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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] [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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Flagellar Phenotypes Impact on Bacterial Transport and Deposition Behavior in Porous Media: Case of Salmonella enterica Serovar Typhimurium. Int J Mol Sci 2022; 23:ijms232214460. [PMID: 36430938 PMCID: PMC9698738 DOI: 10.3390/ijms232214460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Bacterial contamination of groundwater has always been an ecological problem worthy of attention. In this study, Salmonella enterica serovar Typhimurium with different flagellar phenotypes mainly characterized during host-pathogen interaction were analyzed for their transport and deposition behavior in porous media. Column transport experiments and a modified mobile-immobile model were applicated on different strains with flagellar motility (wild-type) or without motility (ΔmotAB), without flagella (ΔflgKL), methylated and unmethylated flagellin (ΔfliB), and different flagella phases (fliCON, fljBON). Results showed that flagella motility could promote bacterial transport and deposition due to their biological advantages of moving and attaching to surfaces. We also found that the presence of non-motile flagella improved bacterial adhesion according to a higher retention rate of the ΔmotAB strain compared to the ΔflgKL strain. This indicated that bacteria flagella and motility both had promoting effects on bacterial deposition in sandy porous media. Flagella phases influenced the bacterial movement; the fliCON strain went faster through the column than the fljBON strain. Moreover, flagella methylation was found to favor bacterial transport and deposition. Overall, flagellar modifications affect Salmonella enterica serovar Typhimurium transport and deposition behavior in different ways in environmental conditions.
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Condemine G, Le Derout B. Identification of new Dickeya dadantii virulence factors secreted by the type 2 secretion system. PLoS One 2022; 17:e0265075. [PMID: 35417462 PMCID: PMC9007343 DOI: 10.1371/journal.pone.0265075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
Dickeya are plant pathogenic bacteria able to provoke disease on a wide range of plants. A type 2 secretion system (T2SS) named Out is necessary for Dickeya virulence. Previous studies showed that the D. dadantii T2SS secretes a wide range of plant cell wall degrading enzymes, including pectinases and a cellulase. However, the full repertoire of exoproteins it can secrete has probably not yet been identified. Secreted proteins possess a signal peptide and are first addressed to the periplasm before their recruitment by Out. T2SS-specific secretion signals remain unknown which prevents in silico identification of T2SS substrates. To identify new Out substrates, we analyzed D. dadantii transcriptome data obtained in plant infection condition and searched for genes strongly induced and encoding proteins with a signal sequence. We identified four new Out-secreted proteins: the expansin YoaJ, the putative virulence factor VirK and two proteins of the DUF 4879 family, SvfA and SvfB. We showed that SvfA and SvfB are required for full virulence of D. dadantii and that svf genes are present in a variable number of copies in other Pectobacteriaceae, up to three in D. fanghzongdai. This work opens the way to the study of the role of non-pectinolytic proteins secreted by the Out pathway in Pectobacteriaceae.
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Affiliation(s)
- Guy Condemine
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
- * E-mail:
| | - Bastien Le Derout
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
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Wang H, Wang Y, Humphris S, Nie W, Zhang P, Wright F, Campbell E, Hu B, Fan J, Toth I. Pectobacterium atrosepticum KDPG aldolase, Eda, participates in the Entner-Doudoroff pathway and independently inhibits expression of virulence determinants. MOLECULAR PLANT PATHOLOGY 2021; 22:271-283. [PMID: 33301200 PMCID: PMC7814964 DOI: 10.1111/mpp.13025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 05/22/2023]
Abstract
Pectobacterium carotovorum has an incomplete Entner-Doudoroff (ED) pathway, including enzyme 2-keto-3-deoxy-6-phosphogluconate aldolase (Eda) but lacking phosphogluconate dehydratase (Edd), while P. atrosepticum (Pba) has a complete pathway. To understand the role of the ED pathway in Pectobacterium infection, mutants of these two key enzymes, Δeda and Δedd, were constructed in Pba SCRI1039. Δeda exhibited significant decreased virulence on potato tubers and colonization in planta and was greatly attenuated in pectinase activity and the ability to use pectin breakdown products, including polygalacturonic acid (PGA) and galacturonic acid. These reduced phenotypes were restored following complementation with an external vector expressing eda. Quantitative reverse transcription PCR analysis revealed that expression of the pectinase genes pelA, pelC, pehN, pelW, and pmeB in Δeda cultured in pyruvate, with or without PGA, was significantly reduced compared to the wild type, while genes for virulence regulators (kdgR, hexR, hexA, and rsmA) remained unchanged. However, Δedd showed similar phenotypes to the wild type. To our knowledge, this is the first demonstration that disruption of eda has a feedback effect on inhibiting pectin degradation and that Eda is involved in building the arsenal of pectinases needed during infection by Pectobacterium.
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Affiliation(s)
- Huan Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
- Institute of Agricultural Science of Taihu Lake DistrictSuzhouChina
| | - Yujie Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Sonia Humphris
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
| | - Weihua Nie
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Pengfei Zhang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Frank Wright
- Bioinformatics and StatisticsJames Hutton InstituteDundeeUK
| | - Emma Campbell
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
| | - Baishi Hu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Jiaqin Fan
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Ian Toth
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
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Niemi O, Laine P, Koskinen P, Pasanen M, Pennanen V, Harjunpää H, Nykyri J, Holm L, Paulin L, Auvinen P, Palva ET, Pirhonen M. Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1. Stand Genomic Sci 2017; 12:87. [PMID: 29276572 PMCID: PMC5738896 DOI: 10.1186/s40793-017-0301-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/05/2017] [Indexed: 01/01/2023] Open
Abstract
Bacteria of the genus Pectobacterium are economically important plant pathogens that cause soft rot disease on a wide variety of plant species. Here, we report the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot model strain isolated from a diseased potato tuber in the early 1980's. The genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349 are protein coding and 102 are RNA genes.
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Affiliation(s)
- Outi Niemi
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Patrik Koskinen
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Miia Pasanen
- Plant Pathology, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ville Pennanen
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Heidi Harjunpää
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Johanna Nykyri
- Plant Pathology, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Liisa Holm
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - E. Tapio Palva
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Minna Pirhonen
- Plant Pathology, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Abstract
Type II secretion (T2S) is one means by which Gram-negative pathogens secrete proteins into the extracellular milieu and/or host organisms. Based upon recent genome sequencing, it is clear that T2S is largely restricted to the Proteobacteria, occurring in many, but not all, genera in the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria classes. Prominent human and/or animal pathogens that express a T2S system(s) include Acinetobacter baumannii, Burkholderia pseudomallei, Chlamydia trachomatis, Escherichia coli, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Vibrio cholerae, and Yersinia enterocolitica T2S-expressing plant pathogens include Dickeya dadantii, Erwinia amylovora, Pectobacterium carotovorum, Ralstonia solanacearum, Xanthomonas campestris, Xanthomonas oryzae, and Xylella fastidiosa T2S also occurs in nonpathogenic bacteria, facilitating symbioses, among other things. The output of a T2S system can range from only one to dozens of secreted proteins, encompassing a diverse array of toxins, degradative enzymes, and other effectors, including novel proteins. Pathogenic processes mediated by T2S include the death of host cells, degradation of tissue, suppression of innate immunity, adherence to host surfaces, biofilm formation, invasion into and growth within host cells, nutrient assimilation, and alterations in host ion flux. The reach of T2S is perhaps best illustrated by those bacteria that clearly use it for both environmental survival and virulence; e.g., L. pneumophila employs T2S for infection of amoebae, growth within lung cells, dampening of cytokines, and tissue destruction. This minireview provides an update on the types of bacteria that have T2S, the kinds of proteins that are secreted via T2S, and how T2S substrates promote infection.
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