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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 MANAGEMENT SCIENCE 2024; 80:687-697. [PMID: 37758685 DOI: 10.1002/ps.7797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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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 DISEASE 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] [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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Wasendorf C, Schmitz-Esser S, Eischeid CJ, Leyhe MJ, Nelson EN, Rahic-Seggerman FM, Sullivan KE, Peters NT. Genome analysis of Erwinia persicina reveals implications for soft rot pathogenicity in plants. Front Microbiol 2022; 13:1001139. [DOI: 10.3389/fmicb.2022.1001139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Soft rot disease causes devastating losses to crop plants all over the world, with up to 90% loss in tropical climates. To better understand this economically important disease, we isolated four soft rot-causing Erwinia persicina strains from rotted vegetables. Notably, E. persicina has only recently been identified as a soft rot pathogen and a comprehensive genomic analysis and comparison has yet to be conducted. Here, we provide the first genomic analysis of E. persicina, compared to Pectobacterium carotovorum, P. carotovorum, and associated Erwinia plant pathogens. We found that E. persicina shares common genomic features with other Erwinia species and P. carotovorum, while having its own unique characteristics as well. The E. persicina strains examined here lack Type II and Type III secretion systems, commonly used to secrete pectolytic enzymes and evade the host immune response, respectively. E. persicina contains fewer putative pectolytic enzymes than P. carotovorum and lacks the Out cluster of the Type II secretion system while harboring a siderophore that causes a unique pink pigmentation during soft rot infections. Interestingly, a putative phenolic acid decarboxylase is present in the E. persicina strains and some soft rot pathogens, but absent in other Erwinia species, thus potentially providing an important factor for soft rot. All four E. persicina isolates obtained here and many other E. persicina genomes contain plasmids larger than 100 kbp that encode proteins likely important for adaptation to plant hosts. This research provides new insights into the possible mechanisms of soft rot disease by E. persicina and potential targets for diagnostic tools and control measures.
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Smoktunowicz M, Jonca J, Stachowska A, May M, Waleron MM, Waleron M, Waleron K. The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes. Pathogens 2022; 11:pathogens11070728. [PMID: 35889973 PMCID: PMC9319320 DOI: 10.3390/pathogens11070728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria of the genus Pectobacterium are globally occurring pathogens that infect a broad spectrum of plants. The plant cell wall degrading enzymes allow them to cause diseases like soft rot and blackleg. Worldwide trade and exchange of plant material together with the accompanying microorganisms contributed to the rapid spread and consequently the acquisition of new traits by bacteria. The 161 pectinolytic strains were isolated from symptomless vegetables and ornamental plants acquired from Polish and foreign local food markets. All strains except four Dickeya isolates were identified as belonging to the Pectobacterium genus by PCR with species-specific primers and recA gene sequencing. The newly isolated bacteria were assigned to eight species, P. versatile (50 strains), P. carotovorum (33), P. brasiliense (27), P. atrosepticum (19), P. parmentieri (12), P. polaris (11), P. parvum (3) and P. odoriferum (2). ERIC PCR and phenotypic characteristics revealed high heterogeneity among P. carotovorum, P. brasiliense and P. versatile isolates. Moreover, a subset of the newly isolated strains was characterised by high tolerance to changing environmental conditions such as salinity, pH and water availability. These bacteria can effectively macerate the tissues of various plants, including potato, chicory and orchid. Our results indicate that Pectobacterium strains isolated from internationally traded, symptomless vegetables and ornamental plants have high potential for adaptation to adverse environmental conditions and to infect various host plants. These features may contribute to the success of the genus Pectobacterium in spreading between different climatic zones and facilitate the colonisation of different ecological niches.
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Affiliation(s)
- Magdalena Smoktunowicz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland;
| | - Joanna Jonca
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Aneta Stachowska
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Michal May
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Michal Mateusz Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
| | - Malgorzata Waleron
- Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland; (J.J.); (A.S.); (M.M.); (M.M.W.)
- Correspondence: (M.W.); (K.W.)
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland;
- Correspondence: (M.W.); (K.W.)
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Han W, Wang J, Li Z, Pan Y, Zhang D, Zhao D, Li Q, Yang Z, Zhu J. First Report of Pectobacterium versatile Causing Aerial Stem Rot of Potato in China. PLANT DISEASE 2022; 106:PDIS06211264PDN. [PMID: 34384251 DOI: 10.1094/pdis-06-21-1264-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Wanxin Han
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Jinhui Wang
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Zheng Li
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Yang Pan
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Dai Zhang
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Dongmei Zhao
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Qian Li
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
| | - Zhihui Yang
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding 071001, China
| | - Jiehua Zhu
- Hebei Agricultural University, College of Plant Protection, Baoding 071001, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding 071001, China
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6
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Ma X, Stodghill P, Gao M, Perry KL, Swingle B. Identification of Pectobacterium versatile Causing Blackleg of Potato in New York State. PLANT DISEASE 2021; 105:2585-2594. [PMID: 33404272 DOI: 10.1094/pdis-09-20-2089-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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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Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco. Microorganisms 2020; 8:microorganisms8060895. [PMID: 32545839 PMCID: PMC7356628 DOI: 10.3390/microorganisms8060895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022] Open
Abstract
Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gapA gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to P. versatile (19%), P. carotovorum (3%), P. polaris (5%), P. brasiliense (56%) and D. dianthicola (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. D. dianthicola were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, D. dianthicola isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of D. dianthicola LAR.16.03.LID was obtained and compared with other D. dianthicola genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a D. dianthicola strain isolated in Morocco that will be suitable for further epidemiological studies.
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Pasanen M, Waleron M, Schott T, Cleenwerck I, Misztak A, Waleron K, Pritchard L, Bakr R, Degefu Y, van der Wolf J, Vandamme P, Pirhonen M. Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence. Int J Syst Evol Microbiol 2020; 70:2440-2448. [PMID: 32100697 PMCID: PMC7395620 DOI: 10.1099/ijsem.0.004057] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/25/2022] Open
Abstract
Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
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Affiliation(s)
- Miia Pasanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Malgorzata Waleron
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | | | - Ilse Cleenwerck
- Ghent University, BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Agnieszka Misztak
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Waleron
- Department of Pharmaceutical Microbiology, Medical University of Gdansk, Gdańsk, Poland
| | - Leighton Pritchard
- Information and Computational Sciences, The James Hutton Institute, Dundee, Scotland, UK
- Present address: Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Ramadan Bakr
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Present address: Department of Agricultural Botany, Faculty of Agriculture, Menoufia University, Shibin Elkom, Egypt
| | | | - Jan van der Wolf
- Wageningen University and Research, Bio-interactions and Plant Health, Wageningen, The Netherlands
| | - Peter Vandamme
- Ghent University, BCCM/LMG Bacteria Collection, Ghent, Belgium
| | - Minna Pirhonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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van den Bosch TJM, Niemi O, Welte CU. Single gene enables plant pathogenic Pectobacterium to overcome host-specific chemical defence. MOLECULAR PLANT PATHOLOGY 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] [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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Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium. Pathogens 2019; 8:pathogens8040247. [PMID: 31756888 PMCID: PMC6963963 DOI: 10.3390/pathogens8040247] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
The Pectobacterium genus comprises pectolytic enterobacteria defined as the causal agents of soft rot, blackleg, and aerial stem rot diseases of potato and economically important crops. In this study, we undertook extensive genome-wide comparative analyses of twelve species that conform the Pectobacterium genus. Bioinformatics approaches outlined a low nucleotide identity of P. parmentieri and P. wasabiae with other species, while P. carotovorum subsp. odoriferum was shown to harbor numerous pseudogenes, which suggests low coding capacity and genomic degradation. The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. The analyses unveiled a noteworthy heterogeneity in the pathogenicity determinants. Specifically, phytotoxins, polysaccharides, iron uptake systems, and the type secretion systems III-V were observed in just some species. Likewise, a comparison of gene clusters encoding antimicrobial compounds put in evidence for high conservation of carotovoricin, whereas a few species possessed the phenazine, carbapenem, and carocins. Moreover, three clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) systems: I-E, I-F, and III-A were identified. Surrounding some CRISPR-Cas regions, different toxin and antitoxin systems were found, which suggests bacterial suicide in the case of an immune system failure. Multiple whole-genome alignments shed light on to the presence of a novel cellobiose phosphotransferase system (PTS) exclusive to P. parmenteri, and an unreported T5SS conserved in almost all species. Several regions that were associated with virulence, microbe antagonism, and adaptive immune systems were predicted within genomic islands, which underscored the essential role that horizontal gene transfer has imparted in the dynamic evolution and speciation of Pectobacterium species. Overall, the results decipher the different strategies that each species has developed to infect their hosts, outcompete for food resources, and defend against bacteriophages. Our investigation provides novel genetic insights that will assist in understanding the pathogenic lifestyle of Pectobacterium, a genus that jeopardizes the agriculture sustainability of important crops worldwide.
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Waleron M, Misztak A, Waleron M, Franczuk M, Jońca J, Wielgomas B, Mikiciński A, Popović T, Waleron K. Pectobacterium zantedeschiae sp. nov. a new species of a soft rot pathogen isolated from Calla lily (Zantedeschia spp.). Syst Appl Microbiol 2019; 42:275-283. [DOI: 10.1016/j.syapm.2018.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 11/24/2022]
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12
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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] [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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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] [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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Draft Genome Sequences of New Genomospecies " Candidatus Pectobacterium maceratum" Strains, Which Cause Soft Rot in Plants. GENOME ANNOUNCEMENTS 2018; 6:6/15/e00260-18. [PMID: 29650577 PMCID: PMC5897815 DOI: 10.1128/genomea.00260-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Investigation of collections of phytopathogenic bacteria has revealed some strains distinct from known Pectobacterium spp. We report here the draft genome sequences of five such strains, isolated during the period of 1947 to 2012. Based on comparative genomics, we propose a new candidate genomospecies of the genus Pectobacterium, “Candidatus Pectobacterium maceratum.”
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