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Zrelovs N, Jansons J, Kazaka T, Kazaks A, Dislers A. Three Phages One Host: Isolation and Characterization of Pantoea agglomerans Phages from a Grasshopper Specimen. Int J Mol Sci 2023; 24:ijms24031820. [PMID: 36768143 PMCID: PMC9915841 DOI: 10.3390/ijms24031820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
The bacterial genus Pantoea comprises species found in a variety of different environmental sources. Pantoea spp. are often recovered from plant material and are capable of both benefitting the plants and acting like phytopathogens. Some species of Pantoea (including P. agglomerans) are considered opportunistic human pathogens capable of causing various infections in immunocompromised subjects. In this study, a strain of P. agglomerans (identified by 16S rRNA gene sequencing) was isolated from a dead specimen of an unidentified Latvian grasshopper species. The retrieved strain of P. agglomerans was then used as a host for the potential retrieval of phages from the same source material. After rounds of plaque purification and propagation, three high-titer lysates corresponding to putatively distinct phages were acquired. Transmission electron microscopy revealed that one of the phages was a myophage with an unusual morphology, while the two others were typical podophages. Whole-genome sequencing (WGS) was performed for each of these isolated phages. Genome de novo assembly and subsequent functional annotation confirmed that three different strictly lytic phages were isolated. Elaborate genomic characterization of the acquired phages was performed to elucidate their place within the so-far-uncovered phage diversity.
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Akmal M, Nishiki I, Zrelovs N, Yoshida T. Complete genome sequence of a novel lytic bacteriophage, PLG-II, specific for Lactococcus garvieae serotype II strains that are pathogenic to fish. Arch Virol 2022; 167:2331-2335. [PMID: 35972540 DOI: 10.1007/s00705-022-05568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/05/2022] [Indexed: 11/02/2022]
Abstract
A novel lytic siphophage, PLG-II, which is specific for Lactococcus garvieae serotype II strains that are pathogenic to fish, was isolated from seawater samples collected from Miyazaki Prefecture, Japan. Whole-genome sequencing showed that the PLG-II genome is a 32,271-bp double-stranded DNA molecule, with an average GC content of 37.74%. It contains 69 open reading frames (ORFs), 43 of which currently have no reliable functional annotation for their product, as well as a single tRNA. Comparative genomics analysis suggests that phage PLG-II might represent a novel species in the genus Uwajimavirus.
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Affiliation(s)
- Muhammad Akmal
- Faculty of Agriculture, University of Miyazaki, Gauken Kibanadai Nishi 1-1, Miyazaki, 889-2192, Japan. .,Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.
| | - Issei Nishiki
- Faculty of Agriculture, University of Miyazaki, Gauken Kibanadai Nishi 1-1, Miyazaki, 889-2192, Japan
| | - Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, Riga, 1067, Latvia
| | - Terutoyo Yoshida
- Faculty of Agriculture, University of Miyazaki, Gauken Kibanadai Nishi 1-1, Miyazaki, 889-2192, Japan
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Korniienko N, Kharina A, Zrelovs N, Jindřichová B, Moravec T, Budzanivska I, Burketová L, Kalachova T. Isolation and Characterization of Two Lytic Phages Efficient Against Phytopathogenic Bacteria From Pseudomonas and Xanthomonas Genera. Front Microbiol 2022; 13:853593. [PMID: 35547140 PMCID: PMC9083414 DOI: 10.3389/fmicb.2022.853593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas syringae is a bacterial pathogen that causes yield losses in various economically important plant species. At the same time, P. syringae pv. tomato (Pst) is one of the best-studied bacterial phytopathogens and a popular model organism. In this study, we report on the isolation of two phages from the market-bought pepper fruit showing symptoms of bacterial speck. These Pseudomonas phages were named Eir4 and Eisa9 and characterized using traditional microbiological methods and whole-genome sequencing followed by various bioinformatics approaches. Both of the isolated phages were capable only of the lytic life cycle and were efficient against several pathovars from Pseudomonas and Xanthomonas genera. With the combination of transmission electron microscopy (TEM) virion morphology inspection and comparative genomics analyses, both of the phages were classified as members of the Autographiviridae family with different degrees of novelty within the known phage diversity. Eir4, but not Eisa9, phage application significantly decreased the propagation of Pst in the leaf tissues of Arabidopsis thaliana plants. The biological properties of Eir4 phage allow us to propose it as a potential biocontrol agent for use in the prevention of Pst-associated bacterioses and also as a model organism for the future research of mechanisms of phage-host interactions in different plant systems.
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Affiliation(s)
- Nataliia Korniienko
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Educational and Scientific Center (ESC) “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Alla Kharina
- Educational and Scientific Center (ESC) “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Rīga, Latvia
| | - Barbora Jindřichová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Tomaš Moravec
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Iryna Budzanivska
- Educational and Scientific Center (ESC) “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Lenka Burketová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Tetiana Kalachova
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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Cernooka E, Rumnieks J, Zrelovs N, Tars K, Kazaks A. Diversity of the lysozyme fold: structure of the catalytic domain from an unusual endolysin encoded by phage Enc34. Sci Rep 2022; 12:5005. [PMID: 35322067 PMCID: PMC8943055 DOI: 10.1038/s41598-022-08765-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/10/2022] [Indexed: 12/02/2022] Open
Abstract
Endolysins are bacteriophage-encoded peptidoglycan-degrading enzymes with potential applications for treatment of multidrug-resistant bacterial infections. Hafnia phage Enc34 encodes an unusual endolysin with an N-terminal enzymatically active domain and a C-terminal transmembrane domain. The catalytic domain of the endolysin belongs to the conserved protein family PHA02564 which has no recognizable sequence similarity to other known endolysin types. Turbidity reduction assays indicate that the Enc34 enzyme is active against peptidoglycan from a variety of Gram-negative bacteria including the opportunistic pathogen Pseudomonas aeruginosa PAO1. The crystal structure of the catalytic domain of the Enc34 endolysin shows a distinctive all-helical architecture that distantly resembles the α-lobe of the lysozyme fold. Conserved catalytically important residues suggest a shared evolutionary history between the Enc34 endolysin and GH73 and GH23 family glycoside hydrolases and propose a molecular signature for substrate cleavage for a large group of peptidoglycan-degrading enzymes.
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Affiliation(s)
- Elina Cernooka
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia
| | - Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia.,Faculty of Biology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia.
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Zrelovs N, Resevica G, Kalnciema I, Niedra H, Lācis G, Bartulsons T, Moročko-Bičevska I, Stalažs A, Drevinska K, Zeltins A, Balke I. First Report of Blackcurrant-Associated Rhabdovirus in Blackcurrants in Latvia. Plant Dis 2022; 106:1078. [PMID: 34491100 DOI: 10.1094/pdis-06-21-1288-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- N Zrelovs
- Bioinformatics Core Facility, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - G Resevica
- Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - I Kalnciema
- Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - H Niedra
- Molecular and Functional Genomics Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - G Lācis
- Unit of Genetics and Breeding, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Dobele, LV-3701, Latvia
| | - T Bartulsons
- Unit of Genetics and Breeding, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Dobele, LV-3701, Latvia
| | - I Moročko-Bičevska
- Unit of Plant Pathology and Entomology, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Dobele, LV-3701, Latvia
| | - A Stalažs
- Unit of Plant Pathology and Entomology, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Dobele, LV-3701, Latvia
| | - K Drevinska
- Unit of Plant Pathology and Entomology, Institute of Horticulture, Latvia University of Life Sciences and Technologies, Dobele, LV-3701, Latvia
| | - A Zeltins
- Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - I Balke
- Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
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Zrelovs N, Lamsters K, Karuss J, Krievans M, Dislers A, Kazaks A. PVJ1 Is Not the First Tailed Temperate Phage Infecting Bacteria from Genus Psychrobacillus. Comment on Liu et al. Isolation and Characterization of the First Temperate Virus Infecting Psychrobacillus from Marine Sediments. Viruses 2022, 14, 108. Viruses 2022; 14:v14030495. [PMID: 35336902 PMCID: PMC8951557 DOI: 10.3390/v14030495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia;
| | - Kristaps Lamsters
- Polar Research Center, Faculty of Geography and Earth Sciences, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (K.L.); (J.K.); (M.K.)
| | - Janis Karuss
- Polar Research Center, Faculty of Geography and Earth Sciences, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (K.L.); (J.K.); (M.K.)
| | - Maris Krievans
- Polar Research Center, Faculty of Geography and Earth Sciences, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (K.L.); (J.K.); (M.K.)
| | - Andris Dislers
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia;
- Correspondence: (A.D.); (A.K.)
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia;
- Correspondence: (A.D.); (A.K.)
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7
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Zrelovs N, Dislers A, Kazaks A. Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth. Microorganisms 2021; 9:1540. [PMID: 34361975 PMCID: PMC8306868 DOI: 10.3390/microorganisms9071540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 12/04/2022] Open
Abstract
While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome annotation elaborated on herein revealed that the genome of Nocturne116 is a 25,554 bp long dsDNA molecule with 10 bp long 3' cos overhangs and a GC content of 37.99%, comprising 52 predicted open reading frames. The complete nucleotide sequence of phage Nocturne116 genome is dissimilar to any of the already sequenced phages, save for a distant link with Lactococcus phage Q54. Functions for only 15/52 of Nocturne116 gene products could be reliably predicted using contemporary comparative genomics approaches, while 22 of its gene products do not yet have any homologous entries in the public biological sequence repositories. Despite the public availability of nearly 350 elucidated Lactococcus phage complete genomes as of now, Nocturne116 firmly stands out as a sole representative of novel phage genus.
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Affiliation(s)
| | - Andris Dislers
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia;
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, LV-1067 Riga, Latvia;
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8
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Zrelovs N, Ustinova M, Silamikelis I, Birzniece L, Megnis K, Rovite V, Freimane L, Silamikele L, Ansone L, Pjalkovskis J, Fridmanis D, Vilne B, Priedite M, Caica A, Gavars M, Perminov D, Storozenko J, Savicka O, Dimina E, Dumpis U, Klovins J. First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity. Front Med (Lausanne) 2021; 8:626000. [PMID: 33889583 PMCID: PMC8055824 DOI: 10.3389/fmed.2021.626000] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/16/2021] [Indexed: 12/19/2022] Open
Abstract
Remaining a major healthcare concern with nearly 29 million confirmed cases worldwide at the time of writing, novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 920 thousand deaths since its outbreak in China, December 2019. First case of a person testing positive for SARS-CoV-2 infection within the territory of the Republic of Latvia was registered on 2nd of March 2020, 9 days prior to the pandemic declaration by WHO. Since then, more than 277,000 tests were carried out confirming a total of 1,464 cases of coronavirus disease 2019 (COVID-19) in the country as of 12th of September 2020. Rapidly reacting to the spread of the infection, an ongoing sequencing campaign was started mid-March in collaboration with the local testing laboratories, with an ultimate goal in sequencing as much local viral isolates as possible, resulting in first full-length SARS-CoV-2 isolate genome sequences from the Baltics region being made publicly available in early April. With 133 viral isolates representing ~9.1% of the total COVID-19 cases during the "first coronavirus wave" in the country (early March, 2020-mid-September, 2020) being completely sequenced as of today, here, we provide a first report on the genetic diversity of Latvian SARS-CoV-2 isolates.
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Affiliation(s)
- Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Monta Ustinova
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Liga Birzniece
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Lauma Freimane
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | | | | | - Dmitry Perminov
- E. Gulbja Laboratorija, Ltd, Riga, Latvia
- Faculty of Biology, University of Latvia, Riga, Latvia
| | - Jelena Storozenko
- Riga Stradins University, Riga, Latvia
- Laboratory Service, Latvian Centre of Infectious Diseases Laboratory, National Microbiology Reference Laboratory, Molecular Biology and Virology Department, Riga East University Hospital, Riga, Latvia
| | - Oksana Savicka
- Riga Stradins University, Riga, Latvia
- Laboratory Service, Latvian Centre of Infectious Diseases Laboratory, National Microbiology Reference Laboratory, Molecular Biology and Virology Department, Riga East University Hospital, Riga, Latvia
| | - Elina Dimina
- Infectious Diseases Surveillance and Immunization Division, Infectious Diseases Risk Analysis and Prevention Department, The Centre for Disease Prevention and Control (CDPC) of Latvia, Riga, Latvia
| | - Uga Dumpis
- Faculty of Medicine, University of Latvia, Riga, Latvia
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Zrelovs N, Kurbatska V, Rudevica Z, Leonchiks A, Fridmanis D. Sorting out the Superbugs: Potential of Sortase A Inhibitors among Other Antimicrobial Strategies to Tackle the Problem of Antibiotic Resistance. Antibiotics (Basel) 2021; 10:164. [PMID: 33562778 PMCID: PMC7916047 DOI: 10.3390/antibiotics10020164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/22/2022] Open
Abstract
Rapid spread of antibiotic resistance throughout the kingdom bacteria is inevitably bringing humanity towards the "post-antibiotic" era. The emergence of so-called "superbugs"-pathogen strains that develop resistance to multiple conventional antibiotics-is urging researchers around the globe to work on the development or perfecting of alternative means of tackling the pathogenic bacteria infections. Although various conceptually different approaches are being considered, each comes with its advantages and drawbacks. While drug-resistant pathogens are undoubtedly represented by both Gram(+) and Gram(-) bacteria, possible target spectrum across the proposed alternative approaches of tackling them is variable. Numerous anti-virulence strategies aimed at reducing the pathogenicity of target bacteria rather than eliminating them are being considered among such alternative approaches. Sortase A (SrtA) is a membrane-associated cysteine protease that catalyzes a cell wall sorting reaction by which surface proteins, including virulence factors, are anchored to the bacterial cell wall of Gram(+) bacteria. Although SrtA inhibition seems perspective among the Gram-positive pathogen-targeted antivirulence strategies, it still remains less popular than other alternatives. A decrease in virulence due to inactivation of SrtA activity has been extensively studied in Staphylococcus aureus, but it has also been demonstrated in other Gram(+) species. In this manuscript, results of past studies on the discovery of novel SrtA inhibitory compounds and evaluation of their potency were summarized and commented on. Here, we discussed the rationale behind the inhibition of SrtA, raised some concerns on the comparability of the results from different studies, and touched upon the possible resistance mechanisms as a response to implementation of such therapy in practice. The goal of this article is to encourage further studies of SrtA inhibitory compounds.
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Affiliation(s)
| | | | | | | | - Davids Fridmanis
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, LV-1067 Riga, Latvia; (N.Z.); (V.K.); (Z.R.); (A.L.)
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Zrelovs N, Dislers A, Kazaks A. Corrigendum: Motley Crew: Overview of the Currently Available Phage Diversity. Front Microbiol 2021; 11:626744. [PMID: 33488568 PMCID: PMC7816127 DOI: 10.3389/fmicb.2020.626744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/18/2020] [Indexed: 12/04/2022] Open
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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Abstract
The first complete genome that was sequenced at the beginning of the sequencing era was that of a phage, since then researchers throughout the world have been steadily describing and publishing genomes from a wide array of phages, uncovering the secrets of the most abundant and diverse biological entities known to man. Currently, we are experiencing an unprecedented rate of novel bacteriophage discovery, which can be seen from the fact that the amount of complete bacteriophage genome entries in public sequence repositories has more than doubled in the past 3 years and is steadily growing without showing any sign of slowing down. The amount of publicly available phage genome-related data can be overwhelming and has been summarized in literature before but quickly becomes out of date. Thus, the aim of this paper is to briefly outline currently available phage diversity data for public acknowledgment that could possibly encourage and stimulate future “depth” studies of particular groups of phages or their gene products.
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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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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Zrelovs N, Cernooka E, Dislers A, Kazaks A. Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87. Arch Virol 2019; 165:737-741. [PMID: 31875246 DOI: 10.1007/s00705-019-04516-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/04/2019] [Indexed: 10/25/2022]
Abstract
The novel bacterial virus Mimir87, infecting the salt-tolerant bacterium Virgibacillus halotolerans, was isolated from worker honey bees. Mimir87 has an elongated head and a long non-contractile tail consistent with members of the Siphoviridae phage family. The phage genome comprises 48,016 base pairs and encodes 68 predicted proteins, to 34 of which a function could be assigned from homology analysis. The phage encodes two metabolism-related transporter proteins previously not observed in bacteriophage genomes. Mimir87 displays some relatedness to several Bacillus and Paenibacillus viruses; however, the overall sequence dissimilarity suggests Mimir87 to be a representative of a new phage genus.
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Affiliation(s)
- Nikita Zrelovs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV-1067, Latvia
| | - Elina Cernooka
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV-1067, Latvia
| | - Andris Dislers
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV-1067, Latvia
| | - Andris Kazaks
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, LV-1067, Latvia.
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