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Vasilyeva AA, Evseev PV, Ignatov AN, Dzhalilov FSU. Pectobacterium punjabense Causing Blackleg and Soft Rot of Potato: The First Report in the Russian Federation. PLANTS (BASEL, SWITZERLAND) 2024; 13:2144. [PMID: 39124263 PMCID: PMC11313954 DOI: 10.3390/plants13152144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/19/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024]
Abstract
Phytopathogenic bacteria of the genus Pectobacterium are responsible for several diseases that affect potato (Solanum tuberosum L.) production worldwide, including blackleg and tuber soft rot. These bacteria are highly diverse, with over 17 different species currently identified. However, some of the recently described species, such as Pectobacterium punjabense, are still poorly understood. In this study, we focused on P. punjabense isolates collected from diseased potato tubers in Russia in 2021. Whole-genome sequencing was used to characterise the genomic diversity of the pathogen and determine the biochemical profiles of the isolated bacteria. The ability of these isolates to cause soft rot symptoms was tested. A comparative assessment of the potential pathogenicity of the Pectobacterium isolates was conducted by infecting potato tubers and measuring the accumulation of biomass in a liquid medium during cultivation at different temperatures. A TaqMan qPCR assay was developed for the highly sensitive and specific characterisation of P. punjabense strains, which can be used in diagnostic systems. This is the first report on P. punjabense causing potato disease in the Russian Federation.
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Affiliation(s)
- 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.N.I.)
| | - 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.N.I.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexandr N. Ignatov
- Department of Plant Protection, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (P.V.E.); (A.N.I.)
- 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; (P.V.E.); (A.N.I.)
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Arizala D, Arif M. Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri. Genome Biol Evol 2024; 16:evae032. [PMID: 38385549 PMCID: PMC10946231 DOI: 10.1093/gbe/evae032] [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: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.
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Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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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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Raina S. Lipopolysaccharides: Regulated Biosynthesis and Structural Diversity. Int J Mol Sci 2023; 24:7498. [PMID: 37108660 PMCID: PMC10145120 DOI: 10.3390/ijms24087498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The cell envelope of Gram-negative bacteria contains two distinct membranes, an inner (IM) and an outer (OM) membrane, separated by the periplasm, a hydrophilic compartment that includes a thin layer of peptidoglycan [...].
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Affiliation(s)
- Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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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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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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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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