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Kang J, Yoon HM, Jung J, Yu S, Choi SY, Bae HW, Cho YH, Chung EH, Lee Y. Pleiotropic effects of N-acylhomoserine lactone synthase ExpI on virulence, competition, and transmission in Pectobacterium carotovorum subsp. carotovorum Pcc21. Pest Manag Sci 2024; 80:687-697. [PMID: 37758685 DOI: 10.1002/ps.7797] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Pectobacterium species are necrotrophic phytopathogenic bacteria that cause soft rot disease in economically important crops. The successful infection of host plants relies on interactions among virulence factors, competition, and transmission within hosts. Pectobacteria primarily produce and secrete plant cell-wall degrading enzymes (PCWDEs) for virulence. The regulation of PCWDEs is controlled by quorum sensing (QS). Thus, the QS system is crucial for disease development in pectobacteria through PCWDEs. RESULTS In this study, we identified a Tn-insertion mutant, M2, in the expI gene from a transposon mutant library of P. carotovorum subsp. carotovorum Pcc21 (hereafter Pcc21). The mutant exhibited reduced production and secretion of PCWDEs, impaired flagellar motility, and increased sensitivity to hydrogen peroxide, resulting in attenuated soft rot symptoms in cabbage and potato tubers. Transcriptomic analysis revealed the down-regulation of genes involved in the production and secretion in the mutant, consistent with the observed phenotype. Furthermore, the Pcc21 wild-type transiently colonized in the gut of Drosophila melanogaster within 12 h after feeding, while the mutant compromised colonization phenotype. Interestingly, Pcc21 produces a bacteriocin, carocin D, to compete with other bacteria. The mutant exhibited up-regulation of carocin D-encoding genes (caroDK) and inhibited the growth of a closely related bacterium, P. wasabiae. CONCLUSION Our results demonstrated the significance of ExpI in the overall pathogenic lifestyle of Pcc21, including virulence, competition, and colonization in plant and insect hosts. These findings suggest that disease outcome is a result of complex interactions mediated by ExpI across multiple steps. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jihee Kang
- Department of Food Science and Biotechnology, CHA University, Pocheon, Republic of Korea
| | - Hye Min Yoon
- Department of Food Science and Biotechnology, CHA University, Pocheon, Republic of Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Seonmi Yu
- Department of Food Science and Biotechnology, CHA University, Pocheon, Republic of Korea
| | - Shin-Yae Choi
- Department of Pharmacy, and Institutes of Pharmaceutical Sciences, CHA University, Seongnam, Republic of Korea
| | - Hee-Won Bae
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - You-Hee Cho
- Department of Pharmacy, and Institutes of Pharmaceutical Sciences, CHA University, Seongnam, Republic of Korea
| | - Eui-Hwan Chung
- Department of Plant Biotechnology, Korea University, Seoul, Republic of Korea
| | - Yunho Lee
- Department of Food Science and Biotechnology, CHA University, Pocheon, Republic of Korea
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Maphosa S, Moleleki LN. A computational and secretome analysis approach reveals exclusive and shared candidate type six secretion system substrates in Pectobacterium brasiliense 1692. Microbiol Res 2024; 278:127501. [PMID: 37976736 DOI: 10.1016/j.micres.2023.127501] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/24/2023] [Accepted: 09/13/2023] [Indexed: 11/19/2023]
Abstract
The type 6 secretion system (T6SS) of Gram-negative bacteria (GNB) has implications for bacterial competition, virulence, and survival. For the broad host range pathogen, Pectobacterium brasiliense 1692, T6SS-mediated competition occurs in a tissue-specific manner. However, no other roles have been investigated. The aim of this study was to identify T6SS-associated proteins under virulence inducing conditions. We used Bastion tools to predict 1479 Pbr1692 secreted proteins. Sixteen percent of these overlap between type 1-4 secretion systems (T1SS-T4SS) and T6SS. Using label-free quantitative mass spectrometry of Pbr1692 T6SS active and T6SS inactive strains' secretomes cultured in minimal media supplemented with host extract, 49 T6SS-associated proteins with varied gene ontology predicted functions were identified. We report 19 and 30 T6SS primary substrates and differentially secreted proteins, respectively, in T6SS mutants versus wild type strains. Of the total 49 T6SS-associated proteins presented in this study, 25 were also predicted using the BastionX platform as T6SS exclusive and shared substrates with T1SS-T4SS. This work provides a list of Pbr1692 T6SS secreted effector candidates. These include a potential antibacterial toxin HNH endonuclease and several predicted virulence proteins, including plant cell wall degrading enzymes. A preliminary basis for potential crosstalk between GNB secretion systems is also highlighted.
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Affiliation(s)
- S Maphosa
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - L N Moleleki
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Hatfield, Pretoria, South Africa
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Mainello-Land AM, Bibi S, Gugino B, Bull CT. Multilocus sequence and phenotypic analysis of Pectobacterium and Dickeya type strains for identification of soft rot Pectobacteriaceae from symptomatic potato stems and tubers in Pennsylvania. Syst Appl Microbiol 2024; 47:126476. [PMID: 38113702 DOI: 10.1016/j.syapm.2023.126476] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023]
Abstract
Outbreaks of potato blackleg and soft rot caused by Pectobacterium species and more recently Dickeya species across the U.S. mid-Atlantic region have caused yield loss due to poor emergence as well as losses from stem and tuber rot. To develop management strategies for soft rot diseases, we must first identify which members of the soft rot Pectobacteriaceae are present in regional potato plantings. However, the rapidly expanding number of soft rot Pectobacteriaceae species and the lack of readily available comparative data for type strains of Pectobacterium and Dickeya hinder quick identification. This manuscript provides a comparative analysis of soft rot Pectobacteriaceae and a comprehensive comparison of type strains from this group using rep-PCR, MLSA and 16S sequence analysis, as well as phenotypic and physiological analyses using Biolog GEN III plates. These data were used to identify isolates cultured from symptomatic potato stems collected between 2016 and 2018. The isolates were characterized for phenotypic traits and by sequence analysis to identify the bacteria from potatoes with blackleg and soft rot symptoms in Pennsylvania potato fields. In this survey, P. actinidiae, P. brasiliense, P. polonicum, P. polaris, P. punjabense, P. parmentieri, and P. versatile were identified from Pennsylvania for the first time. Importantly, the presence of P. actinidiae in Pennsylvania represents the first report of this organism in the U.S. As expected, P. carotorvorum and D. dianthicola were also isolated. In addition to a resource for future work studying the Dickeya and Pectobacterium associated with potato blackleg and soft rot, we provide recommendations for future surveys to monitor for quarantine or emerging soft rot Pectobacteriace regionally.
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Affiliation(s)
- Amanda M Mainello-Land
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaheen Bibi
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Beth Gugino
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
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Ben Moussa H, Pédron J, Hugouvieux-Cotte-Pattat N, Barny MA. Two species with a peculiar evolution within the genus Pectobacterium suggest adaptation to a new environmental niche. Environ Microbiol 2023; 25:2465-2480. [PMID: 37550252 DOI: 10.1111/1462-2920.16479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 08/09/2023]
Abstract
Historically, research on Soft Rot Pectobacteriacea (SRP) has focused on economically important crops and ornamentals and knowledge of these bacteria outside the plant context remains poorly investigated. Recently, two closely related species Pectobacterium aquaticum and Pectobacterium quasiaquaticum were isolated from water and have not been isolated from any plant yet. To identify the distinctive characteristics of these two species, we performed a comparative genomic analysis of 80 genomes representing 19 Pectobacterium species and performed an evolutionary reconstruction. Both water species underwent a reduction in genome size associated with a high pseudogene content. A high gene loss was predicted at the emergence of both species. Among the 199 gene families missing from both P. aquaticum and P. quasiaquaticum genomes but present in at least 80% of other Pectobacterium genomes, COG analysis identified many genes involved in nutrient transport systems. In addition, many type II secreted proteins were also missing in both species. Phenotypic analysis revealed that both species had reduced pectinolytic activity, a biofilm formation defect, were highly motile and had reduced virulence on several plants. These genomic and phenotypic data suggest that the ecological niche of P. aquaticum and P. quasiaquaticum may differ from that of other Pectobacterium species.
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
| | - Jacques Pédron
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
| | | | - Marie-Anne Barny
- Sorbonne Université, INRAE, IRD, CNRS, UPEC, UMR 7618 Institut d'Écologie et des Sciences de l'Environnement de Paris, Paris, France
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Bourigault Y, Dupont CA, Desjardins JB, Doan T, Bouteiller M, Le Guenno H, Chevalier S, Barbey C, Latour X, Cascales E, Merieau A. Pseudomonas fluorescens MFE01 delivers a putative type VI secretion amidase that confers biocontrol against the soft-rot pathogen Pectobacterium atrosepticum. Environ Microbiol 2023; 25:2564-2579. [PMID: 37622480 DOI: 10.1111/1462-2920.16492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
The type VI secretion system (T6SS) is a contractile nanomachine widespread in Gram-negative bacteria. The T6SS injects effectors into target cells including eukaryotic hosts and competitor microbial cells and thus participates in pathogenesis and intermicrobial competition. Pseudomonas fluorescens MFE01 possesses a single T6SS gene cluster that confers biocontrol properties by protecting potato tubers against the phytopathogen Pectobacterium atrosepticum (Pca). Here, we demonstrate that a functional T6SS is essential to protect potato tuber by reducing the pectobacteria population. Fluorescence microscopy experiments showed that MFE01 displays an aggressive behaviour with an offensive T6SS characterized by continuous and intense T6SS firing activity. Interestingly, we observed that T6SS firing is correlated with rounding of Pectobacterium cells, suggesting delivery of a potent cell wall targeting effector. Mutagenesis coupled with functional assays then revealed that a putative T6SS secreted amidase, Tae3Pf , is mainly responsible for MFE01 toxicity towards Pca. Further studies finally demonstrated that Tae3Pf is toxic when produced in the periplasm, and that its toxicity is counteracted by the Tai3Pf inner membrane immunity protein.
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Affiliation(s)
- Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Charly A Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Jonas B Desjardins
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Mathilde Bouteiller
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Hugo Le Guenno
- Plateforme de Microscopie, Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Sylvie Chevalier
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
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Su Y, Li X, Li L, Lukianova A, Tokmakova A, Chen C, Fu L, Tian Y, Shi Y, Xie J, Miroshnikov KA, Yang J, Xie H. Occurrence, Characteristics, and qPCR-Based Identification of Pectobacterium versatile Causing Soft Rot of Chinese Cabbage in China. Plant Dis 2023; 107:2751-2762. [PMID: 36973901 DOI: 10.1094/pdis-12-22-2770-re] [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] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Pectobacterium is one of the most important genera of phytopathogenic bacteria. It can cause soft-rot diseases on a wide range of plant species across the world. In this study, three Pectobacterium strains (KC01, KC02, and KC03) were isolated from soft-rotted Chinese cabbage in Beijing, China. These three strains were identified as Pectobacterium versatile based on phylogenetic analysis of Pectobacterium 16S ribosomal RNA, pmrA, and 504 Pectobacterium core genes, as well as a genomic average nucleotide identity analysis. Their biochemical characteristics were found to be similar to the P. versatile type strain ICMP9168T but differed in response to citric acid, stachyose, D-glucuronic acid, dextrin, and N-acetyl-β-D-mannosamine. All of the tested P. versatile strains showed different carbohydrate utilization abilities compared with P. carotovorum and P. odoriferum, particularly in their ability to utilize D-arabitol, L-rhamnose, and L-serine. Under laboratory conditions, the maceration ability of P. versatile on Chinese cabbage was the highest at 28°C, compared with those at 13, 28, 23, and 33°C. Additionally, P. versatile could infect all of the 17 known Pectobacterium host plants, except for Welsh onion (Allium fistulosum). A SYBR Green quantitative PCR (qPCR) detection system was developed to distinguish P. versatile from other soft-rot bacteria based on the combined performance of melting curve (with a single melting peak at around 85°C) and fluorescence curve (with cycle threshold <30) when the bacterial genomic DNA concentration was in the range of 10 pg/µl to 10 ng/µl. This study is the first to report the presence of P. versatile on Chinese cabbage in China, as well as a specific and sensitive qPCR assay that can be used to quickly identify P. versatile. The work contributes to a better understanding of P. versatile and will facilitate the effective diagnosis of soft-rot disease, ultimately benefitting commercial crop production.
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Affiliation(s)
- Yanyan Su
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaoying Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Anna Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Anna Tokmakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Changlong Chen
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lu Fu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yu Tian
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianbo Xie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Jungang Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hua Xie
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Tsers I, Parfirova O, Moruzhenkova V, Petrova O, Gogoleva N, Vorob’ev V, Gogolev Y, Gorshkov V. A Switch from Latent to Typical Infection during Pectobacterium atrosepticum-Tobacco Interactions: Predicted and True Molecular Players. Int J Mol Sci 2023; 24:13283. [PMID: 37686094 PMCID: PMC10487725 DOI: 10.3390/ijms241713283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both fundamental science and disease management. No studies to date have compared, at the systemic molecular level, the physiological portraits of plants when different infection types (typical and latent) are developed. The only phytopathogenic bacterium for which latent infections were not only widely described but also at least fluently characterized at the molecular level is Pectobacterium atrosepticum (Pba). The present study aimed at the comparison of plant transcriptome responses during typical and latent infections caused by Pba in order to identify and then experimentally verify the key molecular players that act as switchers, turning peaceful plant-Pba coexistence into a typical infection. Based on RNA-Seq, we predicted plant cell wall-, secondary metabolism-, and phytohormone-related genes whose products contributed to the development of the disease or provided asymptomatic plant-Pba interactions. By treatment tests, we confirmed that a switch from latent to typical Pba-caused infection is determined by the plant susceptible responses mediated by the joint action of ethylene and jasmonates.
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Affiliation(s)
- Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Varvara Moruzhenkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
| | - Vladimir Vorob’ev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (I.T.); (O.P.); (V.M.); (O.P.); (N.G.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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Hong SM, Ten LN, Park KT, Back CG, Waleron M, Kang IK, Lee SY, Jung HY. Pectobacterium jejuense sp. nov. Isolated from Cucumber Stem Tissue. Curr Microbiol 2023; 80:308. [PMID: 37528256 DOI: 10.1007/s00284-023-03419-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/16/2023] [Indexed: 08/03/2023]
Abstract
A single Pectobacterium-like strain named 13-115T was isolated from a specimen of diseased cucumber stem tissue collected on Jeju Island, South Korea. The strain presented a rod-like shape and was negative for Gram staining. When grown on R2A medium at 25 °C, strain 13-115T formed round, convex and white colonies. This strain showed growth at temperatures ranging from 10 to 30 °C and tolerated a pH range of 6-9. The strain could also tolerate NaCl concentrations up to 5%. Analysis of the 16S rRNA gene sequence revealed that strain 13-115T exhibited similarity of over 99% with Pectobacterium brasiliense, P. carotovorum, P. polaris, and P. parvum. By conducting multilocus sequence analyses using dnaX, leuS, and recA genes, a separate phylogenetic lineage was discovered between strain 13-115T and other members of the genus Pectobacterium. Moreover, the strain showed relatively low in silico DNA-DNA hybridization (<60.6%) and average nucleotide identity (ANI) (<94.9%) values with recognized Pectobacterium species. The isolate has a genome size of 5,069,478 bp and a genomic G + C content of 52.04 mol%. Major fatty acids identified in the strain included C16:0 (28.99%), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c; 28.85%), and C18:1 ω7c (19.01%). Pathogenicity assay confirmed that the novel strain induced soft rot symptoms in cucumber plants and Koch's postulates were fulfilled. Molecular analysis and phenotypic data indicated that strain 13-115T could be classified as a new species within the Pectobacterium genus, which has been named Pectobacterium jejuense. The type strain is 13-115T (= KCTC 92800T = JCM 35940T).
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Affiliation(s)
- Soo-Min Hong
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Leonid N Ten
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyoung-Taek Park
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Chang-Gi Back
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Malgorzata Waleron
- Intercollegiate Faculty of Biotechnology UG and MUG, 58 Abrahama Street, 80-307, Gdansk, Poland
| | - In-Kyu Kang
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Yeol Lee
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Young Jung
- College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
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9
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Zhang L, Yang T, Zhao Y, Mo Z, Yuan Z, Yang Y, Wang M, Liu H. A Report of Pectobacterium carotovorum subsp. actinidiae Causing Kiwifruit Bacterial Canker in Guangxi, China. Plant Dis 2023; 107:281-287. [PMID: 35971259 DOI: 10.1094/pdis-01-22-0157-re] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A bacterial pathogen strain was isolated from susceptible tissue of Hongyang variety kiwifruit in Zhongfeng Town, Ziyuan County, Guilin City, Guangxi, China. Due to the relatively single variety of kiwifruit in Guangxi, the control technology of fruit farmers is backward, and the climate is humid, which is suitable for the growth of pathogenic bacteria, resulting in frequent occurrence of diseases. In this study, the pathogen strain was identified based on morphological, physiological, and biochemical tests; 16S rRNA gene; PCR detection with specific primers; and Biolog analysis. The results showed that a tobacco allergic reaction could be induced by inoculation with the pathogenic bacteria. Additionally, brown necrotic plaques appeared on kiwifruit leaves, necrotic phloem lesions appeared, and wounds on kiwifruit branches turned brown. The characteristics identified by morphological, physiological, biochemical, and Biolog identification were similar to those caused by Pectobacterium sp. Through 16S rRNA gene sequence analysis and PCR identification with specific primers, bands with a size corresponding to target bands indicated that the pathogen was Pectobacterium carotovorum subsp. actinidiae. This is the first report of kiwifruit canker disease caused by P. carotovorum subsp. actinidiae in Guangxi, China. In addition, through this study, a preliminary understanding of the pathogen has been obtained, which will lay the foundation for the prevention and control of the disease in the future.
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Affiliation(s)
- Lidan Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Tingmi Yang
- Guangxi Academy of Specialty Crops, Guangxi 541004, China
| | - Ying Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Zhitong Mo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Zhixiang Yuan
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Yanchang Yang
- Guangxi Academy of Specialty Crops, Guangxi 541004, China
| | - Mingzhao Wang
- Guangxi Academy of Specialty Crops, Guangxi 541004, China
| | - Hongxia Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing Agricultural University, Nanjing, China
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10
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Ben Moussa H, Bertrand C, Rochelle-Newall E, Fiorini S, Pédron J, Barny MA. The Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys. Phytopathology 2022; 112:1676-1685. [PMID: 35224981 DOI: 10.1094/phyto-12-21-0515-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Claire Bertrand
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Emma Rochelle-Newall
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Sarah Fiorini
- Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Centre de Recherche en Écologie Expérimentale et Prédictive, Paris Sciences & Lettres Research University, UMS 3194, 77140 Saint-Pierre-lès-Nemours, France
| | - Jacques Pédron
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Marie-Anne Barny
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
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11
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Maciag T, Krzyzanowska DM, Rabalski L, Jafra S, Czajkowski R. Complete Genome Sequences of Five Gram-Negative Bacterial Strains Comprising Synthetic Bacterial Consortium "The Great Five" with Antagonistic Activity Against Plant-Pathogenic Pectobacterium spp. and Dickeya spp. Mol Plant Microbe Interact 2022; 35:711-714. [PMID: 35613336 DOI: 10.1094/mpmi-01-22-0020-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Tomasz Maciag
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland
| | - Dorota M Krzyzanowska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, 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
| | - 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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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Jonca J, Waleron M, Czaplewska P, Bogucka A, Steć A, Dziomba S, Jasiecki J, Rychłowski M, Waleron K. Membrane Vesicles of Pectobacterium as an Effective Protein Secretion System. Int J Mol Sci 2021; 22:ijms222212574. [PMID: 34830459 PMCID: PMC8623790 DOI: 10.3390/ijms222212574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Bacteria of genus Pectobacterium are Gram-negative rods of the family Pectobacteriaceae. They are the causative agent of soft rot diseases of crops and ornamental plants. However, their virulence mechanisms are not yet fully elucidated. Membrane vesicles (MVs) are universally released by bacteria and are believed to play an important role in the pathogenicity and survival of bacteria in the environment. Our study investigates the role of MVs in the virulence of Pectobacterium. The results indicate that the morphology and MVs production depend on growth medium composition. In polygalacturonic acid (PGA) supplemented media, Pectobacterium produces large MVs (100–300 nm) and small vesicles below 100 nm. Proteomic analyses revealed the presence of pectate degrading enzymes in the MVs. The pectate plate test and enzymatic assay proved that those enzymes are active and able to degrade pectates. What is more, the pathogenicity test indicated that the MVs derived from Pectobacterium were able to induce maceration of Zantedeschia sp. leaves. We also show that the MVs of β-lactamase producing strains were able to suppress ampicillin activity and permit the growth of susceptible bacteria. Those findings indicate that the MVs of Pectobacterium play an important role in host-pathogen interactions and niche competition with other bacteria. Our research also sheds some light on the mechanism of MVs production. We demonstrate that the MVs production in Pectobacterium strains, which overexpress a green fluorescence protein (GFP), is higher than in wild-type strains. Moreover, proteomic analysis revealed that the GFP was present in the MVs. Therefore, it is possible that protein sequestration into MVs might not be strictly limited to periplasmic proteins. Our research highlights the importance of MVs production as a mechanism of cargo delivery in Pectobacterium and an effective secretion system.
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Affiliation(s)
- Joanna Jonca
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland;
| | - Malgorzata Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland;
- Correspondence: (M.W.); (K.W.)
| | - Paulina Czaplewska
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (P.C.); (A.B.)
| | - Aleksandra Bogucka
- Laboratory of Mass Spectrometry-Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland; (P.C.); (A.B.)
| | - Aleksandra Steć
- Department of Toxicology, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416 Gdansk, Poland; (A.S.); (S.D.)
| | - Szymon Dziomba
- Department of Toxicology, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416 Gdansk, Poland; (A.S.); (S.D.)
| | - Jacek Jasiecki
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. Hallera 107, 80-416 Gdansk, Poland;
| | - Michał Rychłowski
- Laboratory of Virus Molecular Biology, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland;
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, Al. Gen. Hallera 107, 80-416 Gdansk, Poland;
- Correspondence: (M.W.); (K.W.)
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14
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Domingo R, Perez C, Klair D, Vu H, Candelario-Tochiki A, Wang X, Camson A, Uy JN, Salameh M, Arizala D, Dobhal S, Boluk G, Bingham JP, Ochoa-Corona F, Ali ME, Stack JP, Fletcher J, Odani J, Jenkins D, Alvarez AM, Arif M. Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil. Sci Rep 2021; 11:21948. [PMID: 34753982 PMCID: PMC8578433 DOI: 10.1038/s41598-021-01196-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
Pectobacterium parmentieri (formerly Pectobacterium wasabiae), which causes soft rot disease in potatoes, is a newly established species of pectinolytic bacteria within the family Pectobacteriaceae. Despite serious damage caused to the potato industry worldwide, no field-deployable diagnostic tests are available to detect the pathogen in plant samples. In this study, we aimed to develop a reliable, rapid, field-deployable loop-mediated isothermal amplification (LAMP) assay for the specific detection of P. parmentieri. Specific LAMP primers targeting the petF1 gene region, found in P. parmentieri but no other Pectobacterium spp., were designed and validated in silico and in vitro using extensive inclusivity (15 strains of P. parmentieri) and exclusivity (94 strains including all other species in the genus Pectobacterium and host DNA) panels. No false positives or negatives were detected when the assay was tested directly with bacterial colonies, and with infected plant and soil samples. Sensitivity (analytical) assays using serially diluted bacterial cell lysate and purified genomic DNA established the detection limit at 10 CFU/mL and 100 fg (18-20 genome copies), respectively, even in the presence of host crude DNA. Consistent results obtained by multiple users/operators and field tests suggest the assay's applicability to routine diagnostics, seed certification programs, biosecurity, and epidemiological studies.
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Affiliation(s)
- Ryan Domingo
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Cristian Perez
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Diksha Klair
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Huong Vu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Alika Candelario-Tochiki
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Amihan Camson
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jaclyn Nicole Uy
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Mouauia Salameh
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Gamze Boluk
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Francisco Ochoa-Corona
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - James P Stack
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jacqueline Fletcher
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - Jenee Odani
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Daniel Jenkins
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Anne M Alvarez
- 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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Czajkowski R, Rabalski L, Kosinski M, de Neergaard E, Harding S. High-Quality Complete Genome Resource of Pathogenic Bacterium Pectobacterium atrosepticum Strain Green1 Isolated from Potato ( Solanum tuberosum L.) in Greenland. Mol Plant Microbe Interact 2021; 34:1328-1333. [PMID: 34353114 DOI: 10.1094/mpmi-06-21-0130-a] [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] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pectobacterium atrosepticum is a narrow-host-range, pectinolytic, plant-pathogenic bacterium causing blackleg of potato (Solanum tuberosum L.) worldwide. Till present, several P. atrosepticum genomes have been sequenced and characterized in detail; however, all of these genomes have come from P. atrosepticum isolates from plants grown in temperate zones, not from hosts cultivated under different climatic conditions. Herewith, we present the first complete, high-quality genome of the P. atrosepticum strain Green1 isolated from potato plants grown under a subarctic climate in Greenland. The genome of P. atrosepticum strain Green1 consists of one chromosome of 4,959,719 bp, with a GC content of 51% and no plasmids. The genome contains 4,531 annotated features, including 4,179 protein-coding genes, 22 ribosomal RNA genes, 70 transfer RNA genes, 8 noncoding RNA genes, 2 CRISPRs, and 126 pseudogenes. We believe that the information in this first high-quality, complete, closed genome of P. atrosepticum strains isolated from host plants grown in a subarctic agricultural region will provide resources for comparative genomic studies and for analyses targeting climatic adaptation and ecological fitness mechanisms present in P. atrosepticum.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama 58, 80-307 Gdansk, Poland
| | | | - Susanne Harding
- Plant Health in Greenland, Strandgade 39, DK-3000 Helsingør, Denmark
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Gorshkov V, Parfirova O, Petrova O, Gogoleva N, Kovtunov E, Vorob’ev V, Gogolev Y. The Knockout of Enterobactin-Related Gene in Pectobacterium atrosepticum Results in Reduced Stress Resistance and Virulence towards the Primed Plants. Int J Mol Sci 2021; 22:ijms22179594. [PMID: 34502502 PMCID: PMC8431002 DOI: 10.3390/ijms22179594] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Siderophores produced by microorganisms to scavenge iron from the environment have been shown to contribute to virulence and/or stress resistance of some plant pathogenic bacteria. Phytopathogenic bacteria of Pectobacterium genus possess genes for the synthesis of siderophore enterobactin, which role in plant-pathogen interactions has not been elucidated. In the present study we characterized the phenotype of the mutant strain of Pba deficient for the enterobactin-biosynthetic gene entA. We showed that enterobactin may be considered as a conditionally beneficial virulence factor of Pba. The entA knockout did not reduce Pba virulence on non-primed plants; however, salicylic acid-primed plants were more resistant to ΔentA mutant than to the wild type Pba. The reduced virulence of ΔentA mutant towards the primed plants is likely explained by its compromised resistance to oxidative stress.
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Affiliation(s)
- Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Correspondence:
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Evgeny Kovtunov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
| | - Vladimir Vorob’ev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia; (O.P.); (O.P.); (N.G.); (E.K.); (V.V.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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17
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Abstract
Soft rot bacteria classified in the Pectobacteriaceae (SRP), including Pectobacterium and Dickeya spp., are responsible for soft rot and blackleg diseases of potato. Since 2014, blackleg outbreaks caused by D. dianthicola have increased in the United States and Canada. Our previous study found that the most abundant causal organisms of blackleg disease in New York State were P. parmentieri and D. dianthicola, with the latter being the only Dickeya species reported. In the present study, we identified and characterized pathogenic SRP bacteria from 19 potato samples collected in New York State during the 2017 growing season. We used genome sequence comparison to determine the pathogens' species. We found eight P. versatile, one P. atrosepticum, two P. carotovorum, two P. parmentieri, and six D. dianthicola isolates in our 2017 SRP collection. This is the first time that P. versatile has been reported to cause potato blackleg disease in New York State. We determined the phylogenetic relationships between the SRP strains by using 151 single-copy orthologous gene sequences shared among the set of bacteria in our analysis, which provided better resolution than phylogenies constructed with the dnaX gene.
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Affiliation(s)
- Xing Ma
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Paul Stodghill
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, U.S. Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, U.S.A
| | - Miao Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, and Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Keith L Perry
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Bryan Swingle
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, U.S. Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, U.S.A
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Babinska W, Motyka-Pomagruk A, Sledz W, Kowalczyk A, Kaczynski Z, Lojkowska E. The First Polish Isolate of a Novel Species Pectobacterium aquaticum Originates from a Pomeranian Lake. Int J Environ Res Public Health 2021; 18:ijerph18095041. [PMID: 34068828 PMCID: PMC8126228 DOI: 10.3390/ijerph18095041] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022]
Abstract
Pectinolytic bacteria from the genus Pectobacterium cause high economic losses in various crops, vegetables, and ornamentals including potato. Thus far, these strains have been isolated from distinct environments such as rotten or asymptomatic plants, soil, and waterways. The prevalence of soft rot Pectobacteriaceae in different depths of Pomeranian lakes was performed by a qualified scuba diver over 2 years of monitoring. It allowed for the isolation and broad characterization of a strain from the newly established species Pectobacterium aquaticum. Phylogenetic analysis on the sequences of dnaX and recA genes revealed the highest similarity of this strain to P. aquaticum CFBP 8637T. In addition to the determination of analytical profile index (API 20E), we discovered that this strain possesses a smooth form of a lipopolysaccharide with O-polysaccharide consisting of mannose, glucose, and abequose. Moreover, the characterized strain, described as P. aquaticum IFB5637, produced plant-cell–wall-degrading enzymes, such as pectinases, cellulases, proteases, and was capable of macerating potato and chicory tissues under laboratory conditions. In view of more frequent irrigation of seed potato fields resulting from the ongoing climate warming, it is important to monitor the occurrence of potential disease-causing agents in natural waterways.
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Affiliation(s)
- Weronika Babinska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (A.M.-P.); (W.S.)
| | - Agata Motyka-Pomagruk
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (A.M.-P.); (W.S.)
| | - Wojciech Sledz
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (A.M.-P.); (W.S.)
| | - Agnieszka Kowalczyk
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308 Gdansk, Poland; (A.K.); (Z.K.)
| | - Zbigniew Kaczynski
- Laboratory of Structural Biochemistry, Faculty of Chemistry, University of Gdansk, 63 Wita Stwosza, 80-308 Gdansk, Poland; (A.K.); (Z.K.)
| | - Ewa Lojkowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk, 58 Abrahama, 80-307 Gdansk, Poland; (W.B.); (A.M.-P.); (W.S.)
- Correspondence: ; Tel.: +48-725-991-070
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20
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Winn M, Rowlinson M, Wang F, Bering L, Francis D, Levy C, Micklefield J. Discovery, characterization and engineering of ligases for amide synthesis. Nature 2021; 593:391-398. [PMID: 34012085 DOI: 10.1038/s41586-021-03447-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/11/2021] [Indexed: 02/04/2023]
Abstract
Coronatine and related bacterial phytotoxins are mimics of the hormone jasmonyl-L-isoleucine (JA-Ile), which mediates physiologically important plant signalling pathways1-4. Coronatine-like phytotoxins disrupt these essential pathways and have potential in the development of safer, more selective herbicides. Although the biosynthesis of coronatine has been investigated previously, the nature of the enzyme that catalyses the crucial coupling of coronafacic acid to amino acids remains unknown1,2. Here we characterize a family of enzymes, coronafacic acid ligases (CfaLs), and resolve their structures. We found that CfaL can also produce JA-Ile, despite low similarity with the Jar1 enzyme that is responsible for ligation of JA and L-Ile in plants5. This suggests that Jar1 and CfaL evolved independently to catalyse similar reactions-Jar1 producing a compound essential for plant development4,5, and the bacterial ligases producing analogues toxic to plants. We further demonstrate how CfaL enzymes can be used to synthesize a diverse array of amides, obviating the need for protecting groups. Highly selective kinetic resolutions of racemic donor or acceptor substrates were achieved, affording homochiral products. We also used structure-guided mutagenesis to engineer improved CfaL variants. Together, these results show that CfaLs can deliver a wide range of amides for agrochemical, pharmaceutical and other applications.
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Affiliation(s)
- Michael Winn
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Michael Rowlinson
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Fanghua Wang
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Luis Bering
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Daniel Francis
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Colin Levy
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Jason Micklefield
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.
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21
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Petrzik K, Kmoch M, Brázdová S, Ševčík R. Complete genome sequences of novel Berlinvirus and novel Certrevirus lytic for Pectobacterium sp. causing soft rot and black leg disease of potato. Virus Genes 2021; 57:302-305. [PMID: 33914264 DOI: 10.1007/s11262-021-01838-9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022]
Abstract
Two novel dsDNA bacteriophages named Pectobacterium virus CB251 (PcCB251) and Pectobacterium virus CB7V (PcCB7V) targeting plant pathogen Pectobacterium parmentieri have been isolated and sequenced. The PcCB251 genome consists of 40,557 bp with G+C content of 48.6% and contains 47 predicted genes on a single strand. The phage is classified in genus Berlinvirus, family Autographiviridae. The PcCB7V phage has a circular dsDNA genome of 146,054 bp with G+C content of 50.4% and contains 269 predicted protein genes on both strands and 13 tRNA genes. The PcCB7V phage can be classified in genus Certrevirus, subfamily Vequintavirinae. Both novel bacteriophages have narrow host ranges, but they extend the list of candidates for phage-based control of pectolytic bacteria causing soft rot disease of potato.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| | - Martin Kmoch
- Potato Research Institute Havlíčkův Brod, Dobrovského 2366, Havlíčkův Brod, 580 01, Czech Republic
| | - Sára Brázdová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic
| | - Rudolf Ševčík
- University of Chemistry and Technology Prague, Technická 1905/5, Prague 6-Dejvice, Prague, Czech Republic
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22
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Jonkheer EM, Brankovics B, Houwers IM, van der Wolf JM, Bonants PJM, Vreeburg RAM, Bollema R, de Haan JR, Berke L, Smit S, de Ridder D, van der Lee TAJ. The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool. BMC Genomics 2021; 22:265. [PMID: 33849459 PMCID: PMC8045196 DOI: 10.1186/s12864-021-07583-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic diversity underlying virulence and host specificity can be performed at genome level by using a comprehensive comparative approach called pangenomics. A pangenomic approach, using newly developed functionalities in PanTools, was applied to analyze the complex phylogeny of the Pectobacterium genus. We specifically used the pangenome to investigate genetic differences between virulent and avirulent strains of P. brasiliense, a potato blackleg causing species dominantly present in Western Europe. RESULTS Here we generated a multilevel pangenome for Pectobacterium, comprising 197 strains across 19 species, including type strains, with a focus on P. brasiliense. The extensive phylogenetic analysis of the Pectobacterium genus showed robust distinct clades, with most detail provided by 452,388 parsimony-informative single-nucleotide polymorphisms identified in single-copy orthologs. The average Pectobacterium genome consists of 47% core genes, 1% unique genes, and 52% accessory genes. Using the pangenome, we zoomed in on differences between virulent and avirulent P. brasiliense strains and identified 86 genes associated to virulent strains. We found that the organization of genes is highly structured and linked with gene conservation, function, and transcriptional orientation. CONCLUSION The pangenome analysis demonstrates that evolution in Pectobacteria is a highly dynamic process, including gene acquisitions partly in clusters, genome rearrangements, and loss of genes. Pectobacterium species are typically not characterized by a set of species-specific genes, but instead present themselves using new gene combinations from the shared gene pool. A multilevel pangenomic approach, fusing DNA, protein, biological function, taxonomic group, and phenotypes, facilitates studies in a flexible taxonomic context.
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Affiliation(s)
- Eef M Jonkheer
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Balázs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ilse M Houwers
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan M van der Wolf
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robert A M Vreeburg
- Nederlandse Algemene Keuringsdienst voor zaaizaad en pootgoed van landbouwgewassen, Randweg 14, 8304 AS, Emmeloord, The Netherlands
| | - Robert Bollema
- Nederlandse Algemene Keuringsdienst voor zaaizaad en pootgoed van landbouwgewassen, Randweg 14, 8304 AS, Emmeloord, The Netherlands
| | - Jorn R de Haan
- Genetwister Technologies B.V, Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Lidija Berke
- Genetwister Technologies B.V, Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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23
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Zoledowska S, Motyka-Pomagruk A, Misztak A, Lojkowska E. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. Methods Mol Biol 2021; 2242:91-112. [PMID: 33961220 DOI: 10.1007/978-1-0716-1099-2_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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were applied in the studies focused on revealing inter- and intraspecies variation in pectinolytic plant pathogenic bacteria classified to Dickeya solani and Pectobacterium parmentieri. As the described software performed well on the species within the Pectobacteriaceae family, it presumably may be readily utilized on some closely related taxa from the Enterobacteriaceae family. First of all, implementation of various annotation software is discussed and compared. Then, tools computing whole genome comparisons including generation of circular juxtapositions of multiple sequences, revealing the order of synteny blocks or calculation of ANI or Tetra values are presented. Besides, web servers intended either for functional annotation of the genes of interest or for detection of genomic islands, plasmids, prophages, CRISPR/Cas are described. Last but not least, utilization of the software designed for pangenome studies and the further downstream analyses is explained. The presented work not only summarizes broad possibilities assured by the comparative genomic approach but also provides a user-friendly guide that might be easily followed by nonbioinformaticians interested in undertaking similar studies.
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Affiliation(s)
- Sabina Zoledowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
- Institute of Biotechnology and Molecular Medicine, Gdansk, 3 Trzy Lipy, Poland
| | - Agata Motyka-Pomagruk
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
| | - Agnieszka Misztak
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
| | - Ewa Lojkowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland.
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24
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Liu Y, Helmann TC, Stodghill P, Filiatrault MJ. Complete Genome Sequence Resource for the Necrotrophic Plant-Pathogenic Bacterium Pectobacterium carotovorum WPP14. Plant Dis 2021; 105:196-198. [PMID: 32720879 DOI: 10.1094/pdis-05-20-1059-a] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pectobacterium spp. are a major cause of loss in vegetable and ornamental plant production. One of these species, Pectobacterium carotovorum, can cause soft rot disease on many plants, particularly potato. These diseases lead to significant economic loss and pose food security threats by reducing crop yields in the field, in transit, and during storage. The Gram-negative enterobacterium P. carotovorum WPP14 is a particularly virulent strain for which there is no available closed genome, limiting the molecular research for this important pathogen. Here, we report a high-quality complete and annotated genome sequence of P. carotovorum WPP14. The 4,892,225-bp genome was assembled with Nanopore reads and polished with Illumina reads, yielding 394× and 164× coverage, respectively. This closed genome provides a resource for research on improved detection and biology of P. carotovorum, which could translate into improved disease management.
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Affiliation(s)
- Yingyu Liu
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A
| | - Tyler C Helmann
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, U.S.A
| | - Paul Stodghill
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, U.S.A
| | - Melanie J Filiatrault
- School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, U.S.A
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25
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Finney AJ, Buchanan G, Palmer T, Coulthurst SJ, Sargent F. Activation of a [NiFe]-hydrogenase-4 isoenzyme by maturation proteases. Microbiology (Reading) 2020; 166:854-860. [PMID: 32731905 PMCID: PMC7654741 DOI: 10.1099/mic.0.000963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/22/2020] [Indexed: 12/23/2022]
Abstract
Maturation of [NiFe]-hydrogenases often involves specific proteases responsible for cleavage of the catalytic subunits. Escherichia coli HycI is the protease dedicated to maturation of the Hydrogenase-3 isoenzyme, a component of formate hydrogenlyase-1. In this work, it is demonstrated that a Pectobacterium atrosepticum HycI homologue, HyfK, is required for hydrogenase-4 activity, a component of formate hydrogenlyase-2, in that bacterium. The P. atrosepticum ΔhyfK mutant phenotype could be rescued by either P. atrosepticum hyfK or E. coli hycI on a plasmid. Conversely, an E. coli ΔhycI mutant was complemented by either E. coli hycI or P. atrosepticum hyfK in trans. E. coli is a rare example of a bacterium containing both hydrogenase-3 and hydrogenase-4, however the operon encoding hydrogenase-4 has no maturation protease gene. This work suggests HycI should be sufficient for maturation of both E. coli formate hydrogenlyases, however no formate hydrogenlyase-2 activity was detected in any E. coli strains tested here.
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Affiliation(s)
- Alexander J. Finney
- School of Natural & Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Grant Buchanan
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
- Institute of Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Tracy Palmer
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
- Institute of Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Frank Sargent
- School of Natural & Environmental Sciences, Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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26
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Liu Y, Filiatrault MJ. Antibacterial activity and mode of action of potassium tetraborate tetrahydrate against soft-rot bacterial plant pathogens. Microbiology (Reading) 2020; 166:837-848. [PMID: 32639227 PMCID: PMC7654739 DOI: 10.1099/mic.0.000948] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial soft rot caused by the bacteria Dickeya and Pectobacterium is a destructive disease of vegetables, as well as ornamental plants. Several management options exist to help control these pathogens. Because of the limited success of these approaches, there is a need for the development of alternative methods to reduce losses. In this study, we evaluated the effect of potassium tetraborate tetrahydrate (PTB) on the growth of six Dickeya and Pectobacterium spp. Disc diffusion assays showed that Dickeya spp. and Pectobacterium spp. differ in their sensitivity to PTB. Spontaneous PTB-resistant mutants of Pectobacterium were identified and further investigation of the mechanism of PTB resistance was conducted by full genome sequencing. Point mutations in genes cpdB and supK were found in a single Pectobacterium atrosepticum PTB-resistant mutant. Additionally, point mutations in genes prfB (synonym supK) and prmC were found in two independent Pectobacterium brasiliense PTB-resistant mutants. prfB and prmC encode peptide chain release factor 2 and its methyltransferase, respectively. We propose the disruption of translation activity due to PTB leads to Pectobacterium growth inhibition. The P. atrosepticum PTB-resistant mutant showed altered swimming motility. Disease severity was reduced for P. atrosepticum-inoculated potato stems sprayed with PTB. We discuss the potential risk of selecting for bacterial resistance to this chemical.
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Affiliation(s)
- Yingyu Liu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J. Filiatrault
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
- *Correspondence: Melanie J. Filiatrault,
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Fan J, Ma L, Zhao C, Yan J, Che S, Zhou Z, Wang H, Yang L, Hu B. Transcriptome of Pectobacterium carotovorum subsp. carotovorum PccS1 infected in calla plants in vivo highlights a spatiotemporal expression pattern of genes related to virulence, adaptation, and host response. Mol Plant Pathol 2020; 21:871-891. [PMID: 32267092 PMCID: PMC7214478 DOI: 10.1111/mpp.12936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 02/14/2020] [Accepted: 02/29/2020] [Indexed: 06/11/2023]
Abstract
Bacterial pathogens from the genus Pectobacterium cause soft rot in various plants, and result in important economic losses worldwide. We understand much about how these pathogens digest their hosts and protect themselves against plant defences, as well as some regulatory networks in these processes. However, the spatiotemporal expression of genome-wide infection of Pectobacterium remains unclear, although researchers analysed this in some phytopathogens. In the present work, comparing the transcriptome profiles from cellular infection with growth in minimal and rich media, RNA-Seq analyses revealed that the differentially expressed genes (log2 -fold ratio ≥ 1.0) in the cells of Pectobacterium carotovorum subsp. carotovorum PccS1 recovered at a series of time points after inoculation in the host in vivo covered approximately 50% of genes in the genome. Based on the dynamic expression changes in infection, the significantly differentially expressed genes (log2 -fold ratio ≥ 2.0) were classified into five types, and the main expression pattern of the genes for carbohydrate metabolism underlying the processes of infection was identified. The results are helpful to our understanding of the inducement of host plant and environmental adaption of Pectobacterium. In addition, our results demonstrate that maceration caused by PccS1 is due to the depression of callose deposition in the plant for resistance by the pathogenesis-related genes and the superlytic ability of pectinolytic enzymes produced in PccS1, rather than the promotion of plant cell death elicited by the T3SS of bacteria as described in previous work.
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Affiliation(s)
- Jiaqin Fan
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Lin Ma
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Chendi Zhao
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Jingyuan Yan
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Shu Che
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Zhaowei Zhou
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Huan Wang
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Liuke Yang
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Baishi Hu
- Laboratory of BacteriologyDepartment of Plant PathologyNanjing Agricultural UniversityNanjingChina
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28
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Narváez-Barragán DA, Tovar-Herrera OE, Torres M, Rodríguez M, Humphris S, Toth IK, Segovia L, Serrano M, Martínez-Anaya C. Expansin-like Exl1 from Pectobacterium is a virulence factor required for host infection, and induces a defence plant response involving ROS, and jasmonate, ethylene and salicylic acid signalling pathways in Arabidopsis thaliana. Sci Rep 2020; 10:7747. [PMID: 32385404 PMCID: PMC7210985 DOI: 10.1038/s41598-020-64529-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/17/2020] [Indexed: 01/09/2023] Open
Abstract
Expansins are encoded by some phytopathogenic bacteria and evidence indicates that they act as virulence factors for host infection. Here we analysed the expression of exl1 by Pectobacterium brasiliense and Pectobacterium atrosepticum. In both, exl1 gene appears to be under quorum sensing control, and protein Exl1 can be observed in culture medium and during plant infection. Expression of exl1 correlates with pathogen virulence, where symptoms are reduced in a Δexl1 mutant strain of P. atrosepticum. As well as Δexl1 exhibiting less maceration of potato plants, fewer bacteria are observed at distance from the inoculation site. However, bacteria infiltrated into the plant tissue are as virulent as the wild type, suggesting that this is due to alterations in the initial invasion of the tissue. Additionally, swarming from colonies grown on MacConkey soft agar was delayed in the mutant in comparison to the wild type. We found that Exl1 acts on the plant tissue, probably by remodelling of a cell wall component or altering the barrier properties of the cell wall inducing a plant defence response, which results in the production of ROS and the induction of marker genes of the JA, ET and SA signalling pathways in Arabidopsis thaliana. Exl1 inactive mutants fail to trigger such responses. This defence response is protective against Pectobacterium brasiliense and Botrytis cinerea in more than one plant species.
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Affiliation(s)
- Delia A Narváez-Barragán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Omar E Tovar-Herrera
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Martha Torres
- Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, 62110, Cuernavaca, Morelos, Mexico
| | - Mabel Rodríguez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Sonia Humphris
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Ian K Toth
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Lorenzo Segovia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, 62110, Cuernavaca, Morelos, Mexico
| | - Claudia Martínez-Anaya
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
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29
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Narváez-Barragán DA, de Sandozequi A, Rodríguez M, Estrada K, Tovar-Herrera OE, Martínez-Anaya C. Analysis of two Mexican Pectobacterium brasiliense strains reveals an inverted relationship between c-di-GMP levels with exopolysaccharide production and swarming motility. Microbiol Res 2020; 235:126427. [PMID: 32109688 DOI: 10.1016/j.micres.2020.126427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 10/25/2022]
Abstract
Pectobacterium is a diverse genus of phytopathogenic species from soil and water that cause infection either to restricted or multiple plant hosts. Phylogenetic analysis and metabolic fingerprinting of large numbers of genomes have expanded classification of Pectobacterium members. Pectobacterium brasiliense sp. nov has been elevated to the species level having detached from P. carotovorum. Here we present two P. brasiliense strains BF20 and BF45 isolated in Mexico from Opuntia and tobacco, respectively, which cluster into two different groups in whole genome comparisons with other Pectobacterium. We found that BF20 and BF45 strains are phenotypically different as BF45 showed more severe and rapid symptoms in comparison to BF20 in the host models celery and broccoli. Both strains produced similar levels of the main autoinducers, but BF45 shows an additional low abundant autoinducer compared to strain BF20. The two strains had different levels of c-di-GMP, which regulates the transition from motile to sessile lifestyle. In contrast to BF45, BF20 had the highest levels of c-di-GMP, was more motile (swarming), non-flocculant and less proficient in biofilm formation and exopolysaccharide production. Genomic comparisons revealed that differences in c-di-GMP accumulation and perhaps the associated phenotypes might be due to unique c-di-GMP metabolic genes in these two strains. Our results improve our understanding of the associations between phenotype and genotype and how this has shaped the physiology of Pectobacterium strains.
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Affiliation(s)
- Delia A Narváez-Barragán
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Andrés de Sandozequi
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Mabel Rodríguez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Karel Estrada
- Unidad de Secuenciación Masiva y Bioinformática. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Omar E Tovar-Herrera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Claudia Martínez-Anaya
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa, 62210 Cuernavaca, Morelos, México.
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30
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van den Bosch TJM, Niemi O, Welte CU. Single gene enables plant pathogenic Pectobacterium to overcome host-specific chemical defence. Mol Plant Pathol 2020; 21:349-359. [PMID: 31872947 PMCID: PMC7036374 DOI: 10.1111/mpp.12900] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 10/30/2019] [Accepted: 11/27/2019] [Indexed: 05/04/2023]
Abstract
Plants of the Brassicales order, including Arabidopsis and many common vegetables, produce toxic isothiocyanates to defend themselves against pathogens. Despite this defence, plant pathogenic microorganisms like Pectobacterium cause large yield losses in fields and during storage of crops. The bacterial gene saxA was previously found to encode isothiocyanate hydrolase that degrades isothiocyanates in vitro. Here we demonstrate in planta that saxA is a virulence factor that can overcome the chemical defence system of Brassicales plants. Analysis of the distribution of saxA genes in Pectobacterium suggests that saxA from three different phylogenetic origins are present within this genus. Deletion of saxA genes representing two of the most common classes from P. odoriferum and P. versatile resulted in significantly reduced virulence on Arabidopsis thaliana and Brassica oleracea. Furthermore, expressing saxA from a plasmid in a potato-specific P. parmentieri strain that does not naturally harbour this gene significantly increased the ability of the strain to macerate Arabidopsis. These findings suggest that a single gene may have a significant role in defining the host range of a plant pathogen.
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Affiliation(s)
- Tijs J. M. van den Bosch
- Department of MicrobiologyInstitute for Water and Wetland Research, Radboud UniversityNijmegenNetherlands
| | - Outi Niemi
- Viikki Plant Science CentreFaculty of Biological and Environmental SciencesUniversity of HelsinkiFinland
| | - Cornelia U. Welte
- Department of MicrobiologyInstitute for Water and Wetland Research, Radboud UniversityNijmegenNetherlands
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Watson BNJ, Vercoe RB, Salmond GPC, Westra ER, Staals RHJ, Fineran PC. Type I-F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity. Nat Commun 2019; 10:5526. [PMID: 31797922 PMCID: PMC6892833 DOI: 10.1038/s41467-019-13445-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/30/2019] [Indexed: 12/18/2022] Open
Abstract
Type I CRISPR-Cas systems are abundant and widespread adaptive immune systems in bacteria and can greatly enhance bacterial survival in the face of phage infection. Upon phage infection, some CRISPR-Cas immune responses result in bacterial dormancy or slowed growth, which suggests the outcomes for infected cells may vary between systems. Here we demonstrate that type I CRISPR immunity of Pectobacterium atrosepticum leads to suppression of two unrelated virulent phages, ɸTE and ɸM1. Immunity results in an abortive infection response, where infected cells do not survive, but viral propagation is severely decreased, resulting in population protection due to the reduced phage epidemic. Our findings challenge the view of CRISPR-Cas as a system that protects the individual cell and supports growing evidence of abortive infection by some types of CRISPR-Cas systems.
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Affiliation(s)
- Bridget N J Watson
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
- ESI, Biosciences, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Reuben B Vercoe
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Edze R Westra
- ESI, Biosciences, University of Exeter, Cornwall Campus, Penryn, TR10 9FE, UK
| | - Raymond H J Staals
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
- Laboratory of Microbiology, Wageningen University and Research, 6708, WE, Wageningen, The Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand.
- Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand.
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32
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Sun M, Liu H, Huang J, Peng J, Fei F, Zhang Y, Hsiang T, Zheng L. A Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Pectobacterium aroidearum that Causes Soft Rot in Konjac. Int J Mol Sci 2019; 20:ijms20081937. [PMID: 31010197 PMCID: PMC6514923 DOI: 10.3390/ijms20081937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/29/2022] Open
Abstract
Bacterial soft rot caused by Pectobacterium species is a serious disease in konjac (Amorphophallus konjac), a healthy source of starch particularly in East Asia. An effective diagnostic method is crucial to control the disease and reduce losses in konjac production. In this study, we evaluated a loop-mediated isothermal amplification (LAMP) assay with a specific primer set for the rapid and accurate detection of P. aroidearum. A comparative genomics approach was used to identify the specific genes suitable for the design of LAMP primers. The candidate target genes were determined through a first-round comparison with a 50-genome nucleotide database, and subjected to a second-round screening with the GenBank NR database. As a result, nine specific genes of P. aroidearum were selected for LAMP primer design. After screening of the primers, the primer set 1675-1 was chosen for LAMP detection owing to its high specificity and sensitivity. The LAMP assay could detect the presence of P. aroidearum genomic DNA at a concentration as low as 50 fg and 1.2 × 104 CFU/g artificially infected soil within 40 min at 65 °C. Subsequently, this primer set was successfully used to specifically detect P. aroidearum in naturally infected and non-symptomatic plant samples or soil samples from the field. This study indicates that a comparative genomic approach may facilitate the development of highly specific primers for LAMP assays, and a LAMP diagnostic assay with the specific primer set 1675-1 should contribute to the rapid and accurate detection of soft-rot disease in konjac at an early stage.
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Affiliation(s)
- Miaomiao Sun
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hao Liu
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jinbo Peng
- Yichang Academy of Agricultural Science, Yichang 443004, China.
| | - Fuhua Fei
- Yichang Academy of Agricultural Science, Yichang 443004, China.
| | - Ya Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China.
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
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Li X, Ma Y, Liang S, Tian Y, Yin S, Xie S, Xie H. Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle. BMC Genomics 2018; 19:889. [PMID: 30526490 PMCID: PMC6286560 DOI: 10.1186/s12864-018-5269-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/19/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid subspecies, P. carotovorum subsp. brasiliense (Pcb), P. carotovorum subsp. carotovorum (Pcc), and P. carotovorum subsp. odoriferum (Pco). RESULTS Thirty-two P. carotovorum strains had their whole genomes sequenced, including the first complete genome of Pco and another circular genome of Pcb, as well as the high-coverage genome sequences for 30 additional strains covering Pcc, Pcb, and Pco. In combination with 52 other publicly available genome sequences, the comparative genomics study of P. carotovorum and other four closely related species P. polaris, P. parmentieri, P. atrosepticum, and Candidatus P. maceratum was conducted focusing on CRISPR-Cas defense systems and pathogenicity determinants. Our analysis identified two CRISPR-Cas types (I-F and I-E) in Pectobacterium, as well as another I-C type in Dickeya that is not found in Pectobacterium. The core pathogenicity factors (e.g., plant cell wall-degrading enzymes) were highly conserved, whereas some factors (e.g., flagellin, siderophores, polysaccharides, protein secretion systems, and regulatory factors) were varied among these species and/or subspecies. Notably, a novel type of T6SS as well as the sorbitol metabolizing srl operon was identified to be specific to Pco in Pectobacterium. CONCLUSIONS This study not only advances the available knowledge about the genetic differentiation of individual subspecies of P. carotovorum, but also delineates the general genetic features of P. carotovorum by comparison with its four closely related species, thereby substantially enriching the extent of information now available for functional genomic investigations about Pectobacterium.
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Affiliation(s)
- Xiaoying Li
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097 People’s Republic of China
| | - Yali Ma
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097 People’s Republic of China
| | - Shuqing Liang
- Health Time Gene Institute, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Yu Tian
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097 People’s Republic of China
| | - Sanjun Yin
- Health Time Gene Institute, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Sisi Xie
- Health Time Gene Institute, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Hua Xie
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097 People’s Republic of China
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Ahmed FA, Larrea-Sarmiento A, Alvarez AM, Arif M. Genome-informed diagnostics for specific and rapid detection of Pectobacterium species using recombinase polymerase amplification coupled with a lateral flow device. Sci Rep 2018; 8:15972. [PMID: 30374117 PMCID: PMC6206099 DOI: 10.1038/s41598-018-34275-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/15/2018] [Indexed: 11/23/2022] Open
Abstract
Pectobacterium species cause serious bacterial soft rot diseases worldwide on economically important fruit and vegetable crops including tomato and potato. Accurate and simple methods are essential for rapid pathogen identification and timely management of the diseases. Recombinase polymerase amplification (RPA) combined with a lateral flow device (LFD) was developed for specific detection of Pectobacterium sp. directly from infected plant materials with no need for DNA isolation. The specificity of RPA-LFD was tested with 26 Pectobacterium sp. strains and 12 non-Pectobacterium species and no false positive or false negative outcomes were observed. RPA primers and probe for host control were also developed to detect the host genome for enhanced reliability and accuracy of the developed assay. The detection limit of 10 fg was obtained with both sensitivity and spiked sensitivity assays. No inhibitory effects were observed on the RPA assay when targets (pathogen and host) were directly detected from infected potato and tomato sap. The developed RPA assay has numerous applications from routine diagnostics at point-of-care, biosecurity, surveillance and disease management to epidemiological studies. In addition, this tool can also be used to discover reservoir hosts for Pectobacterium species.
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Affiliation(s)
- Firas A Ahmed
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
- Agriculture College, University of Kufa, Al-Najaf, Iraq
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States.
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Zoledowska S, Motyka-Pomagruk A, Sledz W, Mengoni A, Lojkowska E. High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes. BMC Genomics 2018; 19:751. [PMID: 30326842 PMCID: PMC6192338 DOI: 10.1186/s12864-018-5140-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/03/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline. RESULTS The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland. CONCLUSIONS We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.
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Affiliation(s)
- S Zoledowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - A Motyka-Pomagruk
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - W Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - A Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - E Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
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Abstract
Beginning in 2014, outbreaks of blackleg disease compromised potato (Solanum tuberosum) production in the northeastern United States. Disease severity was atypical for plantings with certified seed. During 2016, 43 samples with blackleg symptoms were analyzed, originating from more than 20 farms operating in New York State. A combination of techniques was employed to identify the blackleg pathogens: isolation in vitro, diagnostic PCR assays for Pectobacterium and Dickeya sp., pathogenicity assays, and DNA sequencing. Twenty-three bacterial isolates were obtained, the majority of which were designated D. dianthicola or P. parmentieri; two of the isolates were designated P. atrosepticum. All isolates were pathogenic in stem lesion and tuber soft rot assays and exhibited pectin degrading activity (pitting) in crystal violet pectate agar medium. Phylogenetic analyses of dnaX gene sequences placed all but one of the isolates into clades corresponding to D. dianthicola, P. parmentieri, or P. atrosepticum. One atypical isolate clustered with P. carotovorum subspecies. Data are consistent with the hypothesis that D. dianthicola from New York and the northeast are part of a single clade, and at least three different soft rot bacteria were associated with blackleg during 2016 in New York.
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Affiliation(s)
- Xing Ma
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Allison Schloop
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Bryan Swingle
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Keith L Perry
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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Rossmann S, Dees MW, Perminow J, Meadow R, Brurberg MB. Soft Rot Enterobacteriaceae Are Carried by a Large Range of Insect Species in Potato Fields. Appl Environ Microbiol 2018; 84:e00281-18. [PMID: 29625979 PMCID: PMC5981085 DOI: 10.1128/aem.00281-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
Pathogenic soft rot Enterobacteriaceae (SRE) belonging to the genera Pectobacterium and Dickeya cause diseases in potato and numerous other crops. Seed potatoes are the most important source of infection, but how pathogen-free tubers initially become infected remains an enigma. Since the 1920s, insects have been hypothesized to contribute to SRE transmission. To validate this hypothesis and to map the insect species potentially involved in SRE dispersal, we have analyzed the occurrence of SRE in insects recovered from potato fields over a period of 2 years. Twenty-eight yellow sticky traps were set up in 10 potato fields throughout Norway to attract and trap insects. Total DNA recovered from over 2,000 randomly chosen trapped insects was tested for SRE, using a specific quantitative PCR (qPCR) TaqMan assay, and insects that tested positive were identified by DNA barcoding. Although the occurrence of SRE-carrying insects varied, they were found in all the tested fields. While Delia species were dominant among the insects that carried the largest amount of SRE, more than 80 other SRE-carrying insect species were identified, and they had different levels of abundance. Additionally, the occurrence of SRE in three laboratory-reared insect species was analyzed, and this suggested that SRE are natural members of some insect microbiomes, with herbivorous Delia floralis carrying more SRE than the cabbage moth (Plutella xylostella) and carnivorous green lacewing larvae (Chrysoperla carnea). In summary, the high proportion, variety, and ubiquity of insects that carried SRE show the need to address this source of the pathogens to reduce the initial infection of seed material.IMPORTANCE Soft rot Enterobacteriaceae are among the most important pathogens of a wide range of vegetables and fruits. The bacteria cause severe rots in the field and in storage, leading to considerable harvest losses. In potato, efforts to understand how soft rot bacteria infect and spread between healthy plants have been made for over a century. Early on, fly larvae were implicated in the transmission of these bacteria. This work aimed at investigating the occurrence of soft rot bacteria in insects present in potato fields and at identifying the species of these insects to better understand the potential of this suspected source of transmission. In all tested potato fields, a large proportion of insects were found to carry soft rot bacteria. This suggests a need to give more weight to the role of insects in soft rot ecology and epidemiology to design more effective pest management strategies that integrate this factor.
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Affiliation(s)
- Simeon Rossmann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Merete Wiken Dees
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Juliana Perminow
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Richard Meadow
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - May Bente Brurberg
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Abstract
A powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immunity. Although the benefits of resisting phage infection are evident, this can come at a cost of inhibiting the acquisition of other beneficial genes through HGT. Despite the ability of CRISPR-Cas to limit HGT through conjugation and transformation, its role in transduction is largely overlooked. Transduction is the phage-mediated transfer of bacterial DNA between cells and arguably has the greatest impact on HGT. We demonstrate that in Pectobacterium atrosepticum, CRISPR-Cas can inhibit the transduction of plasmids and chromosomal loci. In addition, we detected phage-mediated transfer of a large plant pathogenicity genomic island and show that CRISPR-Cas can inhibit its transduction. Despite these inhibitory effects of CRISPR-Cas on transduction, its more common role in phage resistance promotes rather than diminishes HGT via transduction by protecting bacteria from phage infection. This protective effect can also increase transduction of phage-sensitive members of mixed populations. CRISPR-Cas systems themselves display evidence of HGT, but little is known about their lateral dissemination between bacteria and whether transduction can contribute. We show that, through transduction, bacteria can acquire an entire chromosomal CRISPR-Cas system, including cas genes and phage-targeting spacers. We propose that the positive effect of CRISPR-Cas phage immunity on enhancing transduction surpasses the rarer cases where gene flow by transduction is restricted.IMPORTANCE The generation of genetic diversity through acquisition of DNA is a powerful contributor to microbial evolution and occurs through transformation, conjugation, and transduction. Of these, transduction, the phage-mediated transfer of bacterial DNA, is arguably the major route for genetic exchange. CRISPR-Cas adaptive immune systems control gene transfer by conjugation and transformation, but transduction has been mostly overlooked. Our results indicate that CRISPR-Cas can impede, but typically enhances the transduction of plasmids, chromosomal genes, and pathogenicity islands. By limiting wild-type phage replication, CRISPR-Cas immunity increases transduction in both phage-resistant and -sensitive members of mixed populations. Furthermore, we demonstrate mobilization of a chromosomal CRISPR-Cas system containing phage-targeting spacers by generalized transduction, which might partly account for the uneven distribution of these systems in nature. Overall, the ability of CRISPR-Cas to promote transduction reveals an unexpected impact of adaptive immunity on horizontal gene transfer, with broader implications for microbial evolution.
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Affiliation(s)
- Bridget N J Watson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Raymond H J Staals
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
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Zoledowska S, Motyka A, Zukowska D, Sledz W, Lojkowska E. Population Structure and Biodiversity of Pectobacterium parmentieri Isolated from Potato Fields in Temperate Climate. Plant Dis 2018; 102:154-164. [PMID: 30673465 DOI: 10.1094/pdis-05-17-0761-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pectobacterium parmentieri (formerly Pectobacterium wasabiae) is a newly established species of pectinolytic plant-pathogenic bacteria responsible for the symptoms of soft rot and blackleg on potato. In this work, we describe biodiversity and the population structure of P. parmentieri strains isolated during two consecutive growing seasons from the seed potato fields in Poland. About 450 samples of diseased potato tubers, potato plants, or accompanying weeds were collected throughout the country and tested for the presence of P. parmentieri by molecular identification methods. We found that P. parmentieri strains commonly occur in almost all regions of Poland. Furthermore, these isolates constituted significant fraction of pectinolytic bacteria from seed potato fields because 16% (2013) and 13% (2014) of the analyzed plant samples were infected with P. parmentieri. Subsequently, a detailed characterization of the obtained strains was conducted basing on repetitive sequences profiling, recA-gene-based phylogeny, and phenotypic features. By applying repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR), we revealed the presence of five distinct genomic profiles among P. parmentieri strains, with profile I being the most abundant (approximately 44%). The performed recA gene-based phylogenetic analysis divided P. parmentieri isolates into two distinct clades, although the strains originating from different years did not group separately. Evaluation of the phenotypic traits playing crucial roles for the virulence of pectinolytic bacteria (namely, pectinase, cellulase and protease activities, and siderophore production, in addition to potato tissue maceration, swimming, and swarming motility) indicated some differences among the characterized strains. To the best of our knowledge, this is the first study that describes biodiversity and the population structure of P. parmentieri isolated in two growing seasons under temperate climate conditions and, hence, illustrates high heterogeneity within this species.
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Affiliation(s)
- Sabina Zoledowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Agata Motyka
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Dominika Zukowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Wojciech Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Ewa Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
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Joshi JR, Burdman S, Lipsky A, Yariv S, Yedidia I. Plant phenolic acids affect the virulence of Pectobacterium aroidearum and P. carotovorum ssp. brasiliense via quorum sensing regulation. Mol Plant Pathol 2016; 17:487-500. [PMID: 26177258 PMCID: PMC6638513 DOI: 10.1111/mpp.12295] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Several studies have reported effects of the plant phenolic acids cinnamic acid (CA) and salicylic acid (SA) on the virulence of soft rot enterobacteria. However, the mechanisms involved in these processes are not yet fully understood. Here, we investigated whether CA and SA interfere with the quorum sensing (QS) system of two Pectobacterium species, P. aroidearum and P. carotovorum ssp. brasiliense, which are known to produce N-acyl-homoserine lactone (AHL) QS signals. Our results clearly indicate that both phenolic compounds affect the QS machinery of the two species, consequently altering the expression of bacterial virulence factors. Although, in control treatments, the expression of QS-related genes increased over time, the exposure of bacteria to non-lethal concentrations of CA or SA inhibited the expression of QS genes, including expI, expR, PC1_1442 (luxR transcriptional regulator) and luxS (a component of the AI-2 system). Other virulence genes known to be regulated by the QS system, such as pecS, pel, peh and yheO, were also down-regulated relative to the control. In agreement with the low levels of expression of expI and expR, CA and SA also reduced the level of the AHL signal. The effects of CA and SA on AHL signalling were confirmed in compensation assays, in which exogenous application of N-(β-ketocaproyl)-l-homoserine lactone (eAHL) led to the recovery of the reduction in virulence caused by the two phenolic acids. Collectively, the results of gene expression studies, bioluminescence assays, virulence assays and compensation assays with eAHL clearly support a mechanism by which CA and SA interfere with Pectobacterium virulence via the QS machinery.
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Affiliation(s)
- Janak Raj Joshi
- Department of Plant Pathology and Microbiology and the Otto Warburg Minerva Center for Agricultural Biotechnology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Saul Burdman
- Department of Plant Pathology and Microbiology and the Otto Warburg Minerva Center for Agricultural Biotechnology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Alexander Lipsky
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Shaked Yariv
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Iris Yedidia
- Department of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
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Tomassetti S, Pontiggia D, Verrascina I, Reca IB, Francocci F, Salvi G, Cervone F, Ferrari S. Controlled expression of pectic enzymes in Arabidopsis thaliana enhances biomass conversion without adverse effects on growth. Phytochemistry 2015; 112:221-30. [PMID: 25242621 DOI: 10.1016/j.phytochem.2014.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/09/2014] [Accepted: 08/28/2014] [Indexed: 05/11/2023]
Abstract
Lignocellulosic biomass from agriculture wastes is a potential source of biofuel, but its use is currently limited by the recalcitrance of the plant cell wall to enzymatic digestion. Modification of the wall structural components can be a viable strategy to overcome this bottleneck. We have previously shown that the expression of a fungal polygalacturonase (pga2 from Aspergillus niger) in Arabidopsis and tobacco plants reduces the levels of de-esterified homogalacturonan in the cell wall and significantly increases saccharification efficiency. However, plants expressing pga2 show stunted growth and reduced biomass production, likely as a consequence of an extensive loss of pectin integrity during the whole plant life cycle. We report here that the expression in Arabidopsis of another pectic enzyme, the pectate lyase 1 (PL1) of Pectobacterium carotovorum, under the control of a chemically inducible promoter, results, after induction of the transgene, in a saccharification efficiency similar to that of plants expressing pga2. However, lines with high levels of transgene induction show reduced growth even in the absence of the inducer. To overcome the problem of plant fitness, we have generated Arabidopsis plants that express pga2 under the control of the promoter of SAG12, a gene expressed only during senescence. These plants expressed pga2 only at late stages of development, and their growth was comparable to that of WT plants. Notably, leaves and stems of transgenic plants were more easily digested by cellulase, compared to WT plants, only during senescence. Expression of cell wall-degrading enzymes at the end of the plant life cycle may be therefore a useful strategy to engineer crops unimpaired in biomass yield but improved for bioconversion.
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Affiliation(s)
- Susanna Tomassetti
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Daniela Pontiggia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Ilaria Verrascina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Ida Barbara Reca
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Fedra Francocci
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Gianni Salvi
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Felice Cervone
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy
| | - Simone Ferrari
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185 Roma, Italy.
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42
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Pour L, Mohammadi M, Khodakaramian G, Moghadam BS. PHENOTYPIC AND MOLECULAR DIFFERENTIATION OF PECTOBACTERIUM AND DICKEYA SPP. CAUSING POTATO TUBER AND STEM ROT IN NORTH-WESTERN PROVINCES OF IRAN. Commun Agric Appl Biol Sci 2015; 80:611-616. [PMID: 27141762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Iran is one of the most important potato-producing countries in Asia and Oceania. Approximately 20 percent of potato cultivation in Iran occurs in the North-western provinces. Pectobacterium and Dickeya species cause important diseases in potato crop. They may incite blackleg and are responsible for tuber soft rot in storage, thereby reducing yield and quality. In order to identify and differentiate the species of soft rot bacteria, potato stems and tubers showing soft rot symptoms were collected from potato fields in North-western Iran. A total of fifty strains belonging to Pectobacterium and Dickeya species were isolated and identified from the infected tissues. Phenotypic characterization revealed a considerable variation among strains thus dividing them into five separate groups. Group 1 strains belonged to Dickeya chrysanthemi that were different from the type strain in malonate utilization. Group 2 strains were similar to Pectobacterium betavascularum but were different from the type strain in utilization of raffinose, citrate and D-sorbitol. Group 3 strains showed more resemblance to P. wasabiae but were different from the type strain with respect to acetoin production. Group 4 strains belonged to P. carotovorum subsp. carotovorum (Pcc) and group 5 strains were identified as intersubspecific of Pcc and P. carotovorum subsp. odoriferum. Polymerase chain reaction using pelY primers identified strains belonging to Pectobacterium species but not P. betavascularum.
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43
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Dankevych LA, Zakharova OM, Mel'nychuk MD, Votselko SK, Patyka VP. [REP-PCR analysis of rapa's bacterial diseases agents]. Mikrobiol Z 2014; 76:17-25. [PMID: 25199341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BOX, ERIC and REP--genomic fingerprints of 12 isolated and 10 typical pathogenic for rape bacterial strains Pseudomonas, Xanthomonas and Pectobacterium genera have been analyzed. The affinity of isolated strains with representatives of P. marginalis pv. marginalis, Pseudomonas fluorescens and Xanthomonas campestris pv. campestris species has been determined.
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Richter C, Dy RL, McKenzie RE, Watson BNJ, Taylor C, Chang JT, McNeil MB, Staals RHJ, Fineran PC. Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res 2014; 42:8516-26. [PMID: 24990370 PMCID: PMC4117759 DOI: 10.1093/nar/gku527] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/23/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼ 350 new spacers acquired in priming events and identified a 5'-protospacer-GG-3' protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2-3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.
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Affiliation(s)
- Corinna Richter
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ron L Dy
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Rebecca E McKenzie
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Bridget N J Watson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Corinda Taylor
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - James T Chang
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Raymond H J Staals
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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Gogoleva NE, Shlykova LV, Gorshkov VI, Daminova AG, Gogolev IV. [The effect of topology of quorum sensing-related genes in Pectobacterium atrosepticumon their expression]. Mol Biol (Mosk) 2014; 48:669-676. [PMID: 25842850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In prokaryotic genomes, the neighboring genes are often located on the complementary DNA strands and adjoin each other by their 5'- or 3'-ends or even overlap by their open reading frames. It was suggested that such gene topology hasfunctional purpose providing the regulation of their expression. For those genes that overlap by their coding 3'-termini this assumption has not been confirmed experimentally. In a broad group of bacteria that belong to proteobacteria such a convergent gene arrangement is typical for functionally connected quorum sensing-related genes "P" and "R" that encode synthases of N-acyl homoserine lactones and their sensors, respectively. In the present study on the example of overlapping quorum sensing-related genes of plant pathogenic bacterium Pectobacterium atrosepticum SCRI1043--expI and expR it was shown that the topology of these genes determines the regula- tion of their expression.
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Laasik E, Põllumaa L, Pasanen M, Mattinen L, Pirhonen M, Mäe A. Expression of nipP.w of Pectobacterium wasabiae is dependent on functional flgKL flagellar genes. Microbiology (Reading) 2014; 160:179-186. [PMID: 24173527 DOI: 10.1099/mic.0.071092-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
While flagellum-driven motility is hypothesized to play a role in the virulence of Pectobacterium species, there is no direct evidence that genes involved in flagellum assembly regulate the synthesis of virulence factors. The purpose of this study was to identify genes that affect the production or secretion of necrosis-inducing protein (Nip) in the strain SCC3193. Transposon mutagenesis of an RpoS strain overexpressing NipP.w was performed, and a mutant associated with decreased necrosis of tobacco leaves was detected. The mutant contained a transposon in the regulatory region upstream of the flagellar genes flgK and flgL. Additional mutants were generated related to the flagellar genes fliC and fliA. The mutation in flgKL, but not those in fliC and fliA, inhibited nipP.w transcription. Moreover, the regulatory effect of the flgKL mutation on nipP.w transcription was partially dependent on the Rcs phosphorelay. Secretion of NipP.w was also dependent on a type II secretion mechanism. Overall, the results of this study indicate that the flgKL mutation is responsible for reduced motility and lower levels of nipP.w expression.
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Affiliation(s)
- Eve Laasik
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Lee Põllumaa
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Miia Pasanen
- Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Finland
| | - Laura Mattinen
- Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Finland
| | - Minna Pirhonen
- Department of Agricultural Sciences, PO Box 27, 00014 University of Helsinki, Finland
| | - Andres Mäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
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des Essarts YR, Sabbah M, Comte A, Soulère L, Queneau Y, Dessaux Y, Hélias V, Faure D. N,N'-alkylated Imidazolium-derivatives act as quorum-sensing inhibitors targeting the Pectobacterium atrosepticum-induced symptoms on potato tubers. Int J Mol Sci 2013; 14:19976-86. [PMID: 24108370 PMCID: PMC3821598 DOI: 10.3390/ijms141019976] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 11/17/2022] Open
Abstract
Bacteria belonging to the Pectobacterium genus are the causative agents of the blackleg and soft-rot diseases that affect potato plants and tubers worldwide. In Pectobacterium, the expression of the virulence genes is controlled by quorum-sensing (QS) and N-acylhomoserine lactones (AHLs). In this work, we screened a chemical library of QS-inhibitors (QSIs) and AHL-analogs to find novel QSIs targeting the virulence of Pectobacterium. Four N,N′-bisalkylated imidazolium salts were identified as QSIs; they were active at the μM range. In potato tuber assays, two of them were able to decrease the severity of the symptoms provoked by P. atrosepticum. This work extends the range of the QSIs acting on the Pectobacterium-induced soft-rot disease.
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Affiliation(s)
- Yannick Raoul des Essarts
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, Gif-sur-Yvette 91198, France; E-Mails: (Y.R.E.); (Y.D.)
- FN3PT/RD3PT, Fédération Nationale des Producteurs de Plants de Pomme de terre, 43-45 Rue de Naples, Paris F-75008, France; E-Mail:
| | - Mohamad Sabbah
- INSA Lyon, ICBMS, UMR 5246, CNRS, Université Lyon 1, INSA-Lyon, CPE-Lyon, Bât J. Verne, 20 av A. Einstein, 69621 Villeurbanne Cedex, France; E-Mails: (M.S.); (L.S.); (Y.Q.)
| | - Arnaud Comte
- Service de Chimiothèque, ICBMS, UMR 5246, CNRS, Université Lyon 1, INSA-Lyon, CPE-Lyon, Bât Curien, 43 bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France; E-Mail:
| | - Laurent Soulère
- INSA Lyon, ICBMS, UMR 5246, CNRS, Université Lyon 1, INSA-Lyon, CPE-Lyon, Bât J. Verne, 20 av A. Einstein, 69621 Villeurbanne Cedex, France; E-Mails: (M.S.); (L.S.); (Y.Q.)
| | - Yves Queneau
- INSA Lyon, ICBMS, UMR 5246, CNRS, Université Lyon 1, INSA-Lyon, CPE-Lyon, Bât J. Verne, 20 av A. Einstein, 69621 Villeurbanne Cedex, France; E-Mails: (M.S.); (L.S.); (Y.Q.)
| | - Yves Dessaux
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, Gif-sur-Yvette 91198, France; E-Mails: (Y.R.E.); (Y.D.)
| | - Valérie Hélias
- FN3PT/RD3PT, Fédération Nationale des Producteurs de Plants de Pomme de terre, 43-45 Rue de Naples, Paris F-75008, France; E-Mail:
- Institut National de la Recherche Agronomique, UMR 1349IGEPP, Le Rheu F-35653, France
| | - Denis Faure
- Centre National de la Recherche Scientifique, Institut des Sciences du Végétal, UPR 2355, Gif-sur-Yvette 91198, France; E-Mails: (Y.R.E.); (Y.D.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-1-69-82-35-77; Fax: +33-1-69-82-36-95
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Nykyri J, Mattinen L, Niemi O, Adhikari S, Kõiv V, Somervuo P, Fang X, Auvinen P, Mäe A, Palva ET, Pirhonen M. Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193. PLoS One 2013; 8:e73718. [PMID: 24040039 PMCID: PMC3767616 DOI: 10.1371/journal.pone.0073718] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/22/2013] [Indexed: 12/18/2022] Open
Abstract
In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.
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Affiliation(s)
- Johanna Nykyri
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Laura Mattinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Outi Niemi
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Satish Adhikari
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Viia Kõiv
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Panu Somervuo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Xin Fang
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Andres Mäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - E. Tapio Palva
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Minna Pirhonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- * E-mail:
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Abstract
Several pectolytic bacterial strains, mainly isolated from monocotyledonous plants and previously identified as Pectobacterium carotovorum, were thought to belong to a novel species after several taxonomic analyses including DNA-DNA hybridization. In 16S rRNA gene sequence analyses, these strains had a similarity of >97.9 % to the 16S rRNA gene sequence of strains representing six other pectobacterial species and subspecies. These strains, represented by strain SCRI 109(T), also showed some unique chemotaxonomic features and quantitative differences in polar lipids, lipoquinones and fatty acids. A specific feature of strain SCRI 109(T) was the presence of DMK-8 lipoquinone, while the dominant fatty acids were the summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c), the unsaturated fatty acid C18 : 1ω7c and straight chain fatty acids, mainly C16 : 0. The DNA G+C content of strain SCRI 109(T) was 50.2 mol%. The taxonomic status of strain SCRI 109(T) and related strains in 16S rRNA gene sequence, chemotaxonomic, and physiological analyses was corroborated by the distinct clustering of these strains in multi-locus sequence analyses. It is proposed that these strains represent a novel species for which the name Pectobacterium aroidearum sp. nov. is proposed; the type strain is SCRI 109(T) ( = NCPPB 929(T) = LMG 2417(T) = ICMP 1522(T)).
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Affiliation(s)
- Shaza Nabhan
- Institute for Plant Disease and Plant Protection, Hannover University, D-30419 Hannover, Germany
| | - Solke H De Boer
- Charlottetown Laboratory, Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PE, C1A 5T1, Canada
| | - Edgar Maiss
- Institute for Plant Disease and Plant Protection, Hannover University, D-30419 Hannover, Germany
| | - Kerstin Wydra
- Centre for Tropical and Subtropical Agriculture and Forestry, Georg-August-University, D-37077 Gottingen, Germany
- Institute for Plant Disease and Plant Protection, Hannover University, D-30419 Hannover, Germany
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50
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Cubitt MF, Hedley PE, Williamson NR, Morris JA, Campbell E, Toth IK, Salmond GPC. A metabolic regulator modulates virulence and quorum sensing signal production in Pectobacterium atrosepticum. Mol Plant Microbe Interact 2013; 26:356-366. [PMID: 23113713 DOI: 10.1094/mpmi-09-12-0210-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant cell wall-degrading enzymes (PCWDE) are key virulence determinants in the pathogenesis of the potato pathogen Pectobacterium atrosepticum. In this study, we report the impact on virulence of a transposon insertion mutation in the metJ gene that codes for the repressor of the methionine biosynthesis regulon. In a mutant strain defective for the small regulatory RNA rsmB, PCWDE are not produced and virulence in potato tubers is almost totally abolished. However, when the metJ gene is disrupted in this background, the rsmB(-) phenotype is suppressed and virulence and PCWDE production are restored. Additionally, when metJ is disrupted, production of the quorum-sensing signal, N-(3-oxohexanoyl)-homoserine lactone, is increased. The metJ mutant strains showed pleiotropic transcriptional impacts affecting approximately a quarter of the genome. Genes involved in methionine biosynthesis were most highly upregulated but many virulence-associated transcripts were also upregulated. This is the first report of the impact of the MetJ repressor on virulence in bacteria.
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Affiliation(s)
- Marion F Cubitt
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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