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Vicente JG, Holub EB. Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. MOLECULAR PLANT PATHOLOGY 2013; 14:2-18. [PMID: 23051837 PMCID: PMC6638727 DOI: 10.1111/j.1364-3703.2012.00833.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BACKGROUND Xanthomonas campestris pv. campestris (Xcc) (Pammel) Dowson is a Gram-negative bacterium that causes black rot, the most important disease of vegetable brassica crops worldwide. Intensive molecular investigation of Xcc is gaining momentum and several whole genome sequences are available. TAXONOMY Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadacea; Genus Xanthomonas; Species X. campestris. HOST RANGE AND SYMPTOMS Xcc can cause disease in a large number of species of Brassicaceae (ex-Cruciferae), including economically important vegetable Brassica crops and a number of other cruciferous crops, ornamentals and weeds, including the model plant Arabidopsis thaliana. Black rot is a systemic vascular disease. Typical disease symptoms include V-shaped yellow lesions starting from the leaf margins and blackening of the veins. RACE STRUCTURE, PATHOGENESIS AND EPIDEMIOLOGY Collections of Xcc isolates have been differentiated into physiological races based on the response of several brassica species lines. Black rot is a seed-borne disease. The disease is favoured by warm, humid conditions and can spread rapidly from rain dispersal and irrigation water. DISEASE CONTROL The control of black rot is difficult and relies on the use of pathogen-free planting material and the elimination of other potential inoculum sources (infected crop debris and cruciferous weeds). Major gene resistance is very rare in B. oleracea (brassica C genome). Resistance is more readily available in other species, including potentially useful sources of broad-spectrum resistance in B. rapa and B. carinata (A and BC genomes, respectively) and in the wild relative A. thaliana. GENOME The reference genomes of three isolates have been released. The genome consists of a single chromosome of approximately 5 100 000 bp, with a GC content of approximately 65% and an average predicted number of coding DNA sequences (CDS) of 4308. IMPORTANT GENES IDENTIFIED Three different secretion systems have been identified and studied in Xcc. The gene clusters xps and xcs encode a type II secretion system and xps genes have been linked to pathogenicity. The role of the type IV secretion system in pathogenicity is still uncertain. The hrp gene cluster encodes a type III secretion system that is associated with pathogenicity. An inventory of candidate effector genes has been assembled based on homology with known effectors. A range of other genes have been associated with virulence and pathogenicity, including the rpf, gum and wxc genes involved in the regulation of the synthesis of extracellular degrading enzymes, xanthan gum and lipopolysaccharides. USEFUL WEBSITE http://www.xanthomonas.org/
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Affiliation(s)
- Joana G Vicente
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
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Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Couloux A, Darrasse A, Gouzy J, Jacques MA, Lauber E, Manceau C, Mangenot S, Poussier S, Segurens B, Szurek B, Verdier V, Arlat M, Gabriel DW, Rott P, Cociancich S. Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels. BMC Genomics 2012; 13:658. [PMID: 23171051 PMCID: PMC3542200 DOI: 10.1186/1471-2164-13-658] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 11/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa-another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. RESULTS Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the "artillery" of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to X. albilineans that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific to X. albilineans were identified, supposing that X. albilineans has a reduced artillery compared to other pathogenic Xanthomonas species. Particular attention has therefore been given to genomic features specific to X. albilineans making it more capable of evading sugarcane surveillance systems or resisting sugarcane defense systems. CONCLUSIONS This study confirms that X. albilineans is a highly distinctive species within the genus Xanthomonas, and opens new perpectives towards a greater understanding of the pathogenicity of this destructive sugarcane pathogen.
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Affiliation(s)
| | - Monique Royer
- CIRAD, UMR BGPI, F-34398 Montpellier Cedex 5, France
| | - Valérie Barbe
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | | | - Ralf Koebnik
- IRD, UMR RPB, F-34394 Montpellier Cedex 5, France
| | - Arnaud Couloux
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | | | - Jérôme Gouzy
- INRA, UMR LIPM, F-31326 Castanet-Tolosan Cedex France
| | | | | | | | - Sophie Mangenot
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | - Stéphane Poussier
- Université de la Réunion, UMR PVBMT, F-97715 Saint-Denis La Réunion, France
| | - Béatrice Segurens
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | - Boris Szurek
- IRD, UMR RPB, F-34394 Montpellier Cedex 5, France
| | | | - Matthieu Arlat
- Université Paul Sabatier, UMR LIPM, F-31326 Castanet-Tolosan Cedex France
| | - Dean W Gabriel
- University of Florida, Plant Pathology Department, Gainesville FL 32605 USA
| | - Philippe Rott
- CIRAD, UMR BGPI, F-34398 Montpellier Cedex 5, France
| | - Stéphane Cociancich
- CIRAD, UMR BGPI, F-34398 Montpellier Cedex 5, France
- UMR BGPI, Campus International de Baillarguet, TA A-54/K, F-34398 Montpellier Cedex 5, France
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Genome sequence of Xanthomonas campestris JX, an industrially productive strain for Xanthan gum. J Bacteriol 2012; 194:4755-6. [PMID: 22887662 DOI: 10.1128/jb.00965-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas campestris JX, a soil bacterium, is an industrially productive strain for xanthan gum. Here we present a 5.0-Mb assembly of its genome sequence. We have annotated 12 coding sequences (CDSs) responsible for xanthan gum biosynthesis, 346 CDSs encoding carbohydrate metabolism, and 69 CDSs related to virulence, defense, and plant disease.
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Zhang X, Abreu JG, Yokota C, MacDonald BT, Singh S, Coburn KLA, Cheong SM, Zhang MM, Ye QZ, Hang HC, Steen H, He X. Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation. Cell 2012; 149:1565-77. [PMID: 22726442 DOI: 10.1016/j.cell.2012.04.039] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 02/17/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
Secreted Wnt morphogens are signaling molecules essential for embryogenesis, pathogenesis, and regeneration and require distinct modifications for secretion, gradient formation, and activity. Whether Wnt proteins can be posttranslationally inactivated during development and homeostasis is unknown. Here we identify, through functional cDNA screening, a transmembrane protein Tiki1 that is expressed specifically in the dorsal Spemann-Mangold Organizer and is required for anterior development during Xenopus embryogenesis. Tiki1 antagonizes Wnt function in embryos and human cells via a TIKI homology domain that is conserved from bacteria to mammals and acts likely as a protease to cleave eight amino-terminal residues of a Wnt protein, resulting in oxidized Wnt oligomers that exhibit normal secretion but minimized receptor-binding capability. Our findings identify a Wnt-specific protease that controls head formation, reveal a mechanism for morphogen inactivation through proteolysis-induced oxidation-oligomerization, and suggest a role of the Wnt amino terminus in evasion of oxidizing inactivation. TIKI proteins may represent potential therapeutic targets.
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Affiliation(s)
- Xinjun Zhang
- The F. M. Kirby Neurobiology Center, Boston Children's Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
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Bart R, Cohn M, Kassen A, McCallum EJ, Shybut M, Petriello A, Krasileva K, Dahlbeck D, Medina C, Alicai T, Kumar L, Moreira LM, Neto JR, Verdier V, Santana MA, Kositcharoenkul N, Vanderschuren H, Gruissem W, Bernal A, Staskawicz BJ. High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance. Proc Natl Acad Sci U S A 2012; 109:E1972-9. [PMID: 22699502 PMCID: PMC3396514 DOI: 10.1073/pnas.1208003109] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cassava bacterial blight (CBB), incited by Xanthomonas axonopodis pv. manihotis (Xam), is the most important bacterial disease of cassava, a staple food source for millions of people in developing countries. Here we present a widely applicable strategy for elucidating the virulence components of a pathogen population. We report Illumina-based draft genomes for 65 Xam strains and deduce the phylogenetic relatedness of Xam across the areas where cassava is grown. Using an extensive database of effector proteins from animal and plant pathogens, we identify the effector repertoire for each sequenced strain and use a comparative sequence analysis to deduce the least polymorphic of the conserved effectors. These highly conserved effectors have been maintained over 11 countries, three continents, and 70 y of evolution and as such represent ideal targets for developing resistance strategies.
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Affiliation(s)
- Rebecca Bart
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Megan Cohn
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Andrew Kassen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Emily J. McCallum
- Department of Biology, Eidgenössische Technische Hochschule, CH-8092 Zurich, Switzerland
| | - Mikel Shybut
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Annalise Petriello
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Douglas Dahlbeck
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Cesar Medina
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Titus Alicai
- National Crops Resources Research Institute–Namulonge, Kampala, Uganda
| | - Lava Kumar
- Germplasm Health Unit, International Institute of Tropical Agriculture, PMB 5320, Ibadan, Nigeria
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Minas Gerais, Brazil
| | - Júlio Rodrigues Neto
- Coleção de Culturas de Fitobactérias, Instituto Biológico Seção de Bacteriologia Fitopatologia, Instituto Biológico–Centro Experimental Central do Instituto Biologico, Laboratório de Bacteriologia Vegetal, 13012-970, Campinas, SP, Brazil
| | - Valerie Verdier
- Bioagricultural Sciences and Pest Management, Institut de Recherche pour le Développement, Unité Mixte de Recherche, Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement-Internationale en Recherche Agronomique pour le Developement-Université Montpellier 2, 34394 Montpellier Cedex 5, France
| | - María Angélica Santana
- Departamento de Biología Celular, Universidad Simón Bolívar, Carretera Nacional Hoyo de la Puerta, Sartenejas, Distrito Capital, Caracas 1080, Venezuela; and
| | - Nuttima Kositcharoenkul
- Plant Protection Research and Development Office, Department of Agriculture, Chatuchak, Bangkok 10900, Thailand
| | - Hervé Vanderschuren
- Department of Biology, Eidgenössische Technische Hochschule, CH-8092 Zurich, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Eidgenössische Technische Hochschule, CH-8092 Zurich, Switzerland
| | - Adriana Bernal
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Brian J. Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
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Zou HS, Song X, Zou LF, Yuan L, Li YR, Guo W, Che YZ, Zhao WX, Duan YP, Chen GY. EcpA, an extracellular protease, is a specific virulence factor required by Xanthomonas oryzae pv. oryzicola but not by X. oryzae pv. oryzae in rice. MICROBIOLOGY-SGM 2012; 158:2372-2383. [PMID: 22700650 DOI: 10.1099/mic.0.059964-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Previously, 12 protease-deficient mutants of the Xanthomonas oryzae pv. oryzicola (Xoc) RS105 strain were recovered from a Tn5-tagged mutant library. In the current study, the Tn5 insertion site in each mutant was mapped. Mutations in genes encoding components of the type II secretion apparatus, cAMP regulatory protein, integral membrane protease subunit, S-adenosylmethionine decarboxylase proenzyme and extracellular protease (ecpA(Xoc)) either partially or completely abolished extracellular protease activity (ECPA) and reduced virulence in rice. Transcription of ecpA(Xoc) was induced in planta in all the mutants except RΔecpA. Complementation of RΔecpA with ecpA(Xoc) in trans restored ECPA, virulence and bacterial growth in planta. Purified EcpA(Xoc) induced chlorosis- and necrosis-like symptoms similar to those induced by the pathogen when injected into rice leaves. Heterologous expression of ecpA(Xoc) conferred ECPA upon the vascular bacterium X. oryzae pv. oryzae (Xoo) and upon non-pathogenic Escherichia coli. Genetic analysis demonstrated that the C-terminal residues of EcpA in Xoo PXO99(A) and Xoc RS105 are different, and a frame shift in ecpA(Xoo) may explain the absence of EcpA activity in Xoo. Collectively, these results suggest that EcpA(Xoc) is a tissue-specific virulence factor for Xoc but not Xoo, although the two pathovars are closely related bacterial pathogens of rice.
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Affiliation(s)
- Hua-Song Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xue Song
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Li-Fang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Liang Yuan
- Department of Plant Pathology, Nanjing Agricultural University, Key Laboratory of Monitoring and Management for Plant Diseases and Insects, Ministry of Agriculture of China, Nanjing 210095, PR China
| | - Yu-Rong Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Wei Guo
- Department of Plant Pathology, Nanjing Agricultural University, Key Laboratory of Monitoring and Management for Plant Diseases and Insects, Ministry of Agriculture of China, Nanjing 210095, PR China
| | - Yi-Zhou Che
- Department of Plant Pathology, Nanjing Agricultural University, Key Laboratory of Monitoring and Management for Plant Diseases and Insects, Ministry of Agriculture of China, Nanjing 210095, PR China
| | - Wen-Xiang Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Key Laboratory of Monitoring and Management for Plant Diseases and Insects, Ministry of Agriculture of China, Nanjing 210095, PR China
| | - Yong-Ping Duan
- Horticultural Research Laboratory, Agricultural Research Service, USDA, Fort Pierce, FL 34945, USA
| | - Gong-You Chen
- Department of Plant Pathology, Nanjing Agricultural University, Key Laboratory of Monitoring and Management for Plant Diseases and Insects, Ministry of Agriculture of China, Nanjing 210095, PR China.,School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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57
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Toward an understanding of the molecular basis of quantitative disease resistance in rice. J Biotechnol 2012; 159:283-90. [DOI: 10.1016/j.jbiotec.2011.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 06/08/2011] [Accepted: 07/06/2011] [Indexed: 11/22/2022]
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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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59
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Hajri A, Brin C, Zhao S, David P, Feng JX, Koebnik R, Szurek B, Verdier V, Boureau T, Poussier S. Multilocus sequence analysis and type III effector repertoire mining provide new insights into the evolutionary history and virulence of Xanthomonas oryzae. MOLECULAR PLANT PATHOLOGY 2012; 13:288-302. [PMID: 21929565 PMCID: PMC6638859 DOI: 10.1111/j.1364-3703.2011.00745.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Multilocus sequence analysis (MLSA) and type III effector (T3E) repertoire mining were performed to gain new insights into the genetic relatedness of Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), two major bacterial pathogens of rice. Based on a collection of 45 African and Asian strains, we first sequenced and analysed three housekeeping genes by MLSA, Bayesian clustering and a median-joining network approach. Second, we investigated the distribution of 32 T3E genes, which are known to be major virulence factors of plant pathogenic bacteria, in all selected strains, by polymerase chain reaction and dot-blot hybridization methods. The diversity observed within housekeeping genes, as well as within T3E repertoires, clearly showed that both pathogens belong to closely related, but distinct, phylogenetic groups. Interestingly, these evolutionary groups are differentiated according to the geographical origin of the strains, suggesting that populations of Xoo and Xoc might be endemic in Africa and Asia, and thus have evolved separately. We further revealed that T3E gene repertoires of both pathogens comprise core and variable gene suites that probably have distinct roles in pathogenicity and different evolutionary histories. In this study, we carried out a functional analysis of xopO, a differential T3E gene between Xoo and Xoc, to determine the involvement of this gene in tissue specificity. Altogether, our data contribute to a better understanding of the evolutionary history of Xoo and Xoc in Africa and Asia, and provide clues for functional studies aiming to understand the virulence, host and tissue specificity of both rice pathogens.
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Affiliation(s)
- Ahmed Hajri
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique, UMR 077 PaVé, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
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Studholme DJ, Wasukira A, Paszkiewicz K, Aritua V, Thwaites R, Smith J, Grant M. Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade. Genes (Basel) 2011; 2:1050-65. [PMID: 24710305 PMCID: PMC3927605 DOI: 10.3390/genes2041050] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 11/04/2011] [Accepted: 11/21/2011] [Indexed: 12/25/2022] Open
Abstract
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.
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Affiliation(s)
- David J Studholme
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Arthur Wasukira
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Konrad Paszkiewicz
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Valente Aritua
- National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda.
| | - Richard Thwaites
- The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK.
| | - Julian Smith
- The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK.
| | - Murray Grant
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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Jalan N, Aritua V, Kumar D, Yu F, Jones JB, Graham JH, Setubal JC, Wang N. Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity. J Bacteriol 2011; 193:6342-57. [PMID: 21908674 PMCID: PMC3209208 DOI: 10.1128/jb.05777-11] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 08/30/2011] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas axonopodis pv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence of X. axonopodis pv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrus Xanthomonas pathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogen X. campestris pv. vesicatoria 85-10, with a completely different host range. We also compared X. axonopodis pv. citrumelo to the genome of citrus canker pathogen X. axonopodis pv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition to pthA, effectors such as xopE3, xopAI, and hrpW were absent from X. axonopodis pv. citrumelo while present in X. axonopodis pv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that of X. axonopodis pv. citri. We also identified unique effectors in X. axonopodis pv. citrumelo that may be related to the different host range as compared to that of X. axonopodis pv. citri. X. axonopodis pv. citrumelo also lacks various genes, such as syrE1, syrE2, and RTX toxin family genes, which were present in X. axonopodis pv. citri. These may be associated with the distinct virulences of X. axonopodis pv. citrumelo and X. axonopodis pv. citri. Comparison of the complete genome sequence of X. axonopodis pv. citrumelo to those of X. axonopodis pv. citri and X. campestris pv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.
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Affiliation(s)
- Neha Jalan
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred, Florida 33850
| | - Valente Aritua
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred, Florida 33850
| | - Dibyendu Kumar
- Interdisciplinary Center for Biotechnology Research, 2033 Mowry Road, University of Florida, Gainesville, Florida 32611
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, 2033 Mowry Road, University of Florida, Gainesville, Florida 32611
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611
| | - James H. Graham
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred, Florida 33850
| | - João C. Setubal
- Virginia Bioinformatics Institute and Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060-0477
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, 700 Experiment Station Road, Lake Alfred, Florida 33850
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Sun W, Liu L, Bent AF. Type III secretion-dependent host defence elicitation and type III secretion-independent growth within leaves by Xanthomonas campestris pv. campestris. MOLECULAR PLANT PATHOLOGY 2011; 12:731-45. [PMID: 21726374 PMCID: PMC6640278 DOI: 10.1111/j.1364-3703.2011.00707.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In many plant-bacterial interactions, loss of the type III secretion system (T3SS) severely reduces bacterial growth, symptom causation and suppression of defences in host plants. In the present study of Xanthomonas campestris pv. campestris (Xcc), Xcc strain B305 grew better than strain B186 in Arabidopsis thaliana after hydathode inoculation, and B305 strains mutated to the loss of T3SS (ΔhrcC and/or ΔhrpE; also ΔhrcCΔflgBC) grew similarly to wild-type B305 in Arabidopsis leaves. Unlike Xcc strain B186, wild-type B305 was relatively inefficient in secreting the exogenous T3S effector AvrBsT, but ΔhrcC and/or ΔhrpE attenuated the disease symptoms caused by Xcc B305, showing that the partially compromised T3SS of this strain still promotes necrotic leaf symptoms. In contrast with the T3SS-dependent defence suppression that has been observed for some other plant pathogenic bacteria, the Xcc B186 and B305 wild-type strains (which are virulent on Arabidopsis) caused greater elicitation of host PR-1 and PR-5 expression and callose deposition in comparison with their respective T3SS mutants. A defence-suppressing/virulence-enhancing activity of the Xcc T3SS effector suite was detectable when co-inoculation with wild-type Xcc B186 increased the growth of ΔhrcC Xcc, but this activity did not prevent the above defence elicitation. Experiments using T3SS mutants and Arabidopsis fls2 mutants suggested that FLS2 does not play a prominent role in restriction of the examined Xcc strains. However, ectopic overexpression of the Pseudomonas syringae effector AvrPto promoted in planta growth of wild-type and ΔhrcC Xcc. In summary, the T3SS components or effector suite from virulent Xcc strains elicit some host defence responses, but suppress other defences and stimulate more severe disease symptoms, AvrPto-disruptable elements other than FLS2 apparently contribute to the host restriction of Xcc, and in some virulent Xcc strains the T3SS is not absolutely required for wild-type levels of bacterial growth within the plant.
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Affiliation(s)
- Wenxian Sun
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol 2011; 193:5450-64. [PMID: 21784931 PMCID: PMC3187462 DOI: 10.1128/jb.05262-11] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 07/11/2011] [Indexed: 01/03/2023] Open
Abstract
Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
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Affiliation(s)
- Adam J Bogdanove
- Department of Plant Pathology, Iowa State University, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA.
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64
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Kimbrel JA, Givan SA, Temple TN, Johnson KB, Chang JH. Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics. MOLECULAR PLANT PATHOLOGY 2011; 12:580-94. [PMID: 21722296 PMCID: PMC6640479 DOI: 10.1111/j.1364-3703.2010.00694.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Xanthomonas hortorum pv. carotae (Xhc) is an economically important pathogen of carrots. Its ability to epiphytically colonize foliar surfaces and infect seeds can result in bacterial blight of carrots when grown in warm and humid regions. We used high-throughput sequencing to determine the genome sequence of isolate M081 of Xhc. The short reads were de novo assembled and the resulting contigs were ordered using a syntenic reference genome sequence from X. campestris pv. campestris ATCC 33913. The improved, high-quality draft genome sequence of Xhc M081 is the first for its species. Despite its distance from other sequenced xanthomonads, Xhc M081 still shared a large inventory of orthologous genes, including many clusters of virulence genes common to other foliar pathogenic species of Xanthomonas. We also mined the genome sequence and identified at least 21 candidate type III effector genes. Two were members of the avrBs2 and xopQ families that demonstrably elicit effector-triggered immunity. We showed that expression in planta of these two type III effectors from Xhc M081 was sufficient to elicit resistance gene-mediated hypersensitive responses in heterologous plants, indicating a possibility for resistance gene-mediated control of Xhc. Finally, we identified regions unique to the Xhc M081 genome sequence, and demonstrated their potential in the design of molecular diagnostics for this pathogen.
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Affiliation(s)
- Jeffrey A Kimbrel
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
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65
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Legaz ME, Blanch M, Piñón D, Santiago R, Fontaniella B, Blanco Y, Solas MT, Vicente C. Sugarcane glycoproteins may act as signals for the production of xanthan in the plant-associated bacterium Xanthomonas albilineans. PLANT SIGNALING & BEHAVIOR 2011; 6:1132-1139. [PMID: 21791980 PMCID: PMC3260710 DOI: 10.4161/psb.6.8.15810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 04/12/2011] [Accepted: 04/12/2011] [Indexed: 05/31/2023]
Abstract
Visual symptoms of leaf scald necrosis in sugarcane (Saccharum officinarum) leaves develop in parallel to the accumulation of a fibrous material invading exocellular spaces and both xylem and phloem. These fibers are produced and secreted by the plant-associated bacterium Xanthomonas albilineans. Electron microscopy and specific staining methods for polysaccharides reveal the polysaccharidic nature of this material. These polysaccharides are not present in healthy leaves or in those from diseased plants without visual symptoms of leaf scald. Bacteria in several leaf tissues have been detected by immunogold labelling. The bacterial polysaccharide is not produced in axenic culture but it is actively synthesized when the microbes invade the host plant. This finding may be due to the production of plant glycoproteins after bacteria infection, which inhibit microbial proteases. In summary, our data are consistent with the existence of a positive feedback loop in which plant-produced glycoproteins act as a cell-to-bacteria signal that promotes xanthan production, by protecting some enzymes of xanthan biosynthesis against from bacterial proteolytic degradation.
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Affiliation(s)
- María-Estrella Legaz
- Intercellular Communication in Plant Symbiosis Team; Instituto del Frío; CSIC; Madrid, Spain
| | - María Blanch
- Department of Plant Food Science and Technology; Instituto del Frío; CSIC; Madrid, Spain
| | - Dolores Piñón
- INICA; National Institute of Sugarcane Research; La Habana, Cuba
| | - Rocío Santiago
- Intercellular Communication in Plant Symbiosis Team; Instituto del Frío; CSIC; Madrid, Spain
| | - Blanca Fontaniella
- Intercellular Communication in Plant Symbiosis Team; Instituto del Frío; CSIC; Madrid, Spain
| | - Yolanda Blanco
- Intercellular Communication in Plant Symbiosis Team; Instituto del Frío; CSIC; Madrid, Spain
| | - María-Teresa Solas
- Department of Cell Biology; Faculty of Biology; Instituto del Frío; CSIC; Madrid, Spain
| | - Carlos Vicente
- Intercellular Communication in Plant Symbiosis Team; Instituto del Frío; CSIC; Madrid, Spain
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66
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Triplett LR, Hamilton JP, Buell CR, Tisserat NA, Verdier V, Zink F, Leach JE. Genomic analysis of Xanthomonas oryzae isolates from rice grown in the United States reveals substantial divergence from known X. oryzae pathovars. Appl Environ Microbiol 2011; 77:3930-7. [PMID: 21515727 PMCID: PMC3131649 DOI: 10.1128/aem.00028-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/09/2011] [Indexed: 12/17/2022] Open
Abstract
The species Xanthomonas oryzae is comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. Although X. oryzae is not considered endemic in the United States, an X. oryzae-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterized X. oryzae pathovars. In the current study, a draft genome sequence from two U.S. Xanthomonas strains revealed that the U.S. strains form a novel clade within the X. oryzae species, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools.
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Affiliation(s)
- L. R. Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - J. P. Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - C. R. Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - N. A. Tisserat
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - V. Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
- UMR RPB, IRD-CIRAD-UM2, BP 64501, 34394 Montpellier Cedex 5, France
| | - F. Zink
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - J. E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523
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67
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Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat Rev Microbiol 2011; 9:344-55. [PMID: 21478901 DOI: 10.1038/nrmicro2558] [Citation(s) in RCA: 303] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant hosts, including many economically important crops. Pathogenic species and pathovars within species show a high degree of host plant specificity and many exhibit tissue specificity, invading either the vascular system or the mesophyll tissue of the host. In this Review, we discuss the insights that functional and comparative genomic studies are providing into the adaptation of this group of bacteria to exploit the extraordinary diversity of plant hosts and different host tissues.
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Affiliation(s)
- Robert P Ryan
- BIOMERIT Research Centre, Department of Microbiology, BioSciences Institute, University College Cork, Ireland
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68
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Ryan RP, Dow JM. Communication with a growing family: diffusible signal factor (DSF) signaling in bacteria. Trends Microbiol 2011; 19:145-52. [PMID: 21227698 DOI: 10.1016/j.tim.2010.12.003] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/19/2010] [Accepted: 12/06/2010] [Indexed: 11/30/2022]
Abstract
Many pathogenic bacteria use cell-cell signaling to regulate the expression of factors contributing to virulence. Bacteria produce signals of diverse structural classes. The signal molecule known as diffusible signal factor (DSF) is a cis-unsaturated fatty acid that was first described in the plant pathogen Xanthomonas campestris. Recent work has shown that structurally related molecules produced by the unrelated bacteria Burkholderia cenocepacia and Pseudomonas aeruginosa regulate virulence, biofilm formation and antibiotic tolerance in these important human pathogens. Furthermore, DSF family signals have been shown to be involved in interspecies signaling that modulates bacterial behavior. An understanding of these diverse signaling mechanisms could suggest strategies for interference, with consequences for disease control.
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Affiliation(s)
- Robert P Ryan
- BIOMERIT Research Centre, Department of Microbiology, Biosciences Institute, University College Cork, Cork, Ireland.
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69
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Mhedbi-Hajri N, Jacques MA, Koebnik R. Adhesion mechanisms of plant-pathogenic Xanthomonadaceae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 715:71-89. [PMID: 21557058 DOI: 10.1007/978-94-007-0940-9_5] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The family Xanthomonadaceae is a wide-spread family of bacteria belonging to the gamma subdivision of the Gram-negative proteobacteria, including the two plant-pathogenic genera Xanthomonas and Xylella, and the related genus Stenotrophomonas. Adhesion is a widely conserved virulence mechanism among Gram-negative bacteria, no matter whether they are human, animal or plant pathogens, since attachment to the host tissue is one of the key early steps of the bacterial infection process. Bacterial attachment to surfaces is mediated by surface structures that are anchored in the bacterial outer membrane and cover a broad group of fimbrial and non-fimbrial structures, commonly known as adhesins. In this chapter, we discuss recent findings on candidate adhesins of plant-pathogenic Xanthomonadaceae, including polysaccharidic (lipopolysaccharides, exopolysaccharides) and proteineous structures (chaperone/usher pili, type IV pili, autotransporters, two-partner-secreted and other outer membrane adhesins), their involvement in the formation of biofilms and their mode of regulation via quorum sensing. We then compare the arsenals of adhesins among different Xanthomonas strains and evaluate their mode of selection. Finally, we summarize the sparse knowledge on specific adhesin receptors in plants and the possible role of RGD motifs in binding to integrin-like plant molecules.
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Affiliation(s)
- Nadia Mhedbi-Hajri
- Pathologie Végétale (UMR077 INRA-Agrocampus Ouest-Université d'Angers), Beaucouzé, France.
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70
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Szczesny R, Jordan M, Schramm C, Schulz S, Cogez V, Bonas U, Büttner D. Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria. THE NEW PHYTOLOGIST 2010; 187:983-1002. [PMID: 20524995 DOI: 10.1111/j.1469-8137.2010.03312.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
*Type II secretion (T2S) systems of many plant-pathogenic bacteria often secrete cell wall-degrading enzymes into the plant apoplast. *Here, we show that the Xps-T2S system from the plant pathogen Xanthomonas campestris pv vesicatoria (Xcv) promotes disease and contributes to the translocation of effector proteins that are delivered into the plant cell by the type III secretion (T3S) system. *The Xcs-T2S system instead lacks an obvious virulence function. However, individual xcs genes can partially complement mutants in homologous xps genes, indicating that they encode functional components of T2S systems. Enzyme activity assays showed that the Xps system contributes to secretion of proteases and xylanases. We identified the virulence-associated xylanase XynC as a substrate of the Xps system. However, homologs of known T2S substrates from other Xanthomonas spp. are not secreted by the T2S systems from Xcv. Thus, T2S systems from Xanthomonas spp. appear to differ significantly in their substrate specificities. *Transcript analyses revealed that expression of xps genes in Xcv is activated by HrpG and HrpX, key regulators of the T3S system. By contrast, expression of xynC and extracellular protease and xylanase activities are repressed by HrpG and HrpX, suggesting that components and substrates of the Xps system are differentially regulated.
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Affiliation(s)
| | | | - Claudia Schramm
- Institut für Biologie, Bereich Genetik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | - Steve Schulz
- Institut für Biologie, Bereich Genetik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | - Virginie Cogez
- Institut für Biologie, Bereich Genetik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | - Ulla Bonas
- Institut für Biologie, Bereich Genetik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | - Daniela Büttner
- Institut für Biologie, Bereich Genetik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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71
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Soto-Suárez M, González C, Piégu B, Tohme J, Verdier V. Genomic comparison between Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, using suppression-subtractive hybridization. FEMS Microbiol Lett 2010; 308:16-23. [DOI: 10.1111/j.1574-6968.2010.01985.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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72
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Lang JM, Hamilton JP, Diaz MGQ, Van Sluys MA, Burgos MRG, Vera Cruz CM, Buell CR, Tisserat NA, Leach JE. Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. PLANT DISEASE 2010; 94:311-319. [PMID: 30754246 DOI: 10.1094/pdis-94-3-0311] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to rapidly identify unique regions for development of highly specific diagnostic markers. A suite of diagnostic primers was selected to monitor diverse loci and to distinguish the rice bacterial blight and bacterial leaf streak pathogens, Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. A subset of these primers was combined into a multiplex polymerase chain reaction set that accurately distinguished the two rice pathogens in a survey of a geographically diverse collection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola, other xanthomonads, and several genera of plant-pathogenic and plant- or seed-associated bacteria. This computational approach for identification of unique loci through whole-genome comparisons is a powerful tool that can be applied to other plant pathogens to expedite development of diagnostic primers.
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Affiliation(s)
- Jillian M Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University (CSU), Fort Collins 80523-1177
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing 48824-1312
| | - Maria Genaleen Q Diaz
- Department of Bioagricultural Sciences and Pest Management, CSU and University of the Philippines, Los Baños, Los Baños, Philippines
| | - Marie Anne Van Sluys
- Department of Bioagricultural Sciences and Pest Management, CSU and Departamento de Botânica, IB-USP, São Paulo 05508-090, Brazil
| | - Ma Ruby G Burgos
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Casiana M Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - C Robin Buell
- Department of Plant Biology, Michigan State University
| | - Ned A Tisserat
- Department of Bioagricultural Sciences and Pest Management, CSU
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, CSU
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73
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Tampakaki AP, Skandalis N, Gazi AD, Bastaki MN, Sarris PF, Charova SN, Kokkinidis M, Panopoulos NJ. Playing the "Harp": evolution of our understanding of hrp/hrc genes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2010; 48:347-370. [PMID: 20455697 DOI: 10.1146/annurev-phyto-073009-114407] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
With the advent of recombinant DNA techniques, the field of molecular plant pathology witnessed dramatic shifts in the 1970s and 1980s. The new and conventional methodologies of bacterial molecular genetics put bacteria center stage. The discovery in the mid-1980s of the hrp/hrc gene cluster and the subsequent demonstration that it encodes a type III secretion system (T3SS) common to Gram negative bacterial phytopathogens, animal pathogens, and plant symbionts was a landmark in molecular plant pathology. Today, T3SS has earned a central role in our understanding of many fundamental aspects of bacterium-plant interactions and has contributed the important concept of interkingdom transfer of effector proteins determining race-cultivar specificity in plant-bacterium pathosystems. Recent developments in genomics, proteomics, and structural biology enable detailed and comprehensive insights into the functional architecture, evolutionary origin, and distribution of T3SS among bacterial pathogens and support current research efforts to discover novel antivirulence drugs.
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74
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Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Cociancich S, Couloux A, Darrasse A, Gouzy J, Jacques MA, Lauber E, Manceau C, Mangenot S, Poussier S, Segurens B, Szurek B, Verdier V, Arlat M, Rott P. The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics 2009; 10:616. [PMID: 20017926 PMCID: PMC2810307 DOI: 10.1186/1471-2164-10-616] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 12/17/2009] [Indexed: 01/21/2023] Open
Abstract
Background The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X. fastidiosa was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess hrp genes which encode a Type III secretion system found in most plant pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group based on phylogenetic analyses with rRNA sequences. Results The complete genome of X. albilineans was sequenced and annotated. X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. Phylogenetic analysis using X. albilineans genomic sequences showed that X. fastidiosa belongs to the Xanthomonas group. Order of divergence of the Xanthomonadaceae revealed that X. albilineans and X. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the Xanthomonas genus. Reductive genome evolutions of the two xylem-limited Xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens. Conclusion The two xylem-limited Xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of X. albilineans differ from those of X. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by X. albilineans, is discussed.
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Affiliation(s)
- Isabelle Pieretti
- CIRAD, UMR 385 BGPI, Campus international de Baillarguet, Montpellier, France.
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75
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Abstract
Plant pathogenic bacteria of the genus Xanthomonas cause a variety of diseases in economically important monocotyledonous and dicotyledonous crop plants worldwide. Successful infection and bacterial multiplication in the host tissue often depend on the virulence factors secreted including adhesins, polysaccharides, LPS and degradative enzymes. One of the key pathogenicity factors is the type III secretion system, which injects effector proteins into the host cell cytosol to manipulate plant cellular processes such as basal defense to the benefit of the pathogen. The coordinated expression of bacterial virulence factors is orchestrated by quorum-sensing pathways, multiple two-component systems and transcriptional regulators such as Clp, Zur, FhrR, HrpX and HpaR. Furthermore, virulence gene expression is post-transcriptionally controlled by the RNA-binding protein RsmA. In this review, we summarize the current knowledge on the infection strategies and regulatory networks controlling secreted virulence factors from Xanthomonas species.
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Affiliation(s)
- Daniela Büttner
- Genetics Department, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
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76
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Hajri A, Brin C, Hunault G, Lardeux F, Lemaire C, Manceau C, Boureau T, Poussier S. A "repertoire for repertoire" hypothesis: repertoires of type three effectors are candidate determinants of host specificity in Xanthomonas. PLoS One 2009; 4:e6632. [PMID: 19680562 PMCID: PMC2722093 DOI: 10.1371/journal.pone.0006632] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/09/2009] [Indexed: 11/21/2022] Open
Abstract
Background The genetic basis of host specificity for animal and plant pathogenic bacteria remains poorly understood. For plant pathogenic bacteria, host range is restricted to one or a few host plant species reflecting a tight adaptation to specific hosts. Methodology/Principal Findings Two hypotheses can be formulated to explain host specificity: either it can be explained by the phylogenetic position of the strains, or by the association of virulence genes enabling a pathological convergence of phylogenically distant strains. In this latter hypothesis, host specificity would result from the interaction between repertoires of bacterial virulence genes and repertoires of genes involved in host defences. To challenge these two hypotheses, we selected 132 Xanthomonas axonopodis strains representative of 18 different pathovars which display different host range. First, the phylogenetic position of each strain was determined by sequencing the housekeeping gene rpoD. This study showed that many pathovars of Xanthomonas axonopodis are polyphyletic. Second, we investigated the distribution of 35 type III effector genes (T3Es) in these strains by both PCR and hybridization methods. Indeed, for pathogenic bacteria T3Es were shown to trigger and to subvert host defences. Our study revealed that T3E repertoires comprise core and variable gene suites that likely have distinct roles in pathogenicity and different evolutionary histories. Our results showed a correspondence between composition of T3E repertoires and pathovars of Xanthomonas axonopodis. For polyphyletic pathovars, this suggests that T3E genes might explain a pathological convergence of phylogenetically distant strains. We also identified several DNA rearrangements within T3E genes, some of which correlate with host specificity of strains. Conclusions/Significance These data provide insight into the potential role played by T3E genes for pathogenic bacteria and support a “repertoire for repertoire” hypothesis that may explain host specificity. Our work provides resources for functional and evolutionary studies aiming at understanding host specificity of pathogenic bacteria, functional redundancy between T3Es and the driving forces shaping T3E repertoires.
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Affiliation(s)
- Ahmed Hajri
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique (INRA), Beaucouzé, France
| | - Chrystelle Brin
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique (INRA), Beaucouzé, France
| | - Gilles Hunault
- Département d'Informatique, Université d'Angers, Angers, France
| | | | | | - Charles Manceau
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique (INRA), Beaucouzé, France
| | - Tristan Boureau
- Département de Biologie, Université d'Angers, Angers, Beaucouzé, France
- * E-mail: (TB); (SP)
| | - Stéphane Poussier
- Département de Sciences Biologiques, Agrocampus Ouest centre d'Angers, Institut National d'Horticulture et de Paysage (INHP), Beaucouzé, France
- * E-mail: (TB); (SP)
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77
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Allen C, Bent A, Charkowski A. Underexplored niches in research on plant pathogenic bacteria. PLANT PHYSIOLOGY 2009; 150:1631-7. [PMID: 19561122 PMCID: PMC2719117 DOI: 10.1104/pp.109.140004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 06/23/2009] [Indexed: 05/09/2023]
Affiliation(s)
- Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin 53706, USA.
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78
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White FF, Yang B. Host and pathogen factors controlling the rice-Xanthomonas oryzae interaction. PLANT PHYSIOLOGY 2009; 150:1677-86. [PMID: 19458115 PMCID: PMC2719118 DOI: 10.1104/pp.109.139360] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 05/17/2009] [Indexed: 05/19/2023]
Affiliation(s)
- Frank F White
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506, USA.
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