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Ouyang X, Liu G, Guo L, Wu G, Xu P, Zhao YL, Tang H. A multifunctional flavoprotein monooxygenase HspB for hydroxylation and C-C cleavage of 6-hydroxy-3-succinoyl-pyridine. Appl Environ Microbiol 2024; 90:e0225523. [PMID: 38415602 PMCID: PMC10952382 DOI: 10.1128/aem.02255-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024] Open
Abstract
Flavoprotein monooxygenases catalyze reactions, including hydroxylation and epoxidation, involved in the catabolism, detoxification, and biosynthesis of natural substrates and industrial contaminants. Among them, the 6-hydroxy-3-succinoyl-pyridine (HSP) monooxygenase (HspB) from Pseudomonas putida S16 facilitates the hydroxylation and C-C bond cleavage of the pyridine ring in nicotine. However, the mechanism for biodegradation remains elusive. Here, we refined the crystal structure of HspB and elucidated the detailed mechanism behind the oxidative hydroxylation and C-C cleavage processes. Leveraging structural information about domains for binding the cofactor flavin adenine dinucleotide (FAD) and HSP substrate, we used molecular dynamics simulations and quantum/molecular mechanics calculations to demonstrate that the transfer of an oxygen atom from the reactive FAD peroxide species (C4a-hydroperoxyflavin) to the C3 atom in the HSP substrate constitutes a rate-limiting step, with a calculated reaction barrier of about 20 kcal/mol. Subsequently, the hydrogen atom was rebounded to the FAD cofactor, forming C4a-hydroxyflavin. The residue Cys218 then catalyzed the subsequent hydrolytic process of C-C cleavage. Our findings contribute to a deeper understanding of the versatile functions of flavoproteins in the natural transformation of pyridine and HspB in nicotine degradation.IMPORTANCEPseudomonas putida S16 plays a pivotal role in degrading nicotine, a toxic pyridine derivative that poses significant environmental challenges. This study highlights a key enzyme, HspB (6-hydroxy-3-succinoyl-pyridine monooxygenase), in breaking down nicotine through the pyrrolidine pathway. Utilizing dioxygen and a flavin adenine dinucleotide cofactor, HspB hydroxylates and cleaves the substrate's side chain. Structural analysis of the refined HspB crystal structure, combined with state-of-the-art computations, reveals its distinctive mechanism. The crucial function of Cys218 was never discovered in its homologous enzymes. Our findings not only deepen our understanding of bacterial nicotine degradation but also open avenues for applications in both environmental cleanup and pharmaceutical development.
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Affiliation(s)
- Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gongquan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lihua Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Clough SE, Elphinstone JG, Friman VP. Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria. J Evol Biol 2024; 37:225-237. [PMID: 38290003 DOI: 10.1093/jeb/voae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/27/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an in vitro experimental evolution approach to investigate if the phytopathogenic Ralstonia solanacearum bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We further asked if tolerance was specific to pairs of R. solanacearum and Pseudomonas strains and certain antimicrobial compounds produced by Pseudomonas. We found that while all R. solanacearum strains could initially be inhibited by Pseudomonas strains, this inhibition decreased following successive subculturing with or without Pseudomonas supernatants. Using separate tolerance assays, we show that the majority of R. solanacearum strains evolved increased tolerance to multiple Pseudomonas strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by Pseudomonas strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.
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Affiliation(s)
- Sophie E Clough
- Department of Biology, University of York, York, United Kingdom
- Department of Biosciences, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - John G Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, York, United Kingdom
| | - Ville-Perti Friman
- Department of Biology, University of York, York, United Kingdom
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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Baroukh C, Cottret L, Pires E, Peyraud R, Guidot A, Genin S. Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex. mSystems 2023; 8:e0008323. [PMID: 37341493 PMCID: PMC10470067 DOI: 10.1128/msystems.00083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/14/2023] [Indexed: 06/22/2023] Open
Abstract
All the strains grouped under the species Ralstonia solanacearum represent a species complex responsible for many diseases on agricultural crops throughout the world. The strains have different lifestyles and host range. Here, we investigated whether specific metabolic pathways contribute to strain diversification. To this end, we carried out systematic comparisons on 11 strains representing the diversity of the species complex. We reconstructed the metabolic network of each strain from its genome sequence and looked for the metabolic pathways differentiating the different reconstructed networks and, by extension, the different strains. Finally, we conducted an experimental validation by determining the metabolic profile of each strain with the Biolog technology. Results revealed that the metabolism is conserved between strains, with a core metabolism composed of 82% of the pan-reactome. The three species composing the species complex could be distinguished according to the presence/absence of some metabolic pathways, in particular, one involving salicylic acid degradation. Phenotypic assays revealed that the trophic preferences on organic acids and several amino acids such as glutamine, glutamate, aspartate, and asparagine are conserved between strains. Finally, we generated mutants lacking the quorum-sensing-dependent regulator PhcA in four diverse strains, and we showed that the phcA-dependent trade-off between growth and production of virulence factors is conserved across the R. solanacearum species complex. IMPORTANCE Ralstonia solanacearum is one of the most important threats to plant health worldwide, causing disease on a very large range of agricultural crops such as tomato or potato. Behind the R. solanacearum name are hundreds of strains with different host range and lifestyle, classified into three species. Studying the differences between strains allows to better apprehend the biology of the pathogens and the specificity of some strains. None of the published genomic comparative studies have focused on the metabolism of the strains so far. We developed a new bioinformatic pipeline to build high-quality metabolic networks and used a combination of metabolic modeling and high-throughput phenotypic Biolog microplates to look for the metabolic differences between 11 strains across the three species. Our study revealed that genes encoding enzymes are overall conserved, with few variations between strains. However, more variations were observed when considering substrate usage. These variations probably result from regulation rather than the presence or absence of enzymes in the genome.
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Affiliation(s)
- Caroline Baroukh
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Emma Pires
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Rémi Peyraud
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alice Guidot
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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In through the Out Door: A Functional Virulence Factor Secretion System Is Necessary for Phage Infection in Ralstonia solanacearum. mBio 2022; 13:e0147522. [PMID: 36314808 PMCID: PMC9765573 DOI: 10.1128/mbio.01475-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
Bacteriophages put intense selective pressure on microbes, which must evolve diverse resistance mechanisms to survive continuous phage attacks. We used a library of spontaneous Bacteriophage Insensitive Mutants (BIMs) to learn how the plant pathogen Ralstonia solanacearum resists the virulent lytic podophage phiAP1. Phenotypic and genetic characterization of many BIMs suggested that the R. solanacearum Type II Secretion System (T2SS) plays a key role in phiAP1 infection. Using precision engineered mutations that permit T2SS assembly but either inactivate the T2SS GspE ATPase or sterically block the secretion portal, we demonstrated that phiAP1 needs a functional T2SS to infect R. solanacearum. This distinction between the static presence of T2SS components, which is necessary but not sufficient for phage sensitivity, and the energized and functional T2SS, which is sufficient, implies that binding interactions alone cannot explain the role of the T2SS in phiAP1 infection. Rather, our results imply that some aspect of the resetting of the T2SS, such as disassembly of the pseudopilus, is required. Because R. solanacearum secretes multiple virulence factors via the T2SS, acquiring resistance to phiAP1 also dramatically reduced R. solanacearum virulence on tomato plants. This acute fitness trade-off suggests this group of phages may be a sustainable control strategy for an important crop disease. IMPORTANCE Ralstonia solanacearum is a destructive plant pathogen that causes lethal bacterial wilt disease in hundreds of diverse plant hosts, including many economically important crops. Phages that kill R. solanacearum could offer effective and environmentally friendly wilt disease control, but only if the bacterium cannot easily evolve resistance. Encouragingly, most R. solanacearum mutants resistant to the virulent lytic phage phiAP1 no longer secreted multiple virulence factors and had much reduced fitness and virulence on tomato plants. Further analysis revealed that phage phiAP1 needs a functional type II secretion system to infect R. solanacearum, suggesting this podophage uses a novel infection mechanism.
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Rincón-Flórez VA, Ray JD, Carvalhais LC, O'Dwyer CA, Subandiyah S, Zulperi D, Drenth A. Diagnostics of Banana Blood Disease. PLANT DISEASE 2022; 106:947-959. [PMID: 34668403 DOI: 10.1094/pdis-07-21-1436-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: 06/13/2023]
Abstract
Blood disease in bananas caused by Ralstonia syzygii subsp. celebesensis is a bacterial wilt disease that causes major yield losses of banana in Indonesia and peninsular Malaysia. The disease has significantly increased its geographic distribution in the past decade. Diagnostic methods are an important component of disease management in vegetatively propagated crops such as banana to constrain incursions of plant pathogens. Therefore, the objectives of this study were (i) to design and rigorously validate a novel banana Blood disease (BBD) real-time PCR assay with a high level of specificity and sensitivity of detection and (ii) to validate published PCR-based diagnostic methods targeting the intergenic region in the megaplasmid ("121 assay" with primer set 121) or the phage tail protein-coding sequence in the bacterial chromosome ("Kubota assay" and "BDB2400 assay" with primer set BDB2400). Assay validation included 339 samples (174 Blood disease bacteria, 51 bacteria associated with banana plants, 51 members of the Ralstonia solanacearum species complex, and 63 samples from symptomatic and healthy plant material). Validation parameters were analytical specificity (inclusivity and exclusivity), selectivity, limit of detection, accuracy, and ruggedness. The 121 assay and our newly developed BBD real-time PCR assay detected all R. syzygii subsp. celebesensis strains with no cross-specificity during validation. Two different PCR assays using the primer set BDB2400 lacked specificity and selectivity. This study reveals that our novel BBD real-time PCR assay and the conventional PCR 121 assay are reliable methods for Blood disease diagnostics, as they comply with all tested validation parameters.
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Affiliation(s)
- Vivian A Rincón-Flórez
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jane D Ray
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cecilia A O'Dwyer
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Siti Subandiyah
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Department of Entomology and Plant Pathology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Dzarifah Zulperi
- Department of Plant Protection, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - André Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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Landry D, González‐Fuente M, Deslandes L, Peeters N. The large, diverse, and robust arsenal of Ralstonia solanacearum type III effectors and their in planta functions. MOLECULAR PLANT PATHOLOGY 2020; 21:1377-1388. [PMID: 32770627 PMCID: PMC7488467 DOI: 10.1111/mpp.12977] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 05/25/2023]
Abstract
The type III secretion system with its delivered type III effectors (T3Es) is one of the main virulence determinants of Ralstonia solanacearum, a worldwide devastating plant pathogenic bacterium affecting many crop species. The pan-effectome of the R. solanacearum species complex has been exhaustively identified and is composed of more than 100 different T3Es. Among the reported strains, their content ranges from 45 to 76 T3Es. This considerably large and varied effectome could be considered one of the factors contributing to the wide host range of R. solanacearum. In order to understand how R. solanacearum uses its T3Es to subvert the host cellular processes, many functional studies have been conducted over the last three decades. It has been shown that R. solanacearum effectors, as those from other plant pathogens, can suppress plant defence mechanisms, modulate the host metabolism, or avoid bacterial recognition through a wide variety of molecular mechanisms. R. solanacearum T3Es can also be perceived by the plant and trigger immune responses. To date, the molecular mechanisms employed by R. solanacearum T3Es to modulate these host processes have been described for a growing number of T3Es, although they remain unknown for the majority of them. In this microreview, we summarize and discuss the current knowledge on the characterized R. solanacearum species complex T3Es.
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Affiliation(s)
- David Landry
- Laboratoire des Interactions Plantes Micro‐organismes (LIPM)INRAE, CNRS, Université de ToulouseCastanet‐TolosanFrance
| | - Manuel González‐Fuente
- Laboratoire des Interactions Plantes Micro‐organismes (LIPM)INRAE, CNRS, Université de ToulouseCastanet‐TolosanFrance
| | - Laurent Deslandes
- Laboratoire des Interactions Plantes Micro‐organismes (LIPM)INRAE, CNRS, Université de ToulouseCastanet‐TolosanFrance
| | - Nemo Peeters
- Laboratoire des Interactions Plantes Micro‐organismes (LIPM)INRAE, CNRS, Université de ToulouseCastanet‐TolosanFrance
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7
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Tan X, Qiu H, Li F, Cheng D, Zheng X, Wang B, Huang M, Li W, Li Y, Sang K, Song B, Du J, Chen H, Xie C. Complete Genome Sequence of Sequevar 14M Ralstonia solanacearum Strain HA4-1 Reveals Novel Type III Effectors Acquired Through Horizontal Gene Transfer. Front Microbiol 2019; 10:1893. [PMID: 31474968 PMCID: PMC6703095 DOI: 10.3389/fmicb.2019.01893] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/31/2019] [Indexed: 01/08/2023] Open
Abstract
Ralstonia solanacearum, which causes bacterial wilt in a broad range of plants, is considered a "species complex" due to its significant genetic diversity. Recently, we have isolated a new R. solanacearum strain HA4-1 from Hong'an county in Hubei province of China and identified it being phylotype I, sequevar 14M (phylotype I-14M). Interestingly, we found that it can cause various disease symptoms among different potato genotypes and display different pathogenic behavior compared to a phylogenetically related strain, GMI1000. To dissect the pathogenic mechanisms of HA4-1, we sequenced its whole genome by combined sequencing technologies including Illumina HiSeq2000, PacBio RS II, and BAC-end sequencing. Genome assembly results revealed the presence of a conventional chromosome, a megaplasmid as well as a 143 kb plasmid in HA4-1. Comparative genome analysis between HA4-1 and GMI1000 shows high conservation of the general virulence factors such as secretion systems, motility, exopolysaccharides (EPS), and key regulatory factors, but significant variation in the repertoire and structure of type III effectors, which could be the determinants of their differential pathogenesis in certain potato species or genotypes. We have identified two novel type III effectors that were probably acquired through horizontal gene transfer (HGT). These novel R. solanacearum effectors display homology to several YopJ and XopAC family members. We named them as RipBR and RipBS. Notably, the copy of RipBR on the plasmid is a pseudogene, while the other on the megaplasmid is normal. For RipBS, there are three copies located in the megaplasmid and plasmid, respectively. Our results have not only enriched the genome information on R. solanacearum species complex by sequencing the first sequevar 14M strain and the largest plasmid reported in R. solanacearum to date but also revealed the variation in the repertoire of type III effectors. This will greatly contribute to the future studies on the pathogenic evolution, host adaptation, and interaction between R. solanacearum and potato.
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Affiliation(s)
- Xiaodan Tan
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Huishan Qiu
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Dong Cheng
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Xueao Zheng
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Bingsen Wang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Mengshu Huang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Wenhao Li
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Yanping Li
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Kangqi Sang
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Botao Song
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Juan Du
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Huilan Chen
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
| | - Conghua Xie
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- National Center for Vegetable Improvement (Central China), Wuhan, China
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da Silva Xavier A, de Almeida JCF, de Melo AG, Rousseau GM, Tremblay DM, de Rezende RR, Moineau S, Alfenas‐Zerbini P. Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex. MOLECULAR PLANT PATHOLOGY 2019; 20:223-239. [PMID: 30251378 PMCID: PMC6637880 DOI: 10.1111/mpp.12750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of an array of short DNA repeat sequences separated by unique spacer sequences that are flanked by associated (Cas) genes. CRISPR-Cas systems are found in the genomes of several microbes and can act as an adaptive immune mechanism against invading foreign nucleic acids, such as phage genomes. Here, we studied the CRISPR-Cas systems in plant-pathogenic bacteria of the Ralstonia solanacearum species complex (RSSC). A CRISPR-Cas system was found in 31% of RSSC genomes present in public databases. Specifically, CRISPR-Cas types I-E and II-C were found, with I-E being the most common. The presence of the same CRISPR-Cas types in distinct Ralstonia phylotypes and species suggests the acquisition of the system by a common ancestor before Ralstonia species segregation. In addition, a Cas1 phylogeny (I-E type) showed a perfect geographical segregation of phylotypes, supporting an ancient acquisition. Ralstoniasolanacearum strains CFBP2957 and K60T were challenged with a virulent phage, and the CRISPR arrays of bacteriophage-insensitive mutants (BIMs) were analysed. No new spacer acquisition was detected in the analysed BIMs. The functionality of the CRISPR-Cas interference step was also tested in R. solanacearum CFBP2957 using a spacer-protospacer adjacent motif (PAM) delivery system, and no resistance was observed against phage phiAP1. Our results show that the CRISPR-Cas system in R. solanacearum CFBP2957 is not its primary antiviral strategy.
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Affiliation(s)
- André da Silva Xavier
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Juliana Cristina Fraleon de Almeida
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Alessandra Gonçalves de Melo
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
| | - Geneviève M. Rousseau
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Rafael Reis de Rezende
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de GénieUniversité LavalQuébec CityQCGIV0A6Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine DentaireUniversité LavalQuébec CityQCGIV0A6Canada
| | - Poliane Alfenas‐Zerbini
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO)Universidade Federal de ViçosaViçosaMG36570‐000Brazil
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Transcriptome and Comparative Genomics Analyses Reveal New Functional Insights on Key Determinants of Pathogenesis and Interbacterial Competition in Pectobacterium and Dickeya spp. Appl Environ Microbiol 2019; 85:AEM.02050-18. [PMID: 30413477 DOI: 10.1128/aem.02050-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023] Open
Abstract
Soft-rot Enterobacteriaceae (SRE), typified by Pectobacterium and Dickeya genera, are phytopathogenic bacteria inflicting soft-rot disease in crops worldwide. By combining genomic information from 100 SRE with whole-transcriptome data sets, we identified novel genomic and transcriptional associations among key pathogenicity themes in this group. Comparative genomics revealed solid linkage between the type I secretion system (T1SS) and the carotovoricin bacteriophage (Ctv) conserved in 96.7% of Pectobacterium genomes. Moreover, their coactivation during infection indicates a novel functional association involving T1SS and Ctv. Another bacteriophage-borne genomic region, mostly confined to less than 10% of Pectobacterium strains, was found, presumably comprising a novel lineage-specific prophage in the genus. We also detected the transcriptional coregulation of a previously predicted toxin/immunity pair (WHH and SMI1_KNR4 families), along with the type VI secretion system (T6SS), which includes hcp and/or vgrG genes, suggesting a role in disease development as T6SS-dependent effectors. Further, we showed that another predicted T6SS-dependent endonuclease (AHH family) exhibited toxicity in ectopic expression assays, indicating antibacterial activity. Additionally, we report the striking conservation of the group 4 capsule (GFC) cluster in 100 SRE strains which consistently features adjacently conserved serotype-specific gene arrays comprising a previously unknown organization in GFC clusters. Also, extensive sequence variations found in gfcA orthologs suggest a serotype-specific role in the GfcABCD machinery.IMPORTANCE Despite the considerable loss inflicted on important crops yearly by Pectobacterium and Dickeya diseases, investigations on key virulence and interbacterial competition assets relying on extensive comparative genomics are still surprisingly lacking for these genera. Such approaches become more powerful over time, underpinned by the growing amount of genomic information in public databases. In particular, our findings point to new functional associations among well-known genomic themes enabling alternative means of neutralizing SRE diseases through disruption of pivotal virulence programs. By elucidating novel transcriptional and genomic associations, this study adds valuable information on virulence candidates that could be decisive in molecular applications in the near future. The utilization of 100 genomes of Pectobacterium and Dickeya strains in this study is unprecedented for comparative analyses in these taxa, and it provides novel insights on the biology of economically important plant pathogens.
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Identification of virulence factors and type III effectors of phylotype I, Indian Ralstonia solanacearum strains Rs-09-161 and Rs-10-244. J Genet 2018. [DOI: 10.1007/s12041-018-0894-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Hayes MM, MacIntyre AM, Allen C. Complete Genome Sequences of the Plant Pathogens Ralstonia solanacearum Type Strain K60 and R. solanacearum Race 3 Biovar 2 Strain UW551. GENOME ANNOUNCEMENTS 2017; 5:e01088-17. [PMID: 28983002 PMCID: PMC5629059 DOI: 10.1128/genomea.01088-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/01/2017] [Indexed: 11/20/2022]
Abstract
Ralstonia solanacearum is a globally distributed plant pathogen that causes bacterial wilt diseases of many crop hosts, threatening both sustenance farming and industrial agriculture. Here, we present closed genome sequences for the R. solanacearum type strain, K60, and the cool-tolerant potato brown rot strain R. solanacearum UW551, a highly regulated U.S. select agent pathogen.
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Affiliation(s)
- Madeline M Hayes
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - April M MacIntyre
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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12
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Bocsanczy AM, Huguet-Tapia JC, Norman DJ. Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence. FRONTIERS IN PLANT SCIENCE 2017; 8:1565. [PMID: 28955357 PMCID: PMC5601409 DOI: 10.3389/fpls.2017.01565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/28/2017] [Indexed: 06/01/2023]
Abstract
Strains of the Ralstonia solanacearum species complex in the phylotype IIB group are capable of causing Bacterial Wilt disease in potato and tomato at temperatures lower than 24°C. The capability of these strains to survive and to incite infection at temperatures colder than their normally tropical boundaries represents a threat to United States agriculture in temperate regions. In this work, we used a comparative genomics approach to identify orthologous genes linked to the lower temperature virulence phenotype. Six R. solanacearum cool virulent (CV) strains were compared to six strains non-pathogenic at low temperature (NPLT). CV strains can cause Bacterial Wilt symptoms at temperatures below 24°C, while NPLT cannot. Four R. solanacearum strains were sequenced for this work in order to complete the comparison. An orthologous genes comparison identified 44 genes present only in CV strains and 19 genes present only in NPLT strains. Gene annotation revealed a high percentage of genes compared with whole genomes in the transcriptional regulator and transport categories. A single nucleotide polymorphism (SNP) analysis identified 265 genes containing conserved non-synonymous SNPs in CV strains. Ten genes in the pathogenicity category were identified in this group. Comparisons of type 3 secretion system, type 6 secretion system (T6SS) clusters, and associated effectors did not indicate a correlation with the CV phenotype except for one T6SS VGR effector potentially associated with the CV phenotype. This is the first R. solanacearum genomic comparative analysis of multiple strains with different temperature related virulence. The candidate genes identified by this comparison are potential factors involved in virulence at low temperatures that need to be investigated. The high percentage of transcriptional regulators among the genes present only in CV strains supports the hypothesis that temperature dependent regulation of virulence genes explains the differential virulence phenotype at low temperatures. This comparison contributes to find new possible connections of temperature dependent virulence to the previously described complex regulatory system involving quorum-sensing, phenotype conversion (phcA), acyl-HSL production and responses to SA. It also added novel candidate T6SS effectors and useful detailed information about the T6SS in R. solanacearum.
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Affiliation(s)
- Ana M. Bocsanczy
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, ApopkaFL, United States
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - David J. Norman
- Mid-Florida Research and Education Center, Department of Plant Pathology, University of Florida, ApopkaFL, United States
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New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations. Appl Environ Microbiol 2017; 83:AEM.03095-16. [PMID: 28003195 DOI: 10.1128/aem.03095-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/13/2016] [Indexed: 12/31/2022] Open
Abstract
Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to R. pseudosolanacearum phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology and population genetics of this bacterium are poorly understood. Until now, the genetic structure of the RSSC has been analyzed on the worldwide and regional scales. Emerging questions regarding evolutionary forces in RSSC adaptation to hosts now require genetic markers that are able to monitor RSSC field populations. In this study, we aimed to evaluate the multilocus variable-number tandem-repeat analysis (MLVA) approach for its ability to discriminate genetically close phylotype I strains and for population genetics studies. We developed a new MLVA scheme (MLVA-7) allowing us to genotype 580 R. pseudosolanacearum phylotype I strains extracted from susceptible and resistant hosts and from different habitats (stem, soil, and rhizosphere). Based on specificity, polymorphism, and the amplification success rate, we selected seven fast-evolving variable-number tandem-repeat (VNTR) markers. The newly developed MLVA-7 scheme showed higher discriminatory power than the previously published MLVA-13 scheme when applied to collections sampled from the same location on different dates and to collections from different locations on very small scales. Our study provides a valuable tool for fine-scale monitoring and microevolution-related study of R. pseudosolanacearum phylotype I populations.IMPORTANCE Understanding the evolutionary dynamics of adaptation of plant pathogens to new hosts or ecological niches has become a key point for the development of innovative disease management strategies, including durable resistance. Whereas the molecular mechanisms underlying virulence or pathogenicity changes have been studied thoroughly, the population genetics of plant pathogen adaptation remains an open, unexplored field, especially for plant-pathogenic bacteria. MLVA has become increasingly popular for epidemiosurveillance and molecular epidemiology studies of plant pathogens. However, this method has been used mostly for genotyping and identification on a regional or global scale. In this study, we developed a new MLVA scheme, targeting phylotype I of the soilborne Ralstonia solanacearum species complex (RSSC), specifically to address the bacterial population genetics on the field scale. Such a MLVA scheme, based on fast-evolving loci, may be a tool of choice for field experimental evolution and spatial genetics studies.
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Prior P, Ailloud F, Dalsing BL, Remenant B, Sanchez B, Allen C. Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species. BMC Genomics 2016; 17:90. [PMID: 26830494 PMCID: PMC4736150 DOI: 10.1186/s12864-016-2413-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/26/2016] [Indexed: 11/26/2022] Open
Abstract
Background The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensively and are less prone to technical and human error. They are thus a technically accessible replacement for species delineation. Here, we use several genomic comparison methods, supported by our own proteomic analyses and metabolic characterization as well as previously published DNA-DNA hybridization analyses, to differentiate members of the Ralstonia solanacearum species complex into three species. This pathogen group consists of diverse and widespread strains that cause bacterial wilt disease on many different plants. Results We used three different methods to compare the complete genomes of 29 strains from the R. solanacearum species complex. In parallel we profiled the proteomes of 73 strains using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). Proteomic profiles together with genomic sequence comparisons consistently and comprehensively described the diversity of the R. solanacearum species complex. In addition, genome-driven functional phenotypic assays excitingly supported an old hypothesis (Hayward et al. (J Appl Bacteriol 69:269–80, 1990)), that closely related members of the R. solanacearum could be identified through a simple assay of anaerobic nitrate metabolism. This assay allowed us to clearly and easily differentiate phylotype II and IV strains from phylotype I and III strains. Further, genomic dissection of the pathway distinguished between proposed subspecies within the current phylotype IV. The assay revealed large scale differences in energy production within the R. solanacearum species complex, indicating coarse evolutionary distance and further supporting a repartitioning of this group into separate species. Conclusions Together, the results of these studies support the proposed division of the R. solanacearum species complex into three species, consistent with recent literature, and demonstrate the utility of proteomic and genomic approaches to delineate bacterial species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2413-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philippe Prior
- UMR PVBMT Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD, Saint Pierre, La Réunion, France. .,Department of Plant Health and Environment (SPE), INRA, Paris, France.
| | - Florent Ailloud
- UMR PVBMT Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD, Saint Pierre, La Réunion, France. .,Anses-Plant Health Laboratory (LSV), 7 chemin de l'IRAT, Saint-Pierre, La Réunion, France.
| | - Beth L Dalsing
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA.
| | - Benoit Remenant
- UMR PVBMT Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD, Saint Pierre, La Réunion, France.
| | - Borja Sanchez
- Department of Plant Health and Environment (SPE), INRA, Paris, France. .,Department of Analytical and Food Chemistry, University of Vigo, Ourense, Spain.
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA.
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Guarischi-Sousa R, Puigvert M, Coll NS, Siri MI, Pianzzola MJ, Valls M, Setubal JC. Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031. Stand Genomic Sci 2016; 11:7. [PMID: 26779304 PMCID: PMC4714475 DOI: 10.1186/s40793-016-0131-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/10/2015] [Indexed: 11/30/2022] Open
Abstract
Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3 biovar 2. Here we report the completely sequenced genome of this strain, the first complete genome for phylotype IIB, sequevar 1, and the fourth for the R. solanacearum species complex. In addition to standard genome annotation, we have carried out a curated annotation of type III effector genes, an important pathogenicity-related class of genes for this organism. We identified 60 effector genes, and observed that this effector repertoire is distinct when compared to those from other phylotype IIB strains. Eleven of the effectors appear to be nonfunctional due to disruptive mutations. We also report a methylome analysis of this genome, the first for a R. solanacearum strain. This analysis helped us note the presence of a toxin gene within a region of probable phage origin, raising the hypothesis that this gene may play a role in this strain's virulence.
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Affiliation(s)
| | - Marina Puigvert
- />Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CRAG), Bellaterra, Catalonia, Spain
| | - Núria S. Coll
- />Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CRAG), Bellaterra, Catalonia, Spain
| | - María Inés Siri
- />Departamento de Biociencias, Cátedra de Microbiología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - María Julia Pianzzola
- />Departamento de Biociencias, Cátedra de Microbiología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Marc Valls
- />Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CRAG), Bellaterra, Catalonia, Spain
| | - João C. Setubal
- />Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- />Biocomplexity Institute, Virginia Tech, Blacksburg, VA USA
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Zhang Y, Qiu S. Phylogenomic analysis of the genus Ralstonia based on 686 single-copy genes. Antonie van Leeuwenhoek 2015; 109:71-82. [PMID: 26494208 DOI: 10.1007/s10482-015-0610-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/16/2015] [Indexed: 12/11/2022]
Abstract
The genus Ralstonia contains species that are devastating plant pathogens, opportunistic human pathogens, and/or important degraders of xenobiotic and recalcitrant compounds. However, significant nomenclature problems exist, especially for the Ralstonia solanacearum species complex which consists of four phylotypes. Phylogenomics of the Ralstonia genus was investigated via a comprehensive analysis of 39 Ralstonia genomes as well as four genomes of Cupriavidus necator (more commonly known by its previous name Ralstonia eutropha). These data revealed 686 single-copy orthologs that could be extracted from the Ralstonia core-genome and used to reconstruct the phylogeny of the genus Ralstonia. The generated tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome. Our data confirmed that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of the genus Ralstonia, e.g. strains of Ralstonia solanacearum phylotype IIA and IIB may represent two subspecies of R. solanacearum, and strains of R. solanacearum phylotype I and III may be classified into two subspecies of Ralstonia pseudosolanacearum. Recently, strains of R. solanacearum phylotype IV were proposed to be reclassified into different subspecies of Ralstonia syzygii; our study, however, showed that phylotype IV strains had high isDDH values (83.8-96.1 %), indicating it may be not appropriate to classify these closely related strains into different subspecies. We also evaluated the performance of six chromosomal housekeeping genes (gdhA, mutS, adk, leuS, rplB and gyrB) used in Ralstonia phylogenetic inference. The multilocus sequence analysis of these six marker genes was able to reliably infer the phylogenetic relationships of the genus Ralstonia.
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Affiliation(s)
- Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
| | - Sai Qiu
- Department of Nematology and Entomology, University of Florida, Gainesville, FL, 32611, USA
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17
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Meng F, Babujee L, Jacobs JM, Allen C. Comparative Transcriptome Analysis Reveals Cool Virulence Factors of Ralstonia solanacearum Race 3 Biovar 2. PLoS One 2015; 10:e0139090. [PMID: 26445498 PMCID: PMC4596706 DOI: 10.1371/journal.pone.0139090] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
While most strains of the plant pathogenic bacterium Ralstonia solanacearum are tropical, the race 3 biovar 2 (R3bv2) subgroup attacks plants in cooler climates. To identify mechanisms underlying this trait, we compared the transcriptional profiles of R. solanacearum R3bv2 strain UW551 and tropical strain GMI1000 at 20°C and 28°C, both in culture and during tomato pathogenesis. 4.2% of the ORFs in the UW551 genome and 7.9% of the GMI1000 ORFs were differentially expressed by temperature in planta. The two strains had distinct transcriptional responses to temperature change. GMI1000 up-regulated several stress response genes at 20°C, apparently struggling to cope with plant defenses. At the cooler temperature, R3bv2 strain UW551 up-regulated a cluster encoding a mannose-fucose binding lectin, LecM; a quorum sensing-dependent protein, AidA; and a related hypothetical protein, AidC. The last two genes are absent from the GMI1000 genome. In UW551, all three genes were positively regulated by the adjacent SolI/R quorum sensing system. These temperature-responsive genes were required for full virulence in R3bv2. Mutants lacking lecM, aidA, or aidC were each significantly more reduced in virulence on tomato at 20°C than at 28°C in both a naturalistic soil soak inoculation assay and when they were inoculated directly into tomato stems. The lecM and aidC mutants also survived poorly in potato tubers at the seed tuber storage temperature of 4°C, and the lecM mutant was defective in biofilm formation in vitro. Together, these results suggest novel mechanisms, including a lectin, are involved in the unique temperate epidemiology of R3bv2.
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Affiliation(s)
- Fanhong Meng
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Lavanya Babujee
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Jonathan M. Jacobs
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States of America
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18
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Huerta AI, Milling A, Allen C. Tropical strains of Ralstonia solanacearum Outcompete race 3 biovar 2 strains at lowland tropical temperatures. Appl Environ Microbiol 2015; 81:3542-51. [PMID: 25769835 PMCID: PMC4407210 DOI: 10.1128/aem.04123-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/10/2015] [Indexed: 01/21/2023] Open
Abstract
Bacterial wilt, caused by members of the heterogenous Ralstonia solanacearum species complex, is an economically important vascular disease affecting many crops. Human activity has widely disseminated R. solanacearum strains, increasing their global agricultural impact. However, tropical highland race 3 biovar 2 (R3bv2) strains do not cause disease in tropical lowlands, even though they are virulent at warm temperatures. We tested the hypothesis that differences in temperature adaptation and competitive fitness explain the uneven geographic distribution of R. solanacearum strains. Using three phylogenetically and ecologically distinct strains, we measured competitive fitness at two temperatures following paired-strain inoculations of their shared host, tomato. Lowland tropical strain GMI1000 was only weakly virulent on tomato under temperate conditions (24°C for day and 19°C for night [24/19°C]), but highland tropical R3bv2 strain UW551 and U.S. warm temperate strain K60 were highly virulent at both 24/19°C and 28°C. Strain K60 was significantly more competitive than both GMI1000 and UW551 in tomato rhizospheres and stems at 28°C, and GMI1000 also outcompeted UW551 at 28°C. The results were reversed at cooler temperatures, at which highland strain UW551 generally outcompeted GMI1000 and K60 in planta. The superior competitive index of UW551 at 24/19°C suggests that adaptation to cool temperatures could explain why only R3bv2 strains threaten highland agriculture. Strains K60 and GMI1000 each produced different bacteriocins that inhibited growth of UW551 in culture. Such interstrain inhibition could explain why R3bv2 strains do not cause disease in tropical lowlands.
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Affiliation(s)
- Alejandra I Huerta
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Annett Milling
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Clarke CR, Studholme DJ, Hayes B, Runde B, Weisberg A, Cai R, Wroblewski T, Daunay MC, Wicker E, Castillo JA, Vinatzer BA. Genome-Enabled Phylogeographic Investigation of the Quarantine Pathogen Ralstonia solanacearum Race 3 Biovar 2 and Screening for Sources of Resistance Against Its Core Effectors. PHYTOPATHOLOGY 2015; 105:597-607. [PMID: 25710204 DOI: 10.1094/phyto-12-14-0373-r] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phylogeographic studies inform about routes of pathogen dissemination and are instrumental for improving import/export controls. Genomes of 17 isolates of the bacterial wilt and potato brown rot pathogen Ralstonia solanacearum race 3 biovar 2 (R3bv2), a Select Agent in the United States, were thus analyzed to get insight into the phylogeography of this pathogen. Thirteen of fourteen isolates from Europe, Africa, and Asia were found to belong to a single clonal lineage while isolates from South America were genetically diverse and tended to carry ancestral alleles at the analyzed genomic loci consistent with a South American origin of R3bv2. The R3bv2 isolates share a core repertoire of 31 type III-secreted effector genes representing excellent candidates to be targeted with resistance genes in breeding programs to develop durable disease resistance. Toward this goal, 27 R3bv2 effectors were tested in eggplant, tomato, pepper, tobacco, and lettuce for induction of a hypersensitive-like response indicative of recognition by cognate resistance receptors. Fifteen effectors, eight of them core effectors, triggered a response in one or more plant species. These genotypes may harbor resistance genes that could be identified and mapped, cloned, and expressed in tomato or potato, for which sources of genetic resistance to R3bv2 are extremely limited.
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Affiliation(s)
- Christopher R Clarke
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - David J Studholme
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Byron Hayes
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Brendan Runde
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Alexandra Weisberg
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Rongman Cai
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Tadeusz Wroblewski
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Marie-Christine Daunay
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Emmanuel Wicker
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Jose A Castillo
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Boris A Vinatzer
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
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20
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Kubota R, Jenkins DM. Real-time duplex applications of loop-mediated AMPlification (LAMP) by assimilating probes. Int J Mol Sci 2015; 16:4786-99. [PMID: 25741765 PMCID: PMC4394449 DOI: 10.3390/ijms16034786] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 12/15/2022] Open
Abstract
Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.
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Affiliation(s)
- Ryo Kubota
- Diagenetix, Inc., Honolulu, HI 96822, USA.
- Department of Molecular Biosciences and Bioengineering, University of Hawai'.i, Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA.
| | - Daniel M Jenkins
- Department of Molecular Biosciences and Bioengineering, University of Hawai'.i, Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA.
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Stulberg MJ, Shao J, Huang Q. A Multiplex PCR Assay to Detect and Differentiate Select Agent Strains of Ralstonia solanacearum. PLANT DISEASE 2015; 99:333-341. [PMID: 30699705 DOI: 10.1094/pdis-05-14-0483-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ralstonia solanacearum race 3 biovar 2 strains are considered select agents by the U.S. government because they are not endemic to the United States and have the potential to cause brown rot in our potato production fields. Simple and accurate methods are needed for quick identification prior to more discriminating but time-consuming verification methods. We developed a multiplex PCR assay that identifies R. solanacearum species complex strains, signals whether the strain detected is a select agent, and controls for false negatives associated with PCR inhibition or unsuccessful DNA extractions in one reaction. We identified unique sequences of non-phage-related DNA for the R. solanacearum species complex strains, and for select agent strains, using in silico genome subtraction. We also designed and included an internal plant DNA control assay. Our multiplex PCR assay correctly identified 90 R. solanacearum species complex strains and 34 select agent strains, while not recognizing five out-group bacterial species. Additionally, the multiplex PCR assay facilitated the detection of plant DNA and R. solanacearum from infected tomato, potato, geranium, and tobacco plants. Our rapid, accurate, and reliable detection assay can help government officials make timely and appropriate recommendations to exclude this bacterium from the United States.
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Affiliation(s)
- Michael J Stulberg
- USDA-ARS, US National Arboretum, Floral and Nursery Plant Research Unit, Beltsville, MD
| | - Jonathan Shao
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, MD
| | - Qi Huang
- USDA-ARS, US National Arboretum, Floral and Nursery Plant Research Unit, Beltsville, MD
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22
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Lowe TM, Ailloud F, Allen C. Hydroxycinnamic Acid Degradation, a Broadly Conserved Trait, Protects Ralstonia solanacearum from Chemical Plant Defenses and Contributes to Root Colonization and Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:286-97. [PMID: 25423265 PMCID: PMC4329107 DOI: 10.1094/mpmi-09-14-0292-fi] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plants produce hydroxycinnamic acid (HCA) defense compounds to combat pathogens, such as the bacterium Ralstonia solanacearum. We showed that an HCA degradation pathway is genetically and functionally conserved across diverse R. solanacearum strains. Further, a feruloyl-CoA synthetase (Δfcs) mutant that cannot degrade HCA was less virulent on tomato plants. To understand the role of HCA degradation in bacterial wilt disease, we tested the following hypotheses: HCA degradation helps the pathogen i) grow, as a carbon source; ii) spread, by reducing HCA-derived physical barriers; and iii) survive plant antimicrobial compounds. Although HCA degradation enabled R. solanacearum growth on HCA in vitro, HCA degradation was dispensable for growth in xylem sap and root exudate, suggesting that HCA are not significant carbon sources in planta. Acetyl-bromide quantification of lignin demonstrated that R. solanacearum infections did not affect the gross quantity or distribution of stem lignin. However, the Δfcs mutant was significantly more susceptible to inhibition by two HCA, namely, caffeate and p-coumarate. Finally, plant colonization assays suggested that HCA degradation facilitates early stages of infection and root colonization. Together, these results indicated that ability to degrade HCA contributes to bacterial wilt virulence by facilitating root entry and by protecting the pathogen from HCA toxicity.
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Affiliation(s)
- Tiffany M. Lowe
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Florent Ailloud
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
- Corresponding Author: Caitilyn Allen; ; 608-262-9578
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23
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Yu H, Hausinger RP, Tang HZ, Xu P. Mechanism of the 6-hydroxy-3-succinoyl-pyridine 3-monooxygenase flavoprotein from Pseudomonas putida S16. J Biol Chem 2014; 289:29158-70. [PMID: 25172510 DOI: 10.1074/jbc.m114.558049] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
6-Hydroxy-3-succinoyl-pyridine (HSP) 3-monooxygenase (HspB), a flavoprotein essential to the pyrrolidine pathway of nicotine degradation, catalyzes pyridine-ring β-hydroxylation, resulting in carbon-carbon cleavage and production of 2,5-dihydroxypyridine. Here, we generated His6-tagged HspB in Escherichia coli, characterized the properties of the recombinant enzyme, and investigated its mechanism of catalysis. In contrast to conclusions reported previously, the second product of the HspB reaction was shown to be succinate, with isotope labeling experiments providing direct evidence that the newly introduced oxygen atom of succinate is derived from H2O. Phylogenetic analysis reveals that HspB is the most closely related to two p-nitrophenol 4-monooxygenases, and the experimental results exhibit that p-nitrophenol is a substrate of HspB. The reduction of HspB (with maxima at 375 and 460 nm, and a shoulder at 485 nm) by NADH was followed by stopped-flow spectroscopy, and the rate constant for reduction was shown to be stimulated by HSP. Reduced HspB reacts with oxygen to form a C(4a)-(hydro)peroxyflavin intermediate with an absorbance maximum at ∼400 nm within the first few milliseconds before converting to the oxidized flavoenzyme species. The formed C(4a)-hydroperoxyflavin intermediate reacts with HSP to form an intermediate that hydrolyzes to the products 2,5-dihydroxypyridine and succinate. The investigation on the catalytic mechanism of a flavoprotein pyridine-ring β-position hydroxylase provides useful information for the biosynthesis of pyridine derivatives.
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Affiliation(s)
- Hao Yu
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China and
| | - Robert P Hausinger
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Hong-Zhi Tang
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China and
| | - Ping Xu
- From the State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China and
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Lohou D, Turner M, Lonjon F, Cazalé AC, Peeters N, Genin S, Vailleau F. HpaP modulates type III effector secretion in Ralstonia solanacearum and harbours a substrate specificity switch domain essential for virulence. MOLECULAR PLANT PATHOLOGY 2014; 15:601-14. [PMID: 24405562 PMCID: PMC6638691 DOI: 10.1111/mpp.12119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many pathogenic bacteria have evolved a type III secretion system (T3SS) to successfully invade their host. This extracellular apparatus allows the translocation of proteins, called type III effectors (T3Es), directly into the host cells. T3Es are virulence factors that have been shown to interfere with the host's immunity or to provide nutrients from the host to the bacteria. The Gram-negative bacterium Ralstonia solanacearum is a worldwide major crop pest whose virulence strongly relies on the T3SS. In R. solanacearum, transcriptional regulation has been extensively studied. However, very few data are available concerning the role played by type III-associated regulators, such as type III chaperones and T3SS control proteins. Here, we characterized HpaP, a putative type III secretion substrate specificity switch (T3S4) protein of R. solanacearum which is not secreted by the bacterium or translocated in the plant cells. HpaP self-interacts and interacts with the PopP1 T3E. HpaP modulates the secretion of early (HrpY pilin) and late (AvrA and PopP1 T3Es) type III substrates. HpaP is dispensable for the translocation of T3Es into the host cells. Finally, we identified two regions of five amino acids in the T3S4 domain that are essential for efficient PopP1 secretion and for HpaP's role in virulence on tomato and Arabidopsis thaliana, but not required for HpaP-HpaP and HpaP-PopP1 interactions. Taken together, our results indicate that HpaP is a putative R. solanacearum T3S4 protein important for full pathogenicity on several hosts, acting as a helper for PopP1 secretion, and repressing AvrA and HrpY secretion.
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Affiliation(s)
- David Lohou
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
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Siri MI, Sanabria A, Boucher C, Pianzzola MJ. New type IV pili-related genes involved in early stages of Ralstonia solanacearum potato infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:712-24. [PMID: 24625029 DOI: 10.1094/mpmi-07-13-0210-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This study provides insights into the pathogenesis of Ralstonia solanacearum, in particular with regards to strains belonging to phylotype IIB, sequevar 1 (IIB-1) and their interaction with potato, its natural host. We performed a comparative genomic analysis among IIB-1 R. solanacearum strains with different levels of virulence in order to identify candidate virulence genes. With this approach, we identified a 33.7-kb deletion in a strain showing reduced virulence on potato. This region contains a cluster of six genes putatively involved in type IV pili (Tfp) biogenesis. Functional analysis suggests that these proteins contribute to several Tfp-related functions such as twitching motility and biofilm formation. In addition, this genetic cluster was found to contribute to early bacterial wilt pathogenesis and colonization fitness of potato roots.
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26
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Safni I, Cleenwerck I, De Vos P, Fegan M, Sly L, Kappler U. Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov. Int J Syst Evol Microbiol 2014; 64:3087-3103. [PMID: 24944341 DOI: 10.1099/ijs.0.066712-0] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Ralstonia solanacearum species complex has long been recognized as a group of phenotypically diverse strains that can be subdivided into four phylotypes. Using a polyphasic taxonomic approach on an extensive set of strains, this study provides evidence for a taxonomic and nomenclatural revision of members of this complex. Data obtained from phylogenetic analysis of 16S-23S rRNA ITS gene sequences, 16S-23S rRNA intergenic spacer (ITS) region sequences and partial endoglucanase (egl) gene sequences and DNA-DNA hybridizations demonstrate that the R. solanacearum species complex comprises three genospecies. One of these includes the type strain of Ralstonia solanacearum and consists of strains of R. solanacearum phylotype II only. The second genospecies includes the type strain of Ralstonia syzygii and contains only phylotype IV strains. This genospecies is subdivided into three distinct groups, namely R. syzygii, the causal agent of Sumatra disease on clove trees in Indonesia, R. solanacearum phylotype IV strains isolated from different host plants mostly from Indonesia, and strains of the blood disease bacterium (BDB), the causal agent of the banana blood disease, a bacterial wilt disease in Indonesia that affects bananas and plantains. The last genospecies is composed of R. solanacearum strains that belong to phylotypes I and III. As these genospecies are also supported by phenotypic data that allow the differentiation of the three genospecies, the following taxonomic proposals are made: emendation of the descriptions of Ralstonia solanacearum and Ralstonia syzygii and descriptions of Ralstonia syzygii subsp. nov. (type strain R 001(T) = LMG 10661(T) = DSM 7385(T)) for the current R. syzygii strains, Ralstonia syzygii subsp. indonesiensis subsp. nov. (type strain UQRS 464(T) = LMG 27703(T) = DSM 27478(T)) for the current R. solanacearum phylotype IV strains, Ralstonia syzygii subsp. celebesensis subsp. nov. (type strain UQRS 627(T) = LMG 27706(T) = DSM 27477(T)) for the BDB strains and Ralstonia pseudosolanacearum sp. nov. (type strain UQRS 461(T) = LMG 9673(T) = NCPPB 1029(T)) for the strains of R. solanacearum phylotypes I and III.
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Affiliation(s)
- Irda Safni
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Paul De Vos
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Mark Fegan
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lindsay Sly
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Queensland 4072, Australia
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Nitrate assimilation contributes to Ralstonia solanacearum root attachment, stem colonization, and virulence. J Bacteriol 2013; 196:949-60. [PMID: 24363343 DOI: 10.1128/jb.01378-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ralstonia solanacearum, an economically important plant pathogen, must attach, grow, and produce virulence factors to colonize plant xylem vessels and cause disease. Little is known about the bacterial metabolism that drives these processes. Nitrate is present in both tomato xylem fluid and agricultural soils, and the bacterium's gene expression profile suggests that it assimilates nitrate during pathogenesis. A nasA mutant, which lacks the gene encoding the catalytic subunit of R. solanacearum's sole assimilatory nitrate reductase, did not grow on nitrate as a sole nitrogen source. This nasA mutant exhibited reduced virulence and delayed stem colonization after soil soak inoculation of tomato plants. The nasA virulence defect was more severe following a period of soil survival between hosts. Unexpectedly, once bacteria reached xylem tissue, nitrate assimilation was dispensable for growth, virulence, and competitive fitness. However, nasA-dependent nitrate assimilation was required for normal production of extracellular polysaccharide (EPS), a major virulence factor. Quantitative analyses revealed that EPS production was significantly influenced by nitrate assimilation when nitrate was not required for growth. The plant colonization delay of the nasA mutant was externally complemented by coinoculation with wild-type bacteria but not by coinoculation with an EPS-deficient epsB mutant. The nasA mutant and epsB mutant did not attach to tomato roots as well as wild-type strain UW551. However, adding either wild-type cells or cell-free EPS improved the root attachment of these mutants. These data collectively suggest that nitrate assimilation promotes R. solanacearum virulence by enhancing root attachment, the initial stage of infection, possibly by modulating EPS production.
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Ralstonia solanacearum requires PopS, an ancient AvrE-family effector, for virulence and To overcome salicylic acid-mediated defenses during tomato pathogenesis. mBio 2013; 4:e00875-13. [PMID: 24281716 PMCID: PMC3870264 DOI: 10.1128/mbio.00875-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During bacterial wilt of tomato, the plant pathogen Ralstonia solanacearum upregulates expression of popS, which encodes a type III-secreted effector in the AvrE family. PopS is a core effector present in all sequenced strains in the R. solanacearum species complex. The phylogeny of popS mirrors that of the species complex as a whole, suggesting that this is an ancient, vertically inherited effector needed for association with plants. A popS mutant of R. solanacearum UW551 had reduced virulence on agriculturally important Solanum spp., including potato and tomato plants. However, the popS mutant had wild-type virulence on a weed host, Solanum dulcamara, suggesting that some species can avoid the effects of PopS. The popS mutant was also significantly delayed in colonization of tomato stems compared to the wild type. Some AvrE-type effectors from gammaproteobacteria suppress salicylic acid (SA)-mediated plant defenses, suggesting that PopS, a betaproteobacterial ortholog, has a similar function. Indeed, the popS mutant induced significantly higher expression of tomato SA-triggered pathogenesis-related (PR) genes than the wild type. Further, pretreatment of roots with SA exacerbated the popS mutant virulence defect. Finally, the popS mutant had no colonization defect on SA-deficient NahG transgenic tomato plants. Together, these results indicate that this conserved effector suppresses SA-mediated defenses in tomato roots and stems, which are R. solanacearum’s natural infection sites. Interestingly, PopS did not trigger necrosis when heterologously expressed in Nicotiana leaf tissue, unlike the AvrE homolog DspEPcc from the necrotroph Pectobacterium carotovorum subsp. carotovorum. This is consistent with the differing pathogenesis modes of necrosis-causing gammaproteobacteria and biotrophic R. solanacearum. The type III-secreted AvrE effector family is widely distributed in high-impact plant-pathogenic bacteria and is known to suppress plant defenses for virulence. We characterized the biology of PopS, the only AvrE homolog made by the bacterial wilt pathogen Ralstonia solanacearum. To our knowledge, this is the first study of R. solanacearum effector function in roots and stems, the natural infection sites of this pathogen. Unlike the functionally redundant R. solanacearum effectors studied to date, PopS is required for full virulence and wild-type colonization of two natural crop hosts. R. solanacearum is a biotrophic pathogen that causes a nonnecrotic wilt. Consistent with this, PopS suppressed plant defenses but did not elicit cell death, unlike AvrE homologs from necrosis-causing plant pathogens. We propose that AvrE family effectors have functionally diverged to adapt to the necrotic or nonnecrotic lifestyle of their respective pathogens.
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Parkinson N, Bryant R, Bew J, Conyers C, Stones R, Alcock M, Elphinstone J. Application of variable-number tandem-repeat typing to discriminate Ralstonia solanacearum strains associated with English watercourses and disease outbreaks. Appl Environ Microbiol 2013; 79:6016-22. [PMID: 23892739 PMCID: PMC3811358 DOI: 10.1128/aem.01219-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/17/2013] [Indexed: 11/20/2022] Open
Abstract
Variable-number tandem-repeat (VNTR) analysis was used for high-resolution discrimination among Ralstonia solanacearum phylotype IIB sequevar 1 (PIIB-1) isolates and further evaluated for use in source tracing. Five tandem-repeat-containing loci (comprising six tandem repeats) discriminated 17 different VNTR profiles among 75 isolates from potato, geranium, bittersweet (Solanum dulcamara), tomato, and the environment. R. solanacearum isolates from crops at three unrelated outbreak sites where river water had been used for irrigation had distinct VNTR profiles that were shared with PIIB-1 isolates from infected bittersweet growing upriver of each site. The VNTR profiling results supported the implication that the source of R. solanacearum at each outbreak was contaminated river water. Analysis of 51 isolates from bittersweet growing in river water at different locations provided a means to evaluate the technique for studying the epidemiology of the pathogen in the environment. Ten different VNTR profiles were identified among bittersweet PIIB-1 isolates from the River Thames. Repeated findings of contiguous river stretches that produced isolates that shared single VNTR profiles supported the hypothesis that the pathogen had disseminated from infected bittersweet plants located upriver. VNTR profiles shared between bittersweet isolates from two widely separated Thames tributaries (River Ray and River Colne) suggested they were independently contaminated with the same clonal type. Some bittersweet isolates had VNTR profiles that were shared with potato isolates collected outside the United Kingdom. It was concluded that VNTR profiling could contribute to further understanding of R. solanacearum epidemiology and assist in control of future disease outbreaks.
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Affiliation(s)
- Neil Parkinson
- Food and Environment Research Agency (FERA), Sand Hutton, York, United Kingdom
| | - Ruth Bryant
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Janice Bew
- Food and Environment Research Agency (FERA), Sand Hutton, York, United Kingdom
| | - Christine Conyers
- Food and Environment Research Agency (FERA), Sand Hutton, York, United Kingdom
| | - Robert Stones
- Food and Environment Research Agency (FERA), Sand Hutton, York, United Kingdom
| | - Michael Alcock
- Food and Environment Research Agency (FERA), Sand Hutton, York, United Kingdom
| | - John Elphinstone
- Food and Environment Research Agency (FERA), Sand Hutton, York, United Kingdom
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30
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Peeters N, Guidot A, Vailleau F, Valls M. Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era. MOLECULAR PLANT PATHOLOGY 2013; 14:651-62. [PMID: 23718203 PMCID: PMC6638647 DOI: 10.1111/mpp.12038] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
UNLABELLED Ralstonia solanacearum is a soil-borne bacterium causing the widespread disease known as bacterial wilt. Ralstonia solanacearum is also the causal agent of Moko disease of banana and brown rot of potato. Since the last R. solanacearum pathogen profile was published 10 years ago, studies concerning this plant pathogen have taken a genomic and post-genomic direction. This was pioneered by the first sequenced and annotated genome for a major plant bacterial pathogen and followed by many more genomes in subsequent years. All molecular features studied now have a genomic flavour. In the future, this will help in connecting the classical field of pathology and diversity studies with the gene content of specific strains. In this review, we summarize the recent research on this bacterial pathogen, including strain classification, host range, pathogenicity determinants, regulation of virulence genes, type III effector repertoire, effector-triggered immunity, plant signalling in response to R. solanacearum, as well as a review of different new pathosystems. TAXONOMY Bacteria; Proteobacteria; β subdivision; Ralstonia group; genus Ralstonia. DISEASE SYMPTOMS Ralstonia solanacearum is the agent of bacterial wilt of plants, characterized by a sudden wilt of the whole plant. Typically, stem cross-sections will ooze a slimy bacterial exudate. In the case of Moko disease of banana and brown rot of potato, there is also visible bacterial colonization of banana fruit and potato tuber. DISEASE CONTROL As a soil-borne pathogen, infected fields can rarely be reused, even after rotation with nonhost plants. The disease is controlled by the use of resistant and tolerant plant cultivars. The prevention of spread of the disease has been achieved, in some instances, by the application of strict prophylactic sanitation practices. USEFUL WEBSITES Stock centre: International Centre for Microbial Resources-French Collection for Plant-associated Bacteria CIRM-CFBP, IRHS UMR 1345 INRA-ACO-UA, 42 rue Georges Morel, 49070 Beaucouzé Cedex, France, http://www.angers-nantes.inra.fr/cfbp/. Ralstonia Genome browser: https://iant.toulouse.inra.fr/R.solanacearum. GMI1000 insertion mutant library: https://iant.toulouse.inra.fr/R.solanacearumGMI1000/GenomicResources. MaGe Genome Browser: https://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?
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Affiliation(s)
- Nemo Peeters
- INRA UMR441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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Lefeuvre P, Cellier G, Remenant B, Chiroleu F, Prior P. Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species. PLoS One 2013; 8:e63155. [PMID: 23723974 PMCID: PMC3665557 DOI: 10.1371/journal.pone.0063155] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/28/2013] [Indexed: 01/11/2023] Open
Abstract
Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.
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Affiliation(s)
- Pierre Lefeuvre
- CIRAD UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France.
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A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences. J Biosci 2013; 38:267-78. [DOI: 10.1007/s12038-013-9312-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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The in planta transcriptome of Ralstonia solanacearum: conserved physiological and virulence strategies during bacterial wilt of tomato. mBio 2012; 3:mBio.00114-12. [PMID: 22807564 PMCID: PMC3413399 DOI: 10.1128/mbio.00114-12] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant xylem fluid is considered a nutrient-poor environment, but the bacterial wilt pathogen Ralstonia solanacearum is well adapted to it, growing to 108 to 109 CFU/g tomato stem. To better understand how R. solanacearum succeeds in this habitat, we analyzed the transcriptomes of two phylogenetically distinct R. solanacearum strains that both wilt tomato, strains UW551 (phylotype II) and GMI1000 (phylotype I). We profiled bacterial gene expression at ~6 × 108 CFU/ml in culture or in plant xylem during early tomato bacterial wilt pathogenesis. Despite phylogenetic differences, these two strains expressed their 3,477 common orthologous genes in generally similar patterns, with about 12% of their transcriptomes significantly altered in planta versus in rich medium. Several primary metabolic pathways were highly expressed during pathogenesis. These pathways included sucrose uptake and catabolism, and components of these pathways were encoded by genes in the scrABY cluster. A UW551 scrA mutant was significantly reduced in virulence on resistant and susceptible tomato as well as on potato and the epidemiologically important weed host Solanum dulcamara. Functional scrA contributed to pathogen competitive fitness during colonization of tomato xylem, which contained ~300 µM sucrose. scrA expression was induced by sucrose, but to a much greater degree by growth in planta. Unexpectedly, 45% of the genes directly regulated by HrpB, the transcriptional activator of the type 3 secretion system (T3SS), were upregulated in planta at high cell densities. This result modifies a regulatory model based on bacterial behavior in culture, where this key virulence factor is repressed at high cell densities. The active transcription of these genes in wilting plants suggests that T3SS has a biological role throughout the disease cycle. Ralstonia solanacearum is a widespread plant pathogen that causes bacterial wilt disease. It inflicts serious crop losses on tropical farmers, with major economic and human consequences. It is also a model for the many destructive microbes that colonize the water-conducting plant xylem tissue, which is low in nutrients and oxygen. We extracted bacteria from infected tomato plants and globally identified the biological functions that R. solanacearum expresses during plant pathogenesis. This revealed the unexpected presence of sucrose in tomato xylem fluid and the pathogen’s dependence on host sucrose for virulence on tomato, potato, and the common weed bittersweet nightshade. Further, R. solanacearum was highly responsive to the plant environment, expressing several metabolic and virulence functions quite differently in the plant than in pure culture. These results reinforce the utility of studying pathogens in interaction with hosts and suggest that selecting for reduced sucrose levels could generate wilt-resistant crops.
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Sequencing of K60, type strain of the major plant pathogen Ralstonia solanacearum. J Bacteriol 2012; 194:2742-3. [PMID: 22535929 DOI: 10.1128/jb.00249-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ralstonia solanacearum is a widespread and destructive plant pathogen. We present the genome of the type strain, K60 (phylotype IIA, sequevar 7). Sequevar 7 strains cause ongoing tomato bacterial wilt outbreaks in the southeastern United States. K60 generally resembles R. solanacearum CFBP2957, a Caribbean tomato isolate, but has almost 360 unique genes.
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Lindeberg M. Genome-enabled perspectives on the composition, evolution, and expression of virulence determinants in bacterial plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:111-132. [PMID: 22559066 DOI: 10.1146/annurev-phyto-081211-173022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genome sequence analyses of bacterial plant pathogens are revealing important insights into the molecular determinants of pathogenicity and, through transcript characterization, responses to environmental conditions, evidence for small RNAs, and validation of uncharacterized genes. Genome comparison sheds further light on the processes impacting pathogen evolution and differences in gene repertoire among isolates contributing to niche specialization. Information derived from pathogen genome analysis is providing tools for use in diagnosis and interference with host-pathogen interactions for the purpose of disease control. However, the existing information infrastructure fails to adequately integrate the increasing numbers of sequence data sets, bioinformatic analyses, and experimental characterization, as required for effective systems-level analysis. Enhanced standardization of data formats at the point of publication is proposed as a possible solution.
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Affiliation(s)
- Magdalen Lindeberg
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, USA.
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Monteiro F, Solé M, van Dijk I, Valls M. A chromosomal insertion toolbox for promoter probing, mutant complementation, and pathogenicity studies in Ralstonia solanacearum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:557-68. [PMID: 22122329 DOI: 10.1094/mpmi-07-11-0201] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We describe here the construction of a delivery system for stable and directed insertion of gene constructs in a permissive chromosomal site of the bacterial wilt pathogen Ralstonia solanacearum. The system consists of a collection of suicide vectors-the Ralstonia chromosome (pRC) series-that carry an integration element flanked by transcription terminators and two sequences of homology to the chromosome of strain GMI1000, where the integration element is inserted through a double recombination event. Unique restriction enzyme sites and a GATEWAY cassette enable cloning of any promoter::gene combination in the integration element. Variants endowed with different selectable antibiotic resistance genes and promoter::gene combinations are described. We show that the system can be readily used in GMI1000 and adapted to other R. solanacearum strains using an accessory plasmid. We prove that the pRC system can be employed to complement a deletion mutation with a single copy of the native gene, and to measure transcription of selected promoters in monocopy both in vitro and in planta. Finally, the system has been used to purify and study secretion type III effectors. These novel genetic tools will be particularly useful for the construction of recombinant bacteria that maintain inserted genes or reporter fusions in competitive situations (i.e., during plant infection).
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Affiliation(s)
- Freddy Monteiro
- Deptartament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645 annex, 08028 Barcelona, Catalonia, Spain
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Ha Y, Kim JS, Denny TP, Schell MA. A Rapid, Sensitive Assay for Ralstonia solanacearum Race 3 Biovar 2 in Plant and Soil Samples Using Magnetic Beads and Real-Time PCR. PLANT DISEASE 2012; 96:258-264. [PMID: 30731804 DOI: 10.1094/pdis-05-11-0426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Ralstonia solanacearum species complex causes economically significant diseases in many plant families worldwide. Although generally limited to the tropics and subtropics, strains designated race 3 biovar 2 (R3Bv2) cause disease in cooler tropical highlands and temperate regions. R3Bv2 has not become established in North America but, due to concerns that it could devastate the U.S. potato industry, it has been designated a Select Agent, and is subject to strict quarantine regulations. Quarantine screening for R3Bv2 requires rapid and robust assays applicable to small populations present in plant tissues or soil, and must distinguish R3Bv2 from the multiple other R. solanacearum subgroups. We developed a 100%-accurate real-time polymerase chain reaction (RT-PCR) assay that can detect R3Bv2 populations >1,000 cells ml-1. However, detection by RT-PCR was inhibited by compounds present in some plant and soil samples. Therefore, we developed simple immunomagnetic separation (IMS) and magnetic capture hybridization (MCH) methods to purify R. solanacearum cells or DNA from PCR inhibitors. When coupled with RT-PCR, these tools permitted detection of R3Bv2 at levels >500 cells ml-1 in stem, tuber, and soil samples when direct RT-PCR failed, and reduced detection time from days to hours. IMS-RT-PCR was usually more sensitive than MCH-RT-PCR, especially at lower population levels.
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Affiliation(s)
| | | | | | - Mark A Schell
- Departments of Plant Pathology and Microbiology, The University of Georgia, Athens 30602
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Bocsanczy AM, Achenbach UCM, Mangravita-Novo A, Yuen JMF, Norman DJ. Comparative effect of low temperature on virulence and twitching motility of Ralstonia solanacearum strains present in Florida. PHYTOPATHOLOGY 2012; 102:185-194. [PMID: 21936660 DOI: 10.1094/phyto-05-11-0145] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt on a wide range of plant hosts. Most strains of R. solanacearum are nonpathogenic below 20°C; however, Race 3 Biovar 2 (R3B2) strains are classified as quarantine pathogens because of their ability to infect crops, cause disease, and survive in temperate climates. We have identified race 1 biovar 1 Phylotype IIB Sequevar 4 strains present in Florida which were able to infect and produce wilt symptoms on potato and tomato at 18°C. Moreover they infected tomato plants at rates similar to strains belonging to R3B2. We determined that strains naturally nonpathogenic at 18°C were able to multiply, move in planta, and cause partial wilt when inoculated directly into the stem, suggesting that low temperature affects virulence of strains differently at early stages of infection. Bacterial growth in vitro was delayed at low temperatures, however it was not attenuated. Twitching motility observed on growing colonies was attenuated in nonpathogenic strains at 18°C, while not affected in the cool virulent ones. Using pilQ as a marker to evaluate the relative expression of the twitching activity of R. solanacearum strains, we confirmed that cool virulent strains maintained a similar level of pilQ expression at both temperatures, while in nonpathogenic strains pilQ was downregulated at 18°C.
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Affiliation(s)
- Ana M Bocsanczy
- Department of Plant Pathology, University of Florida, Apopka, FL 32703, USA
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Genin S, Denny TP. Pathogenomics of the Ralstonia solanacearum species complex. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:67-89. [PMID: 22559068 DOI: 10.1146/annurev-phyto-081211-173000] [Citation(s) in RCA: 322] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network.
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Affiliation(s)
- Stéphane Genin
- INRA, Laboratoire des Interactions Plantes-Microorganismes, UMR441, F-31326 Castanet-Tolosan, France.
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Remigi P, Anisimova M, Guidot A, Genin S, Peeters N. Functional diversification of the GALA type III effector family contributes to Ralstonia solanacearum adaptation on different plant hosts. THE NEW PHYTOLOGIST 2011; 192:976-987. [PMID: 21902695 PMCID: PMC3263339 DOI: 10.1111/j.1469-8137.2011.03854.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/09/2011] [Indexed: 05/23/2023]
Abstract
Type III effectors from phytopathogenic bacteria exhibit a high degree of functional redundancy, hampering the evaluation of their precise contribution to pathogenicity. This is illustrated by the GALA type III effectors from Ralstonia solanacearum, which have been shown to be collectively, but not individually, required for disease on Arabidopsis thaliana and tomato. We investigated evolution, redundancy and diversification of this family in order to understand the individual contribution of the GALA effectors to pathogenicity. From sequences available, we reconstructed GALA phylogeny and performed selection studies. We then focused on the GALAs from the reference strain GMI1000 to examine their ability to suppress plant defense responses and contribution to pathogenicity on three different host plants: A. thaliana, tomato (Lycopersicum esculentum) and eggplant (Solanum melongena). The GALA family is well conserved within R. solanacearum species. Patterns of selection detected on some GALA family members, together with experimental results, show that GALAs underwent functional diversification. We conclude that functional divergence of the GALA family likely accounts for its remarkable conservation during R. solanacearum evolution and could contribute to R. solanacearum's adaptation on several host plants.
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Affiliation(s)
- Philippe Remigi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR441, F-31326 Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR2594, F-31326 Castanet-Tolosan, France
| | - Maria Anisimova
- Department of Computer ScienceETH Zurich, Zurich, Switzerland
- Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Alice Guidot
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR441, F-31326 Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR2594, F-31326 Castanet-Tolosan, France
| | - Stéphane Genin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR441, F-31326 Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR2594, F-31326 Castanet-Tolosan, France
| | - Nemo Peeters
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR441, F-31326 Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR2594, F-31326 Castanet-Tolosan, France
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González A, Plener L, Restrepo S, Boucher C, Genin S. Detection and functional characterization of a large genomic deletion resulting in decreased pathogenicity in Ralstonia solanacearum race 3 biovar 2 strains. Environ Microbiol 2011; 13:3172-85. [DOI: 10.1111/j.1462-2920.2011.02636.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Li Z, Wu S, Bai X, Liu Y, Lu J, Liu Y, Xiao B, Lu X, Fan L. Genome sequence of the tobacco bacterial wilt pathogen Ralstonia solanacearum. J Bacteriol 2011; 193:6088-9. [PMID: 21994922 PMCID: PMC3194909 DOI: 10.1128/jb.06009-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 08/19/2011] [Indexed: 11/20/2022] Open
Abstract
Ralstonia solanacearum is a causal agent of plant bacterial wilt with thousands of distinct strains in a heterogeneous species complex. Here we report the genome sequence of a phylotype IB strain, Y45, isolated from tobacco (Nicotiana tabacum) in China. Compared with the published genomes of eight strains which were isolated from other hosts and habitats, 794 specific genes and many rearrangements/inversion events were identified in the tobacco strain, demonstrating that this strain represents an important node within the R. solanacearum complex.
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Affiliation(s)
- Zefeng Li
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sanling Wu
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuefei Bai
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun Liu
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianfei Lu
- Zhejiang Pesticide Testing Management, Fengqi Road, Hangzhou 310020, China
| | - Yong Liu
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research (Southern) Center, Yuxi 653100, China
| | - Bingguang Xiao
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research (Southern) Center, Yuxi 653100, China
| | - Xiuping Lu
- Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research (Southern) Center, Yuxi 653100, China
| | - Longjiang Fan
- Department of Agronomy & James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
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Remenant B, de Cambiaire JC, Cellier G, Jacobs JM, Mangenot S, Barbe V, Lajus A, Vallenet D, Medigue C, Fegan M, Allen C, Prior P. Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles. PLoS One 2011; 6:e24356. [PMID: 21931687 PMCID: PMC3169583 DOI: 10.1371/journal.pone.0024356] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 08/06/2011] [Indexed: 12/19/2022] Open
Abstract
The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.
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Affiliation(s)
- Benoît Remenant
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
| | - Jean-Charles de Cambiaire
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Gilles Cellier
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), CIRAD, Saint Pierre, La Réunion, France
- Unité Ravageurs et Agents Pathogènes Tropicaux, Agence Nationale de Sécurité Sanitaire, Laboratoire de la Santé des Végétaux, Saint Pierre, La Réunion, France
| | - Jonathan M. Jacobs
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sophie Mangenot
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Valérie Barbe
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Aurélie Lajus
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CNRS-UMR 8030, Evry, France
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - David Vallenet
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CNRS-UMR 8030, Evry, France
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Claudine Medigue
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, CNRS-UMR 8030, Evry, France
- Institut de Génomique, Genoscope, Commissariat à l'Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France
| | - Mark Fegan
- Department of Primary Industries, Biosciences Research Division, Attwood, Victoria, Australia
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Philippe Prior
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Réunion, France
- * E-mail:
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Flores-Cruz Z, Allen C. Necessity of OxyR for the hydrogen peroxide stress response and full virulence in Ralstonia solanacearum. Appl Environ Microbiol 2011; 77:6426-32. [PMID: 21803891 PMCID: PMC3187169 DOI: 10.1128/aem.05813-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 07/21/2011] [Indexed: 01/10/2023] Open
Abstract
The plant pathogen Ralstonia solanacearum, which causes bacterial wilt disease, is exposed to reactive oxygen species (ROS) during tomato infection and expresses diverse oxidative stress response (OSR) genes during midstage disease on tomato. The R. solanacearum genome predicts that the bacterium produces multiple and redundant ROS-scavenging enzymes but only one known oxidative stress response regulator, OxyR. An R. solanacearum oxyR mutant had no detectable catalase activity, did not grow in the presence of 250 μM hydrogen peroxide, and grew poorly in the oxidative environment of solid rich media. This phenotype was rescued by the addition of exogenous catalase, suggesting that oxyR is essential for the hydrogen peroxide stress response. Unexpectedly, the oxyR mutant strain grew better than the wild type in the presence of the superoxide generator paraquat. Gene expression studies indicated that katE, kaG, ahpC1, grxC, and oxyR itself were each differentially expressed in the oxyR mutant background and in response to hydrogen peroxide, suggesting that oxyR is necessary for hydrogen peroxide-inducible gene expression. Additional OSR genes were differentially regulated in response to hydrogen peroxide alone. The virulence of the oxyR mutant strain was significantly reduced in both tomato and tobacco host plants, demonstrating that R. solanacearum is exposed to inhibitory concentrations of ROS in planta and that OxyR-mediated responses to ROS during plant pathogenesis are important for R. solanacearum host adaptation and virulence.
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Affiliation(s)
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706
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Ida K, Suguro M, Suzuki H. High resolution X-ray crystal structures of l-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism. ACTA ACUST UNITED AC 2011; 150:659-69. [DOI: 10.1093/jb/mvr103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Bross CD, Corea ORA, Kaldis A, Menassa R, Bernards MA, Kohalmi SE. Complementation of the pha2 yeast mutant suggests functional differences for arogenate dehydratases from Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:882-890. [PMID: 21388819 DOI: 10.1016/j.plaphy.2011.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 02/08/2011] [Indexed: 05/28/2023]
Abstract
The final steps of phenylalanine (Phe) biosynthesis in bacteria, fungi and plants can occur via phenylpyruvate or arogenate intermediates. These routes are determined by the presence of prephenate dehydratase (PDT, EC4.2.1.51), which forms phenylpyruvate from prephenate, or arogenate dehydratase (ADT, EC4.2.1.91), which forms phenylalanine directly from arogenate. We compared sequences from select yeast species to those of Arabidopsis thaliana. The in silico analysis showed that plant ADTs and yeast PDTs share many common features allowing them to act as dehydratase/decarboxylases. However, plant and yeast sequences clearly group independently conferring distinct substrate specificities. Complementation of the Saccharomyces cerevisiae pha2 mutant, which lacks PDT activity and cannot grow in the absence of exogenous Phe, was used to test the PDT activity of A. thaliana ADTs in vivo. Previous biochemical characterization showed that all six AtADTs had high catalytic activity with arogenate as a substrate, while AtADT1, AtADT2 and AtADT6 also had limited activity with prephenate. Consistent with these results, the complementation test showed AtADT2 readily recovered the pha2 phenotype after ∼6 days growth at 30 °C, while AtADT1 required ∼13 days to show visible growth. By contrast, AtADT6 (lowest PDT activity) and AtADT3-5 (no PDT activity) were unable to recover the phenotype. These results suggest that only AtADT1 and AtADT2, but not the other four ADTs from Arabidopsis, have functional PDT activity in vivo, showing that there are two functional distinct groups. We hypothesize that plant ADTs have evolved to use the arogenate route for Phe synthesis while keeping some residual PDT activity.
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Affiliation(s)
- Crystal D Bross
- Department of Biology, University of Western Ontario, 1151 Richmond Street North, London, Ontario N6A5B7, Canada
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Um HY, Chung E, Lee JH, Lee SW. Improved antibiotic resistance gene cassette for marker exchange mutagenesis in Ralstonia solanacearum and Burkholderia species. J Microbiol 2011; 49:305-8. [PMID: 21538255 DOI: 10.1007/s12275-011-0439-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Accepted: 11/29/2010] [Indexed: 10/18/2022]
Abstract
Marker exchange mutagenesis is a fundamental approach to understanding gene function at a molecular level in bacteria. New plasmids carrying a kanamycin resistance gene or a trimethoprim resistance gene were constructed to provide antibiotic resistance cassettes for marker exchange mutagenesis in Ralstonia solanacearum and many antibiotic-resistant Burkholderia spp. Insertion sequences present in the flanking sequences of the antibiotic resistance cassette were removed to prevent aberrant gene replacement and polar mutation during mutagenesis in wild-type bacteria. Plasmids provided in this study would be convenient for use in gene cassettes for gene replacement in other Gram-negative bacteria.
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Affiliation(s)
- Hae Young Um
- Department of Medical Bioscience, Dong-A University, Busan 604-714, Republic of Korea
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Jeong Y, Cheong H, Choi O, Kim JK, Kang Y, Kim J, Lee S, Koh S, Moon JS, Hwang I. An HrpB-dependent but type III-independent extracellular aspartic protease is a virulence factor of Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2011; 12:373-80. [PMID: 21453432 PMCID: PMC6640462 DOI: 10.1111/j.1364-3703.2010.00679.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The host specificity of Ralstonia solanacearum, the causal organism of bacterial wilt on many solanaceous crops, is poorly understood. To identify a gene conferring host specificity of the bacterium, SL341 (virulent to hot pepper but avirulent to potato) and SL2029 (virulent to potato but avirulent to hot pepper) were chosen as representative strains. We identified a gene, rsa1, from SL2029 that confers avirulence to SL341 in hot pepper. The rsa1 gene encoding an 11.8-kDa protein possessed the perfect consensus hrp(II) box motif upstream of the gene. Although the expression of rsa1 was activated by HrpB, a transcriptional activator for hrp gene expression, Rsa1 protein was secreted in an Hrp type III secretion-independent manner. Rsa1 exhibited weak homology with an aspartic protease, cathepsin D, and possessed protease activity. Two specific aspartic protease inhibitors, pepstatin A and diazoacetyl-d,l-norleucine methyl ester, inhibited the protease activity of Rsa1. Substitution of two aspartic acid residues with alanine at positions 54 and 59 abolished protease activity. The SL2029 rsa1 mutant was much less virulent than the wild-type strain, but did not induce disease symptoms in hot pepper. These data indicate that Rsa1 is an extracellular aspartic protease and plays an important role for the virulence of SL2029 in potato.
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Affiliation(s)
- Yeonhwa Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
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Milling A, Babujee L, Allen C. Ralstonia solanacearum extracellular polysaccharide is a specific elicitor of defense responses in wilt-resistant tomato plants. PLoS One 2011; 6:e15853. [PMID: 21253019 PMCID: PMC3017055 DOI: 10.1371/journal.pone.0015853] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/25/2010] [Indexed: 01/22/2023] Open
Abstract
Ralstonia solanacearum, which causes bacterial wilt of diverse plants, produces copious extracellular polysaccharide (EPS), a major virulence factor. The function of EPS in wilt disease is uncertain. Leading hypotheses are that EPS physically obstructs plant water transport, or that EPS cloaks the bacterium from host plant recognition and subsequent defense. Tomato plants infected with R. solanacearum race 3 biovar 2 strain UW551 and tropical strain GMI1000 upregulated genes in both the ethylene (ET) and salicylic acid (SA) defense signal transduction pathways. The horizontally wilt-resistant tomato line Hawaii7996 activated expression of these defense genes faster and to a greater degree in response to R. solanacearum infection than did susceptible cultivar Bonny Best. However, EPS played different roles in resistant and susceptible host responses to R. solanacearum. In susceptible plants the wild-type and eps− mutant strains induced generally similar defense responses. But in resistant Hawaii7996 tomato plants, the wild-type pathogens induced significantly greater defense responses than the eps− mutants, suggesting that the resistant host recognizes R. solanacearum EPS. Consistent with this idea, purified EPS triggered significant SA pathway defense gene expression in resistant, but not in susceptible, tomato plants. In addition, the eps− mutant triggered noticeably less production of defense-associated reactive oxygen species in resistant tomato stems and leaves, despite attaining similar cell densities in planta. Collectively, these data suggest that bacterial wilt-resistant plants can specifically recognize EPS from R. solanacearum.
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Affiliation(s)
- Annett Milling
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Lavanya Babujee
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Kubota R, LaBarre P, Singleton J, Beddoe A, Weigl BH, Alvarez AM, Jenkins DM. Non-Instrumented Nucleic Acid Amplification (NINA) for Rapid Detection of Ralstonia solanacearum Race 3 Biovar 2. ACTA ACUST UNITED AC 2011; 4:69-80. [PMID: 25485176 DOI: 10.13031/2013.38508] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We report on the use of a non-instrumented device for the implementation of a loop-mediated amplification (LAMP) based assay for the select-agent bacterial-wilt pathogen Ralstonia solanacearum race 3 biovar 2. Heat energy is generated within the device by the exothermic hydration of calcium oxide, and the reaction temperature is regulated by storing latent energy at the melting temperature of a renewable lipid-based engineered phase-change material. Endpoint detection of the LAMP reaction is achieved without opening the reaction tube by observing the fluorescence of an innovative FRET-based hybridization probe with a simple custom fluorometer. Non-instrumented devices could maintain reactions near the design temperature of 63°C for at least an hour. Using this approach DNA extracted from the pathogen could be detected at fewer than ten copies within a 25 μL reaction mix, illustrating the potential of these technologies for simple, powerful agricultural diagnostics in the field. Furthermore, the assay was just as reliable when implemented in a tropical environment at 31°C as it was when implemented in an air-conditioned lab maintained at 22°C, illustrating the potential value of the technology for field conditions in the tropics and subtropics.
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Affiliation(s)
- Ryo Kubota
- Laboratory Manager, Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii
| | - Paul LaBarre
- Technical Officer/Portfolio Leader, Center for POC for Global Health, Program for Appropriate Technologies in Health (PATH), Seattle, Washington
| | - Jered Singleton
- Product Development Technician, Center for POC for Global Health, Program for Appropriate Technologies in Health (PATH), Seattle, Washington
| | - Andy Beddoe
- Product Development Officer, Center for POC for Global Health, Program for Appropriate Technologies in Health (PATH), Seattle, Washington
| | - Bernhard H Weigl
- Director, Center for POC for Global Health, Program for Appropriate Technologies in Health (PATH), Seattle, Washington
| | - Anne M Alvarez
- Professor, Department of Plant and Environmental Protection Sciences
| | - Daniel M Jenkins
- ASABE Member, Associate Professor, Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii
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