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Lauber E, González-Fuente M, Escouboué M, Vicédo C, Luneau JS, Pouzet C, Jauneau A, Gris C, Zhang ZM, Pichereaux C, Carrère S, Deslandes L, Noël LD. Bacterial host adaptation through sequence and structural variations of a single type III effector gene. iScience 2024; 27:109224. [PMID: 38439954 PMCID: PMC10909901 DOI: 10.1016/j.isci.2024.109224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 12/02/2023] [Accepted: 02/08/2024] [Indexed: 03/06/2024] Open
Abstract
Molecular mechanisms underlying quantitative variations of pathogenicity remain elusive. Here, we identified the Xanthomonas campestris XopJ6 effector that triggers disease resistance in cauliflower and Arabidopsis thaliana. XopJ6 is a close homolog of the Ralstoniapseudosolanacearum PopP2 YopJ family acetyltransferase. XopJ6 is recognized by the RRS1-R/RPS4 NLR pair that integrates a WRKY decoy domain mimicking effector targets. We identified a XopJ6 natural variant carrying a single residue substitution in XopJ6 WRKY-binding site that disrupts interaction with WRKY proteins. This mutation allows XopJ6 to evade immune perception while retaining some XopJ6 virulence functions. Interestingly, xopJ6 resides in a Tn3-family transposon likely contributing to xopJ6 copy number variation (CNV). Using synthetic biology, we demonstrate that xopJ6 CNV tunes pathogen virulence on Arabidopsis through gene dosage-mediated modulation of xopJ6 expression. Together, our findings highlight how sequence and structural genetic variations restricted at a particular effector gene contribute to bacterial host adaptation.
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Affiliation(s)
- Emmanuelle Lauber
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Manuel González-Fuente
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Maxime Escouboué
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Céline Vicédo
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Julien S. Luneau
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Cécile Pouzet
- TRI-FRAIB Imaging Platform Facilities, FRAIB, Université de Toulouse, CNRS, UPS, 31320 Castanet-Tolosan, France
| | - Alain Jauneau
- TRI-FRAIB Imaging Platform Facilities, FRAIB, Université de Toulouse, CNRS, UPS, 31320 Castanet-Tolosan, France
| | - Carine Gris
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Carole Pichereaux
- Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FRAIB), Université de Toulouse, CNRS, Université de Toulouse III - Paul Sabatier (UT3), Auzeville-Tolosane, France
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université de Toulouse III - Paul Sabatier (UT3), Toulouse, France
- Infrastructure nationale de protéomique, ProFI, FR 2048, Toulouse, France
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Laurent Deslandes
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, F-31326 Castanet-Tolosan, France
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2
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Agarwal V, Stubits R, Nassrullah Z, Dillon MM. Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks. Front Microbiol 2023; 14:1213261. [PMID: 37476668 PMCID: PMC10356107 DOI: 10.3389/fmicb.2023.1213261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.
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Affiliation(s)
- Viplav Agarwal
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Rachel Stubits
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Zain Nassrullah
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Marcus M. Dillon
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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3
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Genome Sequences of 17 Strains from Eight Races of Xanthomonas campestris pv. campestris. Microbiol Resour Announc 2022; 11:e0027922. [PMID: 35695496 PMCID: PMC9302143 DOI: 10.1128/mra.00279-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas campestris
pv. campestris is a group of phytopathogenic bacteria causing black rot disease on Brassicaceae crops. Here, we report on draft genome sequences of 17 strains representing eight of nine known races of this pathogen, including the pathotype strain CFBP 6865.
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4
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Chen D, Zhong X, Cui J, Li H, Han R, Yue X, Xie J, Kang J. Comparative Genomic Analysis of Xanthomonas campestris pv. campestris Isolates BJSJQ20200612 and GSXT20191014 Provides Novel Insights Into Their Genetic Variability and Virulence. Front Microbiol 2022; 13:833318. [PMID: 35308372 PMCID: PMC8924526 DOI: 10.3389/fmicb.2022.833318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
Black rot is a disease that has a severe impact on cabbage yield and quality in China. Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot of Brassicaceae crops. So far, the whole genomic sequences of more than 30 Xcc isolates have been sequenced; however, little information about genomic variability and virulence has been reported. In this study, 12 Xcc isolates were isolated from diseased cabbage leaves in seven Chinese provinces and two municipalities from July 2019 to November 2020. Pathogenicity analysis showed that isolate GSXT20191014 was more aggressive than BJSJQ20200612 and HRIW 3811 on cabbage inbred line 1371. Both BJSJQ20200612 and GSXT20191014 were sequenced and comparatively analyzed. The results showed that BJSJQ20200612 and GSXT20191014 have a single circular chromosome comprising 5,115,975 and 4,975,682 bp, respectively. Compared to the other six sequenced strains, 26 and 47 variable genomic regions were found in BJSJQ2020061 and GSXT20191014 genomic sequences, respectively. The variable genomic regions could be responsible for the genetic variation in Xcc strains and have led to the differences in type III secreted effector repertoires, virulence factors and secreted proteins between these two strains. Among the identified secreted proteins, two copies of peptidase S8/S53 were found in GSXT20191014-specific chromosomal segments. The common effectors xopR, xopH, avrBs1, and xopAH are found in most Xcc genomes, but they are absent in the GSXT20191014 genome. Variations in the composition of exopolysaccharides (EPS) and lipopolysaccharides (LPS) may aid GSXT20191014 isolate infections to evade recognition by the host immune system. Our results revealed a direct correlation between genomic variability and Xcc virulence. We also developed several markers for detecting BJSJQ20200612 and GSXT20191014 isolates and further tested the rest of our other 10 isolates. Finally, the isolated Xcc strains were classified into three genetic subgroups by specific molecular markers and multilocus sequence typing (MLST) approach. BJSJQ20200612 and GSXT20191014 isolates were also classified into two subgroups of Xcc according to the core-genome-based phylogenetic tree. This study extended our understanding of Xcc genomic features and provided the foundation to further characterize the mechanisms for Xcc virulence and a clue for black rot resistance breeding.
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Affiliation(s)
- Denghui Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Xionghui Zhong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jian Cui
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Hailong Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Rui Han
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Xiangqing Yue
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jungen Kang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
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5
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Complete Genome Sequence of Xanthomonas campestris pv.
campestris
SB80, a Race 4 Strain Isolated from White Head Cabbage in Turkey. Microbiol Resour Announc 2022; 11:e0002222. [PMID: 35191748 PMCID: PMC8928781 DOI: 10.1128/mra.00022-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Here, we report the complete genome sequence of the race 4 strain Xanthomonas campestris pv. campestris SB80, which was isolated from a symptomatic white head cabbage leaf in Samsun Province, Turkey, in 2019. The genome consists of a circular chromosome (5,129,762 bp) with a G+C content of 64.98%, for which 4,159 putative protein-coding genes, 2 rRNA operons, 54 tRNAs, and 86 noncoding RNAs (ncRNAs) were predicted.
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6
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Luneau JS, Cerutti A, Roux B, Carrère S, Jardinaud M, Gaillac A, Gris C, Lauber E, Berthomé R, Arlat M, Boulanger A, Noël LD. Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulence strategies and physiological adaptations at early infection stages. MOLECULAR PLANT PATHOLOGY 2022; 23:159-174. [PMID: 34837293 PMCID: PMC8743013 DOI: 10.1111/mpp.13117] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 06/01/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wild Brassicaceae. Xcc enters the plant tissues preferentially via hydathodes, which are organs localized at leaf margins. To decipher both physiological and virulence strategies deployed by Xcc during early stages of infection, the transcriptomic profile of Xcc was analysed 3 days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and despite a biotrophic lifestyle, 18% of Xcc genes were differentially expressed, including a striking repression of chemotaxis and motility functions. The Xcc full repertoire of virulence factors had not yet been activated but the expression of the HrpG regulon composed of 95 genes, including genes coding for the type III secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulphur and phosphate metabolism was upregulated while limited stress responses were observed 3 days postinfection. We confirmed experimentally that high-affinity phosphate transport is needed for bacterial fitness inside hydathodes. This analysis provides information about the nutritional and stress status of bacteria during the early biotrophic infection stages and helps to decipher the adaptive strategy of Xcc to the hydathode environment.
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Affiliation(s)
- Julien S. Luneau
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Aude Cerutti
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Brice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
- Present address:
Brice Roux, HalioDx, Luminy Biotech EntreprisesMarseille Cedex 9France
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | | | - Antoine Gaillac
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Emmanuelle Lauber
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Richard Berthomé
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Matthieu Arlat
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Alice Boulanger
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
| | - Laurent D. Noël
- LIPME, Université de Toulouse, INRAE, CNRS, Université Paul SabatierCastanet‐TolosanFrance
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7
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González‐Fuente M, Carrère S, Monachello D, Marsella BG, Cazalé A, Zischek C, Mitra RM, Rezé N, Cottret L, Mukhtar MS, Lurin C, Noël LD, Peeters N. EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. MOLECULAR PLANT PATHOLOGY 2020; 21:1257-1270. [PMID: 33245626 PMCID: PMC7488465 DOI: 10.1111/mpp.12965] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 05/16/2023]
Abstract
Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogen's own benefit. However, effectors can also be recognized by host immune proteins, leading to the activation of defence responses. Effectors are thus essential components in determining the outcome of plant-pathogen interactions. Despite major efforts to decipher effector functions, our current knowledge on effector biology is scattered and often limited. In this study, we conducted two systematic large-scale yeast two-hybrid screenings to detect interactions between Arabidopsis thaliana proteins and effectors from two vascular bacterial pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. We then constructed an interactomic network focused on Arabidopsis and effector proteins from a wide variety of bacterial, oomycete, fungal, and invertebrate pathogens. This network contains our experimental data and protein-protein interactions from 2,035 peer-reviewed publications (48,200 Arabidopsis-Arabidopsis and 1,300 Arabidopsis-effector protein interactions). Our results show that effectors from different species interact with both common and specific Arabidopsis interactors, suggesting dual roles as modulators of generic and adaptive host processes. Network analyses revealed that effector interactors, particularly "effector hubs" and bacterial core effector interactors, occupy important positions for network organization, as shown by their larger number of protein interactions and centrality. These interactomic data were incorporated in EffectorK, a new graph-oriented knowledge database that allows users to navigate the network, search for homology, or find possible paths between host and/or effector proteins. EffectorK is available at www.effectork.org and allows users to submit their own interactomic data.
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Affiliation(s)
- Manuel González‐Fuente
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - Dario Monachello
- Institut des Sciences des Plantes de Paris SaclayUEVEINRAECNRSUniversité Paris SudUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Université de ParisGif‐sur‐YvetteFrance
| | | | - Anne‐Claire Cazalé
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - Claudine Zischek
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - Raka M. Mitra
- Department of BiologyCarleton CollegeNorthfieldMNUSA
| | - Nathalie Rezé
- Institut des Sciences des Plantes de Paris SaclayUEVEINRAECNRSUniversité Paris SudUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Université de ParisGif‐sur‐YvetteFrance
| | - Ludovic Cottret
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - M. Shahid Mukhtar
- Department of BiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Claire Lurin
- Institut des Sciences des Plantes de Paris SaclayUEVEINRAECNRSUniversité Paris SudUniversité Paris‐SaclayGif‐sur‐YvetteFrance
- Université de ParisGif‐sur‐YvetteFrance
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
| | - Nemo Peeters
- Laboratoire des Interactions Plantes Micro‐organismes, INRAECNRSUniversité de ToulouseCastanet‐TolosanFrance
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8
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Zhao LN, Ma Y, Yang X, Iqbal A, Ruan CC, Zang LS. Identification of Serratia marcescens isolated from Antheraea pernyi eggs and determination of bacterial pathogenicity and transmission pathway. J Invertebr Pathol 2019; 169:107297. [PMID: 31783030 DOI: 10.1016/j.jip.2019.107297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 01/21/2023]
Abstract
The Chinese oak silkworm, Antheraea pernyi, is an important alternate host for mass production of Trichogramma parasitoids, which play a vital role in the biological control of lepidopterous pests in China. The quality of A. pernyi eggs is particularly important for mass production of these parasitoids. In this study, a pathogenic bacterium, isolated and purified from A. pernyi eggs that had turned gray in color, was identified as Serratia marcescens. We used morphology, biochemistry and 16S rDNA analysis to characterize the strain, which was named "APE strain". Serratia marcescens APE strain was determined to be the causal bacterium associated with the disease in the eggs, verified by a test based on Koch's Postulates. We tested the pathogenicity of S. marcescens APE strain on A. pernyi eggs; the percentage of diseased (gray) eggs reached 57.78% when uninfected eggs were exposed to a concentration of 1 × 109 cfu/mL bacterial suspension for 7 h. S. marcescens was transmitted mechanically by Trichogramma parasitoids. The transmission rate was 25.56%. In a horizontal transmission test, the highest percentage of uninfected eggs that developed infections was 51.43% after being treated with contents of diseased eggs for 12 h. In a vertical transmission test, the number of infected eggs per treated adult female was 63.8-92.3 after treatment with different S. marcescens concentrations, significantly lower than the 304.3 eggs per female in the control group. Furthermore, the percentage of infected (gray) eggs produced by adult moths exposed to bacteria in the larval stage was 80.5-85.3%.
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Affiliation(s)
- Li-Na Zhao
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China; Jilin Agricultural Science and Technology College, Jilin, China
| | - Yue Ma
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China
| | | | - Asim Iqbal
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China
| | - Chang-Chun Ruan
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China.
| | - Lian-Sheng Zang
- Jilin Engineering Research Center of Resource Insects Industrialization, Institute of Biological Control, Jilin Agricultural University, Changchun, China.
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9
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van Hulten M, Chatterjee S, van den Burg HA. Infection Assay for Xanthomonas campestris pv. campestris in Arabidopsis thaliana Mimicking Natural Entry via Hydathodes. Methods Mol Biol 2019; 1991:159-185. [PMID: 31041772 DOI: 10.1007/978-1-4939-9458-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Xanthomonas campestris pv. campestris (Xcc) causes the devastating disease Black rot in Brassicaceae. Typically Xcc enters the plant through specialized organs on the leaf margin, called hydathodes, and spreads from there through the vasculature. In order to mimic natural entry as closely as possible, we here describe a "hydathode guttation"-based entry assay for Xcc in Arabidopsis. This disease assay combines spray inoculation with the induction of guttation and allows reabsorption of guttation droplets by the plant. Moreover, our assay relies on a bioluminescent reporter strain of Xcc to allow direct visualization of both entry and subsequent spreading of Xcc in its host. The assay allows the routine infection from one to two hydathodes per Arabidopsis leaf. Infections are scored 14 days post inoculation, just before the infection goes systemic.
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Affiliation(s)
- Marieke van Hulten
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Sayantani Chatterjee
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands.
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10
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Peňázová E, Kopta T, Jurica M, Pečenka J, Eichmeier A, Pokluda R. Testing of Inoculation Methods and Susceptibility Testing of Perspective Cabbage Breeding Lines (Brassica Oleracea convar. Capitata) to the Black Rot Disease Caused by Xanthomonas Campestris pv. Campestris. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2018. [DOI: 10.11118/actaun201866010139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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11
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Denancé N, Szurek B, Doyle EL, Lauber E, Fontaine-Bodin L, Carrère S, Guy E, Hajri A, Cerutti A, Boureau T, Poussier S, Arlat M, Bogdanove AJ, Noël LD. Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire. THE NEW PHYTOLOGIST 2018; 219:391-407. [PMID: 29677397 DOI: 10.1111/nph.15148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
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Affiliation(s)
- Nicolas Denancé
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Erin L Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Doane University, Crete, NE, 68333, USA
| | - Emmanuelle Lauber
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | | | - Sébastien Carrère
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Endrick Guy
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Ahmed Hajri
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Aude Cerutti
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Tristan Boureau
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Stéphane Poussier
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Matthieu Arlat
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Adam J Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laurent D Noël
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
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12
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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13
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Cerutti A, Jauneau A, Auriac MC, Lauber E, Martinez Y, Chiarenza S, Leonhardt N, Berthomé R, Noël LD. Immunity at Cauliflower Hydathodes Controls Systemic Infection by Xanthomonas campestris pv campestris. PLANT PHYSIOLOGY 2017; 174:700-716. [PMID: 28184011 PMCID: PMC5462019 DOI: 10.1104/pp.16.01852] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/06/2017] [Indexed: 05/20/2023]
Abstract
Hydathodes are water pores found on leaves of a wide range of vascular plants and are the sites of guttation. We report here on the detailed anatomy of cauliflower (Brassicaoleracea) and Arabidopsis (Arabidopsis thaliana) hydathodes. Hydathode surface presents pores resembling stomata giving access to large cavities. Beneath, the epithem is composed of a lacunar and highly vascularized parenchyma offering a direct connection between leaf surface and xylem vessels. Arabidopsis hydathode pores were responsive to ABA and light similar to stomata. The flg22 flagellin peptide, a well-characterized elicitor of plant basal immunity, did not induce closure of hydathode pores in contrast to stomata. Because hydathodes are natural infection routes for several pathogens, we investigated hydathode infection by the adapted vascular phytopathogenic bacterium Xanthomonas campestris pv campestris (Xcc), the causal agent of black rot disease of Brassicaceae. Microscopic observations of hydathodes six days postinoculation indicated a digestion of the epithem cells and a high bacterial multiplication. Postinvasive immunity was shown to limit pathogen growth in the epithem and is actively suppressed by the type III secretion system and its effector proteins. Altogether, these results give a detailed anatomic description of Brassicaceae hydathodes and highlight the efficient use of this tissue as an initial niche for subsequent vascular systemic dissemination of Xcc in distant plant tissues.
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Affiliation(s)
- Aude Cerutti
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Alain Jauneau
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Marie-Christine Auriac
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Emmanuelle Lauber
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Yves Martinez
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Serge Chiarenza
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Nathalie Leonhardt
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Richard Berthomé
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.)
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
| | - Laurent D Noël
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326 Castanet-Tolosan, France (A.C., E.L., R.B., L.D.N.);
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, F-31326 Castanet-Tolosan, France (A.J., M.-C.A., Y.M.); and
- UMR7265, Laboratoire de Biologie du Développement des Plantes, Service de Biologie Végétale et de Microbiologie Environnementales, Institut de Biologie Environnementale et Biotechnologie, Centre National de la Recherche Scientifique-Commissariat à l'Energie Atomique-Université Aix-Marseille, F-13108 Saint Paul-Les-Durance, France (S.C., N.L.)
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Genissel A, Confais J, Lebrun MH, Gout L. Association Genetics in Plant Pathogens: Minding the Gap between the Natural Variation and the Molecular Function. FRONTIERS IN PLANT SCIENCE 2017; 8:1301. [PMID: 28791038 PMCID: PMC5524819 DOI: 10.3389/fpls.2017.01301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/11/2017] [Indexed: 05/05/2023]
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15
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Jacques MA, Arlat M, Boulanger A, Boureau T, Carrère S, Cesbron S, Chen NWG, Cociancich S, Darrasse A, Denancé N, Fischer-Le Saux M, Gagnevin L, Koebnik R, Lauber E, Noël LD, Pieretti I, Portier P, Pruvost O, Rieux A, Robène I, Royer M, Szurek B, Verdier V, Vernière C. Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:163-87. [PMID: 27296145 DOI: 10.1146/annurev-phyto-080615-100147] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.
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Affiliation(s)
- Marie-Agnès Jacques
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Matthieu Arlat
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Alice Boulanger
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Tristan Boureau
- Université Angers, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Sébastien Carrère
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
| | - Sophie Cesbron
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas W G Chen
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Stéphane Cociancich
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Armelle Darrasse
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas Denancé
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Marion Fischer-Le Saux
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Lionel Gagnevin
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Ralf Koebnik
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Emmanuelle Lauber
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Laurent D Noël
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Isabelle Pieretti
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Perrine Portier
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Adrien Rieux
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Isabelle Robène
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Monique Royer
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Boris Szurek
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Valérie Verdier
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Christian Vernière
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
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Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. BMC Genomics 2015; 16:975. [PMID: 26581393 PMCID: PMC4652430 DOI: 10.1186/s12864-015-2190-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/03/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani). RESULTS In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins. CONCLUSIONS This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.
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17
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Genome Sequences of the Race 1 and Race 4 Xanthomonas campestris pv. campestris Strains CFBP 1869 and CFBP 5817. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01023-15. [PMID: 26383661 PMCID: PMC4574366 DOI: 10.1128/genomea.01023-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The draft genome sequences of strains CFBP 1869 and CFBP 5817 have been determined and are the first ones corresponding to race 1 and race 4 strains, which have a predominant agronomic and economic impact on cabbage cultures worldwide.
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18
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Dugé de Bernonville T, Noël LD, SanCristobal M, Danoun S, Becker A, Soreau P, Arlat M, Lauber E. Transcriptional reprogramming and phenotypical changes associated with growth ofXanthomonas campestrispv.campestrisin cabbage xylem sap. FEMS Microbiol Ecol 2014; 89:527-41. [DOI: 10.1111/1574-6941.12345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
- Thomas Dugé de Bernonville
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
| | - Magali SanCristobal
- UMR 1388 Génétique, Physiologie et Systèmes d'Elevage; INRA; Castanet-Tolosan France
- UMR 1388 Génétique, Physiologie et Systèmes d'Elevage; Université de Toulouse INPT ENSAT; Castanet-Tolosan France
- UMR 1388 Génétique, Physiologie et Systèmes d'Elevage; Université de Toulouse INPT ENVT; Toulouse France
| | - Saida Danoun
- Laboratoire de Recherches en Sciences Végétales (LRSV); UMR 5546; Université de Toulouse, UPS; Castanet-Tolosan France
- Laboratoire de Recherches en Sciences Végétales (LRSV); UMR 5546; CNRS; Castanet-Tolosan France
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology; Philipps-Universität Marburg; Marburg Germany
| | - Paul Soreau
- CEA Cadarache; IBEB-SBVME; Research Group in Applied Phytotechnics; UMR 6191 CNRS-CEA; Aix-Marseille University; Saint-Paul-lez-Durance Cedex France
| | - Matthieu Arlat
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
- Université de Toulouse, UPS; Toulouse France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 441; INRA; Castanet-Tolosan France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM); UMR 2594; CNRS; Castanet-Tolosan France
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19
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Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103:80-100. [PMID: 24886836 DOI: 10.1016/j.mimet.2014.05.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 12/29/2022]
Abstract
The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.
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Affiliation(s)
- Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
| | - Hirak R Dash
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Neelam Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Supriya Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
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Akimoto-Tomiyama C, Furutani A, Ochiai H. Real time live imaging of phytopathogenic bacteria Xanthomonas campestris pv. campestris MAFF106712 in 'plant sweet home'. PLoS One 2014; 9:e94386. [PMID: 24736478 PMCID: PMC3988059 DOI: 10.1371/journal.pone.0094386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 03/14/2014] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas is one of the most widespread phytobacteria, causing diseases on a variety of agricultural plants. To develop novel control techniques, knowledge of bacterial behavior inside plant cells is essential. Xanthomonas campestris pv. campestris, a vascular pathogen, is the causal agent of black rot on leaves of Brassicaceae, including Arabidopsis thaliana. Among the X. campestris pv. campestris stocks in the MAFF collection, we selected XccMAFF106712 as a model compatible pathogen for the A. thaliana reference ecotype Columbia (Col-0). Using modified green fluorescent protein (AcGFP) as a reporter, we observed real time XccMAFF106712 colonization in planta with confocal microscopy. AcGFP-expressing bacteria colonized the inside of epidermal cells and the apoplast, as well as the xylem vessels of the vasculature. In the case of the type III mutant, bacteria colonization was never detected in the xylem vessel or apoplast, though they freely enter the xylem vessel through the wound. After 9 days post inoculation with XccMAFF106712, the xylem vessel became filled with bacterial aggregates. This suggests that Xcc colonization can be divided into main four steps, (1) movement in the xylem vessel, (2) movement to the next cell, (3) adhesion to the host plant cells, and (4) formation of bacterial aggregates. The type III mutant abolished at least steps (1) and (2). Better understanding of Xcc colonization is essential for development of novel control techniques for black rot.
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Affiliation(s)
- Chiharu Akimoto-Tomiyama
- Plant-Microbe Interaction Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
- * E-mail:
| | - Ayako Furutani
- Gene Research Center, Ibaraki University, Inashiki, Japan
| | - Hirokazu Ochiai
- Plant-Microbe Interaction Research Unit, Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
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Guy E, Lautier M, Chabannes M, Roux B, Lauber E, Arlat M, Noël LD. xopAC-triggered immunity against Xanthomonas depends on Arabidopsis receptor-like cytoplasmic kinase genes PBL2 and RIPK. PLoS One 2013; 8:e73469. [PMID: 23951354 PMCID: PMC3739749 DOI: 10.1371/journal.pone.0073469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/23/2013] [Indexed: 12/22/2022] Open
Abstract
Xanthomonas campestris pv. campestris (Xcc) colonizes the vascular system of Brassicaceae and ultimately causes black rot. In susceptible Arabidopsis plants, XopAC type III effector inhibits by uridylylation positive regulators of the PAMP-triggered immunity such as the receptor-like cytoplasmic kinases (RLCK) BIK1 and PBL1. In the resistant ecotype Col-0, xopAC is a major avirulence gene of Xcc. In this study, we show that both the RLCK interaction domain and the uridylyl transferase domain of XopAC are required for avirulence. Furthermore, xopAC can also confer avirulence to both the vascular pathogen Ralstonia solanacearum and the mesophyll-colonizing pathogen Pseudomonas syringae indicating that xopAC-specified effector-triggered immunity is not specific to the vascular system. In planta, XopAC-YFP fusions are localized at the plasma membrane suggesting that XopAC might interact with membrane-localized proteins. Eight RLCK of subfamily VII predicted to be localized at the plasma membrane and interacting with XopAC in yeast two-hybrid assays have been isolated. Within this subfamily, PBL2 and RIPK RLCK genes but not BIK1 are important for xopAC-specified effector-triggered immunity and Arabidopsis resistance to Xcc.
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Affiliation(s)
- Endrick Guy
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
| | - Martine Lautier
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Matthieu Chabannes
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
| | - Brice Roux
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
| | - Emmanuelle Lauber
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
| | - Matthieu Arlat
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Laurent D. Noël
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Castanet-Tolosan, France
- * E-mail:
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Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00465-13. [PMID: 23846270 PMCID: PMC3709147 DOI: 10.1128/genomea.00465-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The draft genome sequences of three strains (CN14, CN15, and CN16) that are highly aggressive on Arabidopsis have been determined. These genome sequences present an unexpected genomic diversity in X. campestris pv. campestris, which will be valuable for comparative analyses.
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