51
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Voß S, Betz R, Heidt S, Corradi N, Requena N. RiCRN1, a Crinkler Effector From the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis, Functions in Arbuscule Development. Front Microbiol 2018; 9:2068. [PMID: 30233541 PMCID: PMC6131194 DOI: 10.3389/fmicb.2018.02068] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/13/2018] [Indexed: 01/10/2023] Open
Abstract
Arbuscular mycorrhizal (AM) symbiosis is one of the most prominent and beneficial plant–microbe interactions that facilitates mineral nutrition and confers tolerance to biotic and abiotic stresses. AM fungi colonize the root cortex and develop specialized structures called arbuscules where the nutrient exchange takes place. Arbuscule development is a highly controlled and coordinated process requiring the involvement of many plant proteins recruited at that interface. In contrast, much less is known about the fungal proteins involved in this process. Here, we have identified an AM fungal effector that participates in this developmental step of the symbiosis. RiCRN1 is a crinkler (CRN) effector that belongs to a subfamily of secreted CRN proteins from R. irregularis. CRNs have been so far only functionally characterized in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity. RiCRN1 accumulates during symbiosis establishment parallel to MtPT4, the gene coding for an arbuscule-specific phosphate transporter. Expression in Nicotiana benthamiana leaves and in Medicago truncatula roots suggest that RiCRN1 is not involved in cell death processes. RiCRN1 dimerizes and localizes to nuclear bodies, suggesting that, similar to other CRNs, it functions in the plant nucleus. Downregulation of RiCRN1 using host-induced gene silencing led to an impairment of the symbiosis in M. truncatula and to a reduction of MtPT4, while ectopic expression of RiCRN1, surprisingly, led to a drastic reduction in arbuscule size that correlated with a decrease not only in MtPT4 but also in MtBCP1, a marker for initial stages of arbuscule development. Altogether, our results suggest that a tightly regulated expression in time and space of RiCRN1 is critical for symbiosis progression and for the proper initiation of arbuscule development.
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Affiliation(s)
- Stefanie Voß
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Ruben Betz
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sven Heidt
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Nicolas Corradi
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - Natalia Requena
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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52
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Vetukuri RR, Tripathy S, Malar C M, Panda A, Kushwaha SK, Chawade A, Andreasson E, Grenville-Briggs LJ, Whisson SC. Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora. Genome Biol Evol 2018; 10:2432-2442. [PMID: 30060094 PMCID: PMC6152947 DOI: 10.1093/gbe/evy162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/19/2022] Open
Abstract
Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.
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Affiliation(s)
- Ramesh R Vetukuri
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Mathu Malar C
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Arijit Panda
- Computational Genomics Laboratory, Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Sandeep K Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Department of Biology, Lund University, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Laura J Grenville-Briggs
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Stephen C Whisson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
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53
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Roquigny R, Novinscak A, Arseneault T, Joly DL, Filion M. Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223. BMC Genomics 2018; 19:474. [PMID: 29914352 PMCID: PMC6006673 DOI: 10.1186/s12864-018-4852-1] [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: 12/12/2017] [Accepted: 06/04/2018] [Indexed: 11/13/2022] Open
Abstract
Background Phytophthora infestans is responsible for late blight, one of the most important potato diseases. Phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 isolated in our laboratory shows biocontrol potential against various plant pathogens. To characterize the effect of LBUM223 on the transcriptome of P. infestans, we conducted an in vitro time-course study. Confrontational assay was performed using P. infestans inoculated alone (control) or with LBUM223, its phzC- isogenic mutant (not producing PCA), or exogenically applied PCA. Destructive sampling was performed at 6, 9 and 12 days and the transcriptome of P. infestans was analysed using RNA-Seq. The expression of a subset of differentially expressed genes was validated by RT-qPCR. Results Both LBUM223 and exogenically applied PCA significantly repressed P. infestans’ growth at all times. Compared to the control treatment, transcriptomic analyses showed that the percentages of all P. infestans’ genes significantly altered by LBUM223 and exogenically applied PCA increased as time progressed, from 50 to 61% and from to 32 to 46%, respectively. When applying an absolute cut-off value of 3 fold change or more for all three harvesting times, 207 genes were found significantly differentially expressed by PCA, either produced by LBUM223 or exogenically applied. Gene ontology analysis revealed that both treatments altered the expression of key functional genes involved in major functions like phosphorylation mechanisms, transmembrane transport and oxidoreduction activities. Interestingly, even though no host plant tissue was present in the in vitro system, PCA also led to the overexpression of several genes encoding effectors. The mutant only slightly repressed P. infestans’ growth and barely altered its transcriptome. Conclusions Our study suggests that PCA is involved in P. infestans’ growth repression and led to important transcriptomic changes by both up- and down-regulating gene expression in P. infestans over time. Different metabolic functions were altered and many effectors were found to be upregulated, suggesting their implication in biocontrol. Electronic supplementary material The online version of this article (10.1186/s12864-018-4852-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roxane Roquigny
- Department of Biology, Université de Moncton, Moncton, Canada
| | - Amy Novinscak
- Department of Biology, Université de Moncton, Moncton, Canada
| | - Tanya Arseneault
- Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, Canada
| | - David L Joly
- Department of Biology, Université de Moncton, Moncton, Canada
| | - Martin Filion
- Department of Biology, Université de Moncton, Moncton, Canada.
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54
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Pham J, Stam R, Heredia VM, Csukai M, Huitema E. An NMRA-Like Protein Regulates Gene Expression in Phytophthora capsici to Drive the Infection Cycle on Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:665-677. [PMID: 29419371 DOI: 10.1094/mpmi-07-17-0193-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phytophthora spp. cause devastating disease epidemics on important crop plants and pose a grave threat to global crop production. Critically, Phytophthora pathogens represent a distinct evolutionary lineage in which pathogenicity has been acquired independently. Therefore, there is an urgent need to understand and disrupt the processes that drive infection if we aspire to defeat oomycete pathogens in the field. One area that has received little attention thus far in this respect is the regulation of Phytophthora gene expression during infection. Here, we characterize PcNMRAL1 (Phyca11_505845), a homolog of the Aspergillus nidulans nitrogen metabolite repression regulator NMRA and demonstrate a role for this protein in progression of the Phytophthora capsici infection cycle. PcNmrAL1 is coexpressed with the biotrophic marker gene PcHmp1 (haustorial membrane protein 1) and, when overexpressed, extends the biotrophic infection stage. Microarray analyses revealed that PcNmrAL1 overexpression in P. capsici leads to large-scale transcriptional changes during infection and in vitro. Importantly, detailed analysis reveals that PcNmrAL1 overexpression induces biotrophy-associated genes while repressing those associated with necrotrophy. In addition to factors controlling transcription, translation, and nitrogen metabolism, PcNMRAL1 helps regulate the expression of a considerable effector repertoire in P. capsici. Our data suggests that PcNMRAL1 is a transcriptional regulator that mediates the biotrophy to necrotrophy transition. PcNMRAL1 represents a novel factor that may drive the Phytophthora disease cycle on crops. This study provides the first insight into mechanisms that regulate infection-related processes in Phytophthora spp. and provides a platform for further studies aimed at disabling pathogenesis and preventing crop losses.
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Affiliation(s)
- Jasmine Pham
- 1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, U.K
- 2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Remco Stam
- 3 School for Life Sciences, Weihenstephan Technische Universität München, Freising, Germany; and
| | | | - Michael Csukai
- 4 Syngenta, Jealott's Hill International Research Centre, Bracknell, U.K
| | - Edgar Huitema
- 1 Division of Plant Sciences, University of Dundee, Dundee DD2 5DA, U.K
- 2 Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
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55
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Barchenger DW, Lamour KH, Bosland PW. Challenges and Strategies for Breeding Resistance in Capsicum annuum to the Multifarious Pathogen, Phytophthora capsici. FRONTIERS IN PLANT SCIENCE 2018; 9:628. [PMID: 29868083 PMCID: PMC5962783 DOI: 10.3389/fpls.2018.00628] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Phytophthora capsici is the most devastating pathogen for chile pepper production worldwide and current management strategies are not effective. The population structure of the pathogen is highly variable and few sources of widely applicable host resistance have been identified. Recent genomic advancements in the host and the pathogen provide important insights into the difficulties reported by epidemiological and physiological studies published over the past century. This review highlights important challenges unique to this complex pathosystem and suggests strategies for resistance breeding to help limit losses associated with P. capsici.
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Affiliation(s)
- Derek W. Barchenger
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Kurt H. Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
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56
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Zhang X, Farah N, Rolston L, Ericsson DJ, Catanzariti A, Bernoux M, Ve T, Bendak K, Chen C, Mackay JP, Lawrence GJ, Hardham A, Ellis JG, Williams SJ, Dodds PN, Jones DA, Kobe B. Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P. MOLECULAR PLANT PATHOLOGY 2018; 19:1196-1209. [PMID: 28817232 PMCID: PMC6638141 DOI: 10.1111/mpp.12597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 05/23/2023]
Abstract
The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P-mediated recognition. The first zinc-coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid-binding and chromatin-associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non-conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition.
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Affiliation(s)
- Xiaoxiao Zhang
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Nadya Farah
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Laura Rolston
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Daniel J. Ericsson
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Australian Synchrotron, Macromolecular crystallographyClaytonVictoria 3168Australia
| | - Ann‐Maree Catanzariti
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Thomas Ve
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Institute for Glycomics, Griffith UniversitySouthportQueensland 4222Australia
| | - Katerina Bendak
- School of Molecular BioscienceUniversity of SydneySydneyNew South Wales 2006Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Joel P. Mackay
- School of Molecular BioscienceUniversity of SydneySydneyNew South Wales 2006Australia
| | - Gregory J. Lawrence
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Adrienne Hardham
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Jeffrey G. Ellis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Simon J. Williams
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - David A. Jones
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
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57
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Amaro TMMM, Thilliez GJA, Mcleod RA, Huitema E. Random mutagenesis screen shows that Phytophthora capsici CRN83_152-mediated cell death is not required for its virulence function(s). MOLECULAR PLANT PATHOLOGY 2018; 19:1114-1126. [PMID: 28779542 PMCID: PMC5947615 DOI: 10.1111/mpp.12590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 06/07/2023]
Abstract
With the increasing availability of plant pathogen genomes, secreted proteins that aid infection (effectors) have emerged as key factors that help to govern plant-microbe interactions. The conserved CRN (CRinkling and Necrosis) effector family was first described in oomycetes by their capacity to induce host cell death. Despite recent advances towards the elucidation of CRN virulence functions, the relevance of CRN-induced cell death remains unclear. In planta over-expression of PcCRN83_152, a CRN effector from Phytophthora capsici, causes host cell death and boosts P. capsici virulence. We used these features to ask whether PcCRN83_152-induced cell death is linked to its virulence function. By randomly mutating this effector, we generated PcCRN83_152 variants with no cell death (NCD) phenotypes, which were subsequently tested for activity towards enhanced virulence. We showed that a subset of PcCRN83_152 NCD variants retained their ability to boost P. capsici virulence. Moreover, NCD variants were shown to have a suppressive effect on PcCRN83_152-mediated cell death. Our work shows that PcCRN83_152-induced cell death and virulence function can be separated. Moreover, if these findings hold true for other cell death-inducing CRN effectors, this work, in turn, will provide a framework for studies aimed at unveiling the virulence functions of these effectors.
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Affiliation(s)
- Tiago M. M. M. Amaro
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI), InvergowrieDundee DD2 5DAUK
- Dundee Effector Consortium, JHI, InvergowrieDundee DD2 5DAUK
| | - Gaëtan J. A. Thilliez
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI), InvergowrieDundee DD2 5DAUK
- Dundee Effector Consortium, JHI, InvergowrieDundee DD2 5DAUK
- Cell and Molecular SciencesJHI, InvergowrieDundee DD2 5DAUK
| | - Rory A. Mcleod
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI), InvergowrieDundee DD2 5DAUK
- Dundee Effector Consortium, JHI, InvergowrieDundee DD2 5DAUK
| | - Edgar Huitema
- Division of Plant Sciences, School of Life SciencesUniversity of Dundee at the James Hutton Institute (JHI), InvergowrieDundee DD2 5DAUK
- Dundee Effector Consortium, JHI, InvergowrieDundee DD2 5DAUK
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58
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Gaulin E, Pel MJC, Camborde L, San-Clemente H, Courbier S, Dupouy MA, Lengellé J, Veyssiere M, Le Ru A, Grandjean F, Cordaux R, Moumen B, Gilbert C, Cano LM, Aury JM, Guy J, Wincker P, Bouchez O, Klopp C, Dumas B. Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. BMC Biol 2018; 16:43. [PMID: 29669603 PMCID: PMC5907361 DOI: 10.1186/s12915-018-0508-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/20/2018] [Indexed: 02/07/2023] Open
Abstract
Background Oomycetes are a group of filamentous eukaryotic microorganisms that have colonized all terrestrial and oceanic ecosystems, and they include prominent plant pathogens. The Aphanomyces genus is unique in its ability to infect both plant and animal species, and as such exemplifies oomycete versatility in adapting to different hosts and environments. Dissecting the underpinnings of oomycete diversity provides insights into their specificity and pathogenic mechanisms. Results By carrying out genomic analyses of the plant pathogen A. euteiches and the crustacean pathogen A. astaci, we show that host specialization is correlated with specialized secretomes that are adapted to the deconstruction of the plant cell wall in A. euteiches and protein degradation in A. astaci. The A. euteiches genome is characterized by a large repertoire of small secreted protein (SSP)-encoding genes that are highly induced during plant infection, and are not detected in other oomycetes. Functional analysis revealed an SSP from A. euteiches containing a predicted nuclear-localization signal which shuttles to the plant nucleus and increases plant susceptibility to infection. Conclusion Collectively, our results show that Aphanomyces host adaptation is associated with evolution of specialized secretomes and identify SSPs as a new class of putative oomycete effectors. Electronic supplementary material The online version of this article (10.1186/s12915-018-0508-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France.
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Hélène San-Clemente
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Sarah Courbier
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France.,Present Address: Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Marie-Alexane Dupouy
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Juliette Lengellé
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Marine Veyssiere
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
| | - Aurélie Le Ru
- Fédération de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, 31326, Castanet-Tolosan, France
| | - Frédéric Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Clément Gilbert
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS Université Paris-Sud UMR 9191, IRD 247, Gif sur Yvette, France
| | - Liliana M Cano
- University of Florida, UF/IFAS, Indian River Research and Education Center IRREC, 2199 South Rock Road, Fort Pierce, FL, 34945, USA
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie François-Jacob, Genoscope, F-92057, Evry, France
| | - Julie Guy
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie François-Jacob, Genoscope, F-92057, Evry, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Biologie François-Jacob, Genoscope, CNRS UMR 8030, Université d'Evry, Evry, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, UR875, Plateforme Bioinformatique Genotoul, Castanet-Tolosan, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, CNRS UMR5546 Université de Toulouse, Paul Sabatier, 24, chemin de Borde Rouge BP 42617 Auzeville, 31326, Castanet-Tolosan, France
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59
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Liu Y, Lan X, Song S, Yin L, Dry IB, Qu J, Xiang J, Lu J. In Planta Functional Analysis and Subcellular Localization of the Oomycete Pathogen Plasmopara viticola Candidate RXLR Effector Repertoire. FRONTIERS IN PLANT SCIENCE 2018; 9:286. [PMID: 29706971 PMCID: PMC5908963 DOI: 10.3389/fpls.2018.00286] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/19/2018] [Indexed: 05/20/2023]
Abstract
Downy mildew is one of the most destructive diseases of grapevine, causing tremendous economic loss in the grape and wine industry. The disease agent Plasmopara viticola is an obligate biotrophic oomycete, from which over 100 candidate RXLR effectors have been identified. In this study, 83 candidate RXLR effector genes (PvRXLRs) were cloned from the P. viticola isolate "JL-7-2" genome. The results of the yeast signal sequence trap assay indicated that most of the candidate effectors are secretory proteins. The biological activities and subcellular localizations of all the 83 effectors were analyzed via a heterologous Agrobacterium-mediated Nicotiana benthamiana expression system. Results showed that 52 effectors could completely suppress cell death triggered by elicitin, 10 effectors could partially suppress cell death, 11 effectors were unable to suppress cell death, and 10 effectors themselves triggered cell death. Live-cell imaging showed that the majority of the effectors (76 of 83) could be observed with informative fluorescence signals in plant cells, among which 34 effectors were found to be targeted to both the nucleus and cytosol, 29 effectors were specifically localized in the nucleus, and 9 effectors were targeted to plant membrane system. Interestingly, three effectors PvRXLR61, 86 and 161 were targeted to chloroplasts, and one effector PvRXLR54 was dually targeted to chloroplasts and mitochondria. However, western blot analysis suggested that only PvRXLR86 carried a cleavable N-terminal transit peptide and underwent processing in planta. Many effectors have previously been predicted to target organelles, however, to the best of our knowledge, this is the first study to provide experimental evidence of oomycete effectors targeted to chloroplasts and mitochondria.
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Affiliation(s)
- Yunxiao Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Lan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shiren Song
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ling Yin
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ian B. Dry
- CSIRO Agriculture & Food, Urrbrae, SA, Australia
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jiang Xiang
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
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Dalio RJD, Maximo HJ, Oliveira TS, Dias RO, Breton MC, Felizatti H, Machado M. Phytophthora parasitica Effector PpRxLR2 Suppresses Nicotiana benthamiana Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:481-493. [PMID: 29165046 DOI: 10.1094/mpmi-07-17-0158-fi] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Phytophthora species secrete several classes of effector proteins during interaction with their hosts. These proteins can have multiple functions including modulation of host physiology and immunity. The RxLR effectors have the ability to enter plant cells using the plant machinery. Some of these effectors have been characterized as immunity suppressors; however, very little is known about their functions in the interaction between Phytophthora parasitica and its hosts. Using a bioinformatics pipeline, we have identified 172 candidate RxLR effectors (CREs) in the isolate IAC 01_95 of P. parasitica. Of these 172 CREs, 93 were found to be also present in eight other genomes of P. parasitica, isolated from different hosts and continents. After transcriptomics and gene expression analysis, we have found five CREs to be up-regulated in in-vitro and in-planta samples. Subsequently, we selected three CREs for functional characterization in the model plant Nicotiana benthamiana. We show that PpRxLR2 is able to completely suppress INF-1-induced cell death, whereas PpRxLR3 and PpRxLR5 moderately suppressed N. benthamiana immunity in a less-extensive manner. Moreover, we confirmed the effector-triggered susceptibility activity of these proteins after transient transformation and infection of N. benthamiana plants. All three CREs enhanced virulence of P. parasitica during the interaction with N. benthamiana. These effectors, in particular PpRxLR2, can be targeted for the development of biotechnology-based control strategies of P. parasitica diseases.
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Affiliation(s)
- R J D Dalio
- 1 Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico, Cordeirópolis, SP, Brazil
| | - H J Maximo
- 1 Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico, Cordeirópolis, SP, Brazil
| | - T S Oliveira
- 1 Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico, Cordeirópolis, SP, Brazil
| | - R O Dias
- 2 Instituto de Química, Universidade de São Paulo USP, São Paulo, SP, Brazil; and
| | - M C Breton
- 1 Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico, Cordeirópolis, SP, Brazil
| | - H Felizatti
- 3 Instituto de Matemática, Física e Computação Científica, Universidade Estadual de Campinas Unicamp, Campinas, SP, Brazil
| | - M Machado
- 1 Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico, Cordeirópolis, SP, Brazil
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Lorrain C, Petre B, Duplessis S. Show me the way: rust effector targets in heterologous plant systems. Curr Opin Microbiol 2018; 46:19-25. [PMID: 29454191 DOI: 10.1016/j.mib.2018.01.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/14/2018] [Accepted: 01/31/2018] [Indexed: 11/27/2022]
Abstract
For years, the study of rust fungal effectors has been impeded by the lack of molecular genetic tools in rust pathosystems. The recent use of heterologous plants to perform effector screens (effectoromics)-including effector localisation (cellular targets) and protein interactors (molecular targets) in plant cells-has changed the game. These screens revealed that many candidate effectors from various rust fungi target specific plant cell compartments, including chloroplasts, and associate with specific plant protein complexes. Such information represents unparalleled opportunities to understand how effectors sustain extreme parasitic interactions and obligate biotrophy. Despite their limitations, we here portray how the use of heterologous expression systems has been essential for gaining new insight into rust effectors.
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Affiliation(s)
- Cécile Lorrain
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France
| | - Benjamin Petre
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France
| | - Sébastien Duplessis
- INRA/Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA Centre Grand Est-Nancy, Champenoux, France.
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62
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Hardham AR, Blackman LM. Phytophthora cinnamomi. MOLECULAR PLANT PATHOLOGY 2018; 19:260-285. [PMID: 28519717 PMCID: PMC6637996 DOI: 10.1111/mpp.12568] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/20/2017] [Accepted: 05/11/2017] [Indexed: 05/12/2023]
Abstract
Phytophthora cinnamomi is one of the most devastating plant pathogens in the world. It infects close to 5000 species of plants, including many of importance in agriculture, forestry and horticulture. The inadvertent introduction of P. cinnamomi into natural ecosystems, including a number of recognized Global Biodiversity Hotspots, has had disastrous consequences for the environment and the biodiversity of flora and fauna. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus-like organisms that initiate plant disease through the production of motile zoospores. Disease control is difficult in agricultural and forestry situations and even more challenging in natural ecosystems as a result of the scale of the problem and the limited range of effective chemical inhibitors. The development of sustainable control measures for the future management of P. cinnamomi requires a comprehensive understanding of the cellular and molecular basis of pathogen development and pathogenicity. The application of next-generation sequencing technologies to generate genomic and transcriptomic data promises to underpin a new era in P. cinnamomi research and discovery. The aim of this review is to integrate bioinformatic analyses of P. cinnamomi sequence data with current knowledge of the cellular and molecular basis of P. cinnamomi growth, development and plant infection. The goal is to provide a framework for future research by highlighting potential pathogenicity genes, shedding light on their possible functions and identifying suitable targets for future control measures. TAXONOMY Phytophthora cinnamomi Rands; Kingdom Chromista; Phylum Oomycota or Pseudofungi; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; genus Phytophthora. HOST RANGE Infects about 5000 species of plants, including 4000 Australian native species. Host plants important for agriculture and forestry include avocado, chestnut, macadamia, oak, peach and pineapple. DISEASE SYMPTOMS A root pathogen which causes rotting of fine and fibrous roots, but which can also cause stem cankers. Root damage may inhibit water movement from roots to shoots, leading to dieback of young shoots. USEFUL WEBSITES: http://fungidb.org/fungidb/; http://genome.jgi.doe.gov/Phyci1/Phyci1.home.html; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314365.1; http://www.ncbi.nlm.nih.gov/assembly/GCA_001314505.1.
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Affiliation(s)
- Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and EnvironmentThe Australian National UniversityCanberraACT 2601Australia
| | - Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and EnvironmentThe Australian National UniversityCanberraACT 2601Australia
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Dalio RJD, Herlihy J, Oliveira TS, McDowell JM, Machado M. Effector Biology in Focus: A Primer for Computational Prediction and Functional Characterization. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:22-33. [PMID: 29023190 DOI: 10.1094/mpmi-07-17-0174-fi] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant-pathogen interactions are controlled by a multilayered immune system, which is activated by pathogen recognition in the host. Pathogens secrete effector molecules to interfere with the immune recognition or signaling network and reprogram cell structure or metabolism. Understanding the effector repertoires of diverse pathogens will contribute to unraveling the molecular mechanism of virulence and developing sustainable disease-control strategies for crops and natural ecosystems. Effector functionality has been investigated extensively in only a small number of pathogen species. However, many more pathogen genomes are becoming available, and much can be learned from a broader view of effector biology in diverse pathosystems. The purpose of this review is to summarize methodology for computational prediction of protein effectors, functional characterization of effector proteins and their targets, and the use of effectors as probes to screen for new sources of host resistance. Although these techniques were generally developed in model pathosystems, many of the approaches are directly applicable for exploration and exploitation of effector biology in pathosystems that are less well studied. We hope to facilitate such exploration, which will broaden understanding of the mechanisms that underpin the biological diversity of plant-pathogen interactions, and maximize the impact of new approaches that leverage effector biology for disease control.
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Affiliation(s)
- Ronaldo J D Dalio
- 1 Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IA, Cordeirópolis-SP, Brazil; and
| | - John Herlihy
- 2 Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061-0329, U.S.A
| | - Tiago S Oliveira
- 1 Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IA, Cordeirópolis-SP, Brazil; and
| | - John M McDowell
- 2 Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061-0329, U.S.A
| | - Marcos Machado
- 1 Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IA, Cordeirópolis-SP, Brazil; and
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Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal. mSphere 2017; 2:mSphere00408-17. [PMID: 29202039 PMCID: PMC5700374 DOI: 10.1128/msphere.00408-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles-alveolate-Rhizaria (SAR) supergroup and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. This study investigated the expansion and evolution of effectors in 37 oomycete species in 4 oomycete orders, including Albuginales, Peronosporales, Pythiales, and Saprolegniales species. Our results highlight the large expansions of effector protein families, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, in Phytophthora species. Species-specific expansions, including expansions of chitinases in Aphanomyces astaci and Pythium oligandrum, were detected. Novel effectors which may be involved in suppressing animal immune responses in Ap. astaci and Py. insidiosum were also identified. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located in a number of oomycete species. We also investigated the "RxLR" effector complement of all 37 species and, as expected, observed large expansions in Phytophthora species numbers. Our results provide in-depth sequence information on all putative RxLR effectors from all 37 species. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. IMPORTANCE The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.
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Ah-Fong AMV, Shrivastava J, Judelson HS. Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization. BMC Genomics 2017; 18:764. [PMID: 29017458 PMCID: PMC5635513 DOI: 10.1186/s12864-017-4151-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/02/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND How pathogen genomes evolve to support distinct lifestyles is not well-understood. The oomycete Phytophthora infestans, the potato blight agent, is a largely biotrophic pathogen that feeds from living host cells, which become necrotic only late in infection. The related oomycete Pythium ultimum grows saprophytically in soil and as a necrotroph in plants, causing massive tissue destruction. To learn what distinguishes their lifestyles, we compared their gene contents and expression patterns in media and a shared host, potato tuber. RESULTS Genes related to pathogenesis varied in temporal expression pattern, mRNA level, and family size between the species. A family's aggregate expression during infection was not proportional to size due to transcriptional remodeling and pseudogenization. Ph. infestans had more stage-specific genes, while Py. ultimum tended towards more constitutive expression. Ph. infestans expressed more genes encoding secreted cell wall-degrading enzymes, but other categories such as secreted proteases and ABC transporters had higher transcript levels in Py. ultimum. Species-specific genes were identified including new Pythium genes, perforins, which may disrupt plant membranes. Genome-wide ortholog analyses identified substantial diversified expression, which correlated with sequence divergence. Pseudogenization was associated with gene family expansion, especially in gene clusters. CONCLUSION This first large-scale analysis of transcriptional divergence within oomycetes revealed major shifts in genome composition and expression, including subfunctionalization within gene families. Biotrophy and necrotrophy seem determined by species-specific genes and the varied expression of shared pathogenicity factors, which may be useful targets for crop protection.
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Affiliation(s)
- Audrey M. V. Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Jolly Shrivastava
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521 USA
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Frenken T, Alacid E, Berger SA, Bourne EC, Gerphagnon M, Grossart HP, Gsell AS, Ibelings BW, Kagami M, Küpper FC, Letcher PM, Loyau A, Miki T, Nejstgaard JC, Rasconi S, Reñé A, Rohrlack T, Rojas-Jimenez K, Schmeller DS, Scholz B, Seto K, Sime-Ngando T, Sukenik A, Van de Waal DB, Van den Wyngaert S, Van Donk E, Wolinska J, Wurzbacher C, Agha R. Integrating chytrid fungal parasites into plankton ecology: research gaps and needs. Environ Microbiol 2017; 19:3802-3822. [DOI: 10.1111/1462-2920.13827] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/09/2017] [Accepted: 06/10/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Thijs Frenken
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
| | - Elisabet Alacid
- Departament de Biologia Marina i Oceanografia; Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49; Barcelona 08003 Spain
| | - Stella A. Berger
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
| | - Elizabeth C. Bourne
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straβe 6-8; Berlin D-14195 Germany
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
| | - Mélanie Gerphagnon
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2; Potsdam D-14476 Germany
| | - Alena S. Gsell
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
| | - Bas W. Ibelings
- Department F.-A. Forel for Environmental and Aquatic Sciences & Institute for Environmental Sciences; University of Geneva, 66 Boulevard Carl Vogt; Geneva 4 CH 1211 Switzerland
| | - Maiko Kagami
- Department of Environmental Sciences, Faculty of Science; Toho University, 2-2-1, Miyama; Funabashi Chiba 274-8510 Japan
| | - Frithjof C. Küpper
- Oceanlab, University of Aberdeen, Main Street; Newburgh Scotland AB41 6AA UK
| | - Peter M. Letcher
- Department of Biological Sciences; The University of Alabama, 300 Hackberry Lane; Tuscaloosa AL 35487 USA
| | - Adeline Loyau
- Department of System Ecotoxicology; Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15; 04318 Leipzig Germany
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15; Leipzig 04318 Germany
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Takeshi Miki
- Institute of Oceanography; National Taiwan University, No.1 Section 4, Roosevelt Road; Taipei 10617 Taiwan
- Research Center for Environmental Changes; Academia Sinica, No.128 Section 2, Academia Road, Nankang; Taipei 11529 Taiwan
| | - Jens C. Nejstgaard
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
| | - Serena Rasconi
- WasserCluster Lunz - Biological Station; Inter-University Centre for Aquatic Ecosystem Research, A-3293 Lunz am See; Austria
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia; Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49; Barcelona 08003 Spain
| | - Thomas Rohrlack
- Faculty of Environmental Sciences and Natural Resource Management; Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås; Norway
| | - Keilor Rojas-Jimenez
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
- Universidad Latina de Costa Rica, Campus San Pedro, Apdo; San Jose 10138-1000 Costa Rica
| | - Dirk S. Schmeller
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15; Leipzig 04318 Germany
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Bettina Scholz
- BioPol ehf, Einbúastig 2, Skagaströnd 545; Iceland
- Faculty of Natural Resource Sciences; University of Akureyri, Borgir v. Nordurslod; Akureyri IS 600 Iceland
| | - Kensuke Seto
- Department of Environmental Sciences, Faculty of Science; Toho University, 2-2-1, Miyama; Funabashi Chiba 274-8510 Japan
- Sugadaira Montane Research Center; University of Tsukuba, 1278-294, Sugadaira-Kogen; Ueda, Nagano, 386-2204 Japan
| | - Télesphore Sime-Ngando
- Université Clermont Auvergne, UMR CNRS 6023 LMGE, Laboratoire Microorganismes: Génome et Environnement (LMGE); Campus Universitaire des Cézeaux, Impasse Amélie Murat 1, CS 60026, Aubière, 63178 France
| | - Assaf Sukenik
- Kinneret Limnological Laboratory; Israel Oceanographic & Limnological Research, P.O.Box 447; Migdal, 14950 Israel
| | - Dedmer B. Van de Waal
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
| | - Silke Van den Wyngaert
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
| | - Ellen Van Donk
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
- Department of Biology; University of Utrecht, Padualaan 8; Utrecht TB 3508 The Netherlands
| | - Justyna Wolinska
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Straβe 1-3; Berlin, 14195 Germany
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences; University of Gothenburg, Box 461; Göteborg, 405 30 Sweden
- Gothenburg Global Biodiversity Centre, Box 461; Göteborg, SE-405 30 Sweden
| | - Ramsy Agha
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017. [PMID: 28417959 DOI: 10.1038/srep4655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture &Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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68
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017; 7:46553. [PMID: 28417959 PMCID: PMC5394536 DOI: 10.1038/srep46553] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/22/2017] [Indexed: 12/17/2022] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture & Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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Ali SS, Shao J, Lary DJ, Kronmiller BA, Shen D, Strem MD, Amoako-Attah I, Akrofi AY, Begoude BD, ten Hoopen GM, Coulibaly K, Kebe BI, Melnick RL, Guiltinan MJ, Tyler BM, Meinhardt LW, Bailey BA. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms. Genome Biol Evol 2017; 9:2982378. [PMID: 28186564 PMCID: PMC5381587 DOI: 10.1093/gbe/evx021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/21/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta . Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens.
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Affiliation(s)
- Shahin S. Ali
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Jonathan Shao
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, China
| | - Mary D. Strem
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | | | - B.A. Didier Begoude
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
| | - G. Martijn ten Hoopen
- Regional Laboratory for Biological and Applied Microbiology (IRAD), Yaoundé, Cameroon
- CIRAD, UPR 106 Bioagresseurs, Montpellier, France
| | | | | | - Rachel L. Melnick
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | | | - Brett M. Tyler
- Center for Genome Research and Biocomputing, Oregon State University
- Department of Botany and Plant Pathology, Oregon State University
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
| | - Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, Plant Sciences Institute, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, Maryland
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Amaro TMMM, Thilliez GJA, Motion GB, Huitema E. A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited. FRONTIERS IN PLANT SCIENCE 2017; 8:99. [PMID: 28217133 PMCID: PMC5289972 DOI: 10.3389/fpls.2017.00099] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/17/2017] [Indexed: 05/20/2023]
Abstract
Plant associated microbes rely on secreted virulence factors (effectors) to modulate host immunity and ensure progressive infection. Amongst the secreted protein repertoires defined and studied in pathogens to date, the CRNs (for CRinkling and Necrosis) have emerged as one of only a few highly conserved protein families, spread across several kingdoms. CRN proteins were first identified in plant pathogenic oomycetes where they were found to be modular factors that are secreted and translocated inside host cells by means of a conserved N-terminal domain. Subsequent localization and functional studies have led to the view that CRN C-termini execute their presumed effector function in the host nucleus, targeting processes required for immunity. These findings have led to great interest in this large protein family and driven the identification of additional CRN-like proteins in other organisms. The identification of CRN proteins and subsequent functional studies have markedly increased the number of candidate CRN protein sequences, expanded the range of phenotypes tentatively associated with function and revealed some of their molecular functions toward virulence. The increased number of characterized CRNs also has presented a set of challenges that may impede significant progress in the future. Here, we summarize our current understanding of the CRNs and re-assess some basic assumptions regarding this protein family. We will discuss the latest findings on CRN biology and highlight exciting new hypotheses that have emanated from the field. Finally, we will discuss new approaches to study CRN functions that would lead to a better understanding of CRN effector biology as well as the processes that lead to host susceptibility and immunity.
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Affiliation(s)
- Tiago M. M. M. Amaro
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| | - Gaëtan J. A. Thilliez
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
- Cell and Molecular Sciences, The James Hutton InstituteInvergowrie, UK
| | - Graham B. Motion
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| | - Edgar Huitema
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
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71
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de Vries S, von Dahlen JK, Uhlmann C, Schnake A, Kloesges T, Rose LE. Signatures of selection and host-adapted gene expression of the Phytophthora infestans RNA silencing suppressor PSR2. MOLECULAR PLANT PATHOLOGY 2017; 18:110-124. [PMID: 27503598 PMCID: PMC6638260 DOI: 10.1111/mpp.12465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 08/04/2016] [Indexed: 05/04/2023]
Abstract
Phytophthora infestans is a devastating pathogen in agricultural systems. Recently, an RNA silencing suppressor (PSR2, 'Phytophthora suppressor of RNA silencing 2') has been described in P. infestans. PSR2 has been shown to increase the virulence of Phytophthora pathogens on their hosts. This gene is one of the few effectors present in many economically important Phytophthora species. In this study, we investigated: (i) the evolutionary history of PSR2 within and between species of Phytophthora; and (ii) the interaction between sequence variation, gene expression and virulence. In P. infestans, the highest PiPSR2 expression was correlated with decreased symptom expression. The highest gene expression was observed in the biotrophic phase of the pathogen, suggesting that PSR2 is important during early infection. Protein sequence conservation was negatively correlated with host range, suggesting host range as a driver of PSR2 evolution. Within species, we detected elevated amino acid variation, as observed for other effectors; however, the frequency spectrum of the mutations was inconsistent with strong balancing selection. This evolutionary pattern may be related to the conservation of the host target(s) of PSR2 and the absence of known corresponding R genes. In summary, our study indicates that PSR2 is a conserved effector that acts as a master switch to modify plant gene regulation early during infection for the pathogen's benefit. The conservation of PSR2 and its important role in virulence make it a promising target for pathogen management.
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Affiliation(s)
- Sophie de Vries
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- iGRAD‐Plant Graduate SchoolHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Janina K. von Dahlen
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Constanze Uhlmann
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Anika Schnake
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Thorsten Kloesges
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Laura E. Rose
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- iGRAD‐Plant Graduate SchoolHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- Ceplas, Cluster of Excellence in Plant SciencesHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
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72
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Burroughs AM, Aravind L. RNA damage in biological conflicts and the diversity of responding RNA repair systems. Nucleic Acids Res 2016; 44:8525-8555. [PMID: 27536007 PMCID: PMC5062991 DOI: 10.1093/nar/gkw722] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 12/16/2022] Open
Abstract
RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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73
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Whitham SA, Qi M, Innes RW, Ma W, Lopes-Caitar V, Hewezi T. Molecular Soybean-Pathogen Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:443-68. [PMID: 27359370 DOI: 10.1146/annurev-phyto-080615-100156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.
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Affiliation(s)
- Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
| | - Valéria Lopes-Caitar
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
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74
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Åsman AKM, Fogelqvist J, Vetukuri RR, Dixelius C. Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements. THE NEW PHYTOLOGIST 2016; 211:993-1007. [PMID: 27010746 DOI: 10.1111/nph.13946] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/26/2016] [Indexed: 06/05/2023]
Abstract
Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Recent evidence has suggested that pathogen-derived sRNAs can modulate the expression of plant defense genes. Here, we studied the sRNA classes and functions associated with Phytophthora infestans Argonaute (Ago) proteins. sRNAs were co-immunoprecipitated with three PiAgo proteins and deep sequenced. Twenty- to twenty-two-nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26-nt sRNAs was seen in the PiAgo4-bound sample. The frequencies and sizes of transposable element (TE)-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in the control of different TE classes. We further provide evidence for the involvement of PiAgo1 in the P. infestans microRNA (miRNA) pathway. Protein-coding genes are probably regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing Crinkler (CRN) effectors was bound to PiAgo1, implicating this protein in the regulation of the expanded CRN gene family. The data suggest that PiAgo1 plays an essential role in gene regulation and that at least two RNA silencing pathways regulate TEs in the plant-pathogenic oomycete P. infestans.
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Affiliation(s)
- Anna K M Åsman
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnéan Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnéan Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Resistance Biology Unit, PO Box 102, SE-23053, Alnarp, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnéan Center for Plant Biology, PO Box 7080, SE-75007, Uppsala, Sweden
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75
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Li Q, Zhang M, Shen D, Liu T, Chen Y, Zhou JM, Dou D. A Phytophthora sojae effector PsCRN63 forms homo-/hetero-dimers to suppress plant immunity via an inverted association manner. Sci Rep 2016; 6:26951. [PMID: 27243217 PMCID: PMC4886637 DOI: 10.1038/srep26951] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/05/2016] [Indexed: 11/25/2022] Open
Abstract
Oomycete pathogens produce a large number of effectors to promote infection. Their mode of action are largely unknown. Here we show that a Phytophthora sojae effector, PsCRN63, suppresses flg22-induced expression of FRK1 gene, a molecular marker in pathogen-associated molecular patterns (PAMP)-triggered immunity (PTI). However, PsCRN63 does not suppress upstream signaling events including flg22-induced MAPK activation and BIK1 phosphorylation, indicating that it acts downstream of MAPK cascades. The PsCRN63-transgenic Arabidopsis plants showed increased susceptibility to bacterial pathogen Pseudomonas syringae pathovar tomato (Pst) DC3000 and oomycete pathogen Phytophthora capsici. The callose deposition were suppressed in PsCRN63-transgenic plants compared with the wild-type control plants. Genes involved in PTI were also down-regulated in PsCRN63-transgenic plants. Interestingly, we found that PsCRN63 forms an dimer that is mediated by inter-molecular interactions between N-terminal and C-terminal domains in an inverted association manner. Furthermore, the N-terminal and C-terminal domains required for the dimerization are widely conserved among CRN effectors, suggesting that homo-/hetero-dimerization of Phytophthora CRN effectors is required to exert biological functions. Indeed, the dimerization was required for PTI suppression and cell death-induction activities of PsCRN63.
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Affiliation(s)
- Qi Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.,Center for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingli Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanyu Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Min Zhou
- Center for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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76
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Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L. Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors. Nucleic Acids Res 2016; 44:3513-33. [PMID: 27060143 PMCID: PMC4857004 DOI: 10.1093/nar/gkw221] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/22/2016] [Indexed: 01/13/2023] Open
Abstract
Enzymatic effectors targeting nucleic acids, proteins and other cellular components are the mainstay of conflicts across life forms. Using comparative genomics we identify a large class of eukaryotic proteins, which include effectors from oomycetes, fungi and other parasites. The majority of these proteins have a characteristic domain architecture with one of several N-terminal 'Header' domains, which are predicted to play a role in trafficking of these effectors, including a novel version of the Ubiquitin fold. The Headers are followed by one or more diverse C-terminal domains, such as restriction endonuclease (REase), protein kinase, HNH endonuclease, LK-nuclease (a RNase) and multiple distinct peptidase domains, which are predicted to carry their toxicity determinants. The most common types of these proteins appear to have originated from prokaryotic transposases (e.g. TN7 and Mu) and combine a CDC6/ORC1-STAND clade NTPase domain with a C-terminal REase domain. Other than the so-called Crinkler effectors of oomycetes and fungi, these effectors are encoded by other eukaryotic parasites such as trypanosomatids (the RHS proteins) and the rhizarian Plasmodiophora, and symbionts like Capsaspora Remarkably, we also find these proteins in free-living eukaryotes, including several viridiplantae, fungi, amoebozoans and animals. These versions might either still be transposons or function in other poorly understood eukaryote-specific inter-organismal and inter-genomic conflicts. These include the Medea1 selfish element of Tribolium that spreads via post-zygotic killing. We present a unified mechanism for the recombination-dependent diversification and action of this widespread class of molecular weaponry deployed across diverse conflicts ranging from parasitic to free-living forms.
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Affiliation(s)
- Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Newton D Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Ramirez-Garcés D, Camborde L, Pel MJC, Jauneau A, Martinez Y, Néant I, Leclerc C, Moreau M, Dumas B, Gaulin E. CRN13 candidate effectors from plant and animal eukaryotic pathogens are DNA-binding proteins which trigger host DNA damage response. THE NEW PHYTOLOGIST 2016; 210:602-17. [PMID: 26700936 DOI: 10.1111/nph.13774] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/21/2015] [Indexed: 05/20/2023]
Abstract
To successfully colonize their host, pathogens produce effectors that can interfere with host cellular processes. Here we investigated the function of CRN13 candidate effectors produced by plant pathogenic oomycetes and detected in the genome of the amphibian pathogenic chytrid fungus Batrachochytrium dendrobatidis (BdCRN13). When expressed in Nicotiana, AeCRN13, from the legume root pathogen Aphanomyces euteiches, increases the susceptibility of the leaves to the oomycete Phytophthora capsici. When transiently expressed in amphibians or plant cells, AeCRN13 and BdCRN13 localize to the cell nuclei, triggering aberrant cell development and eventually causing cell death. Using Förster resonance energy transfer experiments in plant cells, we showed that both CRN13s interact with nuclear DNA and trigger plant DNA damage response (DDR). Mutating key amino acid residues in a predicted HNH-like endonuclease motif abolished the interaction of AeCRN13 with DNA, the induction of DDR and the enhancement of Nicotiana susceptibility to P. capsici. Finally, H2AX phosphorylation, a marker of DNA damage, and enhanced expression of genes involved in the DDR were observed in A. euteiches-infected Medicago truncatula roots. These results show that CRN13 from plant and animal eukaryotic pathogens promotes host susceptibility by targeting nuclear DNA and inducing DDR.
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Affiliation(s)
- Diana Ramirez-Garcés
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Alain Jauneau
- CNRS, Plateforme Imagerie-Microscopie Plateforme Imagerie-Microscopie, F-31326, Castanet-Tolosan, France
| | - Yves Martinez
- CNRS, Plateforme Imagerie-Microscopie Plateforme Imagerie-Microscopie, F-31326, Castanet-Tolosan, France
| | - Isabelle Néant
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Catherine Leclerc
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Marc Moreau
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
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Meyer FE, Shuey LS, Naidoo S, Mamni T, Berger DK, Myburg AA, van den Berg N, Naidoo S. Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility. FRONTIERS IN PLANT SCIENCE 2016; 7:191. [PMID: 26973660 PMCID: PMC4773608 DOI: 10.3389/fpls.2016.00191] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 02/04/2016] [Indexed: 05/18/2023]
Abstract
Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nitens plants were stem inoculated with P. cinnamomi and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of P. cinnamomi while 78% of the reads mapped to the Eucalyptus grandis genome. The highest expressed P. cinnamomi gene in planta was a putative crinkler effector (CRN1). Phylogenetic analysis indicated the high similarity of this P. cinnamomi CRN1 to that of Phytophthora infestans. Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related (PR) genes. In particular, a PR-9 peroxidase gene with a high similarity to a Carica papaya PR-9 ortholog previously shown to be suppressed upon infection by Phytophthora palmivora was down-regulated two-fold. This PR-9 gene may represent a cross-species effector target during P. cinnamomi infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by E. nitens that contributed to the susceptible outcome of the interaction.
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Affiliation(s)
- Febé E. Meyer
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Louise S. Shuey
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sitha Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Thandekile Mamni
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Dave K. Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Noëlani van den Berg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
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Gascuel Q, Bordat A, Sallet E, Pouilly N, Carrere S, Roux F, Vincourt P, Godiard L. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates. PLoS One 2016; 11:e0148513. [PMID: 26845339 PMCID: PMC4742249 DOI: 10.1371/journal.pone.0148513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 01/23/2023] Open
Abstract
The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved.
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Affiliation(s)
- Quentin Gascuel
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Amandine Bordat
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Erika Sallet
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Nicolas Pouilly
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Sébastien Carrere
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Fabrice Roux
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Patrick Vincourt
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Laurence Godiard
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
- * E-mail:
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80
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Liu H, Ma X, Yu H, Fang D, Li Y, Wang X, Wang W, Dong Y, Xiao B. Genomes and virulence difference between two physiological races of Phytophthora nicotianae. Gigascience 2016; 5:3. [PMID: 26823972 PMCID: PMC4730604 DOI: 10.1186/s13742-016-0108-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/06/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, races 0 and 1, are predominantly observed in cultivated tobacco fields around the world. Race 0 has been reported to be more aggressive, having a shorter incubation period, and causing worse root rot symptoms, while race 1 causes more severe necrosis. The molecular mechanisms underlying the difference in virulence between race 0 and 1 remain elusive. FINDINGS We assembled and annotated the genomes of P. nicotianae races 0 and 1, which were obtained by a combination of PacBio single-molecular real-time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis revealed a highly expanded ATP-binding cassette transporter gene family in P. nicotianae. Specifically, more RxLR effector genes were found in the genome of race 0 than in that of race 1. In addition, RxLR effector genes were found to be mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome. CONCLUSIONS These results provide not only high quality reference genomes of P. nicotianae, but also insights into the infection mechanisms of P. nicotianae and its co-evolution with the host plant. They also reveal insights into the difference in virulence between the two physiological races.
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Affiliation(s)
- Hui Liu
- />CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiao Ma
- />Yunnan Agricultural University, Kunming, 650100 China
| | - Haiqin Yu
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
| | - Dunhuang Fang
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
| | - Yongping Li
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
| | - Xiao Wang
- />CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wen Wang
- />CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
| | - Yang Dong
- />Yunnan Agricultural University, Kunming, 650100 China
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500 China
| | - Bingguang Xiao
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
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81
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Gascuel Q, Buendia L, Pecrix Y, Blanchet N, Muños S, Vear F, Godiard L. RXLR and CRN Effectors from the Sunflower Downy Mildew Pathogen Plasmopara halstedii Induce Hypersensitive-Like Responses in Resistant Sunflower Lines. FRONTIERS IN PLANT SCIENCE 2016; 7:1887. [PMID: 28066456 PMCID: PMC5165252 DOI: 10.3389/fpls.2016.01887] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/29/2016] [Indexed: 05/20/2023]
Abstract
Plasmopara halstedii is an obligate biotrophic oomycete causing downy mildew disease on sunflower, Helianthus annuus, an economically important oil crop. Severe symptoms of the disease (e.g., plant dwarfism, leaf bleaching, sporulation and production of infertile flower) strongly impair seed yield. Pl resistance genes conferring resistance to specific P. halstedii pathotypes were located on sunflower genetic map but yet not cloned. They are present in cultivated lines to protect them against downy mildew disease. Among the 16 different P. halstedii pathotypes recorded in France, pathotype 710 is frequently found, and therefore continuously controlled in sunflower by different Pl genes. High-throughput sequencing of cDNA from P. halstedii led us to identify potential effectors with the characteristic RXLR or CRN motifs described in other oomycetes. Expression of six P. halstedii putative effectors, five RXLR and one CRN, was analyzed by qRT-PCR in pathogen spores and in the pathogen infecting sunflower leaves and selected for functional analyses. We developed a new method for transient expression in sunflower plant leaves and showed for the first time subcellular localization of P. halstedii effectors fused to a fluorescent protein in sunflower leaf cells. Overexpression of the CRN and of 3 RXLR effectors induced hypersensitive-like cell death reactions in some sunflower near-isogenic lines resistant to pathotype 710 and not in susceptible corresponding lines, suggesting they could be involved in Pl loci-mediated resistances.
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Affiliation(s)
- Quentin Gascuel
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Luis Buendia
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Yann Pecrix
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Nicolas Blanchet
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
| | | | - Laurence Godiard
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de ToulouseCastanet Tolosan, France
- *Correspondence: Laurence Godiard,
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82
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Petre B, Lorrain C, Saunders DG, Win J, Sklenar J, Duplessis S, Kamoun S. Rust fungal effectors mimic host transit peptides to translocate into chloroplasts. Cell Microbiol 2015; 18:453-65. [DOI: 10.1111/cmi.12530] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 09/22/2015] [Accepted: 09/29/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory; Norwich Research Park; Norwich NR4 7UH UK
- INRA, UMR 1136 Interactions Arbres/Microorganismes; Centre INRA Nancy Lorraine; Champenoux 54280 France
- Université de Lorraine; UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy 54506 France
| | - Cécile Lorrain
- The Sainsbury Laboratory; Norwich Research Park; Norwich NR4 7UH UK
- INRA, UMR 1136 Interactions Arbres/Microorganismes; Centre INRA Nancy Lorraine; Champenoux 54280 France
- Université de Lorraine; UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy 54506 France
| | - Diane G.O. Saunders
- The Sainsbury Laboratory; Norwich Research Park; Norwich NR4 7UH UK
- The Genome Analysis Centre; Norwich Research Park; Norwich NR4 7UH UK
- The John Innes Centre; Norwich Research Park; Norwich NR4 7UH UK
| | - Joe Win
- The Sainsbury Laboratory; Norwich Research Park; Norwich NR4 7UH UK
| | - Jan Sklenar
- The Sainsbury Laboratory; Norwich Research Park; Norwich NR4 7UH UK
| | - Sébastien Duplessis
- INRA, UMR 1136 Interactions Arbres/Microorganismes; Centre INRA Nancy Lorraine; Champenoux 54280 France
- Université de Lorraine; UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies; Vandoeuvre-lès-Nancy 54506 France
| | - Sophien Kamoun
- The Sainsbury Laboratory; Norwich Research Park; Norwich NR4 7UH UK
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83
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Chaudhari P, Ahmed B, Joly DL, Germain H. Effector biology during biotrophic invasion of plant cells. Virulence 2015; 5:703-9. [PMID: 25513771 PMCID: PMC4189876 DOI: 10.4161/viru.29652] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Several obligate biotrophic phytopathogens, namely oomycetes and fungi, invade and feed on living plant cells through specialized structures known as haustoria. Deploying an arsenal of secreted proteins called effectors, these pathogens balance their parasitic propagation by subverting plant immunity without sacrificing host cells. Such secreted proteins, which are thought to be delivered by haustoria, conceivably reprogram host cells and instigate structural modifications, in addition to the modulation of various cellular processes. As effectors represent tools to assist disease resistance breeding, this short review provides a bird’s eye view on the relationship between the virulence function of effectors and their subcellular localization in host cells.
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Affiliation(s)
- Prateek Chaudhari
- a Groupe de Recherche en Biologie Végétale; Département de Chimie, Biochimie et Physique; Université du Québec à Trois-Rivières; Trois-Rivières, QC Canada
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84
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Fu L, Zhu C, Ding X, Yang X, Morris PF, Tyler BM, Zhang X. Characterization of Cell-Death-Inducing Members of the Pectate Lyase Gene Family in Phytophthora capsici and Their Contributions to Infection of Pepper. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:766-75. [PMID: 25775270 DOI: 10.1094/mpmi-11-14-0352-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Pectate lyases (PL) play a critical role in pectin degradation. PL have been extensively studied in major bacterial and fungal pathogens of a wide range of plant species. However, the contribution of PL to infection by oomycete pathogens remains largely unknown. Here, we cloned 22 full-length pectate lyase (PcPL) genes from a highly aggressive strain of Phytophthora capsici SD33. Of these, PVX agroinfiltration revealed that 12 PcPL genes were found to be highly induced during infection of pepper by SD33 but the induction level was twofold less in a mildly aggressive strain, YN07. The four genes with the highest transcript levels as measured by by quantitative reverse-transcription polymerase chain reaction (PcPL1, PcPL15, PcPL16, and PcPL20) also produced a severe cell death response following transient expression in pepper leaves but the other eight PcPL genes did not. Overexpression of these four genes increased the virulence of SD33 on pepper slightly, and increased it more substantially during infection of tobacco. Overexpression of the genes in YN07 restored its aggressiveness to near that of SD33. Gene silencing experiments with the 12 PcPL genes produced diverse patterns of silencing of PcPL genes, from which it could be inferred from regression analysis that PcPL1, PcPL16, and PcPL20 could account for nearly all of the contributions of the PcPL genes to virulence.
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Affiliation(s)
- Li Fu
- 1 Department of Plant Pathology, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong, 271018, China
| | - Chunyuan Zhu
- 1 Department of Plant Pathology, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong, 271018, China
| | - Xiaomeng Ding
- 1 Department of Plant Pathology, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong, 271018, China
| | - Xiaoyan Yang
- 1 Department of Plant Pathology, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong, 271018, China
| | - Paul F Morris
- 2 Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 U.S.A
| | - Brett M Tyler
- 3 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, 97331, U.S.A
| | - Xiuguo Zhang
- 1 Department of Plant Pathology, Shandong Agricultural University, No. 61, Daizong Street, Taian, Shandong, 271018, China
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85
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Zhang M, Ahmed Rajput N, Shen D, Sun P, Zeng W, Liu T, Juma Mafurah J, Dou D. A Phytophthora sojae cytoplasmic effector mediates disease resistance and abiotic stress tolerance in Nicotiana benthamiana. Sci Rep 2015; 5:10837. [PMID: 26039925 PMCID: PMC4454142 DOI: 10.1038/srep10837] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/05/2015] [Indexed: 11/29/2022] Open
Abstract
Each oomycete pathogen encodes a large number of effectors. Some effectors can be used in crop disease resistance breeding, such as to accelerate R gene cloning and utilisation. Since cytoplasmic effectors may cause acute physiological changes in host cells at very low concentrations, we assume that some of these effectors can serve as functional genes for transgenic plants. Here, we generated transgenic Nicotiana benthamiana plants that express a Phytophthora sojae CRN (crinkling and necrosis) effector, PsCRN115. We showed that its expression did not significantly affect the growth and development of N. benthamiana, but significantly improved disease resistance and tolerance to salt and drought stresses. Furthermore, we found that expression of heat-shock-protein and cytochrome-P450 encoding genes were unregulated in PsCRN115-transgenic N. benthamiana based on digital gene expression profiling analyses, suggesting the increased plant defence may be achieved by upregulation of these stress-related genes in transgenic plants. Thus, PsCRN115 may be used to improve plant tolerance to biotic and abiotic stresses.
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Affiliation(s)
- Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Nasir Ahmed Rajput
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- Department of Plant Pathology, Sindh Agriculture University, Tandojam, Pakistan
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Peng Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Wentao Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Tingli Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Joseph Juma Mafurah
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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86
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Petre B, Saunders DGO, Sklenar J, Lorrain C, Win J, Duplessis S, Kamoun S. Candidate Effector Proteins of the Rust Pathogen Melampsora larici-populina Target Diverse Plant Cell Compartments. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:689-700. [PMID: 25650830 DOI: 10.1094/mpmi-01-15-0003-r] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalog of secreted proteins, some of which have been considered candidate effectors. Unraveling how these proteins function in host cells is a key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localization and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria, and discrete cellular bodies. We also used coimmunoprecipitation (coIP) and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and TOPLESS-related protein 4 from poplar by in planta coIP. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.
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Affiliation(s)
- Benjamin Petre
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, U.K
- 2 INRA, UMR 1136 Interactions Arbres/Microorganismes, Centre INRA Nancy Lorraine, 54280 Champenoux, France
- 3 Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, 54506 Vandoeuvre-lès-Nancy, France
| | - Diane G O Saunders
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, U.K
- 4 The Genome Analysis Centre, Norwich Research Park, NR4 7UH Norwich, U.K
- 5 The John Innes Centre, Norwich Research Park, NR4 7UH Norwich, U.K
| | - Jan Sklenar
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, U.K
| | - Cécile Lorrain
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, U.K
- 2 INRA, UMR 1136 Interactions Arbres/Microorganismes, Centre INRA Nancy Lorraine, 54280 Champenoux, France
- 3 Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, 54506 Vandoeuvre-lès-Nancy, France
| | - Joe Win
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, U.K
| | - Sébastien Duplessis
- 2 INRA, UMR 1136 Interactions Arbres/Microorganismes, Centre INRA Nancy Lorraine, 54280 Champenoux, France
- 3 Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, 54506 Vandoeuvre-lès-Nancy, France
| | - Sophien Kamoun
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, U.K
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87
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Mafurah JJ, Ma H, Zhang M, Xu J, He F, Ye T, Shen D, Chen Y, Rajput NA, Dou D. A Virulence Essential CRN Effector of Phytophthora capsici Suppresses Host Defense and Induces Cell Death in Plant Nucleus. PLoS One 2015; 10:e0127965. [PMID: 26011314 PMCID: PMC4444017 DOI: 10.1371/journal.pone.0127965] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
Phytophthora capsici is a soil-borne plant pathogen with a wide range of hosts. The pathogen secretes a large array of effectors during infection of host plants, including Crinkler (CRN) effectors. However, it remains largely unknown on the roles of these effectors in virulence especially in P. capsici. In this study, we identified a cell death-inducing CRN effector PcCRN4 using agroinfiltration approach. Transient expression of PcCRN4 gene induced cell death in N. benthamiana, N. tabacum and Solanum lycopersicum. Overexpression of the gene in N. benthamiana enhanced susceptibility to P. capsici. Subcellular localization results showed that PcCRN4 localized to the plant nucleus, and the localization was required for both of its cell death-inducing activity and virulent function. Silencing PcCRN4 gene in P. capsici significantly reduced pathogen virulence. The expression of the pathogenesis-related gene PR1b in N. benthamiana was significantly induced when plants were inoculated with PcCRN4-silenced P. capsici transformant compared to the wilt-type. Callose deposits were also abundant at sites inoculated with PcCRN4-silenced transformant, indicating that silencing of PcCRN4 in P. capsici reduced the ability of the pathogen to suppress plant defenses. Transcriptions of cell death-related genes were affected when PcCRN4-silenced line were inoculated on Arabidopsis thaliana, suggesting that PcCRN4 may induce cell death by manipulating cell death-related genes. Overall, our results demonstrate that PcCRN4 is a virulence essential effector and it needs target to the plant nucleus to suppress plant immune responses.
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Affiliation(s)
- Joseph Juma Mafurah
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huifei Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng He
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingyue Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanyu Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nasir Ahmed Rajput
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
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Kamoun S, Furzer O, Jones JDG, Judelson HS, Ali GS, Dalio RJD, Roy SG, Schena L, Zambounis A, Panabières F, Cahill D, Ruocco M, Figueiredo A, Chen XR, Hulvey J, Stam R, Lamour K, Gijzen M, Tyler BM, Grünwald NJ, Mukhtar MS, Tomé DFA, Tör M, Van Den Ackerveken G, McDowell J, Daayf F, Fry WE, Lindqvist-Kreuze H, Meijer HJG, Petre B, Ristaino J, Yoshida K, Birch PRJ, Govers F. The Top 10 oomycete pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2015; 16:413-34. [PMID: 25178392 PMCID: PMC6638381 DOI: 10.1111/mpp.12190] [Citation(s) in RCA: 464] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.
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Affiliation(s)
- Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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89
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Gascuel Q, Martinez Y, Boniface MC, Vear F, Pichon M, Godiard L. The sunflower downy mildew pathogen Plasmopara halstedii. MOLECULAR PLANT PATHOLOGY 2015; 16:109-22. [PMID: 25476405 PMCID: PMC6638465 DOI: 10.1111/mpp.12164] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
UNLABELLED Downy mildew of sunflower is caused by Plasmopara halstedii (Farlow) Berlese & de Toni. Plasmopara halstedii is an obligate biotrophic oomycete pathogen that attacks annual Helianthus species and cultivated sunflower, Helianthus annuus. Depending on the sunflower developmental stage at which infection occurs, the characteristic symptoms range from young seedling death, plant dwarfing, leaf bleaching and sporulation to the production of infertile flowers. Downy mildew attacks can have a great economic impact on sunflower crops, and several Pl resistance genes are present in cultivars to protect them against the disease. Nevertheless, some of these resistances have been overcome by the occurrence of novel isolates of the pathogen showing increased virulence. A better characterization of P. halstedii infection and dissemination mechanisms, and the identification of the molecular basis of the interaction with sunflower, is a prerequisite to efficiently fight this pathogen. This review summarizes what is currently known about P. halstedii, provides new insights into its infection cycle on resistant and susceptible sunflower lines using scanning electron and light microscopy imaging, and sheds light on the pathogenicity factors of P. halstedii obtained from recent molecular data. TAXONOMY Kingdom Stramenopila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Plasmopara; Species Plasmopara halstedii. DISEASE SYMPTOMS Sunflower seedling damping off, dwarfing of the plant, bleaching of leaves, starting from veins, and visible white sporulation, initially on the lower side of cotyledons and leaves. Plasmopara halstedii infection may severely impact sunflower seed yield. INFECTION PROCESS In spring, germination of overwintered sexual oospores leads to sunflower root infection. Intercellular hyphae are responsible for systemic plant colonization and the induction of disease symptoms. Under humid and fresh conditions, dissemination structures are produced by the pathogen on all plant organs to release asexual zoosporangia. These zoosporangia play an important role in pathogen dissemination, as they release motile zoospores that are responsible for leaf infections on neighbouring plants. DISEASE CONTROL Disease control is obtained by both chemical seed treatment (mefenoxam) and the deployment of dominant major resistance genes, denoted Pl. However, the pathogen has developed fungicide resistance and has overcome some plant resistance genes. Research for more sustainable strategies based on the identification of the molecular basis of the interaction are in progress. USEFUL WEBSITES http://www.heliagene.org/HP, http://lipm-helianthus.toulouse.inra.fr/dokuwiki/doku.php?id=start, https://www.heliagene.org/PlasmoparaSpecies (soon available).
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Affiliation(s)
- Quentin Gascuel
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
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90
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Analysis of putative apoplastic effectors from the nematode, Globodera rostochiensis, and identification of an expansin-like protein that can induce and suppress host defenses. PLoS One 2015; 10:e0115042. [PMID: 25606855 PMCID: PMC4301866 DOI: 10.1371/journal.pone.0115042] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/18/2014] [Indexed: 12/01/2022] Open
Abstract
The potato cyst nematode, Globodera rostochiensis, is an important pest of potato. Like other pathogens, plant parasitic nematodes are presumed to employ effector proteins, secreted into the apoplast as well as the host cytoplasm, to alter plant cellular functions and successfully infect their hosts. We have generated a library of ORFs encoding putative G. rostochiensis putative apoplastic effectors in vectors for expression in planta. These clones were assessed for morphological and developmental effects on plants as well as their ability to induce or suppress plant defenses. Several CLAVATA3/ESR-like proteins induced developmental phenotypes, whereas predicted cell wall-modifying proteins induced necrosis and chlorosis, consistent with roles in cell fate alteration and tissue invasion, respectively. When directed to the apoplast with a signal peptide, two effectors, an ubiquitin extension protein (GrUBCEP12) and an expansin-like protein (GrEXPB2), suppressed defense responses including NB-LRR signaling induced in the cytoplasm. GrEXPB2 also elicited defense response in species- and sequence-specific manner. Our results are consistent with the scenario whereby potato cyst nematodes secrete effectors that modulate host cell fate and metabolism as well as modifying host cell walls. Furthermore, we show a novel role for an apoplastic expansin-like protein in suppressing intra-cellular defense responses.
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91
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Zhang M, Li Q, Liu T, Liu L, Shen D, Zhu Y, Liu P, Zhou JM, Dou D. Two cytoplasmic effectors of Phytophthora sojae regulate plant cell death via interactions with plant catalases. PLANT PHYSIOLOGY 2015; 167:164-75. [PMID: 25424308 PMCID: PMC4281015 DOI: 10.1104/pp.114.252437] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 11/23/2014] [Indexed: 05/18/2023]
Abstract
Plant pathogenic oomycetes, such as Phytophthora sojae, secrete an arsenal of host cytoplasmic effectors to promote infection. We have shown previously that P. sojae PsCRN63 (for crinkling- and necrosis-inducing proteins) induces programmed cell death (PCD) while PsCRN115 blocks PCD in planta; however, they are jointly required for full pathogenesis. Here, we find that PsCRN63 alone or PsCRN63 and PsCRN115 together might suppress the immune responses of Nicotiana benthamiana and demonstrate that these two cytoplasmic effectors interact with catalases from N. benthamiana and soybean (Glycine max). Transient expression of PsCRN63 increases hydrogen peroxide (H(2)O(2)) accumulation, whereas PsCRN115 suppresses this process. Transient overexpression of NbCAT1 (for N. benthamiana CATALASE1) or GmCAT1 specifically alleviates PsCRN63-induced PCD. Suppression of the PsCRN63-induced PCD by PsCRN115 is compromised when catalases are silenced in N. benthamiana. Interestingly, the NbCAT1 is recruited into the plant nucleus in the presence of PsCRN63 or PsCRN115; NbCAT1 and GmCAT1 are destabilized when PsCRN63 is coexpressed, and PsCRN115 inhibits the processes. Thus, PsCRN63/115 manipulates plant PCD through interfering with catalases and perturbing H(2)O(2) homeostasis. Furthermore, silencing of catalase genes enhances susceptibility to Phytophthora capsici, indicating that catalases are essential for plant resistance. Taken together, we suggest that P. sojae secretes these two effectors to regulate plant PCD and H(2)O(2) homeostasis through direct interaction with catalases and, therefore, overcome host immune responses.
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Affiliation(s)
- Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Qi Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Tingli Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Li Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Ye Zhu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Peihan Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Jian-Min Zhou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China (M.Z., Q.L., T.L., L.L., D.S., Y.Z., P.L., D.D.); andCenter for Genome Biology and State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (Q.L., J.-M.Z.)
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92
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Hadwiger LA. Anatomy of a nonhost disease resistance response of pea to Fusarium solani: PR gene elicitation via DNase, chitosan and chromatin alterations. FRONTIERS IN PLANT SCIENCE 2015; 6:373. [PMID: 26124762 PMCID: PMC4464173 DOI: 10.3389/fpls.2015.00373] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/11/2015] [Indexed: 05/18/2023]
Abstract
Of the multiplicity of plant pathogens in nature, only a few are virulent on a given plant species. Conversely, plants develop a rapid "nonhost" resistance response to the majority of the pathogens. The anatomy of the nonhost resistance of pea endocarp tissue against a pathogen of bean, Fusarium solani f.sp. phaseoli (Fsph) and the susceptibility of pea to F. solani f sp. pisi (Fspi) has been described cytologically, biochemically and molecular-biologically. Cytological changes have been followed by electron microscope and stain differentiation under white and UV light. The induction of changes in transcription, protein synthesis, expression of pathogenesis-related (PR) genes, and increases in metabolic pathways culminating in low molecular weight, antifungal compounds are described biochemically. Molecular changes initiated by fungal signals to host organelles, primarily to chromatin within host nuclei, are identified according to source of the signal and the mechanisms utilized in activating defense genes. The functions of some PR genes are defined. A hypothesis based on this data is developed to explain both why fungal growth is suppressed in nonhost resistance and why growth can continue in a susceptible reaction.
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Affiliation(s)
- Lee A. Hadwiger
- *Correspondence: Lee A. Hadwiger, Department of Plant Pathology, Washington State University, 100 Dairy Road, Pullman, WA 99163-6430, USA
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Chen XR, Zhang BY, Xing YP, Li QY, Li YP, Tong YH, Xu JY. Transcriptomic analysis of the phytopathogenic oomycete Phytophthora cactorum provides insights into infection-related effectors. BMC Genomics 2014; 15:980. [PMID: 25406848 PMCID: PMC4289400 DOI: 10.1186/1471-2164-15-980] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022] Open
Abstract
Background Phytophthora cactorum, a hemibiotrophic oomycete pathogen, can cause destructive diseases on numerous crops worldwide, leading to essential economic losses every year. However, little has been known about its molecular pathogenicity mechanisms. To gain insight into its repertoire of effectors, the P. cactorum transcriptome was investigated using Illumina RNA-seq. Results We first demonstrated an in vitro inoculation method that can be used to mimic natural cyst germination on host plants. Over 28 million cDNA reads were obtained for five life cycle stages (mycelium, sporangium, zoospore, cyst and germinating cyst) and de novo assembled into 21,662 unique genes. By comparisons with 11 public databases, 88.99% of the unique genes were annotated, including 15,845 mapped to the gene models of the annotated relative Phytophthora infestans. Using TribeMCL, 5,538 gene families conserved across P. cactorum and other three completely sequenced Phytophthora pathogen species were determined. In silico analyses revealed that 620 P. cactorum effector homologues including 94 RXLR effector candidates matched known or putative virulence genes in other oomycetes. About half of the RXLR effector candidates were predicted to share a conserved structure unit, termed the WY-domain fold. A subset of the effector genes were checked and validated by PCR amplification. Transcriptional experiments indicated that effector genes were differentially expressed during the life cycle and host infection stages of P. cactorum. Ectopic expression in Nicotiana benthamiana revealed that RXLR, elicitin and NLP effectors can trigger plant cell death. These effectors are highly conserved across oomycete species. Single nucleotide polymorphisms for RXLR effectors were detected in a collection of P. cactorum isolates from different countries and hosts. Conclusions This study demonstrates the comprehensive sequencing, de novo assembly, and analyses of the transcriptome of P. cactorum life cycle stages. In the absence of genome sequence, transcriptome data is important for infection-related gene discovery in P. cactorum, as demonstrated here for the effector genes. The first look at the transcriptome and effector arsenal of P. cactorum provides valuable data to elucidate the pathogenicity basis of this broad-host-range pathogen. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-980) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Ren Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
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94
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Eves-van den Akker S, Lilley CJ, Jones JT, Urwin PE. Identification and characterisation of a hyper-variable apoplastic effector gene family of the potato cyst nematodes. PLoS Pathog 2014; 10:e1004391. [PMID: 25255291 PMCID: PMC4177990 DOI: 10.1371/journal.ppat.1004391] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/11/2014] [Indexed: 11/18/2022] Open
Abstract
Sedentary endoparasitic nematodes are obligate biotrophs that modify host root tissues, using a suite of effector proteins to create and maintain a feeding site that is their sole source of nutrition. Using assumptions about the characteristics of genes involved in plant-nematode biotrophic interactions to inform the identification strategy, we provide a description and characterisation of a novel group of hyper-variable extracellular effectors termed HYP, from the potato cyst nematode Globodera pallida. HYP effectors comprise a large gene family, with a modular structure, and have unparalleled diversity between individuals of the same population: no two nematodes tested had the same genetic complement of HYP effectors. Individuals vary in the number, size, and type of effector subfamilies. HYP effectors are expressed throughout the biotrophic stages in large secretory cells associated with the amphids of parasitic stage nematodes as confirmed by in situ hybridisation. The encoded proteins are secreted into the host roots where they are detectable by immunochemistry in the apoplasm, between the anterior end of the nematode and the feeding site. We have identified HYP effectors in three genera of plant parasitic nematodes capable of infecting a broad range of mono- and dicotyledon crop species. In planta RNAi targeted to all members of the effector family causes a reduction in successful parasitism. Sedentary plant parasitic nematodes are pathogens that invade plant roots and establish a feeding site. The feeding site is a specialist structure used by the nematode to support its development within the plant. The nematode secretes a suite of proteins, termed ‘effector proteins’ that are responsible for initiating and maintaining the feeding site. The nematode must also evade recognition by the plant defence systems throughout its lifecycle that can last for many weeks. We describe a diverse and variable effector gene family (HYP), the products of which are secreted into the plant by the nematode and are required for successful infection. The variability and modular structure of this gene family can lead to the production of a large array of effector proteins. This diversity may allow the nematodes to combat any resistance mechanisms developed by the plant. Each nematode tested within a population is genetically unique in terms of these effector genes. We found huge variation in the number, size and type of HYP effectors at the level of the individual. This may explain some of the difficulties in breeding nematode resistant plants and has profound implications for those working with other plant pathogens.
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Affiliation(s)
- Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | | | - John T. Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Peter E. Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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95
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Transcriptome analysis of the entomopathogenic oomycete Lagenidium giganteum reveals putative virulence factors. Appl Environ Microbiol 2014; 80:6427-36. [PMID: 25107973 DOI: 10.1128/aem.02060-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A combination of 454 pyrosequencing and Sanger sequencing was used to sample and characterize the transcriptome of the entomopathogenic oomycete Lagenidium giganteum. More than 50,000 high-throughput reads were annotated through homology searches. Several selected reads served as seeds for the amplification and sequencing of full-length transcripts. Phylogenetic analyses inferred from full-length cellulose synthase alignments revealed that L giganteum is nested within the peronosporalean galaxy and as such appears to have evolved from a phytopathogenic ancestor. In agreement with the phylogeny reconstructions, full-length L. giganteum oomycete effector orthologs, corresponding to the cellulose-binding elicitor lectin (CBEL), crinkler (CRN), and elicitin proteins, were characterized by domain organizations similar to those of pathogenicity factors of plant-pathogenic oomycetes. Importantly, the L. giganteum effectors provide a basis for detailing the roles of canonical CRN, CBEL, and elicitin proteins in the infectious process of an oomycete known principally as an animal pathogen. Finally, phylogenetic analyses and genome mining identified members of glycoside hydrolase family 5 subfamily 27 (GH5_27) as putative virulence factors active on the host insect cuticle, based in part on the fact that GH5_27 genes are shared by entomopathogenic oomycetes and fungi but are underrepresented in nonentomopathogenic genomes. The genomic resources gathered from the L. giganteum transcriptome analysis strongly suggest that filamentous entomopathogens (oomycetes and fungi) exhibit convergent evolution: they have evolved independently from plant-associated microbes, have retained genes indicative of plant associations, and may share similar cores of virulence factors, such as GH5_27 enzymes, that are absent from the genomes of their plant-pathogenic relatives.
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96
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Meijer HJG, Mancuso FM, Espadas G, Seidl MF, Chiva C, Govers F, Sabidó E. Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans. Mol Cell Proteomics 2014; 13:2101-13. [PMID: 24872595 PMCID: PMC4125740 DOI: 10.1074/mcp.m113.035873] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 05/09/2014] [Indexed: 11/06/2022] Open
Abstract
Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes, and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focused on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyze P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses, and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.
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Affiliation(s)
- Harold J G Meijer
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Francesco M Mancuso
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Guadalupe Espadas
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael F Seidl
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; ‖Centre for BioSystems Genomics, Droevendaalsesteeg, 16708 PB Wageningen, The Netherlands
| | - Cristina Chiva
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francine Govers
- From the ‡Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; ‖Centre for BioSystems Genomics, Droevendaalsesteeg, 16708 PB Wageningen, The Netherlands
| | - Eduard Sabidó
- §Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain; ¶Proteomics Unit, Universitat Pompeu Fabra (UPF), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain;
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Bozkurt TO, Richardson A, Dagdas YF, Mongrand S, Kamoun S, Raffaele S. The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans. PLANT PHYSIOLOGY 2014; 165:1005-1018. [PMID: 24808104 PMCID: PMC4081318 DOI: 10.1104/pp.114.235804] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Filamentous pathogens such as the oomycete Phytophthora infestans infect plants by developing specialized structures termed haustoria inside the host cells. Haustoria are thought to enable the secretion of effector proteins into the plant cells. Haustorium biogenesis, therefore, is critical for pathogen accommodation in the host tissue. Haustoria are enveloped by a specialized host-derived membrane, the extrahaustorial membrane (EHM), which is distinct from the plant plasma membrane. The mechanisms underlying the biogenesis of the EHM are unknown. Remarkably, several plasma membrane-localized proteins are excluded from the EHM, but the remorin REM1.3 accumulates around P. infestans haustoria. Here, we used overexpression, colocalization with reporter proteins, and superresolution microscopy in cells infected by P. infestans to reveal discrete EHM domains labeled by REM1.3 and the P. infestans effector AVRblb2. Moreover, SYNAPTOTAGMIN1, another previously identified perihaustorial protein, localized to subdomains that are mainly not labeled by REM1.3 and AVRblb2. Functional characterization of REM1.3 revealed that it is a susceptibility factor that promotes infection by P. infestans. This activity, and REM1.3 recruitment to the EHM, require the REM1.3 membrane-binding domain. Our results implicate REM1.3 membrane microdomains in plant susceptibility to an oomycete pathogen.
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Affiliation(s)
- Tolga O Bozkurt
- Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom (T.O.B., A.R., Y.F.D., S.K., S.R.);Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom (T.O.B.);John Innes Centre, Norwich NR4 7UH, United Kingdom (A.R.);Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique-Université Bordeaux Segalen-Institut National de la Recherche Agronomique, F-33883 Villenave d'Ornon cedex, France (S.M.); andLaboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441 Institut National de la Recherche Agronomique-Unité Mixte de Recherche 2594 Centre National de la Recherche Scientifique, F-31326 Castanet-Tolosan, France (S.R.)
| | - Annis Richardson
- Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom (T.O.B., A.R., Y.F.D., S.K., S.R.);Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom (T.O.B.);John Innes Centre, Norwich NR4 7UH, United Kingdom (A.R.);Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique-Université Bordeaux Segalen-Institut National de la Recherche Agronomique, F-33883 Villenave d'Ornon cedex, France (S.M.); andLaboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441 Institut National de la Recherche Agronomique-Unité Mixte de Recherche 2594 Centre National de la Recherche Scientifique, F-31326 Castanet-Tolosan, France (S.R.)
| | - Yasin F Dagdas
- Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom (T.O.B., A.R., Y.F.D., S.K., S.R.);Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom (T.O.B.);John Innes Centre, Norwich NR4 7UH, United Kingdom (A.R.);Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique-Université Bordeaux Segalen-Institut National de la Recherche Agronomique, F-33883 Villenave d'Ornon cedex, France (S.M.); andLaboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441 Institut National de la Recherche Agronomique-Unité Mixte de Recherche 2594 Centre National de la Recherche Scientifique, F-31326 Castanet-Tolosan, France (S.R.)
| | - Sébastien Mongrand
- Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom (T.O.B., A.R., Y.F.D., S.K., S.R.);Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom (T.O.B.);John Innes Centre, Norwich NR4 7UH, United Kingdom (A.R.);Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique-Université Bordeaux Segalen-Institut National de la Recherche Agronomique, F-33883 Villenave d'Ornon cedex, France (S.M.); andLaboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441 Institut National de la Recherche Agronomique-Unité Mixte de Recherche 2594 Centre National de la Recherche Scientifique, F-31326 Castanet-Tolosan, France (S.R.)
| | - Sophien Kamoun
- Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom (T.O.B., A.R., Y.F.D., S.K., S.R.);Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom (T.O.B.);John Innes Centre, Norwich NR4 7UH, United Kingdom (A.R.);Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique-Université Bordeaux Segalen-Institut National de la Recherche Agronomique, F-33883 Villenave d'Ornon cedex, France (S.M.); andLaboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441 Institut National de la Recherche Agronomique-Unité Mixte de Recherche 2594 Centre National de la Recherche Scientifique, F-31326 Castanet-Tolosan, France (S.R.)
| | - Sylvain Raffaele
- Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom (T.O.B., A.R., Y.F.D., S.K., S.R.);Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom (T.O.B.);John Innes Centre, Norwich NR4 7UH, United Kingdom (A.R.);Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique-Université Bordeaux Segalen-Institut National de la Recherche Agronomique, F-33883 Villenave d'Ornon cedex, France (S.M.); andLaboratoire des Interactions Plantes-Microorganismes, Unité Mixte de Recherche 441 Institut National de la Recherche Agronomique-Unité Mixte de Recherche 2594 Centre National de la Recherche Scientifique, F-31326 Castanet-Tolosan, France (S.R.)
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98
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Rajput NA, Zhang M, Ru Y, Liu T, Xu J, Liu L, Mafurah JJ, Dou D. Phytophthora sojae effector PsCRN70 suppresses plant defenses in Nicotiana benthamiana. PLoS One 2014; 9:e98114. [PMID: 24858571 PMCID: PMC4032284 DOI: 10.1371/journal.pone.0098114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 04/28/2014] [Indexed: 11/19/2022] Open
Abstract
Phytophthora sojae, an oomycete pathogen, produces a large number of effector proteins that enter into host cells. The Crinklers (Crinkling and Necrosis, CRN) are cytoplasmic effectors that are conserved in oomycete pathogens and their encoding genes are highly expressed at the infective stages in P. sojae. However, their roles in pathogenesis are largely unknown. Here, we functionally characterized an effector PsCRN70 by transiently and stably overexpressing it in Nicotiana benthamiana. We demonstrated that PsCRN70 was localized to the plant cell nucleus and suppressed cell death elicited by all the tested cell death-inducing proteins, including BAX, PsAvh241, PsCRN63, PsojNIP and R3a/Avr3a. Overexpression of the PsCRN70 gene in N. benthamiana enhanced susceptibility to P. parasitica. The H2O2 accumulation in the PsCRN70-transgenic plants was reduced compared to the GFP-lines. The transcriptional levels of the defense-associated genes, including PR1b, PR2b, ERF1 and LOX, were also down-regulated in the PsCRN70-transgenic lines. Our results suggest that PsCRN70 may function as a universal suppressor of the cell death induced by many elicitors, the host H2O2 accumulation and the expression of defense-associated genes, and therefore promotes pathogen infection.
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Affiliation(s)
- Nasir Ahmed Rajput
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yanyan Ru
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Tingli Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jing Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Li Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Joseph Juma Mafurah
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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99
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Rodriguez PA, Stam R, Warbroek T, Bos JIB. Mp10 and Mp42 from the aphid species Myzus persicae trigger plant defenses in Nicotiana benthamiana through different activities. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:30-9. [PMID: 24006884 DOI: 10.1094/mpmi-05-13-0156-r] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Aphids are phloem-feeding insects that, like other plant parasites, deliver effectors inside their host to manipulate host responses. The Myzus persicae (green peach aphid) candidate effectors Mp10 and Mp42 were previously found to reduce aphid fecundity upon intracellular transient overexpression in Nicotiana benthamiana. We performed functional analyses of these proteins to investigate whether they activate defenses through similar activities. We employed a range of functional characterization experiments based on intracellular transient overexpression in N. benthamiana to determine the subcellular localization of Mp10 and Mp42 and investigate their role in activating plant defense signaling. Mp10 and Mp42 showed distinct subcellular localization in planta, suggesting that they target different host compartments. Also, Mp10 reduced the levels of Agrobacterium-mediated overexpression of proteins. This reduction was not due to an effect on Agrobacterium viability. Transient overexpression of Mp10 but not Mp42 activated jasmonic acid and salicylic acid signaling pathways and decreased susceptibility to the hemibiotrophic plant pathogen Phytophthora capsici. We found that two candidate effectors from the broad-host-range aphid M. persicae can trigger aphid defenses through different mechanisms. Importantly, we found that some (candidate) effectors such as Mp10 interfere with Agrobacterium-based overexpression assays, an important tool to study effector activity and function.
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100
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Stam R, Mantelin S, McLellan H, Thilliez G. The role of effectors in nonhost resistance to filamentous plant pathogens. FRONTIERS IN PLANT SCIENCE 2014; 5:582. [PMID: 25426123 PMCID: PMC4224059 DOI: 10.3389/fpls.2014.00582] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/08/2014] [Indexed: 05/18/2023]
Abstract
In nature, most plants are resistant to a wide range of phytopathogens. However, mechanisms contributing to this so-called nonhost resistance (NHR) are poorly understood. Besides constitutive defenses, plants have developed two layers of inducible defense systems. Plant innate immunity relies on recognition of conserved pathogen-associated molecular patterns (PAMPs). In compatible interactions, pathogenicity effector molecules secreted by the invader can suppress host defense responses and facilitate the infection process. Additionally, plants have evolved pathogen-specific resistance mechanisms based on recognition of these effectors, which causes secondary defense responses. The current effector-driven hypothesis is that NHR in plants that are distantly related to the host plant is triggered by PAMP recognition that cannot be efficiently suppressed by the pathogen, whereas in more closely related species, nonhost recognition of effectors would play a crucial role. In this review we give an overview of current knowledge of the role of effector molecules in host and NHR and place these findings in the context of the model. We focus on examples from filamentous pathogens (fungi and oomycetes), discuss their implications for the field of plant-pathogen interactions and relevance in plant breeding strategies for development of durable resistance in crops.
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Affiliation(s)
- Remco Stam
- Division of Plant Sciences, University of Dundee – The James Hutton InstituteDundee, UK
- *Correspondence: Remco Stam, Division of Plant Sciences, University of Dundee – The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK e-mail:
| | - Sophie Mantelin
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Hazel McLellan
- Division of Plant Sciences, University of Dundee – The James Hutton InstituteDundee, UK
| | - Gaëtan Thilliez
- Division of Plant Sciences, University of Dundee – The James Hutton InstituteDundee, UK
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
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