namely RSF1 and RSL2, which are members of the genus Chiangmaivirus (family: Myoviridae; order: Caudovirales). Interestingly, FLC6 could also lyse two strains of Ralstonia pseudosolanacearum, the causal agent of bacterial wilt, suggesting that FLC6 has a broad host range that may make it especially advantageous as a bio-control agent for several bacterial diseases in economically important crops. The novel jumbo phage FLC6 may enable leaf litter compost to suppress several bacterial diseases and may itself be useful for controlling plant diseases in crop cultivation.
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Affiliation(s)
- Ryota Sasaki
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Sugihiro Ando
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Kumiko Ito
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8538, Japan;
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai 980-0845, Japan; (R.S.); (S.M.); (S.A.); (K.I.)
- Correspondence: ; Tel.: +81-812-2757-4300
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18
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Lee Y, Son B, Cha Y, Ryu S. Characterization and Genomic Analysis of PALS2, a Novel Staphylococcus Jumbo Bacteriophage. Front Microbiol 2021; 12:622755. [PMID: 33763042 PMCID: PMC7982418 DOI: 10.3389/fmicb.2021.622755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/09/2021] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that can be frequently encountered in clinical and food-processing surroundings. Among the various countermeasures, bacteriophages have been considered to be promising alternatives to antibiotics. In this study, the bacteriophage PALS2 was isolated from bird feces, and the genomic and biological characteristics of this phage were investigated. PALS2 was determined to belong to the Myoviridae family and exhibited extended host inhibition that persisted for up to 24 h with repeated bursts of 12 plaque-forming units/cell. The complete genome of PALS2 measured 268,746 base pairs (bp), indicating that PALS2 could be classified as a jumbo phage. The PALS2 genome contained 279 ORFs and 1 tRNA covering asparagine, and the majority of predicted PALS2 genes encoded hypothetical proteins. Additional genes involved in DNA replication and repair, nucleotide metabolism, and genes encoding multisubunit RNA polymerase were identified in the PALS2 genome, which is a common feature of typical jumbo phages. Comparative genomic analysis indicated that PALS2 is a phiKZ-related virus and is more similar to typical jumbo phages than to staphylococcal phages. Additionally, the effective antimicrobial activities of phage PALS2 suggest its possible use as a biocontrol agent in various clinical and food processing environments.
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Affiliation(s)
- Yoona Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yoyeon Cha
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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19
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Kumar M, Sarma DK, Shubham S, Kumawat M, Verma V, Nina PB, JP D, Kumar S, Singh B, Tiwari RR. Futuristic Non-antibiotic Therapies to Combat Antibiotic Resistance: A Review. Front Microbiol 2021; 12:609459. [PMID: 33574807 PMCID: PMC7870489 DOI: 10.3389/fmicb.2021.609459] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
The looming problem of resistance to antibiotics in microorganisms is a global health concern. The drug-resistant microorganisms originating from anthropogenic sources and commercial livestock farming have posed serious environmental and health challenges. Antibiotic-resistant genes constituting the environmental "resistome" get transferred to human and veterinary pathogens. Hence, deciphering the origin, mechanism and extreme of transfer of these genetic factors into pathogens is extremely important to develop not only the therapeutic interventions to curtail the infections, but also the strategies to avert the menace of microbial drug-resistance. Clinicians, researchers and policymakers should jointly come up to develop the strategies to prevent superfluous exposure of pathogens to antibiotics in non-clinical settings. This article highlights the present scenario of increasing antimicrobial-resistance in pathogenic bacteria and the clinical importance of unconventional or non-antibiotic therapies to thwart the infectious pathogenic microorganisms.
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Affiliation(s)
- Manoj Kumar
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Swasti Shubham
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Manoj Kumawat
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, SGPGIMS, Lucknow, India
| | | | - Devraj JP
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Santosh Kumar
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
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20
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Kumar P, Meghvansi MK, Kamboj DV. Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii. Front Microbiol 2021; 12:644013. [PMID: 33569047 PMCID: PMC7868345 DOI: 10.3389/fmicb.2021.644013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
Citrobacter species often occur in sewage, food, soil, wastewater, and in the intestinal tract of animals and humans. Citrobacter spp. cause urinary tract infections (UTIs) and infantile meningitis in humans. Due to the presence of plasmid-encoded resistance genes, Citrobacter spp. are often resistant to many antibiotics. In this study, Citrobacter virus HCF1, a novel virulent bacteriophage capable of killing Citrobacter amalonaticus and Citrobacter freundii, was isolated from the sewage water. The isolated bacteriophage was characterized with respect to transmission electron microscopy, one-step growth curve, host range, in vitro efficacy, storage stability, and environmental stress tolerance. The one-step growth curve analysis revealed that the latent period of HCF1 was 30 min and the estimated burst size was 121 plaque-forming units (PFU) per bacterial cell. Host range testing indicated that the HCF1 was specific to the Citrobacter genus. In vitro efficacy assay in the effluent of an anaerobic biodigester showed that the HCF1 completely eliminated the host within 4 and 5 h at MOI:100 and MOI:10, respectively, thereby indicating its potential for combating C. amalonaticus infections. The isolated bacteriophage is considerably stable and tolerant to environmental stress. Furthermore, the complete genome of HCF1 was sequenced using Oxford Nanopore sequencing and the data were subjected to detailed bioinformatic analyses. NCBI-BLASTn analysis revealed that the HCF1 genome had a query coverage of 15-21% and a maximum similarity of 77.27-78.49% with 11 bacteriophages of the Drexlerviridae family. Detailed bioinformatic analysis of the genome profile suggests that HCF1 is a novel T1svirus belonging to the Tempevirinae subfamily of the Drexlerviridae family.
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Affiliation(s)
| | | | - Dev V. Kamboj
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
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21
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Kassa T. Bacteriophages Against Pathogenic Bacteria and Possibilities for Future Application in Africa. Infect Drug Resist 2021; 14:17-31. [PMID: 33442273 PMCID: PMC7797301 DOI: 10.2147/idr.s284331] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/24/2020] [Indexed: 12/21/2022] Open
Abstract
Bacteriophages (phages) are viruses that infect prokaryotic cells. Phages exist in many shapes and sizes with the majority of them being less than 100 nm in size. Essentially, the majority of phages identified are double-stranded DNA virions with the remaining few being found as RNA or single-stranded DNA viruses. These biological entities are plentiful in different environments, especially in wet sources. Treatment of a bacterial disease using phage application has been documented in the pre-antibiotic era. Different studies have emerging to value the efficacy of phage use in in-vitro and in-vivo based systems against specific bacterial agents of humans, animals or plant diseases. The process represents a natural and nontoxic framework to avert infections due to pathogenic and antimicrobial-resistant bacteria. Most of the published researches on the usefulness of phages against disease-causing bacteria (including antimicrobial-resistant strains) of humans, animals or plants are emerging from the US and European countries with very few studies available from Africa. This review assesses published articles in the area of phage applications against pathogenic or antimicrobial-resistant bacteria from experimental, clinical and field settings. The knowledge and skill of isolating lytic phages against bacteria can be operational for its simpler procedures and economic benefit. Future studies in Africa and other emerging countries may consider in-house phage preparations for effective control and eradication of pathogenic and multidrug resistant bacteria of humans, animals and plants.
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Affiliation(s)
- Tesfaye Kassa
- School of Medical Laboratory Science, Institute of Health, Jimma University, Jimma, Ethiopia
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22
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Kwon J, Kim SG, Kim HJ, Giri SS, Kim SW, Lee SB, Park SC. Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04. Viruses 2020; 13:v13010027. [PMID: 33375688 PMCID: PMC7823757 DOI: 10.3390/v13010027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/11/2022] Open
Abstract
The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.
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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: 14] [Impact Index Per Article: 3.5] [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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24
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Atzinger A, Lawrence JG. Selection for ancient periodic motifs that do not impart DNA bending. PLoS Genet 2020; 16:e1009042. [PMID: 33022009 PMCID: PMC7537859 DOI: 10.1371/journal.pgen.1009042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/11/2020] [Indexed: 11/19/2022] Open
Abstract
A ~10-11 bp periodicity in dinucleotides imparting DNA bending, with shorter periods found in organisms with positively-supercoiled DNA and longer periods found in organisms with negatively-supercoiled DNA, was previously suggested to assist in DNA compaction. However, when measured with more robust methods, variation in the observed periods between organisms with different growth temperatures is not consistent with that hypothesis. We demonstrate that dinucleotide periodicity does not arise solely by mutational biases but is under selection. We found variation between genomes in both the period and the suite of dinucleotides that are periodic. Whereas organisms with similar growth temperatures have highly variable periods, differences in periods increase with phylogenetic distance between organisms. In addition, while the suites of dinucleotides under selection for periodicity become more dissimilar among more distantly-related organisms, there is a core set of dinucleotides that are strongly periodic among genomes in all domains of life. Notably, this core set of periodic motifs are not involved in DNA bending. These data indicate that dinucleotide periodicity is an ancient genomic architecture which may play a role in shaping the evolution of genes and genomes.
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Affiliation(s)
- Aletheia Atzinger
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, United States of America
| | - Jeffrey G Lawrence
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, United States of America
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25
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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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26
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Zrelovs N, Dislers A, Kazaks A. Novel Erwinia persicina Infecting Phage Midgardsormr38 Within the Context of Temperate Erwinia Phages. Front Microbiol 2020; 11:1245. [PMID: 32636815 PMCID: PMC7317114 DOI: 10.3389/fmicb.2020.01245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/15/2020] [Indexed: 11/17/2022] Open
Abstract
Prophages or prophage remnants are found in chromosomes of many bacterial strains and might increase the environmental fitness and/or virulence of their hosts. Up to this date, complete genome sequences of only seven temperate bacteriophages infecting bacteria from genus Erwinia, comprising of mostly phytopathogenic bacteria, are available publicly. No attempts to analyze the global diversity of temperate Erwinia phages and establish relationships between cultured temperate Erwinia phages and prophages were yet made. In this study, we have isolated, sequenced, and described novel Erwinia persicina infecting bacteriophage "Midgardsormr38" and placed it in the context of previously described Erwinia sp. temperate phages and putative prophages derived from chromosomes of publicly available complete genomes of Erwinia sp. to broaden and investigate diversity of temperate Erwinia phages based on their genomic contents. The study revealed more than 50 prophage or prophage remnant regions in the genomes of different Erwinia species. At least 5 of them seemed to be intact and might represent novel inducible Erwinia phages. Given the enormous bacteriophage diversity, attempts to establish evolutionary relationships between temperate Erwinia phages revealed at least five different clusters of temperate phages sharing higher degree of similarity.
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Affiliation(s)
- Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Andris Dislers
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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27
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Wagemans J, Tsonos J, Holtappels D, Fortuna K, Hernalsteens JP, De Greve H, Estrozi LF, Bacia-Verloop M, Moriscot C, Noben JP, Schoehn G, Lavigne R. Structural Analysis of Jumbo Coliphage phAPEC6. Int J Mol Sci 2020; 21:ijms21093119. [PMID: 32354127 PMCID: PMC7247149 DOI: 10.3390/ijms21093119] [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: 04/16/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of Escherichia coli virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.
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Affiliation(s)
- Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Jessica Tsonos
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Department of Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium;
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
| | - Dominique Holtappels
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | - Kiandro Fortuna
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
| | | | - Henri De Greve
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
- VIB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium
| | - Leandro F. Estrozi
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Maria Bacia-Verloop
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
| | - Christine Moriscot
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, Integrated Structural Biology Grenoble (ISBG), F-38042 Grenoble, France;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Agoralaan D, 3590 Hasselt, Belgium;
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France; (L.F.E.); (M.B.-V.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21—box 2462, 3001 Leuven, Belgium; (J.W.); (J.T.); (D.H.); (K.F.)
- Correspondence: (G.S.); (R.L.); Tel.: +33-4-5742-8568 (G.S.); +32-16-3795-24 (R.L.)
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28
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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: 26] [Impact Index Per Article: 6.5] [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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29
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Knecht LE, Veljkovic M, Fieseler L. Diversity and Function of Phage Encoded Depolymerases. Front Microbiol 2020; 10:2949. [PMID: 31998258 PMCID: PMC6966330 DOI: 10.3389/fmicb.2019.02949] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages of the Podoviridae family often exhibit so-called depolymerases as structural components of the virion. These enzymes appear as tail spike proteins (TSPs). After specific binding to capsular polysaccharides (CPS), exopolysaccharides (EPS) or lipopolysaccharide (LPS) of the host bacteria, polysaccharide-repeating units are specifically cleaved. Finally, the phage reaches the last barrier, the cell wall, injects its DNA, and infects the cell. Recently, similar enzymes from bacteriophages of the Ackermannviridae, Myoviridae, and Siphoviridae families were also described. In this mini-review the diversity and function of phage encoded CPS-, EPS-, and LPS-degrading depolymerases is summarized. The function of the enzymes is described in terms of substrate specificity and applications in biotechnology.
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Affiliation(s)
- Leandra E Knecht
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Marjan Veljkovic
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
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