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Evseev PV, Tarakanov RI, Vo HTN, Suzina NE, Vasilyeva AA, Ignatov AN, Miroshnikov KA, Dzhalilov FSU. Characterisation of New Foxunavirus Phage Murka with the Potential of Xanthomonas campestris pv. campestris Control. Viruses 2024; 16:198. [PMID: 38399973 PMCID: PMC10892653 DOI: 10.3390/v16020198] [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: 10/21/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Phages of phytopathogenic bacteria are considered to be promising agents for the biological control of bacterial diseases in plants. This paper reports on the isolation and characterisation of a new Xanthomonas campestris pv. campestris phage, Murka. Phage morphology and basic kinetic characteristics of the infection were determined, and a phylogenomic analysis was performed. The phage was able to lyse a reasonably broad range (64%, 9 of the 14 of the Xanthomonas campestris pv. campestris strains used in the study) of circulating strains of the cabbage black rot pathogen. This lytic myovirus has a DNA genome of 44,044 bp and contains 83 predicted genes. Taxonomically, it belongs to the genus Foxunavirus. This bacteriophage is promising for use as a possible means of biological control of cabbage black rot.
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Affiliation(s)
- Peter V. Evseev
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.A.V.); (A.N.I.); (K.A.M.); (F.S.-U.D.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Rashit I. Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.A.V.); (A.N.I.); (K.A.M.); (F.S.-U.D.)
| | - Ha T. N. Vo
- Faculty of Agronomy, Nong Lam University, Quarter 6, Thu Duc District, Ho Chi Minh City 721400, Vietnam;
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, Prosp. Nauki, 5, 142290 Pushchino, Russia;
| | - Anna A. Vasilyeva
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.A.V.); (A.N.I.); (K.A.M.); (F.S.-U.D.)
| | - Alexander N. Ignatov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.A.V.); (A.N.I.); (K.A.M.); (F.S.-U.D.)
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
| | - Konstantin A. Miroshnikov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.A.V.); (A.N.I.); (K.A.M.); (F.S.-U.D.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.A.V.); (A.N.I.); (K.A.M.); (F.S.-U.D.)
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Letarov AV. Bacterial Virus Forcing of Bacterial O-Antigen Shields: Lessons from Coliphages. Int J Mol Sci 2023; 24:17390. [PMID: 38139217 PMCID: PMC10743462 DOI: 10.3390/ijms242417390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In most Gram-negative bacteria, outer membrane (OM) lipopolysaccharide (LPS) molecules carry long polysaccharide chains known as the O antigens or O polysaccharides (OPS). The OPS structure varies highly from strain to strain, with more than 188 O serotypes described in E. coli. Although many bacteriophages recognize OPS as their primary receptors, these molecules can also screen OM proteins and other OM surface receptors from direct interaction with phage receptor-binding proteins (RBP). In this review, I analyze the body of evidence indicating that most of the E. coli OPS types robustly shield cells completely, preventing phage access to the OM surface. This shield not only blocks virulent phages but also restricts the acquisition of prophages. The available data suggest that OPS-mediated OM shielding is not merely one of many mechanisms of bacterial resistance to phages. Rather, it is an omnipresent factor significantly affecting the ecology, phage-host co-evolution and other related processes in E. coli and probably in many other species of Gram-negative bacteria. The phages, in turn, evolved multiple mechanisms to break through the OPS layer. These mechanisms rely on the phage RBPs recognizing the OPS or on using alternative receptors exposed above the OPS layer. The data allow one to forward the interpretation that, regardless of the type of receptors used, primary receptor recognition is always followed by the generation of a mechanical force driving the phage tail through the OPS layer. This force may be created by molecular motors of enzymatically active tail spikes or by virion structural re-arrangements at the moment of infection.
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Affiliation(s)
- Andrey V Letarov
- Winogradsky Institute of Micrbiology, Research Center Fundamentals of Biotechnology RAS, pr. 60-letiya Oktyabrya 7 bld. 2, Moscow 117312, Russia
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3
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Kowalczyk A, Kaczyńska N, Motyka-Pomagruk A, Śledź W, Łojkowska E, Kaczyński Z. The chemical structure of the O-antigen and enterobacterial common antigen of Pectobacterium brasiliense NCPPB 4609 TS. Carbohydr Res 2023; 534:108983. [PMID: 37980861 DOI: 10.1016/j.carres.2023.108983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/21/2023]
Abstract
Pectobacterium brasiliense is a widely distributed phytopathogenic bacterium that causes diseases such as soft rot and blackleg, leading to significant yield losses in potatoes as well as other vegetables and ornamental plants. Lipopolysaccharide (LPS) is an important virulence factor that plays an essential role in colonisation of plant tissues and overcoming the host defence mechanisms. The O-polysaccharide from the LPS of P. brasiliense strain NCPPB 4609TS (=CFBP 6617TS = LMG 21371TS = IFB5390) was structurally characterised using spectroscopic techniques and chemical methods. The analyses revealed that the polysaccharide repeating unit consists of Gal, GlcN and an unusual 3-amino-3,6-dideoxyglucose decorated with (R)-3-hydroxybutyric acid according to the structure shown below: In addition, another polysaccharide was isolated from bacterial cells, analysis of which led to the identification of an enterobacterial common antigen, containing N-acetyl-d-glucosamine, N-acetyl-d-mannosaminouronic acid, and 4-acetamido-4,6-dideoxy-d-galactose.
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Affiliation(s)
- Agnieszka Kowalczyk
- Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308, Gdansk, Poland.
| | - Natalia Kaczyńska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdansk, Poland; Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdansk, Poland
| | - Agata Motyka-Pomagruk
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdansk, Poland; Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdansk, Poland
| | - Wojciech Śledź
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdansk, Poland; Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdansk, Poland
| | - Ewa Łojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307, Gdansk, Poland; Research & Development Laboratory, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 20 Podwale Przedmiejskie, 80-824, Gdansk, Poland
| | - Zbigniew Kaczyński
- Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308, Gdansk, Poland
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Sokolova D, Smolarska A, Bartnik P, Rabalski L, Kosinski M, Narajczyk M, Krzyżanowska DM, Rajewska M, Mruk I, Czaplewska P, Jafra S, Czajkowski R. Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta. Sci Rep 2023; 13:7534. [PMID: 37160956 PMCID: PMC10169776 DOI: 10.1038/s41598-023-34803-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/07/2023] [Indexed: 05/11/2023] Open
Abstract
Lytic bacteriophages able to infect and kill Dickeya spp. can be readily isolated from virtually all Dickeya spp. containing environments, yet little is known about the selective pressure those viruses exert on their hosts. Two spontaneous D. solani IPO 2222 mutants (0.8% of all obtained mutants), DsR34 and DsR207, resistant to infection caused by lytic phage vB_Dsol_D5 (ΦD5) were identified in this study that expressed a reduced ability to macerate potato tuber tissues compared to the wild-type, phage-susceptible D. solani IPO 2222 strain. Genome sequencing revealed that genes encoding: secretion protein HlyD (in mutant DsR34) and elongation factor Tu (EF-Tu) (in mutant DsR207) were altered in these strains. These mutations impacted the DsR34 and DsR207 proteomes. Features essential for the ecological success of these mutants in a plant environment, including their ability to use various carbon and nitrogen sources, production of plant cell wall degrading enzymes, ability to form biofilms, siderophore production, swimming and swarming motility and virulence in planta were assessed. Compared to the wild-type strain, D. solani IPO 2222, mutants DsR34 and DsR207 had a reduced ability to macerate chicory leaves and to colonize and cause symptoms in growing potato plants.
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Affiliation(s)
- Daryna Sokolova
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, 148 Academika Zabolotnoho St., Kyiv, 03143, Ukraine
| | - Anna Smolarska
- Department of Cancer Biology, Institute of Biology, Warsaw, University of Life Sciences (SGGW), J. Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Przemysław Bartnik
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Dorota M Krzyżanowska
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama, 58, 80-307, Gdansk, Poland
| | - Inez Mruk
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307, Gdansk, Poland
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307, Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama, 58, 80-307, Gdansk, Poland
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, A. Abrahama 58, 80-307, Gdansk, Poland.
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5
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Szulta S, Kowalczyk A, Czerwicka-Pach M, Motyka-Pomagruk A, Śledź W, Kaczyńska N, Łojkowska E, Kaczyński Z. The chemical structure of the O-polysaccharide isolated from the lipopolysaccharide of Pectobacterium brasiliense IFB5527, a phytopathogenic bacterium of high economic importance. Carbohydr Res 2023; 527:108806. [PMID: 37058948 DOI: 10.1016/j.carres.2023.108806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 04/08/2023]
Abstract
Pectobacterium brasiliense is a widespread plant pathogenic bacterium classified to the Pectobacteriaceae family, which causes significant economic losses because of the developed soft rot and blackleg symptoms on potatoes and a wide spectrum of crops, vegetables, and ornamentals. One of the key virulence factors is a lipopolysaccharide due to its involvement in efficient colonisation of plant tissues and overcoming the host defence mechanisms. Thus, we structurally characterised the O-polysaccharide from the LPS of P. brasiliense strain IFB5527 (HAFL05) using chemical methods followed by GLC and GLC-MS as well as 1D and 2D NMR spectroscopy. The analyses revealed that the polysaccharide repeating unit consists of Fuc, Glc, GlcN and an unusual N-formylated 6-deoxy amino sugar, Qui3NFo, and has the structure shown below.
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Affiliation(s)
- Sylwia Szulta
- Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. J. Hallera 107, 80-416, Gdansk, Poland
| | - Agnieszka Kowalczyk
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | | | - Agata Motyka-Pomagruk
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama, 58, 80-307, Gdansk, Poland
| | - Wojciech Śledź
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama, 58, 80-307, Gdansk, Poland
| | - Natalia Kaczyńska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama, 58, 80-307, Gdansk, Poland
| | - Ewa Łojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, Abrahama, 58, 80-307, Gdansk, Poland
| | - Zbigniew Kaczyński
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland.
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6
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Klumpp J, Dunne M, Loessner MJ. A perfect fit: Bacteriophage receptor-binding proteins for diagnostic and therapeutic applications. Curr Opin Microbiol 2023; 71:102240. [PMID: 36446275 DOI: 10.1016/j.mib.2022.102240] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022]
Abstract
Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to specifically infect and kill bacteria, phages and their encoded endolysins and receptor-binding proteins (RBPs) have enormous potential for development into precision antimicrobials for treatment of bacterial infections and microbial disbalances; or as biocontrol agents to tackle bacterial contaminations during various biotechnological processes. The extraordinary binding specificity of phages and RBPs can be exploited in various areas of bacterial diagnostics and monitoring, from food production to health care. We review and describe the distinctive features of phage RBPs, explain why they are attractive candidates for use as therapeutics and in diagnostics, discuss recent applications using RBPs, and finally provide our perspective on how synthetic technology and artificial intelligence-driven approaches will revolutionize how we use these tools in the future.
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Affiliation(s)
- Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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7
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Kowalczyk A, Babińska-Wensierska W, Lojkowska E, Kaczyński Z. The structure of O-polysaccharide isolated from the type strain of Pectobacterium versatile CFBP6051 T containing an erwiniose - higher branched monosaccharide. Carbohydr Res 2023; 524:108743. [PMID: 36669445 DOI: 10.1016/j.carres.2023.108743] [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: 12/08/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Utilizing sugar, methylation, and absolute configurations analyses as well as NMR spectroscopy, the chemical repeating unit of the O-specific polysaccharide of Pectobacteriumversatile CFBP6051T was identified as: The polymer contains residues of an unusual, higher-branched monosaccharide, named erwiniose (3,6,8-trideoxy-4-C-(R-1-hydroxyethyl)-d-gulo-octose). Comparison of the P. versatile CFBP6051T O-polysaccharide with those isolated from strains of other Pectobacterium species indicated high differentiation in their structures within this genus.
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Affiliation(s)
- Agnieszka Kowalczyk
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308, Gdansk, Poland
| | - Weronika Babińska-Wensierska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, 58 Abrahama, 80-307, Gdansk, Poland
| | - Ewa Lojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk & Medical University of Gdansk, 58 Abrahama, 80-307, Gdansk, Poland
| | - Zbigniew Kaczyński
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308, Gdansk, Poland.
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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] [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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Kowalczyk A, Szpakowska N, Babinska W, Motyka-Pomagruk A, Sledz W, Lojkowska E, Kaczyński Z. The structure of an abequose - containing O-polysaccharide isolated from Pectobacterium aquaticum IFB5637. Carbohydr Res 2022; 522:108696. [DOI: 10.1016/j.carres.2022.108696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
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10
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Pectobacterium versatile Bacteriophage Possum: A Complex Polysaccharide-Deacetylating Tail Fiber as a Tool for Host Recognition in Pectobacterial Schitoviridae. Int J Mol Sci 2022; 23:ijms231911043. [PMID: 36232343 PMCID: PMC9569702 DOI: 10.3390/ijms231911043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Novel, closely related phages Possum and Horatius infect Pectobacterium versatile, a phytopathogen causing soft rot in potatoes and other essential plants. Their properties and genomic composition define them as N4-like bacteriophages of the genus Cbunavirus, a part of a recently formed family Schitoviridae. It is proposed that the adsorption apparatus of these phages consists of tail fibers connected to the virion through an adapter protein. Tail fibers possess an enzymatic domain. Phage Possum uses it to deacetylate O-polysaccharide on the surface of the host strain to provide viral attachment. Such an infection mechanism is supposed to be common for all Cbunavirus phages and this feature should be considered when designing cocktails for phage control of soft rot.
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Tarakanov RI, Lukianova AA, Evseev PV, Pilik RI, Tokmakova AD, Kulikov EE, Toshchakov SV, Ignatov AN, Dzhalilov FSU, Miroshnikov KA. Ayka, a Novel Curtobacterium Bacteriophage, Provides Protection against Soybean Bacterial Wilt and Tan Spot. Int J Mol Sci 2022; 23:ijms231810913. [PMID: 36142829 PMCID: PMC9502298 DOI: 10.3390/ijms231810913] [Citation(s) in RCA: 7] [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: 08/25/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
Diseases caused by the Gram-positive bacterium Curtobacteriumflaccumfaciens pv. flaccumfaciens (Cff) inflict substantial economic losses in soybean cultivation. Use of specific bacterial viruses (bacteriophages) for treatment of seeds and plants to prevent the development of bacterial infections is a promising approach for bioprotection in agriculture. Phage control has been successfully tested for a number of staple crops. However, this approach has never been applied to treat bacterial diseases of legumes caused by Cff, and no specific bacteriophages have been known to date. This paper presents detailed characteristics of the first lytic bacteriophage infecting this pathogen. Phage Ayka, related to φ29-like (Salasmaviridae) viruses, but representing a new subfamily, was shown to control the development of bacterial wilt and tan spot in vitro and in greenhouse plants.
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Affiliation(s)
- Rashit I. Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia
| | - Anna A. Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Roksana I. Pilik
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
| | - Anna D. Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, National Research University, Institutskiy Per, 9, Dolgoprudny, 141701 Moscow, Russia
| | - Eugene E. Kulikov
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, National Research University, Institutskiy Per, 9, Dolgoprudny, 141701 Moscow, Russia
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prosp. 60-Letia Oktyabrya, 7-2, 117312 Moscow, Russia
| | - Stepan V. Toshchakov
- Center for Genome Research, National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123098 Moscow, Russia
| | - Alexander N. Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia
- Correspondence: (F.S.-U.D.); (K.A.M.); Tel.: +7-(495)-335-5588 (K.A.M.)
| | - Konstantin A. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Correspondence: (F.S.-U.D.); (K.A.M.); Tel.: +7-(495)-335-5588 (K.A.M.)
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12
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Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection. Sci Rep 2022; 12:10725. [PMID: 35750797 PMCID: PMC9232599 DOI: 10.1038/s41598-022-14956-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Resistance to bacteriophage infections protects bacteria in phage-replete environments, enabling them to survive and multiply in the presence of their viral predators. However, such resistance may confer costs for strains, reducing their ecological fitness as expressed as competitiveness for resources or virulence or both. There is limited knowledge about such costs paid by phage-resistant plant pathogenic bacteria in their natural habitats. This study analyzed the costs of phage resistance paid by the phytopathogenic pectinolytic bacterium Dickeya solani both in vitro and in potato (Solanum tuberosum L.) plants. Thirteen Tn5 mutants of D. solani IPO 2222 were identified that exhibited resistance to infection by lytic bacteriophage vB_Dsol_D5 (ΦD5). The genes disrupted in these mutants encoded proteins involved in the synthesis of bacterial envelope components (viz. LPS, EPS and capsule). Although phage resistance did not affect most of the phenotypes of ΦD5-resistant D. solani such as growth rate, production of effectors, swimming and swarming motility, use of various carbon and nitrogen sources and biofilm formation evaluated in vitro, all phage resistant mutants were significantly compromised in their ability to survive on leaf surfaces as well as to grow within and cause disease symptoms in potato plants.
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13
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Bujak K, Decewicz P, Kitowicz M, Radlinska M. Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. Viruses 2022; 14:1016. [PMID: 35632757 PMCID: PMC9145550 DOI: 10.3390/v14051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host-pathogen pairs were derived from the same sampling location-the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4-25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.
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Affiliation(s)
| | | | | | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.B.); (P.D.); (M.K.)
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14
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Tarakanov RI, Lukianova AA, Evseev PV, Toshchakov SV, Kulikov EE, Ignatov AN, Miroshnikov KA, Dzhalilov FSU. Bacteriophage Control of Pseudomonas savastanoi pv. glycinea in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:938. [PMID: 35406917 PMCID: PMC9003214 DOI: 10.3390/plants11070938] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Bacterial viruses (bacteriophages) have been considered as potential agents for the biological control of bacterial phytopathogens due to their safety and host specificity. Pseudomonas savastanoi pv. glycinea (Psg) is a causative agent of the bacterial spotting of soybean (Glycine max Willd). The harm caused by this bacterium to crop production and the development of antibiotic resistance in Psg and other pathogenic microorganisms has led to the pursuit of alternative management strategies. In this study, three Psg-specific lytic bacteriophages were isolated from soybean field soil in geographically distant regions of Russia, and their potential for protective action on plants was assessed. Sequencing of phage genomes has revealed their close relatedness and attribution to the genus Ghunavirus, subfamily Studiervirinae, family Autographiviridae. Extensive testing of the biological properties of P421, the representative of the isolated phage group, has demonstrated a relatively broad host range covering closely related Pseudomonas species and stability over wide temperature (4-40 °C) and pH (pH 4-7) ranges, as well as stability under ultraviolet irradiation for 30 min. Application of the phages to prevent, and treat, Psg infection of soybean plants confirms that they are promising as biocontrol agents.
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Affiliation(s)
- Rashit I. Tarakanov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (A.A.L.); (A.N.I.)
| | - Anna A. Lukianova
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (A.A.L.); (A.N.I.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Stepan V. Toshchakov
- Center for Genome Research, National Research Center “Kurchatov Institute”, Kurchatov Sq. 1, 123098 Moscow, Russia;
| | - Eugene E. Kulikov
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prosp. 60-letia Oktyabrya 7-2, 117312 Moscow, Russia;
| | - Alexander N. Ignatov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (A.A.L.); (A.N.I.)
- Agrobiotechnology Department, Agrarian and Technological Institute, Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya Str. 6, 117198 Moscow, Russia
| | - Konstantin A. Miroshnikov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (A.A.L.); (A.N.I.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (A.A.L.); (A.N.I.)
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15
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Ossowska K, Motyka-Pomagruk A, Kaczyńska N, Kowalczyk A, Sledz W, Lojkowska E, Kaczyński Z. Heterogenicity within the LPS Structure in Relation to the Chosen Genomic and Physiological Features of the Plant Pathogen Pectobacterium parmentieri. Int J Mol Sci 2022; 23:ijms23042077. [PMID: 35216191 PMCID: PMC8879369 DOI: 10.3390/ijms23042077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022] Open
Abstract
Pectobacterium parmentieri is a pectinolytic plant pathogenic bacterium causing high economic losses of cultivated plants. The highly devastating potential of this phytopathogen results from the efficient production of plant cell wall-degrading enzymes, i.e., pectinases, cellulases and proteases, in addition to the impact of accessory virulence factors such as motility, siderophores, biofilm and lipopolysaccharide (LPS). LPS belongs to pathogen-associated molecular patterns (PAMPs) and plays an important role in plant colonization and interaction with the defense systems of the host. Therefore, we decided to investigate the heterogeneity of O-polysaccharides (OPS) of LPS of different strains of P. parmentieri, in search of an association between the selected genomic and phenotypic features of the strains that share an identical structure of the OPS molecule. In the current study, OPS were isolated from the LPS of two P. parmentieri strains obtained either in Finland in the 1980s (SCC3193) or in Poland in 2013 (IFB5432). The purified polysaccharides were analyzed by utilizing 1D and 2D NMR spectroscopy (1H, DQF-COSY, TOCSY, ROESY, HSQC, HSQC-TOCSY and HMBC) in addition to chemical methods. Sugar and methylation analyses of native polysaccharides, absolute configuration assignment of constituent monosaccharides and NMR spectroscopy data revealed that these two P. parmentieri strains isolated in different countries possess the same structure of OPS with a very rare residue of 5,7-diamino-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (pseudaminic acid) substituted in the position C-8: →3)-β-d-Galf-(1→3)-α-d-Galp-(1→8)-β-Pse4Ac5Ac7Ac-(2→6)-α-d-Glcp-(1→6)-β-d-Glcp-(1→. The previous study indicated that three other P. parmentieri strains, namely IFB5427, IFB5408 and IFB5443, exhibit a different OPS molecule than SCC3193 and IFB5432. The conducted biodiversity-oriented assays revealed that the P. parmentieri IFB5427 and IFB5408 strains possessing the same OPS structure yielded the highest genome-wide similarity, according to average nucleotide identity analyses, in addition to the greatest ability to macerate chicory tissue among the studied P. parmentieri strains. The current research demonstrated a novel OPS structure, characteristic of at least two P. parmentieri strains (SCC3193 and IFB5432), and discussed the observed heterogenicity in the OPS of P. parmentieri in a broad genomic and phenotype-related context.
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Affiliation(s)
- Karolina Ossowska
- Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308 Gdansk, Poland; (K.O.); (A.K.)
| | - Agata Motyka-Pomagruk
- Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (A.M.-P.); (N.K.); (W.S.); (E.L.)
| | - Natalia Kaczyńska
- Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (A.M.-P.); (N.K.); (W.S.); (E.L.)
| | - Agnieszka Kowalczyk
- Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308 Gdansk, Poland; (K.O.); (A.K.)
| | - Wojciech Sledz
- Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (A.M.-P.); (N.K.); (W.S.); (E.L.)
| | - Ewa Lojkowska
- Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (A.M.-P.); (N.K.); (W.S.); (E.L.)
| | - Zbigniew Kaczyński
- Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308 Gdansk, Poland; (K.O.); (A.K.)
- Correspondence:
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16
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Novel Acinetobacter baumannii Bacteriophage Aristophanes Encoding Structural Polysaccharide Deacetylase. Viruses 2021; 13:v13091688. [PMID: 34578271 PMCID: PMC8471582 DOI: 10.3390/v13091688] [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: 07/27/2021] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 02/01/2023] Open
Abstract
Acinetobacter baumannii appears to be one of the most crucial nosocomial pathogens. A possible component of antimicrobial therapy for infections caused by extremely drug-resistant A. baumannii strains may be specific lytic bacteriophages or phage-derived enzymes. In the present study, we observe the biological features, genomic organization, and phage–host interaction strategy of novel virulent bacteriophage Aristophanes isolated on A. baumannii strain having K26 capsular polysaccharide structure. According to phylogenetic analysis phage Aristophanes can be classified as a representative of a new distinct genus of the subfamily Beijerinckvirinae of the family Autographiviridae. This is the first reported A. baumannii phage carrying tailspike deacetylase, which caused O-acetylation of one of the K26 sugar residues.
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17
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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18
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Bartnik P, Jafra S, Narajczyk M, Czaplewska P, Czajkowski R. Pectobacterium parmentieri SCC 3193 Mutants with Altered Synthesis of Cell Surface Polysaccharides Are Resistant to N4-Like Lytic Bacteriophage ϕA38 (vB_Ppp_A38) but Express Decreased Virulence in Potato ( Solanum tuberosum L.) Plants. Int J Mol Sci 2021; 22:7346. [PMID: 34298965 PMCID: PMC8304393 DOI: 10.3390/ijms22147346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 01/15/2023] Open
Abstract
Pectobacterium parmentieri is a Gram-negative plant-pathogenic bacterium able to infect potato (Solanum tuberosum L.). Little is known about lytic bacteriophages infecting P. parmentieri and how phage-resistance influences the environmental fitness and virulence of this species. A lytic phage vB_Ppp_A38 (ϕA38) has been previously isolated and characterized as a potential biological control agent for the management of P. parmentieri. In this study, seven P. parmentieri SCC 3193 Tn5 mutants were identified that exhibited resistance to infection caused by vB_Ppp_A38 (ϕA38). The genes disrupted in these seven mutants encoded proteins involved in the assembly of O-antigen, sugar metabolism, and the production of bacterial capsule exopolysaccharides. The potential of A38-resistant P. parmentieri mutants for plant colonization and pathogenicity as well as other phenotypes expected to contribute to the ecological fitness of P. parmentieri, including growth rate, use of carbon and nitrogen sources, production of pectinolytic enzymes, proteases, cellulases, and siderophores, swimming and swarming motility, presence of capsule and flagella as well as the ability to form biofilm were assessed. Compared to the wild-type P. parmentieri strain, all phage-resistant mutants exhibited a reduced ability to colonize and to cause symptoms in growing potato (S. tuberosum L.) plants. The implications of bacteriophage resistance on the ecological fitness of P. parmentieri are discussed.
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Affiliation(s)
- Przemyslaw Bartnik
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland;
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19
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Use of a Specific Phage Cocktail for Soft Rot Control on Ware Potatoes: A Case Study. Viruses 2021; 13:v13061095. [PMID: 34201375 PMCID: PMC8229397 DOI: 10.3390/v13061095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 01/15/2023] Open
Abstract
Using bacteriophages (bacterial viruses) to control pathogenic bacteria is a promising approach in horticulture. However, the application of this strategy in real conditions requires compliance with particular technological and environmental restraints. The presented paper concerns the process of phage selection to create a cocktail that is efficient against the circulating causal agents of potato soft rot. The resulting phage cocktail causes a complete lysis of a mixture of circulating pectobacterial strains in vitro. In the context of being used to treat ware potatoes during off-season storage, the protocol of phage application via the humidity maintenance system was designed. The phage cocktail was shown to reduce the population of Pectobacterium spp. 10–12-fold, achieving a population that was below a symptomatic threshold.
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20
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Oulghazi S, Sarfraz S, Zaczek-Moczydłowska MA, Khayi S, Ed-Dra A, Lekbach Y, Campbell K, Novungayo Moleleki L, O’Hanlon R, Faure D. Pectobacterium brasiliense: Genomics, Host Range and Disease Management. Microorganisms 2021; 9:E106. [PMID: 33466309 PMCID: PMC7824751 DOI: 10.3390/microorganisms9010106] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.
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Affiliation(s)
- Said Oulghazi
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Sohaib Sarfraz
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Maja A. Zaczek-Moczydłowska
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Slimane Khayi
- Biotechnology Research Unit, CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Abdelaziz Ed-Dra
- Department of Biology, Faculty of Sciences, Moulay Ismaïl University, BP.11201, Zitoune Meknes 50000, Morocco; (S.O.); (A.E.-D.)
| | - Yassir Lekbach
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China;
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast BT9 5DL, UK; (M.A.Z.-M.); (K.C.)
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Richard O’Hanlon
- Agri-Food and Biosciences Institute, 18a Newforge Lane, Belfast BT9 5PX, UK;
- Department of Agriculture, Food and the Marine, D02 WK12 Dublin 2, Ireland
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France
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21
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Evseev PV, Lukianova AA, Shneider MM, Korzhenkov AA, Bugaeva EN, Kabanova AP, Miroshnikov KK, Kulikov EE, Toshchakov SV, Ignatov AN, Miroshnikov KA. Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches. Microorganisms 2020; 8:E1707. [PMID: 33142811 PMCID: PMC7693777 DOI: 10.3390/microorganisms8111707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 01/25/2023] Open
Abstract
Black leg and soft rot are devastating diseases causing up to 50% loss of potential potato yield. The search for, and characterization of, bacterial viruses (bacteriophages) suitable for the control of these diseases is currently a sought-after task for agricultural microbiology. Isolated lytic Pectobacterium bacteriophages Q19, PP47 and PP81 possess a similar broad host range but differ in their genomic properties. The genomic features of characterized phages have been described and compared to other Studiervirinae bacteriophages. Thorough phylogenetic analysis has clarified the taxonomy of the phages and their positioning relative to other genera of the Autographiviridae family. Pectobacterium phage Q19 seems to represent a new genus not described previously. The genomes of the phages are generally similar to the genome of phage T7 of the Teseptimavirus genus but possess a number of specific features. Examination of the structure of the genes and proteins of the phages, including the tail spike protein, underlines the important role of horizontal gene exchange in the evolution of these phages, assisting their adaptation to Pectobacterium hosts. The results provide the basis for the development of bacteriophage-based biocontrol of potato soft rot as an alternative to the use of antibiotics.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | - Anna A. Lukianova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Mikhail M. Shneider
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
| | | | - Eugenia N. Bugaeva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Anastasia P. Kabanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Eugene E. Kulikov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Stepan V. Toshchakov
- Winogradsky Institute of Microbiology, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, 117312 Moscow, Russia; (K.K.M.); (E.E.K.); (S.V.T.)
| | - Alexander N. Ignatov
- Research Center “PhytoEngineering” Ltd., Rogachevo, 141880 Moscow Region, Russia;
| | - Konstantin A. Miroshnikov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (A.A.L.); (M.M.S.); (E.N.B.); (A.P.K.)
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Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide. Int J Mol Sci 2020; 21:ijms21093170. [PMID: 32365879 PMCID: PMC7246868 DOI: 10.3390/ijms21093170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/17/2022] Open
Abstract
Phytopathogenic bacteria belonging to the Pectobacterium and Dickeya genera (soft-rot Pectobacteriaceae) are in the focus of agriculture-related microbiology because of their diversity, their substantial negative impact on the production of potatoes and vegetables, and the prospects of bacteriophage applications for disease control. Because of numerous amendments in the taxonomy of P. carotovorum, there are still a few studied sequenced strains among this species. The present work reports on the isolation and characterization of the phage infectious to the type strain of P. carotovorum. The phage Arno 160 is a lytic Podovirus representing a potential new genus of the subfamily Autographivirinae. It recognizes O-polysaccahride of the host strain and depolymerizes it in the process of infection using a rhamnosidase hydrolytic mechanism. Despite the narrow host range of this phage, it is suitable for phage control application.
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