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Louet C, Duplessis S, Frey P, Petre B. A survey of highly cited studies on plant pathogen effectors during the last two decades (2000-2020). FRONTIERS IN PLANT SCIENCE 2022; 13:920281. [PMID: 36544874 PMCID: PMC9762492 DOI: 10.3389/fpls.2022.920281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Plant effector biology is a research area that describes how plant-associated organisms modulate host structures and function to promote colonization by using small molecules (effectors). In this article, we analyzed 249 highly cited publications focused on plant pathogen effectors (i.e., Highly Influential studies on plant Pathogen Effectors; thereafter HIPEs) published between 2000 and 2020. This analysis identifies countries, organizations, and journals that contributed HIPEs, and reveals the evolution of research trends, model molecules, and model organisms over the last two decades. We notably show an increasing proportion of studies focused on effectors of biotrophic and hemibiotrophic fungi upon time. Our snapshot of the highly influential plant effector biology papers may help new comers in the field to gain an analytical understanding of this research area.
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Gu B, Shao G, Gao W, Miao J, Wang Q, Liu X, Tyler BM. Transcriptional Variability Associated With CRISPR-Mediated Gene Replacements at the Phytophthora sojae Avr1b-1 Locus. Front Microbiol 2021; 12:645331. [PMID: 33815332 PMCID: PMC8012851 DOI: 10.3389/fmicb.2021.645331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
Transcriptional plasticity enables oomycetes to rapidly adapt to environmental challenges including emerging host resistance. For example, the soybean pathogen Phytophthora sojae can overcome resistance conferred by the host resistance gene Rps1b through natural silencing of its corresponding effector gene, Avr1b-1. With the Phytophthora CRISPR/Cas9 genome editing system, it is possible to generate site-specific knock-out (KO) and knock-in (KI) mutants and to investigate the biological functions of target genes. In this study, the Avr1b-1 gene was deleted from the P. sojae genome using a homology-directed recombination strategy that replaced Avr1b-1 with a gene encoding the fluorescent protein mCherry. As expected, all selected KO transformants gained virulence on Rps1b plants, while infection of plants lacking Rps1b was not compromised. When a sgRNA-resistant version of Avr1b-1 was reintroduced into the Avr1b-1 locus of an Avr1b KO transformant, KI transformants with a well-transcribed Avr1b-1 gene were unable to infect Rps1b-containing soybeans. However, loss of expression of the incoming Avr1b-1 gene was frequently observed in KI transformants, which resulted in these transformants readily infecting Rps1b soybeans. A similar variability in the expression levels of the incoming gene was observed with AVI- or mCherry-tagged Avr1b-1 constructs. Our results suggest that Avr1b-1 may be unusually susceptible to transcriptional variation.
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Affiliation(s)
- Biao Gu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Guangda Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wenxin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Brett M Tyler
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
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Tomczynska I, Stumpe M, Doan TG, Mauch F. A Phytophthora effector protein promotes symplastic cell-to-cell trafficking by physical interaction with plasmodesmata-localised callose synthases. THE NEW PHYTOLOGIST 2020; 227:1467-1478. [PMID: 32396661 DOI: 10.1111/nph.16653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/20/2020] [Indexed: 05/03/2023]
Abstract
Pathogen effectors act as disease promoting factors that target specific host proteins with roles in plant immunity. Here, we investigated the function of the RxLR3 effector of the plant-pathogen Phytophthora brassicae. Arabidopsis plants expressing a FLAG-RxLR3 fusion protein were used for co-immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify host targets of RxLR3. Fluorescently labelled fusion proteins were used for analysis of subcellular localisation and function of RxLR3. Three closely related members of the callose synthase family, CalS1, CalS2 and CalS3, were identified as targets of RxLR3. RxLR3 co-localised with the plasmodesmal marker protein PDLP5 (PLASMODESMATA-LOCALISED PROTEIN 5) and with plasmodesmata-associated deposits of the β-1,3-glucan polymer callose. In line with a function as an inhibitor of plasmodesmal callose synthases (CalS) enzymes, callose depositions were reduced and cell-to-cell trafficking was promoted in the presence of RxLR3. Plasmodesmal callose deposition in response to infection was compared with wild-type suppressed in RxLR3-expressing Arabidopsis lines. Our results implied a virulence function of the RxLR3 effector as a positive regulator of plasmodesmata transport and provided evidence for competition between P. brassicae and Arabidopsis for control of cell-to-cell trafficking.
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Affiliation(s)
- Iga Tomczynska
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
| | - Tu Giang Doan
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
| | - Felix Mauch
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland
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Thines M, Sharma R, Rodenburg SYA, Gogleva A, Judelson HS, Xia X, van den Hoogen J, Kitner M, Klein J, Neilen M, de Ridder D, Seidl MF, van den Ackerveken G, Govers F, Schornack S, Studholme DJ. The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:742-753. [PMID: 32237964 DOI: 10.1094/mpmi-07-19-0211-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here, we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was around 35.4 Mbp in length, with an N50 scaffold length of around 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of around 40.1 kbp. From the repeat-masked genome, 9,049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16% of the genome consists of repetitive sequences, and, based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of P. belbahrii. P. belbahrii has undergone a high degree of convergent evolution with other obligate parasitic pathogen groups, reflecting its obligate biotrophic lifestyle. Features of its secretome, signaling networks, and promoters are presented, and some patterns are hypothesized to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
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Affiliation(s)
- Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Rahul Sharma
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Anna Gogleva
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521 U.S.A
| | - Xiaojuan Xia
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manon Neilen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guido van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
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Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. Arms race: diverse effector proteins with conserved motifs. PLANT SIGNALING & BEHAVIOR 2019; 14:1557008. [PMID: 30621489 PMCID: PMC6351098 DOI: 10.1080/15592324.2018.1557008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.
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Affiliation(s)
- Liping Liu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou 434025, China; Chu Wu College of Horticulture & Gardening, Yangtze University, Jingzhou 434025, China
| | - Chu Wu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
- Institute of Plant Ecology and Environmental Restoration, Yangtze University, Jingzhou, China
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Deb D, Mackey D, Opiyo SO, McDowell JM. Application of alignment-free bioinformatics methods to identify an oomycete protein with structural and functional similarity to the bacterial AvrE effector protein. PLoS One 2018; 13:e0195559. [PMID: 29641586 PMCID: PMC5895030 DOI: 10.1371/journal.pone.0195559] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 11/23/2022] Open
Abstract
Diverse plant pathogens export effector proteins to reprogram host cells. One of the most challenging goals in the molecular plant-microbe field is to functionally characterize the complex repertoires of effectors secreted by these pathogens. For bacterial pathogens, the predominant class of effectors is delivered to host cells by Type III secretion. For oomycetes, the predominant class of effectors is defined by a signal peptide that mediates secretion from the oomycete and a conserved RxLR motif. Downy mildew pathogens and Phytophthora species maintain hundreds of candidate RxLR effector genes in their genomes. Although no primary sequence similarity is evident between bacterial Type III effectors (T3Es) and oomycete RXLR effectors, some bacterial and oomycete effectors have convergently evolved to target the same host proteins. Such effectors might have evolved domains that are functionally similar but sequence-unrelated. We reasoned that alignment-free bioinformatics approaches could be useful to identify structural similarities between bacterial and oomycete effectors. To test this approach, we used partial least squares regression, alignment-free bioinformatics methods to identify effector proteins from the genome of the oomycete Hyaloperonospora arabidopsidis that are similar to the well-studied AvrE1 effector from Pseudomonas syringae. This approach identified five RxLR proteins with putative structural similarity to AvrE1. We focused on one, HaRxL23, because it is an experimentally validated effector and it is conserved between distantly related oomycetes. Several experiments indicate that HaRxL23 is functionally similar to AvrE1, including the ability to partially rescue an AvrE1 loss-of-function mutant. This study provides an example of how an alignment-free bioinformatics approach can identify functionally similar effector proteins in the absence of primary sequence similarity. This approach could be useful to identify effectors that have convergently evolved regardless of whether the shared host target is known.
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Affiliation(s)
- Devdutta Deb
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - David Mackey
- Departments of Horticulture and Crop Science and Molecular Genetics, Ohio State University, Columbus, Ohio, United States of America
| | - Stephen O. Opiyo
- Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (SOO); (JMM)
| | - John M. McDowell
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail: (SOO); (JMM)
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7
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Woods-Tör A, Studholme DJ, Cevik V, Telli O, Holub EB, Tör M. A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:265. [PMID: 29545818 PMCID: PMC5838922 DOI: 10.3389/fpls.2018.00265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/14/2018] [Indexed: 05/23/2023]
Abstract
The pathosystem of Arabidopsis thaliana and diploid biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) has been a model for investigating the molecular basis of Flor's gene-for-gene hypothesis. The isolates Hpa-Noks1 and Hpa-Cala2 are virulent on Arabidopsis accession RMX-A02 whilst an F1 generated from a cross between these two isolates was avirulent. The F2 progeny segregated 3,1 (avirulent, virulent), indicating a single major effect AVR locus in this pathogen. SNP-based linkage mapping confirmed a single AVR locus within a 14 kb map interval containing two genes encoding putative effectors. The Hpa-Cala2 allele of one gene, designated H. arabidopsidiscryptic1 (HAC1), encodes a protein with a signal peptide and an RxLR/dEER motif, and triggers a defense response in RMX-A02. The second gene is heterozygous in Hpa-Cala2. One allele, designated Suppressor ofHAC1Cala2 (S-HAC1Cala2 ) encodes a protein with a signal peptide and a dKEE motif with no RxLR motif; the other allele (s-hac1Cala2 ) encodes a protein with a signal peptide, a dEEE motif and is divergent in sequence from the S-HAC1Cala2 allele. In selfed progeny from Hpa-Cala2, dominant S-HAC1Cala2 allele carrying progeny correlates with virulence in RMX-A02, whereas homozygous recessive s-hac1Cala2 carrying progeny were avirulent. Genetic investigations suggested other heterozygous suppressor loci might exist in the Hpa-Cala2 genome.
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Affiliation(s)
- Alison Woods-Tör
- Institute of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - David J. Studholme
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Volkan Cevik
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Osman Telli
- Institute of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Eric B. Holub
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Mahmut Tör
- Institute of Science and the Environment, University of Worcester, Worcester, United Kingdom
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Bournaud C, Gillet FX, Murad AM, Bresso E, Albuquerque EVS, Grossi-de-Sá MF. Meloidogyne incognita PASSE-MURAILLE (MiPM) Gene Encodes a Cell-Penetrating Protein That Interacts With the CSN5 Subunit of the COP9 Signalosome. FRONTIERS IN PLANT SCIENCE 2018; 9:904. [PMID: 29997646 PMCID: PMC6029430 DOI: 10.3389/fpls.2018.00904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/07/2018] [Indexed: 05/11/2023]
Abstract
The pathogenicity of phytonematodes relies on secreted virulence factors to rewire host cellular pathways for the benefits of the nematode. In the root-knot nematode (RKN) Meloidogyne incognita, thousands of predicted secreted proteins have been identified and are expected to interact with host proteins at different developmental stages of the parasite. Identifying the host targets will provide compelling evidence about the biological significance and molecular function of the predicted proteins. Here, we have focused on the hub protein CSN5, the fifth subunit of the pleiotropic and eukaryotic conserved COP9 signalosome (CSN), which is a regulatory component of the ubiquitin/proteasome system. We used affinity purification-mass spectrometry (AP-MS) to generate the interaction network of CSN5 in M. incognita-infected roots. We identified the complete CSN complex and other known CSN5 interaction partners in addition to unknown plant and M. incognita proteins. Among these, we described M. incognita PASSE-MURAILLE (MiPM), a small pioneer protein predicted to contain a secretory peptide that is up-regulated mostly in the J2 parasitic stage. We confirmed the CSN5-MiPM interaction, which occurs in the nucleus, by bimolecular fluorescence complementation (BiFC). Using MiPM as bait, a GST pull-down assay coupled with MS revealed some common protein partners between CSN5 and MiPM. We further showed by in silico and microscopic analyses that the recombinant purified MiPM protein enters the cells of Arabidopsis root tips in a non-infectious context. In further detail, the supercharged N-terminal tail of MiPM (NTT-MiPM) triggers an unknown host endocytosis pathway to penetrate the cell. The functional meaning of the CSN5-MiPM interaction in the M. incognita parasitism is discussed. Moreover, we propose that the cell-penetrating properties of some M. incognita secreted proteins might be a non-negligible mechanism for cell uptake, especially during the steps preceding the sedentary parasitic phase.
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Affiliation(s)
- Caroline Bournaud
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- *Correspondence: Caroline Bournaud
| | | | - André M. Murad
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
| | - Emmanuel Bresso
- Université de Lorraine, Centre National de la Recherche Scientifique, Inria, Laboratoire Lorrain de Recherche en Informatique et ses Applications, Nancy, France
| | | | - Maria F. Grossi-de-Sá
- Embrapa Genetic Resources and Biotechnology, Brasília, Brazil
- Post-Graduation Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil
- Maria F. Grossi-de-Sá
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9
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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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10
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Yu Y, Hube B, Kämper J, Meyer V, Krappmann S. When green and red mycology meet: Impressions from an interdisciplinary forum on virulence mechanisms of phyto- and human-pathogenic fungi. Virulence 2017; 8:1435-1444. [PMID: 28723316 DOI: 10.1080/21505594.2017.1356502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Fungal infections pose a constant threat to plants and humans, but detailed knowledge about pathogenesis, immunity, or virulence is rather scarce. Due to the fact that a certain overlap in the armoury of infection exists between plant- and human-pathogenic fungi, an interdisciplinary forum was held in October 2016 at the Institute for Clinical Microbiology, Immunology and Hygiene in Erlangen under the organisational umbrella from two special interest groups of German microbial societies. Scientific exchange and intense discussion of this timely topic was fostered by bringing together renowned experts in their respective fields to present their thoughts and recent findings in the course of a plenary lecture and six themed sessions, accompanied by oral and poster contributions of young researchers. By targeting the topic of fungal virulence mechanisms from various angles and in the context of plant and human hosts, some common grounds and exciting perspectives could be deduced during this vibrant scientific event.
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Affiliation(s)
- Yidong Yu
- a Institute for Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen and Friedrich-Alexander University (FAU) Erlangen-Nürnberg , Erlangen , Bavaria , Germany
| | - Bernhard Hube
- b Department of Microbial Pathogenicity Mechanisms , Hans Knöll Institute , Jena , Thuringia , Germany
| | - Jörg Kämper
- c Department of Genetics , Institute of Applied Biosciences, Karlsruhe Institute of Technology , Karlsruhe , Baden-Wuerttemberg , Germany
| | - Vera Meyer
- d Institute of Biotechnology , Department of Applied and Molecular Microbiology, Technische Universität Berlin , Berlin , Germany
| | - Sven Krappmann
- a Institute for Clinical Microbiology, Immunology and Hygiene, University Hospital Erlangen and Friedrich-Alexander University (FAU) Erlangen-Nürnberg , Erlangen , Bavaria , Germany
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Wang S, Boevink PC, Welsh L, Zhang R, Whisson SC, Birch PRJ. Delivery of cytoplasmic and apoplastic effectors from Phytophthora infestans haustoria by distinct secretion pathways. THE NEW PHYTOLOGIST 2017; 216:205-215. [PMID: 28758684 PMCID: PMC5601276 DOI: 10.1111/nph.14696] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/05/2017] [Indexed: 05/17/2023]
Abstract
The potato blight pathogen Phytophthora infestans secretes effector proteins that are delivered inside (cytoplasmic) or can act outside (apoplastic) plant cells to neutralize host immunity. Little is known about how and where effectors are secreted during infection, yet such knowledge is essential to understand and combat crop disease. We used transient Agrobacterium tumefaciens-mediated in planta expression, transformation of P. infestans with fluorescent protein fusions and confocal microscopy to investigate delivery of effectors to plant cells during infection. The cytoplasmic effector Pi04314, expressed as a monomeric red fluorescent protein (mRFP) fusion protein with a signal peptide to secrete it from plant cells, did not passively re-enter the cells upon secretion. However, Pi04314-mRFP expressed in P. infestans was translocated from haustoria, which form intimate interactions with plant cells, to accumulate at its sites of action in the host nucleus. The well-characterized apoplastic effector EPIC1, a cysteine protease inhibitor, was also secreted from haustoria. EPIC1 secretion was inhibited by brefeldin A (BFA), demonstrating that it is delivered by conventional Golgi-mediated secretion. By contrast, Pi04314 secretion was insensitive to BFA treatment, indicating that the cytoplasmic effector follows an alternative route for delivery into plant cells. Phytophthora infestans haustoria are thus sites for delivery of both apoplastic and cytoplasmic effectors during infection, following distinct secretion pathways.
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Affiliation(s)
- Shumei Wang
- Division of Plant SciencesUniversity of Dundee (at JHI)Errol RoadInvergowrieDundeeDD2 5DAUK
| | - Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Lydia Welsh
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Ruofang Zhang
- Potato Engineering and Technology Research Centre of Inner Mongolia UniversityWest College Road 235Hohhot010021China
| | - Stephen C. Whisson
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Division of Plant SciencesUniversity of Dundee (at JHI)Errol RoadInvergowrieDundeeDD2 5DAUK
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
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12
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Whisson SC, Boevink PC, Wang S, Birch PR. The cell biology of late blight disease. Curr Opin Microbiol 2016; 34:127-135. [PMID: 27723513 PMCID: PMC5340842 DOI: 10.1016/j.mib.2016.09.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/01/2016] [Accepted: 09/08/2016] [Indexed: 11/12/2022]
Abstract
The Phytophthora haustorium is a major site of secretion during infection. The host endocytic cycle contributes to biogenesis of the Extra-Haustorial Membrane. RXLR effectors manipulate host processes at diverse subcellular locations. They directly manipulate the activity or location of immune proteins. They also promote the activity of endogenous negative regulators of immunity.
Late blight, caused by the oomycete Phytophthora infestans, is a major global disease of potato and tomato. Cell biology is teaching us much about the developmental stages associated with infection, especially the haustorium, which is a site of intimate interaction and molecular exchange between pathogen and host. Recent observations suggest a role for the plant endocytic cycle in specific recruitment of host proteins to the Extra-Haustorial Membrane, emphasising the unique nature of this membrane compartment. In addition, there has been a strong focus on the activities of RXLR effectors, which are delivered into plant cells to modulate and manipulate host processes. RXLR effectors interact directly with diverse plant proteins at a range of subcellular locations to promote disease.
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Affiliation(s)
- Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK
| | - Shumei Wang
- Division of Plant Sciences, University of Dundee, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Paul Rj Birch
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA, UK; Division of Plant Sciences, University of Dundee, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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13
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Contributions of host cellular trafficking and organization to the outcomes of plant-pathogen interactions. Semin Cell Dev Biol 2016; 56:163-173. [DOI: 10.1016/j.semcdb.2016.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 05/16/2016] [Accepted: 05/20/2016] [Indexed: 11/23/2022]
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14
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Oomycete interactions with plants: infection strategies and resistance principles. Microbiol Mol Biol Rev 2016; 79:263-80. [PMID: 26041933 DOI: 10.1128/mmbr.00010-15] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Oomycota include many economically significant microbial pathogens of crop species. Understanding the mechanisms by which oomycetes infect plants and identifying methods to provide durable resistance are major research goals. Over the last few years, many elicitors that trigger plant immunity have been identified, as well as host genes that mediate susceptibility to oomycete pathogens. The mechanisms behind these processes have subsequently been investigated and many new discoveries made, marking a period of exciting research in the oomycete pathology field. This review provides an introduction to our current knowledge of the pathogenic mechanisms used by oomycetes, including elicitors and effectors, plus an overview of the major principles of host resistance: the established R gene hypothesis and the more recently defined susceptibility (S) gene model. Future directions for development of oomycete-resistant plants are discussed, along with ways that recent discoveries in the field of oomycete-plant interactions are generating novel means of studying how pathogen and symbiont colonizations overlap.
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15
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Helliwell EE, Vega-Arreguín J, Shi Z, Bailey B, Xiao S, Maximova SN, Tyler BM, Guiltinan MJ. Enhanced resistance in Theobroma cacao against oomycete and fungal pathogens by secretion of phosphatidylinositol-3-phosphate-binding proteins. PLANT BIOTECHNOLOGY JOURNAL 2016. [PMID: 26214158 DOI: 10.1111/pbi.12436] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The internalization of some oomycete and fungal pathogen effectors into host plant cells has been reported to be blocked by proteins that bind to the effectors' cell entry receptor, phosphatidylinositol-3-phosphate (PI3P). This finding suggested a novel strategy for disease control by engineering plants to secrete PI3P-binding proteins. In this study, we tested this strategy using the chocolate tree Theobroma cacao. Transient expression and secretion of four different PI3P-binding proteins in detached leaves of T. cacao greatly reduced infection by two oomycete pathogens, Phytophthora tropicalis and Phytophthora palmivora, which cause black pod disease. Lesion size and pathogen growth were reduced by up to 85%. Resistance was not conferred by proteins lacking a secretory leader, by proteins with mutations in their PI3P-binding site, or by a secreted PI4P-binding protein. Stably transformed, transgenic T. cacao plants expressing two different PI3P-binding proteins showed substantially enhanced resistance to both P. tropicalis and P. palmivora, as well as to the fungal pathogen Colletotrichum theobromicola. These results demonstrate that secretion of PI3P-binding proteins is an effective way to increase disease resistance in T. cacao, and potentially in other plants, against a broad spectrum of pathogens.
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Affiliation(s)
- Emily E Helliwell
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Julio Vega-Arreguín
- Virginia Bioinformatics Institute and Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Zi Shi
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bryan Bailey
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research & Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Siela N Maximova
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
- Virginia Bioinformatics Institute and Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Mark J Guiltinan
- Department of Plant Science and Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA, USA
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16
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Export of malaria proteins requires co-translational processing of the PEXEL motif independent of phosphatidylinositol-3-phosphate binding. Nat Commun 2016; 7:10470. [PMID: 26832821 PMCID: PMC4740378 DOI: 10.1038/ncomms10470] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 12/09/2015] [Indexed: 11/08/2022] Open
Abstract
Plasmodium falciparum exports proteins into erythrocytes using the Plasmodium export element (PEXEL) motif, which is cleaved in the endoplasmic reticulum (ER) by plasmepsin V (PMV). A recent study reported that phosphatidylinositol-3-phosphate (PI(3)P) concentrated in the ER binds to PEXEL motifs and is required for export independent of PMV, and that PEXEL motifs are functionally interchangeable with RxLR motifs of oomycete effectors. Here we show that the PEXEL does not bind PI(3)P, and that this lipid is not concentrated in the ER. We find that RxLR motifs cannot mediate export in P. falciparum. Parasites expressing a mutated version of KAHRP, with the PEXEL motif repositioned near the signal sequence, prevented PMV cleavage. This mutant possessed the putative PI(3)P-binding residues but is not exported. Reinstatement of PEXEL to its original location restores processing by PMV and export. These results challenge the PI(3)P hypothesis and provide evidence that PEXEL position is conserved for co-translational processing and export.
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17
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Lyu X, Shen C, Fu Y, Xie J, Jiang D, Li G, Cheng J. A Small Secreted Virulence-Related Protein Is Essential for the Necrotrophic Interactions of Sclerotinia sclerotiorum with Its Host Plants. PLoS Pathog 2016; 12:e1005435. [PMID: 26828434 PMCID: PMC4735494 DOI: 10.1371/journal.ppat.1005435] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/11/2016] [Indexed: 12/28/2022] Open
Abstract
Small, secreted proteins have been found to play crucial roles in interactions between biotrophic/hemi-biotrophic pathogens and plants. However, little is known about the roles of these proteins produced by broad host-range necrotrophic phytopathogens during infection. Here, we report that a cysteine-rich, small protein SsSSVP1 in the necrotrophic phytopathogen Sclerotinia sclerotiorum was experimentally confirmed to be a secreted protein, and the secretion of SsSSVP1 from hyphae was followed by internalization and cell-to-cell movement independent of a pathogen in host cells. SsSSVP1∆SP could induce significant plant cell death and targeted silencing of SsSSVP1 resulted in a significant reduction in virulence. Through yeast two-hybrid (Y2H), coimmunoprecipitation (co-IP) and bimolecular fluorescence complementation (BiFC) assays, we demonstrated that SsSSVP1∆SP interacted with QCR8, a subunit of the cytochrome b-c1 complex of mitochondrial respiratory chain in plants. Double site-directed mutagenesis of two cysteine residues (C38 and C44) in SsSSVP1∆SP had significant effects on its homo-dimer formation, SsSSVP1∆SP-QCR8 interaction and plant cell death induction, indicating that partial cysteine residues surely play crucial roles in maintaining the structure and function of SsSSVP1. Co-localization and BiFC assays showed that SsSSVP1∆SP might hijack QCR8 to cytoplasm before QCR8 targeting into mitochondria, thereby disturbing its subcellular localization in plant cells. Furthermore, virus induced gene silencing (VIGS) of QCR8 in tobacco caused plant abnormal development and cell death, indicating the cell death induced by SsSSVP1∆SP might be caused by the SsSSVP1∆SP-QCR8 interaction, which had disturbed the QCR8 subcellular localization and hence disabled its biological functions. These results suggest that SsSSVP1 is a potential effector which may manipulate plant energy metabolism to facilitate the infection of S. sclerotiorum. Our findings indicate novel roles of small secreted proteins in the interactions between host-non-specific necrotrophic fungi and plants, and highlight the significance to illuminate the pathogenic mechanisms of this type of interaction.
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Affiliation(s)
- Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Cuicui Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jiatao Xie
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
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18
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Anderson RG, Deb D, Fedkenheuer K, McDowell JM. Recent Progress in RXLR Effector Research. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1063-72. [PMID: 26125490 DOI: 10.1094/mpmi-01-15-0022-cr] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.
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Affiliation(s)
- Ryan G Anderson
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Devdutta Deb
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Kevin Fedkenheuer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - John M McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
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19
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Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, Lazar N, Daverdin G, Balesdent MH, Choi DHY, Tyler BM, Rouxel T, van Tilbeurgh H, Fudal I. Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:610-24. [PMID: 26082394 DOI: 10.1111/tpj.12913] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 05/13/2023]
Abstract
The avirulence gene AvrLm4-7 of Leptosphaeria maculans, the causal agent of stem canker in Brassica napus (oilseed rape), confers a dual specificity of recognition by two resistance genes (Rlm4 and Rlm7) and is strongly involved in fungal fitness. In order to elucidate the biological function of AvrLm4-7 and understand the specificity of recognition by Rlm4 and Rlm7, the AvrLm4-7 protein was produced in Pichia pastoris and its crystal structure was determined. It revealed the presence of four disulfide bridges, but no close structural analogs could be identified. A short stretch of amino acids in the C terminus of the protein, (R/N)(Y/F)(R/S)E(F/W), was well-conserved among AvrLm4-7 homologs. Loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. Loss of recognition by Rlm7 is governed by more complex mutational patterns, including gene loss or drastic modifications of the protein structure. Three point mutations altered residues in the well-conserved C-terminal motif or close to the glycine involved in Rlm4-mediated recognition, resulting in the loss of Rlm7-mediated recognition. Transient expression in Nicotiana benthamiana (tobacco) and particle bombardment experiments on leaves from oilseed rape suggested that AvrLm4-7 interacts with its cognate R proteins inside the plant cell, and can be translocated into plant cells in the absence of the pathogen. Translocation of AvrLm4-7 into oilseed rape leaves is likely to require the (R/N)(Y/F)(R/S)E(F/W) motif as well as an RAWG motif located in a nearby loop that together form a positively charged region.
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Affiliation(s)
- Karine Blondeau
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Françoise Blaise
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marc Graille
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Shiv D Kale
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Juliette Linglin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Audrey Labarde
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Noureddine Lazar
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Guillaume Daverdin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Danielle H Y Choi
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Thierry Rouxel
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Herman van Tilbeurgh
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Isabelle Fudal
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
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20
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Gong X, Hurtado O, Wang B, Wu C, Yi M, Giraldo M, Valent B, Goodin M, Farman M. pFPL Vectors for High-Throughput Protein Localization in Fungi: Detecting Cytoplasmic Accumulation of Putative Effector Proteins. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:107-121. [PMID: 25390188 DOI: 10.1094/mpmi-05-14-0144-ta] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
As part of a large-scale project whose goal was to identify candidate effector proteins in Magnaporthe oryzae, we developed a suite of vectors that facilitate high-throughput protein localization experiments in fungi. These vectors utilize Gateway recombinational cloning to place a gene's promoter and coding sequences upstream and in frame with enhanced cyan fluorescent protein, green fluorescent protein (GFP), monomeric red fluorescence protein (mRFP), and yellow fluorescent protein or a nucleus-targeted mCHERRY variant. The respective Gateway cassettes were incorporated into Agrobacterium-based plasmids to allow efficient fungal transformation using hygromycin or geneticin resistance selection. mRFP proved to be more sensitive than the GFP spectral variants for monitoring proteins secreted in planta; and extensive testing showed that Gateway-derived fusion proteins produced localization patterns identical to their "directly fused" counterparts. Use of plasmid for fungal protein localization (pFPL) vectors with two different selectable markers provided a convenient way to label fungal cells with different fluorescent proteins. We demonstrate the utility of the pFPL vectors for identifying candidate effector proteins and we highlight a number of important factors that must be taken into consideration when screening for proteins that are translocated across the host plasma membrane.
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22
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Sperschneider J, Williams AH, Hane JK, Singh KB, Taylor JM. Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors. FRONTIERS IN PLANT SCIENCE 2015; 6:1168. [PMID: 26779196 PMCID: PMC4688413 DOI: 10.3389/fpls.2015.01168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/07/2015] [Indexed: 05/03/2023]
Abstract
The steadily increasing number of sequenced fungal and oomycete genomes has enabled detailed studies of how these eukaryotic microbes infect plants and cause devastating losses in food crops. During infection, fungal and oomycete pathogens secrete effector molecules which manipulate host plant cell processes to the pathogen's advantage. Proteinaceous effectors are synthesized intracellularly and must be externalized to interact with host cells. Computational prediction of secreted proteins from genomic sequences is an important technique to narrow down the candidate effector repertoire for subsequent experimental validation. In this study, we benchmark secretion prediction tools on experimentally validated fungal and oomycete effectors. We observe that for a set of fungal SwissProt protein sequences, SignalP 4 and the neural network predictors of SignalP 3 (D-score) and SignalP 2 perform best. For effector prediction in particular, the use of a sensitive method can be desirable to obtain the most complete candidate effector set. We show that the neural network predictors of SignalP 2 and 3, as well as TargetP were the most sensitive tools for fungal effector secretion prediction, whereas the hidden Markov model predictors of SignalP 2 and 3 were the most sensitive tools for oomycete effectors. Thus, previous versions of SignalP retain value for oomycete effector prediction, as the current version, SignalP 4, was unable to reliably predict the signal peptide of the oomycete Crinkler effectors in the test set. Our assessment of subcellular localization predictors shows that cytoplasmic effectors are often predicted as not extracellular. This limits the reliability of secretion predictions that depend on these tools. We present our assessment with a view to informing future pathogenomics studies and suggest revised pipelines for secretion prediction to obtain optimal effector predictions in fungi and oomycetes.
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Affiliation(s)
- Jana Sperschneider
- CSIRO Agriculture Flagship, Centre for Environment and Life SciencesPerth, WA, Australia
- *Correspondence: Jana Sperschneider
| | - Angela H. Williams
- CSIRO Agriculture Flagship, Centre for Environment and Life SciencesPerth, WA, Australia
- The Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - James K. Hane
- Department of Environment and Agriculture, CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin UniversityPerth, WA, Australia
- Curtin Institute for Computation, Curtin UniversityPerth, WA, Australia
| | - Karam B. Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life SciencesPerth, WA, Australia
- The Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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An immunity-triggering effector from the Barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution. PLoS Pathog 2014; 10:e1004223. [PMID: 24992661 PMCID: PMC4081816 DOI: 10.1371/journal.ppat.1004223] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 05/15/2014] [Indexed: 11/19/2022] Open
Abstract
The basidiomycete smut fungus Ustilago hordei was previously shown to comprise isolates that are avirulent on various barley host cultivars. Through genetic crosses we had revealed that a dominant avirulence locus UhAvr1 which triggers immunity in barley cultivar Hannchen harboring resistance gene Ruh1, resided within an 80-kb region. DNA sequence analysis of this genetically delimited region uncovered the presence of 7 candidate secreted effector proteins. Sequence comparison of their coding sequences among virulent and avirulent parental and field isolates could not distinguish UhAvr1 candidates. Systematic deletion and complementation analyses revealed that UhAvr1 is UHOR_10022 which codes for a small effector protein of 171 amino acids with a predicted 19 amino acid signal peptide. Virulence in the parental isolate is caused by the insertion of a fragment of 5.5 kb with similarity to a common U. hordei transposable element (TE), interrupting the promoter of UhAvr1 and thereby changing expression and hence recognition of UhAVR1p. This rearrangement is likely caused by activities of TEs and variation is seen among isolates. Using GFP-chimeric constructs we show that UhAvr1 is induced only in mated dikaryotic hyphae upon sensing and infecting barley coleoptile cells. When infecting Hannchen, UhAVR1p causes local callose deposition and the production of reactive oxygen species and necrosis indicative of the immune response. UhAvr1 does not contribute significantly to overall virulence. UhAvr1 is located in a cluster of ten effectors with several paralogs and over 50% of TEs. This cluster is syntenous with clusters in closely-related U. maydis and Sporisorium reilianum. In these corn-infecting species, these clusters harbor however more and further diversified homologous effector families but very few TEs. This increased variability may have resulted from past selection pressure by resistance genes since U. maydis is not known to trigger immunity in its corn host.
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Abstract
Fungal and oomycete plant parasites are among the most devastating pathogens of food crops. These microbes secrete effector proteins inside plant cells to manipulate host processes and facilitate colonization. How these effectors reach the host cytoplasm remains an unclear and debated area of plant research. In this article, we examine recent conflicting findings that have generated discussion in the field. We also highlight promising approaches based on studies of both parasite and host during infection. Ultimately, this knowledge may inform future broad spectrum strategies for protecting crops from such pathogens.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- INRA, Interactions Arbres/Microorganismes, UMR 1136, Champenoux, France
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Abstract
Live-cell imaging assisted by fluorescent markers has been fundamental to understanding the focused secretory 'warfare' that occurs between plants and biotrophic pathogens that feed on living plant cells. Pathogens succeed through the spatiotemporal deployment of a remarkably diverse range of effector proteins to control plant defences and cellular processes. Some effectors can be secreted by appressoria even before host penetration, many enter living plant cells where they target diverse subcellular compartments and others move into neighbouring cells to prepare them before invasion. This Review summarizes the latest advances in our understanding of the cell biology of biotrophic interactions between plants and their eukaryotic filamentous pathogens based on in planta analyses of effectors.
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Sperschneider J, Gardiner DM, Taylor JM, Hane JK, Singh KB, Manners JM. A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi. BMC Genomics 2013; 14:807. [PMID: 24252298 PMCID: PMC3914424 DOI: 10.1186/1471-2164-14-807] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 11/15/2013] [Indexed: 11/25/2022] Open
Abstract
Background Fungal pathogens cause devastating losses in economically important cereal crops by utilising pathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus far been identified by selecting small, cysteine-rich peptides from the secretome despite increasing evidence that not all effectors share these attributes. Results We take advantage of the availability of sequenced fungal genomes and present an unbiased method for finding putative pathogen proteins and secreted effectors in a query genome via comparative hidden Markov model analyses followed by unsupervised protein clustering. Our method returns experimentally validated fungal effectors in Stagonospora nodorum and Fusarium oxysporum as well as the N-terminal Y/F/WxC-motif from the barley powdery mildew pathogen. Application to the cereal pathogen Fusarium graminearum reveals a secreted phosphorylcholine phosphatase that is characteristic of hemibiotrophic and necrotrophic cereal pathogens and shares an ancient selection process with bacterial plant pathogens. Three F. graminearum protein clusters are found with an enriched secretion signal. One of these putative effector clusters contains proteins that share a [SG]-P-C-[KR]-P sequence motif in the N-terminal and show features not commonly associated with fungal effectors. This motif is conserved in secreted pathogenic Fusarium proteins and a prime candidate for functional testing. Conclusions Our pipeline has successfully uncovered conservation patterns, putative effectors and motifs of fungal pathogens that would have been overlooked by existing approaches that identify effectors as small, secreted, cysteine-rich peptides. It can be applied to any pathogenic proteome data, such as microbial pathogen data of plants and other organisms.
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Affiliation(s)
- Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Centre for Environment and Life Sciences, Perth, Western Australia, Australia.
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Ve T, Williams SJ, Catanzariti AM, Rafiqi M, Rahman M, Ellis JG, Hardham AR, Jones DA, Anderson PA, Dodds PN, Kobe B. Structures of the flax-rust effector AvrM reveal insights into the molecular basis of plant-cell entry and effector-triggered immunity. Proc Natl Acad Sci U S A 2013; 110:17594-9. [PMID: 24101475 PMCID: PMC3808616 DOI: 10.1073/pnas.1307614110] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fungal and oomycete pathogens cause some of the most devastating diseases in crop plants, and facilitate infection by delivering a large number of effector molecules into the plant cell. AvrM is a secreted effector protein from flax rust (Melampsora lini) that can internalize into plant cells in the absence of the pathogen, binds to phosphoinositides (PIPs), and is recognized directly by the resistance protein M in flax (Linum usitatissimum), resulting in effector-triggered immunity. We determined the crystal structures of two naturally occurring variants of AvrM, AvrM-A and avrM, and both reveal an L-shaped fold consisting of a tandem duplicated four-helix motif, which displays similarity to the WY domain core in oomycete effectors. In the crystals, both AvrM variants form a dimer with an unusual nonglobular shape. Our functional analysis of AvrM reveals that a hydrophobic surface patch conserved between both variants is required for internalization into plant cells, whereas the C-terminal coiled-coil domain mediates interaction with M. AvrM binding to PIPs is dependent on positive surface charges, and mutations that abrogate PIP binding have no significant effect on internalization, suggesting that AvrM binding to PIPs is not essential for transport of AvrM across the plant membrane. The structure of AvrM and the identification of functionally important surface regions advance our understanding of the molecular mechanisms underlying how effectors enter plant cells and how they are detected by the plant immune system.
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Affiliation(s)
- Thomas Ve
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ann-Maree Catanzariti
- Plant Science Division, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Maryam Rafiqi
- Plant Science Division, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Institute of Phytopathology and Applied Zoology, Research Centre for BioSystems, Land Use, and Nutrition, Justus Liebig University, 35390 Giessen, Germany
| | - Motiur Rahman
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia; and
| | - Jeffrey G. Ellis
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, ACT 2601, Australia
| | - Adrienne R. Hardham
- Plant Science Division, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - David A. Jones
- Plant Science Division, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Peter A. Anderson
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia; and
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, ACT 2601, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
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Abstract
Over the past decade, considerable advances have been made in understanding the molecular mechanisms that underpin the arms race between plant pathogens and their hosts. Alongside genomic, bioinformatic, proteomic, biochemical and cell biological analyses of plant-pathogen interactions, three-dimensional structural studies of virulence proteins deployed by pathogens to promote infection, in some cases complexed with their plant cell targets, have uncovered key insights into the functions of these molecules. Structural information on plant immune receptors, which regulate the response to pathogen attack, is also starting to emerge. Structural studies of bacterial plant pathogen-host systems have been leading the way, but studies of filamentous plant pathogens are gathering pace. In this Review, we summarize the key developments in the structural biology of plant pathogen-host interactions.
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Lapin D, Van den Ackerveken G. Susceptibility to plant disease: more than a failure of host immunity. TRENDS IN PLANT SCIENCE 2013; 18:546-54. [PMID: 23790254 DOI: 10.1016/j.tplants.2013.05.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/15/2013] [Accepted: 05/21/2013] [Indexed: 05/23/2023]
Abstract
Susceptibility to infectious diseases caused by pathogens affects most plants in their natural habitat and leads to yield losses in agriculture. However, plants are not helpless because their immune system can deal with the vast majority of attackers. Nevertheless, adapted pathogens are able to circumvent or avert host immunity making plants susceptible to these uninvited guests. In addition to the failure of the plant immune system, there are other host processes that contribute to plant disease susceptibility. In this review, we discuss recent studies that show the active role played by the host in supporting disease, focusing mainly on biotrophic stages of infection. Plants attract pathogens, enable their entry and accommodation, and facilitate nutrient provision.
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Affiliation(s)
- Dmitry Lapin
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Jaouannet M, Rosso MN. Effectors of root sedentary nematodes target diverse plant cell compartments to manipulate plant functions and promote infection. PLANT SIGNALING & BEHAVIOR 2013; 8:25507. [PMID: 23857349 PMCID: PMC4002590 DOI: 10.4161/psb.25507] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Sedentary plant-parasitic nematodes maintain a biotrophic relationship with their hosts over a period of several weeks and induce the differentiation of root cells into specialized feeding cells. Nematode effectors, which are synthesized in the esophageal glands and injected into the plant tissue through the syringe-like stylet, play a central role in these processes. Previous work on nematode effectors has shown that the apoplasm is targeted during invasion of the host while the cytoplasm is targeted during the induction and the maintenance of the feeding site. A large number of candidate effectors potentially secreted by the nematode into the plant tissues to promote infection have now been identified. This work has shown that the targeting and the role of effectors are more complex than previously thought. This review will not cover the prolific recent findings in nematode effector function but will instead focus on recent selected examples that illustrate the variety of plant cell compartments that effectors are addressed to in order reach their plant targets.
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Affiliation(s)
- Maëlle Jaouannet
- Cell and Molecular Sciences; The James Hutton Institute; Dundee, UK
- Correspondence to: Maëlle Jaouannet,
| | - Marie-Noëlle Rosso
- INRA; Aix-Marseille Université; UMR 1163; Biotechnologie des Champignons Filamenteux; Marseille, France
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Yi M, Valent B. Communication between filamentous pathogens and plants at the biotrophic interface. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:587-611. [PMID: 23750888 DOI: 10.1146/annurev-phyto-081211-172916] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fungi and oomycetes that colonize living plant tissue form extensive interfaces with plant cells in which the cytoplasm of the microorganism is closely aligned with the host cytoplasm for an extended distance. In all cases, specialized biotrophic hyphae function to hijack host cellular processes across an interfacial zone consisting of a hyphal plasma membrane, a specialized interfacial matrix, and a plant-derived membrane. The interface is the site of active secretion by both players. This cross talk at the interface determines the winner in adversarial relationships and establishes the partnership in mutualistic relationships. Fungi and oomycetes secrete many specialized effector proteins for controlling the host, and they can stimulate remarkable cellular reorganization even in distant plant cells. Breakthroughs in live-cell imaging of fungal and oomycete encounter sites, including live-cell imaging of pathogens secreting fluorescently labeled effector proteins, have led to recent progress in understanding communication across the interface.
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Affiliation(s)
- Mihwa Yi
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506-5502, USA.
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