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Licciardello G, Caruso P, Bella P, Boyer C, Smith MW, Pruvost O, Robene I, Cubero J, Catara V. Pathotyping Citrus Ornamental Relatives with Xanthomonas citri pv. citri and X. citri pv. aurantifolii Refines Our Understanding of Their Susceptibility to These Pathogens. Microorganisms 2022; 10:microorganisms10050986. [PMID: 35630430 PMCID: PMC9148020 DOI: 10.3390/microorganisms10050986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Xanthomonas citri pv. citri (Xcc) and X. citri pv. aurantifolii (Xca) are causal agents of Citrus Bacterial Canker (CBC), a devastating disease that severely affects citrus plants. They are harmful organisms not reported in Europe or the Mediterranean Basin. Host plants are in the Rutaceae family, including the genera Citrus, Poncirus, and Fortunella, and their hybrids. In addition, other genera of ornamental interest are reported as susceptible, but results are not uniform and sometimes incongruent. We evaluated the susceptibility of 32 ornamental accessions of the Rutaceae family belonging to the genera Citrus, Fortunella, Atalantia, Clausena, Eremocitrus, Glycosmis, Microcitrus, Murraya, Casimiroa, Calodendrum, and Aegle, and three hybrids to seven strains of Xcc and Xca. Pathotyping evaluation was assessed by scoring the symptomatic reactions on detached leaves. High variability in symptoms and bacterial population was shown among the different strains in the different hosts, indicative of complex host–pathogen interactions. The results are mostly consistent with past findings, with the few discrepancies probably due to our more complete experimental approach using multiple strains of the pathogen and multiple hosts. Our work supports the need to regulate non-citrus Rutaceae plant introductions into areas, like the EU and Mediterranean, that are currently free of this economically important pathogen.
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Affiliation(s)
- Grazia Licciardello
- Dipartimento di Agricoltura Alimentazione e Ambiente, Università degli Studi di Catania, 95130 Catania, Italy;
- Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura-Consiglio per la Ricerca in Agricoltura e L’analisi Dell’Economia Agraria (CREA), 95024 Acireale, Italy;
| | - Paola Caruso
- Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura-Consiglio per la Ricerca in Agricoltura e L’analisi Dell’Economia Agraria (CREA), 95024 Acireale, Italy;
| | - Patrizia Bella
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy;
| | - Claudine Boyer
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), 97410 Saint Pierre, La Réunion, France; (C.B.); (O.P.); (I.R.)
| | - Malcolm W. Smith
- Department of Agriculture & Fisheries, Bundaberg Research Station, Bundaberg, QLD 4670, Australia;
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), 97410 Saint Pierre, La Réunion, France; (C.B.); (O.P.); (I.R.)
| | - Isabelle Robene
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), 97410 Saint Pierre, La Réunion, France; (C.B.); (O.P.); (I.R.)
| | - Jaime Cubero
- Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain;
| | - Vittoria Catara
- Dipartimento di Agricoltura Alimentazione e Ambiente, Università degli Studi di Catania, 95130 Catania, Italy;
- Correspondence: ; Tel.: +39-095-714-7370
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Duan S, Long Y, Cheng S, Li J, Ouyang Z, Wang N. Rapid Evaluation of the Resistance of Citrus Germplasms Against Xanthomonas citri subsp. citri. PHYTOPATHOLOGY 2022; 112:765-774. [PMID: 34495678 DOI: 10.1094/phyto-04-21-0175-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas citri subsp. citri (Xcc) is the causal agent of citrus bacterial canker (CBC), one of the most devastating citrus diseases. Most commercial citrus varieties are susceptible to CBC. However, some citrus varieties and wild citrus germplasms are CBC resistant and are promising in genetic increases in citrus resistance against CBC. We aimed to evaluate citrus germplasms for resistance against CBC. First, we developed a rapid evaluation method based on enhanced yellow fluorescent protein (eYFP)-labeled Xcc. The results demonstrated that eYFP does not affect the growth and virulence of Xcc. Xcc-eYFP allows measurement of bacterial titers but is more efficient and rapid than the plate colony counting method. Next, we evaluated citrus germplasms collected in China. Based on symptoms and bacterial titers, we identified that two citrus germplasms ('Ichang' papeda and 'Huapi' kumquat) are resistant, whereas eight citrus germplasms ('Chongyi' wild mandarin, 'Mangshan' wild mandarin, 'Ledong' kumquat, 'Dali' citron, 'Yiliang' citron, 'Longyan' kumquat, 'Bawang' kumquat, and 'Daoxian' wild mandarin) are tolerant. In summary, we have developed a rapid evaluation method to test the resistance of citrus plants against CBC. This method was successfully used to identify two highly canker-resistant citrus germplasms and eight citrus germplasms with canker tolerance. These results could be leveraged in traditional breeding contexts or be used to identify canker resistance genes to increase the disease resistance of commercial citrus varieties via biotechnological approaches.
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Affiliation(s)
- Shuo Duan
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Yunfei Long
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Shuyuan Cheng
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL 33850, U.S.A
| | - Zhigang Ouyang
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL 33850, U.S.A
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3
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Teper D, Xu J, Pandey SS, Wang N. PthAW1, a Transcription Activator-Like Effector of Xanthomonas citri subsp. citri, Promotes Host-Specific Immune Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1033-1047. [PMID: 33970668 DOI: 10.1094/mpmi-01-21-0026-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Citrus canker disease caused by Xanthomonas citri subsp. citri is one of the most destructive diseases in citrus. X. citri subsp. citri pathotypes display different host ranges. X. citri subsp. citri strain A (XccA) causes canker disease in most commercial citrus varieties, whereas strain AW (XccAW), which is genetically similar to XccA, infects only lime and alemow. Understanding the mechanism that determines the host range of pathogens is critical to investigating and utilizing host resistance. We hypothesized that XccAW would undergo mutations in genes that restrict its host range when artificially inoculated into incompatible citrus varieties. To test this hypothesis, we used an experimental evolution approach to identify phenotypic traits and genetic loci associated with the adaptation of XccAW to incompatible sweet orange. Repeated inoculation and reisolation cycles improved the ability of three independent XccAW strains to colonize sweet orange. Adapted XccAW strains displayed increased expression of type III secretion system and effector genes. Genome sequencing analysis indicated that two of the adapted strains harbored mutations in pthAW1, a transcription activator-like effector (TALE) gene, that corresponded to the removal of one or two repeats from the central DNA-binding repeat region. Introduction of the original but not the adapted pthAW1 variants into XccA abolished its ability to cause canker symptoms in sweet orange, Meyer lemon, and clementine but not in other XccAW-resistant citrus varieties. The original pthAW1, when expressed in XccA, induced ion leakage and the expression of pathogenesis-related genes but had no effect on CsLOB1 expression in sweet orange. Our study has identified a novel host-specific avirulence TALE and demonstrated active adaptive rearrangements of the TALE repeat array during host adaptation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
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Gopalan-Nair R, Jardinaud MF, Legrand L, Landry D, Barlet X, Lopez-Roques C, Vandecasteele C, Bouchez O, Genin S, Guidot A. Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato. Mol Biol Evol 2021; 38:1792-1808. [PMID: 33306125 PMCID: PMC8097285 DOI: 10.1093/molbev/msaa320] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics, and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia solanacearum to overcome the quantitative resistance of the tomato cultivar Hawaii 7996. After serial passaging over 300 generations, we observed pathogen adaptation to within-plant environment of the resistant cultivar but no plant resistance breakdown. Genomic sequence analysis of the adapted clones revealed few genetic alterations, but we provide evidence that all but one were gain of function mutations. Transcriptomic analyses revealed that even if different adaptive events occurred in independently evolved clones, there is convergence toward a global rewiring of the virulence regulatory network as evidenced by largely overlapping gene expression profiles. A subset of four transcription regulators, including HrpB, the activator of the type 3 secretion system regulon and EfpR, a global regulator of virulence and metabolic functions, emerged as key nodes of this regulatory network that are frequently targeted to redirect the pathogen’s physiology and improve its fitness in adverse conditions. Significant transcriptomic variations were also detected in evolved clones showing no genomic polymorphism, suggesting that epigenetic modifications regulate expression of some of the virulence network components and play a major role in adaptation as well.
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Affiliation(s)
| | | | - Ludovic Legrand
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - David Landry
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Xavier Barlet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRAE, US 1426, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alice Guidot
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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5
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Dutta A, Hartmann FE, Francisco CS, McDonald BA, Croll D. Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments. THE ISME JOURNAL 2021; 15:1402-1419. [PMID: 33452474 PMCID: PMC8115182 DOI: 10.1038/s41396-020-00859-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
The adaptive potential of pathogens in novel or heterogeneous environments underpins the risk of disease epidemics. Antagonistic pleiotropy or differential resource allocation among life-history traits can constrain pathogen adaptation. However, we lack understanding of how the genetic architecture of individual traits can generate trade-offs. Here, we report a large-scale study based on 145 global strains of the fungal wheat pathogen Zymoseptoria tritici from four continents. We measured 50 life-history traits, including virulence and reproduction on 12 different wheat hosts and growth responses to several abiotic stressors. To elucidate the genetic basis of adaptation, we used genome-wide association mapping coupled with genetic correlation analyses. We show that most traits are governed by polygenic architectures and are highly heritable suggesting that adaptation proceeds mainly through allele frequency shifts at many loci. We identified negative genetic correlations among traits related to host colonization and survival in stressful environments. Such genetic constraints indicate that pleiotropic effects could limit the pathogen's ability to cause host damage. In contrast, adaptation to abiotic stress factors was likely facilitated by synergistic pleiotropy. Our study illustrates how comprehensive mapping of life-history trait architectures across diverse environments allows to predict evolutionary trajectories of pathogens confronted with environmental perturbations.
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Affiliation(s)
- Anik Dutta
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E. Hartmann
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland ,grid.417885.70000 0001 2185 8223Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Carolina Sardinha Francisco
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland ,Present Address: Environmental Genomics Group, Botanical Institute, CAU Kiel, Germany
| | - Bruce A. McDonald
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- grid.10711.360000 0001 2297 7718Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Yamamoto K, Kusada H, Kamagata Y, Tamaki H. Parallel Evolution of Enhanced Biofilm Formation and Phage-Resistance in Pseudomonas aeruginosa during Adaptation Process in Spatially Heterogeneous Environments. Microorganisms 2021; 9:569. [PMID: 33801971 PMCID: PMC7999436 DOI: 10.3390/microorganisms9030569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/22/2021] [Accepted: 03/06/2021] [Indexed: 11/16/2022] Open
Abstract
An opportunistic pathogen Pseudomonas aeruginosa has a versatile phenotype and high evolutionary potential to adapt to various natural habitats. As the organism normally lives in spatially heterogeneous and polymicrobial environments from open fields to the inside of hosts, adaptation to abiotic (spatial heterogeneity) and biotic factors (interspecies interactions) is a key process to proliferate. However, our knowledge about the adaptation process of P. aeruginosa in spatially heterogeneous environments associated with other species is limited. We show herein that the evolutionary dynamics of P. aeruginosa PAO1 in spatially heterogeneous environments with Staphylococcus aureus known to coexist in vivo is dictated by two distinct core evolutionary trajectories: (i) the increase of biofilm formation and (ii) the resistance to infection by a filamentous phage which is retained in the PAO1 genome. Hyperbiofilm and/or pili-deficient phage-resistant variants were frequently selected in the laboratory evolution experiment, indicating that these are key adaptive traits under spatially structured conditions. On the other hand, the presence of S. aureus had only a marginal effect on the emergence and maintenance of these variants. These results show key adaptive traits of P. aeruginosa and indicate the strong selection pressure conferred by spatial heterogeneity, which might overwhelm the effect of interspecies interactions.
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Affiliation(s)
- Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 0628517, Hokkaido, Japan
- Bioproduction Research Institute, AIST, Tsukuba 3058566, Ibaraki, Japan; (H.K.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 3058577, Ibaraki, Japan
| | - Hiroyuki Kusada
- Bioproduction Research Institute, AIST, Tsukuba 3058566, Ibaraki, Japan; (H.K.); (Y.K.)
| | - Yoichi Kamagata
- Bioproduction Research Institute, AIST, Tsukuba 3058566, Ibaraki, Japan; (H.K.); (Y.K.)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, AIST, Tsukuba 3058566, Ibaraki, Japan; (H.K.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 3058577, Ibaraki, Japan
- Biotechnology Research Center, University of Tokyo, Bunkyo-ku, Tokyo 1138657, Japan
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7
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Teper D, Wang N. Consequences of adaptation of TAL effectors on host susceptibility to Xanthomonas. PLoS Genet 2021; 17:e1009310. [PMID: 33465093 PMCID: PMC7845958 DOI: 10.1371/journal.pgen.1009310] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/29/2021] [Accepted: 12/11/2020] [Indexed: 12/03/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are virulence factors of Xanthomonas that induce the expression of host susceptibility (S) genes by specifically binding to effector binding elements (EBEs) in their promoter regions. The DNA binding specificity of TALEs is dictated by their tandem repeat regions, which are highly variable between different TALEs. Mutation of the EBEs of S genes is being utilized as a key strategy to generate resistant crops against TALE-dependent pathogens. However, TALE adaptations through rearrangement of their repeat regions is a potential obstacle for successful implementation of this strategy. We investigated the consequences of TALE adaptations in the citrus pathogen Xanthomonas citri subsp. citri (Xcc), in which PthA4 is the TALE required for pathogenicity, whereas CsLOB1 is the corresponding susceptibility gene, on host resistance. Seven TALEs, containing two-to-nine mismatching-repeats to the EBEPthA4 that were unable to induce CsLOB1 expression, were introduced into Xcc pthA4:Tn5 and adaptation was simulated by repeated inoculations into and isolations from sweet orange for a duration of 30 cycles. While initially all strains failed to promote disease, symptoms started to appear between 9–28 passages in four TALEs, which originally harbored two-to-five mismatches. Sequence analysis of adapted TALEs identified deletions and mutations within the TALE repeat regions which enhanced putative affinity to the CsLOB1 promoter. Sequence analyses suggest that TALEs adaptations result from recombinations between repeats of the TALEs. Reintroduction of these adapted TALEs into Xcc pthA4:Tn5 restored the ability to induce the expression of CsLOB1, promote disease symptoms and colonize host plants. TALEs harboring seven-to-nine mismatches were unable to adapt to overcome the incompatible interaction. Our study experimentally documented TALE adaptations to incompatible EBE and provided strategic guidance for generation of disease resistant crops against TALE-dependent pathogens. Mutation of the EBEs of susceptibility (S) genes via genome editing and utilization of naturally occurring EBE variants have been used to generate disease resistant plants. However, TALE adaptations may lead to resistance loss, limiting the long-term efficacy of the strategy. We utilized an experimental evolution approach to test TALEs adaptations in the Xanthomonas citri-citrus pathosystem using designer TALEs that cannot recognize the EBE of host targets. We identified adaptive TALE mutations and deletions that occurred during less than 30 cycles of repeated infections, which reconstituted the virulence on the host. Adaptive variants originated from TALEs that harbored a small number of mismatches (≤5) to the EBE, whereas designer TALEs that harbored larger number of mismatches (≥7) to the EBE failed to adapt in the duration of this study. Our study experimentally demonstrates adaptive rearrangements of TALEs during host adaptation and suggests that the potential durability in the resistance of modified crops should be a significant factor to be considered prior to their introduction into the field.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
- * E-mail:
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8
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Teper D, Xu J, Li J, Wang N. The immunity of Meiwa kumquat against Xanthomonas citri is associated with a known susceptibility gene induced by a transcription activator-like effector. PLoS Pathog 2020; 16:e1008886. [PMID: 32931525 PMCID: PMC7518600 DOI: 10.1371/journal.ppat.1008886] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/25/2020] [Accepted: 08/14/2020] [Indexed: 12/22/2022] Open
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating diseases in citrus. Meiwa kumquat (Fortunella crassifolia) has shown a durable resistance against Xcc. Here, we aimed to characterize the mechanisms responsible for such a durable resistance by characterizing the transcriptional and physiological responses of Meiwa kumquat to Xcc. Inoculation of Meiwa kumquat with Xcc promoted immune responses such as upregulation of PR genes, accumulation of salicylic acid, hypersensitive response (HR)-like cell death and early leaf abscission. Hypertrophy and hyperplasia symptoms, which are known to be caused by Xcc-induction of the canker susceptibility gene LOB1 through the transcription activator-like effector (TALE) PthA4, always appear prior to the development of cell death. Mutation of pthA4 in Xcc abolished the induction of LOB1, canker symptoms, cell death, and leaf abscission and reduced the expression of PR genes in inoculated kumquat leaves without reducing Xcc titers in planta. Transcriptome analysis demonstrated that PthA4 promotes plant biotic and abiotic stress responses and the biosynthesis of abscisic acid. Transcriptional induction of LOB1 homologs in Meiwa kumquat by Xcc pthA4 mutant strains carrying a repertoire of designer TALEs promoted the elicitation of HR-like phenotype and leaf abscission, suggesting that kumquat response to Xcc is associated with upregulation of LOB1. Our study suggests a novel mechanism of plant resistance to Xanthomonas via elicitation of immune responses by upregulation of a host susceptibility gene.
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Affiliation(s)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, United States of America
- * E-mail:
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9
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Su Q, Chen Y, Wang B, Huang C, Han S, Yuan G, Zhang Q, He H. Epidemiology and genetic diversity of zoonotic pathogens in urban rats (Rattus spp.) from a subtropical city, Guangzhou, southern China. Zoonoses Public Health 2020; 67:534-545. [PMID: 32452163 DOI: 10.1111/zph.12717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/13/2022]
Abstract
Commensal rats (Rattus spp.), which are globally distributed, harbour many pathogens responsible for significant human diseases. Despite this, we have a poor understanding of the epidemiology and genetic diversity of some recently neglected zoonotic pathogens, such as Leptospira spp., Bartonella spp. and hepatitis E virus (HEV), which constitute a major public health threat. Thus, we surveyed the occurrences, co-infection and genetic diversity of these pathogens in 129 urban rats from China. For Rattus tanezumi, the prevalences of Leptospira spp., Bartonella spp. and HEV infection were 6.67%, 0% and 46.67%, respectively. The prevalences of Leptospira spp., Bartonella spp. and HEV infection were 57.89%, 9.65% and 57.89% for Rattus norvegicus respectively. Leptospira spp. and HEV infections were more likely to occur in mature R. norvegicus. Phylogenetic analyses showed that pathogenic Leptospira interrogans and Leptospira borgpetersenii might exist. We also found that Bartonella spp. showed high similarity to Bartonella elizabethae, Bartonella rochalimae and Bartonella tribocorum, which are implicated in human disease. Dual and triple infections were both detected. Moreover, dual infections with Leptospira spp. and HEV represented the most frequent co-infection, and there was a significantly positive association between them. High genetic diversity was observed in genes segments from Leptospira, Bartonella and HEV. Our results first discover the occurrence of multiple co-infections and genetic diversity of Leptospira, Bartonella and HEV in commensal rats from China. Altogether, the present study provides an insight into evaluating the risk of rat-borne zoonoses in urban China.
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Affiliation(s)
- Qianqian Su
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Chen
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chengmei Huang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Han
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guohui Yuan
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingxun Zhang
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxuan He
- National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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10
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Murata MM, Omar AA, Mou Z, Chase CD, Grosser JW, Graham JH. Novel Plastid-Nuclear Genome Combinations Enhance Resistance to Citrus Canker in Cybrid Grapefruit. FRONTIERS IN PLANT SCIENCE 2019; 9:1858. [PMID: 30666259 PMCID: PMC6330342 DOI: 10.3389/fpls.2018.01858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/30/2018] [Indexed: 05/23/2023]
Abstract
Host disease resistance is the most desirable strategy for control of citrus canker, a disease caused by a gram-negative bacterium Xanthomonas citri subsp. citri. However, no resistant commercial citrus cultivar has been identified. Cybridization, a somatic hybridization approach that combines the organelle and nuclear genomes from different species, was used to create cybrids between citrus canker resistant 'Meiwa' kumquat (Fortunella crassifolia Swingle snym. Citrus japonica Thunb.) and susceptible grapefruit (Citrus paradisi Macfad) cultivars. From these fusions, cybrids with grapefruit nucleus, kumquat mitochondria and kumquat chloroplasts and cybrids with grapefruit nucleus, kumquat mitochondria and grapefruit chloroplasts were generated. These cybrids showed a range of citrus canker response, but all cybrids with kumquat chloroplasts had a significantly lower number of lesions and lower Xanthomonas citri subsp. citri populations than the grapefruit controls. Cybrids with grapefruit chloroplasts had a significantly higher number of lesions than those with kumquat chloroplasts. To understand the role of chloroplasts in the cybrid disease defense, quantitative PCR was performed on both cybrid types and their parents to examine changes in gene expression during Xanthomonas citri subsp. citri infection. The results revealed chloroplast influences on nuclear gene expression, since isonuclear cybrids and 'Marsh' grapefruit had different gene expression profiles. In addition, only genotypes with kumquat chloroplasts showed an early up-regulation of reactive oxygen species genes upon Xanthomonas citri subsp. citri infection. These cybrids have the potential to enhance citrus canker resistance in commercial grapefruit orchards. They also serve as models for understanding the contribution of chloroplasts to plant disease response and raise the question of whether other alien chloroplast genotypes would condition similar results.
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Affiliation(s)
- Mayara M. Murata
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Ahmad A. Omar
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
- Biochemistry Department, Zagazig University, Zagazig, Egypt
| | - Zhonglin Mou
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Christine D. Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - James H. Graham
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
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Wang R, Dong L, He R, Wang Q, Chen Y, Qu L, Zhang YA. Comparative genomic analyses reveal the features for adaptation to nematodes in fungi. DNA Res 2018; 25:4791394. [PMID: 29315395 PMCID: PMC6014366 DOI: 10.1093/dnares/dsx053] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/06/2017] [Indexed: 12/20/2022] Open
Abstract
Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application.
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Affiliation(s)
- Ruizhen Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Botany, Beijing Botanical Garden, Beijing 100093, China
| | - Leiming Dong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Ran He
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Botany, Beijing Botanical Garden, Beijing 100093, China
| | - Qinghua Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yuequ Chen
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Forestry Resources Protection Institute, Jilin Provincial Academy of Forestry Sciences, Changchun 130031, China
| | - Liangjian Qu
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yong-An Zhang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
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12
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Marasco R, Rolli E, Fusi M, Michoud G, Daffonchio D. Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. MICROBIOME 2018; 6:3. [PMID: 29298729 PMCID: PMC5751889 DOI: 10.1186/s40168-017-0391-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/18/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit. However, V. vinifera cultivars are invariably grafted onto the rootstocks of other Vitis species and hybrids. It has been hypothesized that the plant species determines the microbiome of the root endosphere and, as a consequence, the aerial endosphere. In this work, we test the first part of this hypothesis. We investigate whether different rootstocks influence the bacteria selected from the surrounding soil, affecting the bacterial diversity and potential functionality of the rhizosphere and root endosphere. METHODS Bacterial microbiomes from both the root tissues and the rhizosphere of Barbera cultivars, both ungrafted and grafted on four different rootstocks, cultivated in the same soil from the same vineyard, were characterized by 16S rRNA high-throughput sequencing. To assess the influence of the root genotype on the bacterial communities' recruitment in the root system, (i) the phylogenetic diversity coupled with the predicted functional profiles and (ii) the co-occurrence bacterial networks were determined. Cultivation-dependent approaches were used to reveal the plant-growth promoting (PGP) potential associated with the grafted and ungrafted root systems. RESULTS Richness, diversity and bacterial community networking in the root compartments were significantly influenced by the rootstocks. Complementary to a shared bacterial microbiome, different subsets of soil bacteria, including those endowed with PGP traits, were selected by the root system compartments of different rootstocks. The interaction between the root compartments and the rootstock exerted a unique selective pressure that enhanced niche differentiation, but rootstock-specific bacterial communities were still recruited with conserved PGP traits. CONCLUSION While the rootstock significantly influences the taxonomy, structure and network properties of the bacterial community in grapevine roots, a homeostatic effect on the distribution of the predicted and potential functional PGP traits was found.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Eleonora Rolli
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133, Milano, Italy
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133, Milano, Italy.
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Voitenko OS, Dhroso A, Feldmann A, Korkin D, Kalinina OV. Patterns of amino acid conservation in human and animal immunodeficiency viruses. Bioinformatics 2017; 32:i685-i692. [PMID: 27587690 DOI: 10.1093/bioinformatics/btw441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION Due to their high genomic variability, RNA viruses and retroviruses present a unique opportunity for detailed study of molecular evolution. Lentiviruses, with HIV being a notable example, are one of the best studied viral groups: hundreds of thousands of sequences are available together with experimentally resolved three-dimensional structures for most viral proteins. In this work, we use these data to study specific patterns of evolution of the viral proteins, and their relationship to protein interactions and immunogenicity. RESULTS We propose a method for identification of two types of surface residues clusters with abnormal conservation: extremely conserved and extremely variable clusters. We identify them on the surface of proteins from HIV and other animal immunodeficiency viruses. Both types of clusters are overrepresented on the interaction interfaces of viral proteins with other proteins, nucleic acids or low molecular-weight ligands, both in the viral particle and between the virus and its host. In the immunodeficiency viruses, the interaction interfaces are not more conserved than the corresponding proteins on an average, and we show that extremely conserved clusters coincide with protein-protein interaction hotspots, predicted as the residues with the largest energetic contribution to the interaction. Extremely variable clusters have been identified here for the first time. In the HIV-1 envelope protein gp120, they overlap with known antigenic sites. These antigenic sites also contain many residues from extremely conserved clusters, hence representing a unique interacting interface enriched both in extremely conserved and in extremely variable clusters of residues. This observation may have important implication for antiretroviral vaccine development. AVAILABILITY AND IMPLEMENTATION A Python package is available at https://bioinf.mpi-inf.mpg.de/publications/viral-ppi-pred/ CONTACT voitenko@mpi-inf.mpg.de or kalinina@mpi-inf.mpg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Olga S Voitenko
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, Saarbrücken 66123, Germany, Graduate School for Computer Science, Saarland University, Campus E1 3, Saarbrücken 66123, Germany
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Anna Feldmann
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, Saarbrücken 66123, Germany, Graduate School for Computer Science, Saarland University, Campus E1 3, Saarbrücken 66123, Germany
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, Saarbrücken 66123, Germany
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Meaden S, Koskella B. Adaptation of the pathogen, Pseudomonas syringae, during experimental evolution on a native vs. alternative host plant. Mol Ecol 2017; 26:1790-1801. [PMID: 28207977 PMCID: PMC6849854 DOI: 10.1111/mec.14060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022]
Abstract
The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within‐host growth rate will vary among host genotypes/species and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also those experiencing opportunistic infections on novel hosts or that spill over among host populations. There is very little empirical data, however, regarding how adaptation to one host might directly influence infectivity and growth on another. We took an experimental evolution approach to examine short‐term adaptation of the plant pathogen, Pseudomonas syringae pathovar tomato, to its native tomato host compared with an alternative host, Arabidopsis, in either the presence or absence of bacteriophages. After four serial passages (20 days of selection in planta), we measured bacterial growth of selected lines in leaves of either the focal or alternative host. We found that passage through Arabidopsis led to greater within‐host bacterial densities in both hosts than did passage through tomato. Whole genome resequencing of evolved isolates identified numerous single nucleotide polymorphisms based on our novel draft assembly for strain PT23. However, there was no clear pattern of clustering among plant selection lines at the genetic level despite the phenotypic differences observed. Together, the results emphasize that previous host associations can influence the within‐host growth rate of pathogens.
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Affiliation(s)
- Sean Meaden
- University of Exeter, Penryn Campus, Penryn, Cornwall, TR11 4EH, UK.,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
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15
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Perrier A, Peyraud R, Rengel D, Barlet X, Lucasson E, Gouzy J, Peeters N, Genin S, Guidot A. Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum. PLoS Pathog 2016; 12:e1006044. [PMID: 27911943 PMCID: PMC5135139 DOI: 10.1371/journal.ppat.1006044] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/05/2016] [Indexed: 11/18/2022] Open
Abstract
Experimental evolution of the plant pathogen Ralstonia solanacearum, where bacteria were maintained on plant lineages for more than 300 generations, revealed that several independent single mutations in the efpR gene from populations propagated on beans were associated with fitness gain on bean. In the present work, novel allelic efpR variants were isolated from populations propagated on other plant species, thus suggesting that mutations in efpR were not solely associated to a fitness gain on bean, but also on additional hosts. A transcriptomic profiling and phenotypic characterization of the efpR deleted mutant showed that EfpR acts as a global catabolic repressor, directly or indirectly down-regulating the expression of multiple metabolic pathways. EfpR also controls virulence traits such as exopolysaccharide production, swimming and twitching motilities and deletion of efpR leads to reduced virulence on tomato plants after soil drenching inoculation. We studied the impact of the single mutations that occurred in efpR during experimental evolution and found that these allelic mutants displayed phenotypic characteristics similar to the deletion mutant, although not behaving as complete loss-of-function mutants. These adaptive mutations therefore strongly affected the function of efpR, leading to an expanded metabolic versatility that should benefit to the evolved clones. Altogether, these results indicated that EfpR is a novel central player of the R. solanacearum virulence regulatory network. Independent mutations therefore appeared during experimental evolution in the evolved clones, on a crucial node of this network, to favor adaptation to host vascular tissues through regulatory and metabolic rewiring. Among plant pathogens of major economic and food crops, Ralstonia solanacearum, the causal agent of bacterial wilt, is recognized as one of the most destructive plant bacterial diseases. In addition, the emergence of new pathotypes, more aggressive and adapted to new hosts, has been reported. During an evolution experiment of R. solanacearum, where bacteria were maintained on plant lineages for more than 300 generations, we demonstrated that several single mutations in the regulatory gene efpR were associated with fitness gain on plants. However, the function of the EfpR regulator was totally unknown. In this work, we provided evidence that EfpR controls several metabolic pathways and important virulence traits of R. solanacearum. We then demonstrated that the single mutations selected in the efpR gene during the evolution experiment strongly alter the efpR expression, and thus enlarge the metabolic capacities of the bacterial cell. Altogether, our study reveals that EfpR is a novel key component of the complex regulatory network of the R. solanacearum cell, tightly linking the bacterial metabolism to virulence in response to multiple environmental signals.
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Affiliation(s)
- Anthony Perrier
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Rémi Peyraud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - David Rengel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Xavier Barlet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Nemo Peeters
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- * E-mail: (SG); (AG)
| | - Alice Guidot
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- * E-mail: (SG); (AG)
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Bartoli C, Roux F, Lamichhane JR. Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective. MOLECULAR PLANT PATHOLOGY 2016; 17:303-10. [PMID: 26062772 PMCID: PMC6638374 DOI: 10.1111/mpp.12284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rapid emergence of new bacterial diseases negatively affects both human health and agricultural productivity. Although the molecular mechanisms underlying these disease emergences are shared between human- and plant-pathogenic bacteria, not much effort has been made to date to understand disease emergences caused by plant-pathogenic bacteria. In particular, there is a paucity of information in the literature on the role of environmental habitats in which plant-pathogenic bacteria evolve and on the stress factors to which these microbes are unceasingly exposed. In this microreview, we focus on three molecular mechanisms underlying pathogenicity in bacteria, namely mutations, genomic rearrangements and the acquisition of new DNA sequences through horizontal gene transfer (HGT). We briefly discuss the role of these mechanisms in bacterial disease emergence and elucidate how the environment can influence the occurrence and regulation of these molecular mechanisms by directly impacting disease emergence. The understanding of such molecular evolutionary mechanisms and their environmental drivers will represent an important step towards predicting bacterial disease emergence and developing sustainable management strategies for crops.
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Affiliation(s)
- Claudia Bartoli
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
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17
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Kung F, Kaur S, Smith AA, Yang X, Wilder CN, Sharma K, Buyuktanir O, Pal U. A Borrelia burgdorferi Surface-Exposed Transmembrane Protein Lacking Detectable Immune Responses Supports Pathogen Persistence and Constitutes a Vaccine Target. J Infect Dis 2016; 213:1786-95. [PMID: 26747708 DOI: 10.1093/infdis/jiw013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/30/2015] [Indexed: 01/29/2023] Open
Abstract
Borrelia burgdorferi harbors a limited set of transmembrane surface proteins, most of which constitute key targets of humoral immune responses. Here we show that BB0405, a conserved membrane-spanning protein of unknown function, fails to evoke detectable antibody responses despite its extracellular exposure. bb0405 is a member of an operon and ubiquitously expressed throughout the rodent-tick infection cycle. The gene product serves an essential function in vivo, as bb0405-deletion mutants are unable to transmit from ticks and establish infection in mammalian hosts. Despite the lack of BB0405-specific immunoglobulin M or immunoglobulin G antibodies during natural infection, mice immunized with a recombinant version of the protein elicited high-titer and remarkably long-lasting antibody responses, conferring significant host protection against tick-borne infection. Taken together, these studies highlight the essential role of an apparently immune-invisible borrelial transmembrane protein in facilitating infection and its usefulness as a target of protective host immunity blocking the transmission of B. burgdorferi.
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Affiliation(s)
- Faith Kung
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
| | - Simarjot Kaur
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
| | - Alexis A Smith
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
| | - Xiuli Yang
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
| | - Cara N Wilder
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
| | - Kavita Sharma
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
| | - Ozlem Buyuktanir
- Department of Microbiology, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Utpal Pal
- Department of Veterinary Medicine, University of Maryland-College Park and Virginia-Maryland Regional College of Veterinary Medicine, College Park
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18
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Zhang Y, Jalan N, Zhou X, Goss E, Jones JB, Setubal JC, Deng X, Wang N. Positive selection is the main driving force for evolution of citrus canker-causing Xanthomonas. THE ISME JOURNAL 2015; 9:2128-38. [PMID: 25689023 PMCID: PMC4579464 DOI: 10.1038/ismej.2015.15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 12/13/2022]
Abstract
Understanding the evolutionary history and potential of bacterial pathogens is critical to prevent the emergence of new infectious bacterial diseases. Xanthomonas axonopodis subsp. citri (Xac) (synonym X. citri subsp. citri), which causes citrus canker, is one of the hardest-fought plant bacterial pathogens in US history. Here, we sequenced 21 Xac strains (14 XacA, 3 XacA* and 4 XacA(w)) with different host ranges from North America and Asia and conducted comparative genomic and evolutionary analyses. Our analyses suggest that acquisition of beneficial genes and loss of detrimental genes most likely allowed XacA to infect a broader range of hosts as compared with XacA(w) and XacA*. Recombination was found to have occurred frequently on the relative ancient branches, but rarely on the young branches of the clonal genealogy. The ratio of recombination/mutation ρ/θ was 0.0790±0.0005, implying that the Xac population was clonal in structure. Positive selection has affected 14% (395 out of 2822) of core genes of the citrus canker-causing Xanthomonas. The genes affected are enriched in 'carbohydrate transport and metabolism' and 'DNA replication, recombination and repair' genes (P<0.05). Many genes related to virulence, especially genes involved in the type III secretion system and effectors, are affected by positive selection, further highlighting the contribution of positive selection to the evolution of citrus canker-causing Xanthomonas. Our results suggest that both metabolism and virulence genes provide advantages to endow XacA with higher virulence and a wider host range. Our analysis advances our understanding of the genomic basis of specialization by positive selection in bacterial evolution.
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Affiliation(s)
- Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Neha Jalan
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Xiaofeng Zhou
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Erica Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Xiaoling Deng
- Department of Plant Pathology, South China Agricultural University, Guangzhou, Guangdong, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
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Guidot A, Jiang W, Ferdy JB, Thébaud C, Barberis P, Gouzy J, Genin S. Multihost experimental evolution of the pathogen Ralstonia solanacearum unveils genes involved in adaptation to plants. Mol Biol Evol 2014; 31:2913-28. [PMID: 25086002 DOI: 10.1093/molbev/msu229] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ralstonia solanacearum, the causal agent of a lethal bacterial wilt plant disease, infects an unusually wide range of hosts. These hosts can further be split into plants where R. solanacearum is known to cause disease (original hosts) and those where this bacterium can grow asymptomatically (distant hosts). Moreover, this pathogen is able to adapt to many plants as supported by field observations reporting emergence of strains with enlarged pathogenic properties. To investigate the genetic bases of host adaptation, we conducted evolution experiments by serial passages of a single clone of the pathogen on three original and two distant hosts over 300 bacterial generations and then analyzed the whole-genome of nine evolved clones. Phenotypic analysis of the evolved clones showed that the pathogen can increase its fitness on both original and distant hosts although the magnitude of fitness increase was greater on distant hosts. Only few genomic modifications were detected in evolved clones compared with the ancestor but parallel evolutionary changes in two genes were observed in independent evolved populations. Independent mutations in the regulatory gene efpR were selected for in three populations evolved on beans, a distant host. Reverse genetic approaches confirmed that these mutations were associated with fitness gain on bean plants. This work provides a first step toward understanding the within-host evolutionary dynamics of R. solanacearum during infection and identifying bacterial genes subjected to in planta selection. The discovery of EfpR as a determinant conditioning host adaptation of the pathogen illustrates how experimental evolution coupled with whole-genome sequencing is a potent tool to identify novel molecular players involved in central life-history traits.
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Affiliation(s)
- Alice Guidot
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Wei Jiang
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Jean-Baptiste Ferdy
- UPS-CNRS-ENFA, Laboratoire Évolution et Diversité Biologique (EDB), UMR5174, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- UPS-CNRS-ENFA, Laboratoire Évolution et Diversité Biologique (EDB), UMR5174, Université Paul Sabatier, Toulouse, France
| | - Patrick Barberis
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Jérôme Gouzy
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Stéphane Genin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
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Jayamani E, Mylonakis E. Effector triggered manipulation of host immune response elicited by different pathotypes of Escherichia coli. Virulence 2014; 5:733-9. [PMID: 25513774 PMCID: PMC4189879 DOI: 10.4161/viru.29948] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/08/2014] [Accepted: 07/15/2014] [Indexed: 12/28/2022] Open
Abstract
Effectors are virulence factors that are secreted by bacteria during an infection in order to subvert cellular processes or induce the surveillance system of the host. Pathogenic microorganisms encode effectors, toxins and components of secretion systems that inject the effectors to the host. Escherichia coli is part of the innocuous commensal microbial flora of the gastrointestinal tract. However, pathogenic E. coli can cause diarrheal and extraintestinal diseases. Pathogenic E. coli uses secretion systems to inject an array of effector proteins directly into the host cells. Herein, we discuss the effectors secreted by different pathotypes of E. coli and provide an overview of strategies employed by effectors to target the host cellular and subcellular processes as well as their role in triggering host immune response.
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Affiliation(s)
- Elamparithi Jayamani
- Division of Infectious Diseases; Rhode Island Hospital; Alpert Medical School of Brown University; Providence, RI USA
| | - Eleftherios Mylonakis
- Division of Infectious Diseases; Rhode Island Hospital; Alpert Medical School of Brown University; Providence, RI USA
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