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Pradeu T, Thomma BPHJ, Girardin SE, Lemaitre B. The conceptual foundations of innate immunity: Taking stock 30 years later. Immunity 2024; 57:613-631. [PMID: 38599162 DOI: 10.1016/j.immuni.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
While largely neglected over decades during which adaptive immunity captured most of the attention, innate immune mechanisms have now become central to our understanding of immunology. Innate immunity provides the first barrier to infection in vertebrates, and it is the sole mechanism of host defense in invertebrates and plants. Innate immunity also plays a critical role in maintaining homeostasis, shaping the microbiota, and in disease contexts such as cancer, neurodegeneration, metabolic syndromes, and aging. The emergence of the field of innate immunity has led to an expanded view of the immune system, which is no longer restricted to vertebrates and instead concerns all metazoans, plants, and even prokaryotes. The study of innate immunity has given rise to new concepts and language. Here, we review the history and definition of the core concepts of innate immunity, discussing their value and fruitfulness in the long run.
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Affiliation(s)
- Thomas Pradeu
- CNRS UMR 5164 ImmunoConcept, University of Bordeaux, Bordeaux, France; Department of Biological and Medical Sciences, University of Bordeaux, Bordeaux, France; Presidential Fellow, Chapman University, Orange, CA, USA.
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Bruno Lemaitre
- Global Health Institute, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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2
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Torres DE, Kramer HM, Tracanna V, Fiorin GL, Cook DE, Seidl MF, Thomma BPHJ. Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nat Commun 2024; 15:1701. [PMID: 38402218 PMCID: PMC10894299 DOI: 10.1038/s41467-024-45884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024] Open
Abstract
The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.
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Affiliation(s)
- David E Torres
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vittorio Tracanna
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Manhattan, KS, USA
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany.
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3
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Chavarro-Carrero EA, Snelders NC, Torres DE, Kraege A, López-Moral A, Petti GC, Punt W, Wieneke J, García-Velasco R, López-Herrera CJ, Seidl MF, Thomma BPHJ. The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathog 2024; 20:e1011866. [PMID: 38236788 PMCID: PMC10796067 DOI: 10.1371/journal.ppat.1011866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.
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Affiliation(s)
- Edgar A. Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Nick C. Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - David E. Torres
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anton Kraege
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ana López-Moral
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Gabriella C. Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Wilko Punt
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Jan Wieneke
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Rómulo García-Velasco
- Laboratory of Phytopathology, Tenancingo University Center, Autonomous University of the State of Mexico, Tenancingo, State of Mexico, Mexico
| | - Carlos J. López-Herrera
- CSIC, Instituto de Agricultura Sostenible, Dept. Protección de Cultivos, C/Alameda del Obispo s/n, Córdoba, Spain
| | - Michael F. Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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Rovenich H, Thomma BPHJ. Battle of the bugs: how an oomycete pathogen shapes the microbiota of its host. New Phytol 2023; 239:2064-2066. [PMID: 37430388 DOI: 10.1111/nph.19133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
This article is a Commentary on Gómez‐Pérez et al. (2023), 239: 2320–2334.
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Affiliation(s)
- Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Zülpicher Straße 47b, 50674, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Zülpicher Straße 47b, 50674, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zülpicher Straße 47b, 50674, Cologne, Germany
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5
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Weiland P, Dempwolff F, Steinchen W, Freibert S, Tian H, Glatter T, Martin R, Thomma BPHJ, Bange G, Altegoer F. Structural and functional analysis of the cerato-platanin-like protein Cpl1 suggests diverging functions in smut fungi. Mol Plant Pathol 2023; 24:768-787. [PMID: 37171083 PMCID: PMC10257043 DOI: 10.1111/mpp.13349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/28/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Plant-pathogenic fungi are causative agents of the majority of plant diseases and can lead to severe crop loss in infected populations. Fungal colonization is achieved by combining different strategies, such as avoiding and counteracting the plant immune system and manipulating the host metabolome. Of major importance are virulence factors secreted by fungi, which fulfil diverse functions to support the infection process. Most of these proteins are highly specialized, with structural and biochemical information often absent. Here, we present the atomic structures of the cerato-platanin-like protein Cpl1 from Ustilago maydis and its homologue Uvi2 from Ustilago hordei. Both proteins adopt a double-Ψβ-barrel architecture reminiscent of cerato-platanin proteins, a class so far not described in smut fungi. Our structure-function analysis shows that Cpl1 binds to soluble chitin fragments via two extended grooves at the dimer interface of the two monomer molecules. This carbohydrate-binding mode has not been observed previously and expands the repertoire of chitin-binding proteins. Cpl1 localizes to the cell wall of U. maydis and might synergize with cell wall-degrading and decorating proteins during maize infection. The architecture of Cpl1 harbouring four surface-exposed loop regions supports the idea that it might play a role in the spatial coordination of these proteins. While deletion of cpl1 has only mild effects on the virulence of U. maydis, a recent study showed that deletion of uvi2 strongly impairs U. hordei virulence. Our structural comparison between Cpl1 and Uvi2 reveals sequence variations in the loop regions that might explain a diverging function.
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Affiliation(s)
- Paul Weiland
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Sven‐Andreas Freibert
- Center for Synthetic Microbiology (SYNMIKRO), Institute of CytobiologyPhilipps‐University MarburgMarburgGermany
- Protein Biochemistry and Spectroscopy Core Facility, Institute of CytobiologyPhilipps‐University MarburgMarburgGermany
| | - Hui Tian
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Timo Glatter
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Roman Martin
- Faculty of Mathematics and Computer SciencePhilipps‐University MarburgMarburgGermany
| | - Bart P. H. J. Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Florian Altegoer
- Center for Synthetic Microbiology (SYNMIKRO), Faculty of ChemistryPhilipps‐University MarburgMarburgGermany
- Max‐Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Institute of MicrobiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
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6
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Snelders NC, Boshoven JC, Song Y, Schmitz N, Fiorin GL, Rovenich H, van den Berg GCM, Torres DE, Petti GC, Prockl Z, Faino L, Seidl MF, Thomma BPHJ. A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria. New Phytol 2023; 237:944-958. [PMID: 36300791 DOI: 10.1111/nph.18576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
| | - Jordi C Boshoven
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Yin Song
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Natalie Schmitz
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Gabriella C Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Zoe Prockl
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- Department of Ambiental Biology, Sapienza University of Rome, 00185, Rome, Italy
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
| | - Bart P H J Thomma
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
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7
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Tian H, Fiorin GL, Kombrink A, Mesters JR, Thomma BPHJ. Fungal dual-domain LysM effectors undergo chitin-induced intermolecular, and not intramolecular, dimerization. Plant Physiol 2022; 190:2033-2044. [PMID: 35997573 PMCID: PMC9614474 DOI: 10.1093/plphys/kiac391] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Chitin is a homopolymer of β-(1,4)-linked N-acetyl-D-glucosamine (GlcNAc) and a major structural component of fungal cell walls. In plants, chitin acts as a microbe-associated molecular pattern (MAMP) that is recognized by lysin motif (LysM)-containing plant cell surface-localized pattern recognition receptors (PRRs) that activate a plethora of downstream immune responses. To deregulate chitin-induced plant immunity and successfully establish infection, many fungal pathogens secrete LysM domain-containing effector proteins during host colonization. The LysM effector Ecp6 from the tomato (Solanum lycopersicum) leaf mold fungus Cladosporium fulvum can outcompete plant PRRs for chitin binding because two of its three LysM domains cooperate to form a composite groove with ultra-high (pM) chitin-binding affinity. However, most functionally characterized LysM effectors contain only two LysMs, including Magnaporthe oryzae MoSlp1, Verticillium dahliae Vd2LysM, and Colletotrichum higginsianum ChElp1 and ChElp2. Here, we performed modeling, structural, and functional analyses to investigate whether such dual-domain LysM effectors can also form ultra-high chitin-binding affinity grooves through intramolecular LysM dimerization. However, our study suggests that intramolecular LysM dimerization does not occur. Rather, our data support the occurrence of intermolecular LysM dimerization for these effectors, associated with a substantially lower chitin binding affinity than monitored for Ecp6. Interestingly, the intermolecular LysM dimerization allows for the formation of polymeric complexes in the presence of chitin. Possibly, such polymers may precipitate at infection sites to eliminate chitin oligomers, and thus suppress the activation of chitin-induced plant immunity.
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Affiliation(s)
- Hui Tian
- University of Cologne, Institute for Plant Sciences, 50674 Cologne, Germany
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Anja Kombrink
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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8
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:6590816. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, CologneGermany
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9
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Snelders NC, Petti GC, van den Berg GCM, Seidl MF, Thomma BPHJ. An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation. Proc Natl Acad Sci U S A 2021; 118:e2110968118. [PMID: 34853168 PMCID: PMC8670511 DOI: 10.1073/pnas.2110968118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Microbes typically secrete a plethora of molecules to promote niche colonization. Soil-dwelling microbes are well-known producers of antimicrobials that are exploited to outcompete microbial coinhabitants. Also, plant pathogenic microbes secrete a diversity of molecules into their environment for niche establishment. Upon plant colonization, microbial pathogens secrete so-called effector proteins that promote disease development. While such effectors are typically considered to exclusively act through direct host manipulation, we recently reported that the soil-borne, fungal, xylem-colonizing vascular wilt pathogen Verticillium dahliae exploits effector proteins with antibacterial properties to promote host colonization through the manipulation of beneficial host microbiota. Since fungal evolution preceded land plant evolution, we now speculate that a subset of the pathogen effectors involved in host microbiota manipulation evolved from ancient antimicrobial proteins of terrestrial fungal ancestors that served in microbial competition prior to the evolution of plant pathogenicity. Here, we show that V. dahliae has co-opted an ancient antimicrobial protein as effector, named VdAMP3, for mycobiome manipulation in planta. We show that VdAMP3 is specifically expressed to ward off fungal niche competitors during resting structure formation in senescing mesophyll tissues. Our findings indicate that effector-mediated microbiome manipulation by plant pathogenic microbes extends beyond bacteria and also concerns eukaryotic members of the plant microbiome. Finally, we demonstrate that fungal pathogens can exploit plant microbiome-manipulating effectors in a life stage-specific manner and that a subset of these effectors has evolved from ancient antimicrobial proteins of fungal ancestors that likely originally functioned in manipulation of terrestrial biota.
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Affiliation(s)
- Nick C Snelders
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht 3584CH, The Netherlands
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
| | - Gabriella C Petti
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht 3584CH, The Netherlands
| | - Bart P H J Thomma
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne D-50674, Germany;
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen 6708PB, The Netherlands
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10
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Pruitt RN, Locci F, Wanke F, Zhang L, Saile SC, Joe A, Karelina D, Hua C, Fröhlich K, Wan WL, Hu M, Rao S, Stolze SC, Harzen A, Gust AA, Harter K, Joosten MHAJ, Thomma BPHJ, Zhou JM, Dangl JL, Weigel D, Nakagami H, Oecking C, Kasmi FE, Parker JE, Nürnberger T. The EDS1-PAD4-ADR1 node mediates Arabidopsis pattern-triggered immunity. Nature 2021; 598:495-499. [PMID: 34497423 DOI: 10.1038/s41586-021-03829-0] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/16/2021] [Indexed: 02/08/2023]
Abstract
Plants deploy cell-surface and intracellular leucine rich-repeat domain (LRR) immune receptors to detect pathogens1. LRR receptor kinases and LRR receptor proteins at the plasma membrane recognize microorganism-derived molecules to elicit pattern-triggered immunity (PTI), whereas nucleotide-binding LRR proteins detect microbial effectors inside cells to confer effector-triggered immunity (ETI). Although PTI and ETI are initiated in different host cell compartments, they rely on the transcriptional activation of similar sets of genes2, suggesting pathway convergence upstream of nuclear events. Here we report that PTI triggered by the Arabidopsis LRR receptor protein RLP23 requires signalling-competent dimers of the lipase-like proteins EDS1 and PAD4, and of ADR1 family helper nucleotide-binding LRRs, which are all components of ETI. The cell-surface LRR receptor kinase SOBIR1 links RLP23 with EDS1, PAD4 and ADR1 proteins, suggesting the formation of supramolecular complexes containing PTI receptors and transducers at the inner side of the plasma membrane. We detected similar evolutionary patterns in LRR receptor protein and nucleotide-binding LRR genes across Arabidopsis accessions; overall higher levels of variation in LRR receptor proteins than in LRR receptor kinases are consistent with distinct roles of these two receptor families in plant immunity. We propose that the EDS1-PAD4-ADR1 node is a convergence point for defence signalling cascades, activated by both surface-resident and intracellular LRR receptors, in conferring pathogen immunity.
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Affiliation(s)
- Rory N Pruitt
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Federica Locci
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Friederike Wanke
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Lisha Zhang
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Svenja C Saile
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Anna Joe
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Darya Karelina
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chenlei Hua
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Katja Fröhlich
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Wei-Lin Wan
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Meijuan Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shaofei Rao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Sara C Stolze
- Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrea A Gust
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Klaus Harter
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | | | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands.,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne University, Cologne, Germany
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jeffery L Dangl
- Department of Biology, Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hirofumi Nakagami
- Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Claudia Oecking
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Farid El Kasmi
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne University, Cologne, Germany.
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany. .,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa.
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11
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Harting R, Starke J, Kusch H, Pöggeler S, Maurus I, Schlüter R, Landesfeind M, Bulla I, Nowrousian M, de Jonge R, Stahlhut G, Hoff KJ, Aßhauer KP, Thürmer A, Stanke M, Daniel R, Morgenstern B, Thomma BPHJ, Kronstad JW, Braus‐Stromeyer SA, Braus GH. A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. Mol Plant Pathol 2021; 22:939-953. [PMID: 33955130 PMCID: PMC8295516 DOI: 10.1111/mpp.13071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/30/2021] [Indexed: 05/04/2023]
Abstract
Amphidiploid fungal Verticillium longisporum strains Vl43 and Vl32 colonize the plant host Brassica napus but differ in their ability to cause disease symptoms. These strains represent two V. longisporum lineages derived from different hybridization events of haploid parental Verticillium strains. Vl32 and Vl43 carry same-sex mating-type genes derived from both parental lineages. Vl32 and Vl43 similarly colonize and penetrate plant roots, but asymptomatic Vl32 proliferation in planta is lower than virulent Vl43. The highly conserved Vl43 and Vl32 genomes include less than 1% unique genes, and the karyotypes of 15 or 16 chromosomes display changed genetic synteny due to substantial genomic reshuffling. A 20 kb Vl43 lineage-specific (LS) region apparently originating from the Verticillium dahliae-related ancestor is specific for symptomatic Vl43 and encodes seven genes, including two putative transcription factors. Either partial or complete deletion of this LS region in Vl43 did not reduce virulence but led to induction of even more severe disease symptoms in rapeseed. This suggests that the LS insertion in the genome of symptomatic V. longisporum Vl43 mediates virulence-reducing functions, limits damage on the host plant, and therefore tames Vl43 from being even more virulent.
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Affiliation(s)
- Rebekka Harting
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Jessica Starke
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Harald Kusch
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Stefanie Pöggeler
- Department of Genetics of Eukaryotic MicroorganismsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Isabel Maurus
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Rabea Schlüter
- Imaging Center of the Department of BiologyUniversity of GreifswaldGreifswaldGermany
| | - Manuel Landesfeind
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Ingo Bulla
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
| | - Minou Nowrousian
- Department of Molecular and Cellular BotanyRuhr‐Universität BochumBochumGermany
| | - Ronnie de Jonge
- Plant–Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtNetherlands
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | - Gertrud Stahlhut
- Department of Genetics of Eukaryotic MicroorganismsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Katharina J. Hoff
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
- Center for Functional Genomics of MicrobesUniversity of GreifswaldGreifswaldGermany
| | - Kathrin P. Aßhauer
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Andrea Thürmer
- Department of Genomic and Applied MicrobiologyInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Mario Stanke
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
- Center for Functional Genomics of MicrobesUniversity of GreifswaldGreifswaldGermany
| | - Rolf Daniel
- Department of Genomic and Applied MicrobiologyInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Burkhard Morgenstern
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | | | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCCanada
| | - Susanna A. Braus‐Stromeyer
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
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12
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Torres DE, Thomma BPHJ, Seidl MF. Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae. Genome Biol Evol 2021; 13:evab135. [PMID: 34100895 PMCID: PMC8290119 DOI: 10.1093/gbe/evab135] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, University of Cologne, Germany
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
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13
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Tian H, MacKenzie CI, Rodriguez‐Moreno L, van den Berg GCM, Chen H, Rudd JJ, Mesters JR, Thomma BPHJ. Three LysM effectors of Zymoseptoria tritici collectively disarm chitin-triggered plant immunity. Mol Plant Pathol 2021; 22:683-693. [PMID: 33797163 PMCID: PMC8126183 DOI: 10.1111/mpp.13055] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 05/09/2023]
Abstract
Chitin is a major structural component of fungal cell walls and acts as a microbe-associated molecular pattern (MAMP) that, on recognition by a plant host, triggers the activation of immune responses. To avoid the activation of these responses, the Septoria tritici blotch (STB) pathogen of wheat, Zymoseptoria tritici, secretes LysM effector proteins. Previously, the LysM effectors Mg1LysM and Mg3LysM were shown to protect fungal hyphae against host chitinases. Furthermore, Mg3LysM, but not Mg1LysM, was shown to suppress chitin-induced reactive oxygen species (ROS) production. Whereas initially a third LysM effector gene was disregarded as a presumed pseudogene, we now provide functional data to show that this gene also encodes a LysM effector, named Mgx1LysM, that is functional during wheat colonization. While Mg3LysM confers a major contribution to Z. tritici virulence, Mgx1LysM and Mg1LysM contribute to Z. tritici virulence with smaller effects. All three LysM effectors display partial functional redundancy. We furthermore demonstrate that Mgx1LysM binds chitin, suppresses the chitin-induced ROS burst, and is able to protect fungal hyphae against chitinase hydrolysis. Finally, we demonstrate that Mgx1LysM is able to undergo chitin-induced polymerization. Collectively, our data show that Z. tritici utilizes three LysM effectors to disarm chitin-triggered wheat immunity.
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Affiliation(s)
- Hui Tian
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Institute for Plant SciencesCluster of Excellence on Plant Sciences (CEPLAS)University of CologneCologneGermany
| | - Craig I. MacKenzie
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
| | - Luis Rodriguez‐Moreno
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Departamento de Biología Celular, Genética y FisiologíaUniversidad de MálagaMálagaSpain
| | | | - Hongxin Chen
- Department of Bio‐Interactions and Crop ProtectionRothamsted ResearchHarpendenUK
| | - Jason J. Rudd
- Department of Bio‐Interactions and Crop ProtectionRothamsted ResearchHarpendenUK
| | | | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
- Institute for Plant SciencesCluster of Excellence on Plant Sciences (CEPLAS)University of CologneCologneGermany
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14
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Kramer HM, Cook DE, van den Berg GCM, Seidl MF, Thomma BPHJ. Three putative DNA methyltransferases of Verticillium dahliae differentially contribute to DNA methylation that is dispensable for growth, development and virulence. Epigenetics Chromatin 2021; 14:21. [PMID: 33941240 PMCID: PMC8091789 DOI: 10.1186/s13072-021-00396-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic control mechanism that in many fungi is restricted to genomic regions containing transposable elements (TEs). Two DNA methyltransferases, Dim2 and Dnmt5, are known to perform methylation at cytosines in fungi. While most ascomycete fungi encode both Dim2 and Dnmt5, only few functional studies have been performed in species containing both. METHODS In this study, we report functional analysis of both Dim2 and Dnmt5 in the plant pathogenic fungus Verticillium dahliae. RESULTS Our results show that Dim2, but not Dnmt5 or the putative sexual-cycle-related DNA methyltransferase Rid, is responsible for the majority of DNA methylation under the tested conditions. Single or double DNA methyltransferase mutants did not show altered development, virulence, or transcription of genes or TEs. In contrast, Hp1 and Dim5 mutants that are impacted in chromatin-associated processes upstream of DNA methylation are severely affected in development and virulence and display transcriptional reprogramming in specific hypervariable genomic regions (so-called adaptive genomic regions) that contain genes associated with host colonization. As these adaptive genomic regions are largely devoid of DNA methylation and of Hp1- and Dim5-associated heterochromatin, the differential transcription is likely caused by pleiotropic effects rather than by differential DNA methylation. CONCLUSION Overall, our study suggests that Dim2 is the main DNA methyltransferase in V. dahliae and, in conjunction with work on other fungi, is likely the main active DNMT in ascomycetes, irrespective of Dnmt5 presence. We speculate that Dnmt5 and Rid act under specific, presently enigmatic, conditions or, alternatively, act in DNA-associated processes other than DNA methylation.
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Affiliation(s)
- H Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany.
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15
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Chavarro‐Carrero EA, Vermeulen JP, E. Torres D, Usami T, Schouten HJ, Bai Y, Seidl MF, Thomma BPHJ. Comparative genomics reveals the in planta-secreted Verticillium dahliae Av2 effector protein recognized in tomato plants that carry the V2 resistance locus. Environ Microbiol 2021; 23:1941-1958. [PMID: 33078534 PMCID: PMC8246953 DOI: 10.1111/1462-2920.15288] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/12/2022]
Abstract
Plant pathogens secrete effector molecules during host invasion to promote colonization. However, some of these effectors become recognized by host receptors to mount a defence response and establish immunity. Recently, a novel resistance was identified in wild tomato, mediated by the single dominant V2 locus, to control strains of the soil-borne vascular wilt fungus Verticillium dahliae that belong to race 2. With comparative genomics of race 2 strains and resistance-breaking race 3 strains, we identified the avirulence effector that activates V2 resistance, termed Av2. We identified 277 kb of race 2-specific sequence comprising only two genes encoding predicted secreted proteins that are expressed during tomato colonization. Subsequent functional analysis based on genetic complementation into race 3 isolates and targeted deletion from the race 1 isolate JR2 and race 2 isolate TO22 confirmed that one of the two candidates encodes the avirulence effector Av2 that is recognized in V2 tomato plants. Two Av2 allelic variants were identified that encode Av2 variants that differ by a single acid. Thus far, a role in virulence could not be demonstrated for either of the two variants.
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Affiliation(s)
| | - Jasper P. Vermeulen
- Laboratory of PhytopathologyWageningen University and ResearchWageningen6708 PBThe Netherlands
- Laboratory of Plant BreedingWageningen University and ResearchWageningen6708 PBThe Netherlands
| | - David E. Torres
- Laboratory of PhytopathologyWageningen University and ResearchWageningen6708 PBThe Netherlands
- Theoretical Biology and Bioinformatics Group, Department of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Toshiyuki Usami
- Graduate School of HorticultureChiba UniversityMatsudo, Chiba271‐8510Japan
| | - Henk J. Schouten
- Laboratory of Plant BreedingWageningen University and ResearchWageningen6708 PBThe Netherlands
| | - Yuling Bai
- Laboratory of Plant BreedingWageningen University and ResearchWageningen6708 PBThe Netherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen University and ResearchWageningen6708 PBThe Netherlands
- Theoretical Biology and Bioinformatics Group, Department of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen University and ResearchWageningen6708 PBThe Netherlands
- Cluster of Excellence on Plant Sciences (CEPLAS)University of Cologne, Botanical InstituteCologneGermany
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16
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Ebert MK, Rangel LI, Spanner RE, Taliadoros D, Wang X, Friesen TL, de Jonge R, Neubauer JD, Secor GA, Thomma BPHJ, Stukenbrock EH, Bolton MD. Identification and characterization of Cercospora beticola necrosis-inducing effector CbNip1. Mol Plant Pathol 2021; 22:301-316. [PMID: 33369055 PMCID: PMC7865086 DOI: 10.1111/mpp.13026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 05/30/2023]
Abstract
Cercospora beticola is a hemibiotrophic fungus that causes cercospora leaf spot disease of sugar beet (Beta vulgaris). After an initial symptomless biotrophic phase of colonization, necrotic lesions appear on host leaves as the fungus switches to a necrotrophic lifestyle. The phytotoxic secondary metabolite cercosporin has been shown to facilitate fungal virulence for several Cercospora spp. However, because cercosporin production and subsequent cercosporin-initiated formation of reactive oxygen species is light-dependent, cell death evocation by this toxin is only fully ensured during a period of light. Here, we report the discovery of the effector protein CbNip1 secreted by C. beticola that causes enhanced necrosis in the absence of light and, therefore, may complement light-dependent necrosis formation by cercosporin. Infiltration of CbNip1 protein into sugar beet leaves revealed that darkness is essential for full CbNip1-triggered necrosis, as light exposure delayed CbNip1-triggered host cell death. Gene expression analysis during host infection shows that CbNip1 expression is correlated with symptom development in planta. Targeted gene replacement of CbNip1 leads to a significant reduction in virulence, indicating the importance of CbNip1 during colonization. Analysis of 89 C. beticola genomes revealed that CbNip1 resides in a region that recently underwent a selective sweep, suggesting selection pressure exists to maintain a beneficial variant of the gene. Taken together, CbNip1 is a crucial effector during the C. beticola-sugar beet disease process.
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Affiliation(s)
- Malaika K. Ebert
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNorth DakotaUSA
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
- Present address:
Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Lorena I. Rangel
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
| | - Rebecca E. Spanner
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNorth DakotaUSA
| | - Demetris Taliadoros
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Christian‐Albrechts University of KielKielGermany
| | - Xiaoyun Wang
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
- Present address:
Institute of BiotechnologyCornell UniversityIthacaNew YorkUSA
| | - Timothy L. Friesen
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNorth DakotaUSA
| | - Ronnie de Jonge
- Plant‐Microbe InteractionsDepartment of BiologyUtrecht UniversityUtrechtNetherlands
- Department of Plant Systems BiologyVIBGhentBelgium
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
| | - Jonathan D. Neubauer
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
| | - Gary A. Secor
- Department of Plant PathologyNorth Dakota State UniversityFargoNorth DakotaUSA
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Eva H. Stukenbrock
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Christian‐Albrechts University of KielKielGermany
| | - Melvin D. Bolton
- Edward T. Schafer Agricultural Research CenterUSDA Agricultural Research ServiceFargoNorth DakotaUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNorth DakotaUSA
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17
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Hanika K, Schipper D, Chinnappa S, Oortwijn M, Schouten HJ, Thomma BPHJ, Bai Y. Impairment of Tomato WAT1 Enhances Resistance to Vascular Wilt Fungi Despite Severe Growth Defects. Front Plant Sci 2021; 12:721674. [PMID: 34589102 PMCID: PMC8473820 DOI: 10.3389/fpls.2021.721674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/25/2021] [Indexed: 05/18/2023]
Abstract
Verticillium dahliae is a particularly notorious vascular wilt pathogen of tomato and poses a reoccurring challenge to crop protection as limited qualitative resistance is available. Therefore, alternative approaches for crop protection are pursued. One such strategy is the impairment of disease susceptibility (S) genes, which are plant genes targeted by pathogens to promote disease development. In Arabidopsis and cotton, the Walls Are Thin 1 (WAT1) gene has shown to be a S gene for V. dahliae. In this study, we identified the tomato WAT1 homolog Solyc04g080940 (SlWAT1). Transient and stable silencing of SlWAT1, based on virus-induced gene silencing (VIGS) and RNAi, respectively, did not consistently lead to reduced V. dahliae susceptibility in tomato. However, CRISPR-Cas9 tomato mutant lines carrying targeted deletions in SlWAT1 showed significantly enhanced resistance to V. dahliae, and furthermore also to Verticillium albo-atrum and Fusarium oxysporum f. sp. lycopersici (Fol). Thus, disabling the tomato WAT1 gene resulted in broad-spectrum resistance to various vascular pathogens in tomato. Unfortunately these tomato CRISPR mutant lines suffered from severe growth defects. In order to overcome the pleiotropic effect caused by the impairment of the tomato WAT1 gene, future efforts should be devoted to identifying tomato SlWAT1 mutant alleles that do not negatively impact tomato growth and development.
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Affiliation(s)
- Katharina Hanika
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Danny Schipper
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Shravya Chinnappa
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Marian Oortwijn
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Henk J. Schouten
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Yuling Bai,
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18
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Cook DE, Kramer HM, Torres DE, Seidl MF, Thomma BPHJ. A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen. eLife 2020; 9:e62208. [PMID: 33337321 PMCID: PMC7781603 DOI: 10.7554/elife.62208] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus Verticillium dahliae. We identified incomplete DNA methylation of repetitive elements, associated with specific genomic compartments originally defined as Lineage-Specific (LS) regions that contain genes involved in host adaptation. Further chromatin characterization revealed associations with features such as H3 Lys-27 methylated histones (H3K27me3) and accessible DNA. Machine learning trained on chromatin data identified twice as much LS DNA as previously recognized, which was validated through orthogonal analysis, and we propose to refer to this DNA as adaptive genomic regions. Our results provide evidence that specific chromatin profiles define adaptive genomic regions, and highlight how different epigenetic factors contribute to the organization of these regions.
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Affiliation(s)
- David E Cook
- Department of Plant Pathology, Kansas State UniversityManhattanUnited States
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
| | - David E Torres
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht UniversityUtrechtNetherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht UniversityUtrechtNetherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
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Snelders NC, Rovenich H, Petti GC, Rocafort M, van den Berg GCM, Vorholt JA, Mesters JR, Seidl MF, Nijland R, Thomma BPHJ. Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins. Nat Plants 2020; 6:1365-1374. [PMID: 33139860 DOI: 10.1038/s41477-020-00799-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 09/29/2020] [Indexed: 05/23/2023]
Abstract
During colonization of their hosts, pathogens secrete effector proteins to promote disease development through various mechanisms. Increasing evidence shows that the host microbiome plays a crucial role in health, and that hosts actively shape their microbiomes to suppress disease. We proposed that pathogens evolved to manipulate host microbiomes to their advantage in turn. Here, we show that the previously identified virulence effector VdAve1, secreted by the fungal plant pathogen Verticillium dahliae, displays antimicrobial activity and facilitates colonization of tomato and cotton through the manipulation of their microbiomes by suppressing antagonistic bacteria. Moreover, we show that VdAve1, and also the newly identified antimicrobial effector VdAMP2, are exploited for microbiome manipulation in the soil environment, where the fungus resides in absence of a host. In conclusion, we demonstrate that a fungal plant pathogen uses effector proteins to modulate microbiome compositions inside and outside the host, and propose that pathogen effector catalogues represent an untapped resource for new antibiotics.
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Affiliation(s)
- Nick C Snelders
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hanna Rovenich
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Gabriella C Petti
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Mercedes Rocafort
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Jeroen R Mesters
- Institute of Biochemistry, University of Lübeck, Center for Structural and Cell Biology in Medicine, Lübeck, Germany
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Reindert Nijland
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Marine Animal Ecology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands.
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Botanical Institute, Cologne, Germany.
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20
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Seidl MF, Kramer HM, Cook DE, Fiorin GL, van den Berg GCM, Faino L, Thomma BPHJ. Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium. mBio 2020; 11:e01714-20. [PMID: 32900804 PMCID: PMC7482064 DOI: 10.1128/mbio.01714-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
Centromeres are chromosomal regions that are crucial for chromosome segregation during mitosis and meiosis, and failed centromere formation can contribute to chromosomal anomalies. Despite this conserved function, centromeres differ significantly between and even within species. Thus far, systematic studies into the organization and evolution of fungal centromeres remain scarce. In this study, we identified the centromeres in each of the 10 species of the fungal genus Verticillium and characterized their organization and evolution. Chromatin immunoprecipitation of the centromere-specific histone CenH3 (ChIP-seq) and chromatin conformation capture (Hi-C) followed by high-throughput sequencing identified eight conserved, large (∼150-kb), AT-, and repeat-rich regional centromeres that are embedded in heterochromatin in the plant pathogen Verticillium dahliae Using Hi-C, we similarly identified repeat-rich centromeres in the other Verticillium species. Strikingly, a single degenerated long terminal repeat (LTR) retrotransposon is strongly associated with centromeric regions in some but not all Verticillium species. Extensive chromosomal rearrangements occurred during Verticillium evolution, of which some could be linked to centromeres, suggesting that centromeres contributed to chromosomal evolution. The size and organization of centromeres differ considerably between species, and centromere size was found to correlate with the genome-wide repeat content. Overall, our study highlights the contribution of repetitive elements to the diversity and rapid evolution of centromeres within the fungal genus VerticilliumIMPORTANCE The genus Verticillium contains 10 species of plant-associated fungi, some of which are notorious pathogens. Verticillium species evolved by frequent chromosomal rearrangements that contribute to genome plasticity. Centromeres are instrumental for separation of chromosomes during mitosis and meiosis, and failed centromere functionality can lead to chromosomal anomalies. Here, we used a combination of experimental techniques to identify and characterize centromeres in each of the Verticillium species. Intriguingly, we could strongly associate a single repetitive element to the centromeres of some of the Verticillium species. The presence of this element in the centromeres coincides with increased centromere sizes and genome-wide repeat expansions. Collectively, our findings signify a role of repetitive elements in the function, organization, and rapid evolution of centromeres in a set of closely related fungal species.
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Affiliation(s)
- Michael F Seidl
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | | | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Environmental Biology Department, Sapienza Università di Roma, Rome, Italy
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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21
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Sánchez-Vallet A, Tian H, Rodriguez-Moreno L, Valkenburg DJ, Saleem-Batcha R, Wawra S, Kombrink A, Verhage L, de Jonge R, van Esse HP, Zuccaro A, Croll D, Mesters JR, Thomma BPHJ. A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization. PLoS Pathog 2020; 16:e1008652. [PMID: 32574207 PMCID: PMC7337405 DOI: 10.1371/journal.ppat.1008652] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 07/06/2020] [Accepted: 05/25/2020] [Indexed: 12/25/2022] Open
Abstract
Plants trigger immune responses upon recognition of fungal cell wall chitin, followed by the release of various antimicrobials, including chitinase enzymes that hydrolyze chitin. In turn, many fungal pathogens secrete LysM effectors that prevent chitin recognition by the host through scavenging of chitin oligomers. We previously showed that intrachain LysM dimerization of the Cladosporium fulvum effector Ecp6 confers an ultrahigh-affinity binding groove that competitively sequesters chitin oligomers from host immune receptors. Additionally, particular LysM effectors are found to protect fungal hyphae against chitinase hydrolysis during host colonization. However, the molecular basis for the protection of fungal cell walls against hydrolysis remained unclear. Here, we determined a crystal structure of the single LysM domain-containing effector Mg1LysM of the wheat pathogen Zymoseptoria tritici and reveal that Mg1LysM is involved in the formation of two kinds of dimers; a chitin-dependent dimer as well as a chitin-independent homodimer. In this manner, Mg1LysM gains the capacity to form a supramolecular structure by chitin-induced oligomerization of chitin-independent Mg1LysM homodimers, a property that confers protection to fungal cell walls against host chitinases. Chitin plays a central role in plant-fungi interactions, since it is a major component of the fungal cell wall that is targeted by host hydrolytic enzymes to inhibit the growth of fungal pathogens on the one hand, and release chitin fragments that are recognized by host immune receptors to activate further immune responses on the other hand. In turn, many fungal pathogens secrete chitin binding LysM effectors to which currently two functions have been assigned. Most LysM effectors that were functionally characterized to date function to prevent chitin recognition by host immune receptors through chitin sequestration. Additionally, some LysM effectors were shown to protect fungal hyphae against hydrolysis by host chitinases. The crystal structure of Mg1LysM from the Septoria blotch pathogen of wheat, Zymoseptoria tritici, revealed that chitin-induced dimerization of two Mg1LysM protomers through high affinity binding is required for hyphal protection against chitinases. Since Mg1LysM also forms ligand-independent homodimers, a supramolecular structure can be formed in which chitin-induced oligomerization of Mg1LysM ligand-independent homodimers form a contiguous Mg1LysM higher ordered structure that is anchored to the chitin in the fungal cell wall to prevent hydrolysis by host chitinases.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Hui Tian
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Luis Rodriguez-Moreno
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Dirk-Jan Valkenburg
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Raspudin Saleem-Batcha
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
| | - Stephan Wawra
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Anja Kombrink
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Leonie Verhage
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Ronnie de Jonge
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - H. Peter van Esse
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Daniel Croll
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Jeroen R. Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
- * E-mail: (JRM); (BPHJT)
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University& Research, Wageningen, The Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
- * E-mail: (JRM); (BPHJT)
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Fiorin GL, Sánchez-Vallet A, Thomma BPHJ, Pereira GAG, Teixeira PJPL. MAMP-triggered Medium Alkalinization of Plant Cell Cultures. Bio Protoc 2020; 10:e3588. [PMID: 33659555 PMCID: PMC7842674 DOI: 10.21769/bioprotoc.3588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/18/2020] [Accepted: 01/26/2020] [Indexed: 11/02/2022] Open
Abstract
Plants recognize a wide variety of microbial molecules to detect and respond to potential invaders. Recognition of Microbe-Associated Molecular Patterns (MAMPs) by cell surface receptors initiate a cascade of biochemical responses that include, among others, ion fluxes across the plasma membrane. A consequence of such event is a decrease in the concentration of extracellular H+ ions, which can be experimentally detected in plant cell suspensions as a shift in the pH of the medium. Thus, similarly to reactive oxygen species (ROS) accumulation, phosphorylation of MAP kinases and induction of defense-related genes, MAMP-induced medium alkalinization can be used as a proxy for the activation of plant immune responses. Here, we describe a detailed protocol for the measurement of medium alkalinization of tobacco BY-2 cell suspensions upon treatment with two different MAMPs: chitohexamers derived from fungal cell walls (NAG6; N-acetylglucosamine) and the flagellin epitope flg22, found in the bacterial flagellum. This method provides a reliable and fast platform to access MAMP-Triggered Immunity (MTI) in tobacco cell suspensions and can be easily adapted to other plant species as well as to other MAMPs.
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Affiliation(s)
- Gabriel L. Fiorin
- Graduate Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, Brazil
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas, Campinas, Brazil
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
| | - Andrea Sánchez-Vallet
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Switzerland
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, The Netherlands
| | - Gonçalo A. G. Pereira
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo J. P. L. Teixeira
- Laboratório de Genética e Imunologia de Plantas, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), Piracicaba, Brazil
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23
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Zeng T, Rodriguez‐Moreno L, Mansurkhodzaev A, Wang P, van den Berg W, Gasciolli V, Cottaz S, Fort S, Thomma BPHJ, Bono J, Bisseling T, Limpens E. A lysin motif effector subverts chitin-triggered immunity to facilitate arbuscular mycorrhizal symbiosis. New Phytol 2020; 225:448-460. [PMID: 31596956 PMCID: PMC6916333 DOI: 10.1111/nph.16245] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/24/2019] [Indexed: 05/13/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi greatly improve mineral uptake by host plants in nutrient-depleted soil and can intracellularly colonize root cortex cells in the vast majority of higher plants. However, AM fungi possess common fungal cell wall components such as chitin that can be recognized by plant chitin receptors to trigger immune responses, raising the question as to how AM fungi effectively evade chitin-triggered immune responses during symbiosis. In this study, we characterize a secreted lysin motif (LysM) effector identified from the model AM fungal species Rhizophagus irregularis, called RiSLM. RiSLM is one of the highest expressed effector proteins in intraradical mycelium during the symbiosis. In vitro binding assays show that RiSLM binds chitin-oligosaccharides and can protect fungal cell walls from chitinases. Moreover, RiSLM efficiently interferes with chitin-triggered immune responses, such as defence gene induction and reactive oxygen species production in Medicago truncatula. Although RiSLM also binds to symbiotic (lipo)chitooligosaccharides it does not interfere significantly with symbiotic signalling in Medicago. Host-induced gene silencing of RiSLM greatly reduces fungal colonization levels. Taken together, our results reveal a key role for AM fungal LysM effectors to subvert chitin-triggered immunity in symbiosis, pointing to a common role for LysM effectors in both symbiotic and pathogenic fungi.
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Affiliation(s)
- Tian Zeng
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Luis Rodriguez‐Moreno
- Department of Plant SciencesLaboratory of PhytopathologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Artem Mansurkhodzaev
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Peng Wang
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Willy van den Berg
- Laboratory of BiochemistryWageningen University & Research6708 WEWageningenthe Netherlands
| | | | - Sylvain Cottaz
- CNRSCERMAVUniversity Grenoble AlpesUPR 530138041GrenobleFrance
| | - Sébastien Fort
- CNRSCERMAVUniversity Grenoble AlpesUPR 530138041GrenobleFrance
| | - Bart P. H. J. Thomma
- Department of Plant SciencesLaboratory of PhytopathologyWageningen University & Research6708 PBWageningenthe Netherlands
| | | | - Ton Bisseling
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
| | - Erik Limpens
- Laboratory of Molecular BiologyWageningen University & Research6708 PBWageningenthe Netherlands
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Volk H, Marton K, Flajšman M, Radišek S, Tian H, Hein I, Podlipnik Č, Thomma BPHJ, Košmelj K, Javornik B, Berne S. Chitin-Binding Protein of Verticillium nonalfalfae Disguises Fungus from Plant Chitinases and Suppresses Chitin-Triggered Host Immunity. Mol Plant Microbe Interact 2019; 32:1378-1390. [PMID: 31063047 DOI: 10.1094/mpmi-03-19-0079-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During fungal infections, plant cells secrete chitinases, which digest chitin in the fungal cell walls. The recognition of released chitin oligomers via lysin motif (LysM)-containing immune host receptors results in the activation of defense signaling pathways. We report here that Verticillium nonalfalfae, a hemibiotrophic xylem-invading fungus, prevents these digestion and recognition processes by secreting a carbohydrate-binding motif 18 (CBM18)-chitin-binding protein, VnaChtBP, which is transcriptionally activated specifically during the parasitic life stages. VnaChtBP is encoded by the Vna8.213 gene, which is highly conserved within the species, suggesting high evolutionary stability and importance for the fungal lifestyle. In a pathogenicity assay, however, Vna8.213 knockout mutants exhibited wilting symptoms similar to the wild-type fungus, suggesting that Vna8.213 activity is functionally redundant during fungal infection of hop. In a binding assay, recombinant VnaChtBP bound chitin and chitin oligomers in vitro with submicromolar affinity and protected fungal hyphae from degradation by plant chitinases. Moreover, the chitin-triggered production of reactive oxygen species from hop suspension cells was abolished in the presence of VnaChtBP, indicating that VnaChtBP also acts as a suppressor of chitin-triggered immunity. Using a yeast-two-hybrid assay, circular dichroism, homology modeling, and molecular docking, we demonstrated that VnaChtBP forms dimers in the absence of ligands and that this interaction is stabilized by the binding of chitin hexamers with a similar preference in the two binding sites. Our data suggest that, in addition to chitin-binding LysM (CBM50) and Avr4 (CBM14) fungal effectors, structurally unrelated CBM18 effectors have convergently evolved to prevent hydrolysis of the fungal cell wall against plant chitinases and to interfere with chitin-triggered host immunity.
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Affiliation(s)
- Helena Volk
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Kristina Marton
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Marko Flajšman
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - Hui Tian
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ingo Hein
- The James Hutton Institute (JHI), Invergowrie, Dundee DD2 5DA, Scotland, U.K
- The University of Dundee, School of Life Sciences, Division of Plant Sciences at the JHI, Invergowrie
| | - Črtomir Podlipnik
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Katarina Košmelj
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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25
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Depotter JRL, Shi-Kunne X, Missonnier H, Liu T, Faino L, van den Berg GCM, Wood TA, Zhang B, Jacques A, Seidl MF, Thomma BPHJ. Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation. Mol Ecol 2019; 28:3482-3495. [PMID: 31282048 PMCID: PMC6771948 DOI: 10.1111/mec.15168] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/23/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two‐speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so‐called lineage‐specific regions, that are enriched in in planta‐induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage‐specific regions and the core genome. Unanticipated, lineage‐specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage‐specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage‐specific regions of V. dahliae.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands.,Department of Crops and Agronomy, National Institute of Agricultural Botany, Cambridge, UK
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hélène Missonnier
- Département des Sciences Agronomiques et Agroalimentaires, Equipe Agrophysiologie et Agromolécules, Institut National Polytechnique de Toulouse - Ecole d'Ingénieurs de Purpan, Université de Toulouse, Toulouse, France
| | - Tingli Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Cambridge, UK
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Alban Jacques
- Département des Sciences Agronomiques et Agroalimentaires, Equipe Agrophysiologie et Agromolécules, Institut National Polytechnique de Toulouse - Ecole d'Ingénieurs de Purpan, Université de Toulouse, Toulouse, France
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
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26
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Zhang Z, Song Y, Liu CM, Thomma BPHJ. Correction: Mutational Analysis of the Ve1 Immune Receptor That Mediates Verticillium Resistance in Tomato. PLoS One 2019; 14:e0220402. [PMID: 31335905 PMCID: PMC6650063 DOI: 10.1371/journal.pone.0220402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Shi-Kunne X, Jové RDP, Depotter JRL, Ebert MK, Seidl MF, Thomma BPHJ. In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae. FEMS Microbiol Lett 2019; 366:5475643. [PMID: 31004487 PMCID: PMC6502550 DOI: 10.1093/femsle/fnz081] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/23/2019] [Indexed: 01/07/2023] Open
Abstract
Fungi are renowned producers of natural compounds, also known as secondary metabolites (SMs) that display a wide array of biological activities. Typically, the genes that are involved in the biosynthesis of SMs are located in close proximity to each other in so-called secondary metabolite clusters. Many plant-pathogenic fungi secrete SMs during infection in order to promote disease establishment, for instance as cytocoxic compounds. Verticillium dahliae is a notorious plant pathogen that can infect over 200 host plants worldwide. However, the SM repertoire of this vascular pathogen remains mostly uncharted. To unravel the potential of V. dahliae to produce SMs, we performed in silico predictions and in-depth analyses of its secondary metabolite clusters. Using distinctive traits of gene clusters and the conserved signatures of core genes 25 potential SM gene clusters were identified. Subsequently, phylogenetic and comparative genomics analyses were performed, revealing that two putative siderophores, ferricrocin and TAFC, DHN-melanin and fujikurin may belong to the SM repertoire of V. dahliae.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Roger de Pedro Jové
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands,Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, CB3 0LE Cambridge, United Kingdom
| | - Malaika K Ebert
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands,Corresponding author: Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Tel: 0031-317-484536; Fax: 0031-317-483412; E-mail:
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28
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Ebert MK, Spanner RE, de Jonge R, Smith DJ, Holthusen J, Secor GA, Thomma BPHJ, Bolton MD. Gene cluster conservation identifies melanin and perylenequinone biosynthesis pathways in multiple plant pathogenic fungi. Environ Microbiol 2019; 21:913-927. [PMID: 30421572 PMCID: PMC7379194 DOI: 10.1111/1462-2920.14475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
Abstract
Perylenequinones are a family of structurally related polyketide fungal toxins with nearly universal toxicity. These photosensitizing compounds absorb light energy which enables them to generate reactive oxygen species that damage host cells. This potent mechanism serves as an effective weapon for plant pathogens in disease or niche establishment. The sugar beet pathogen Cercospora beticola secretes the perylenequinone cercosporin during infection. We have shown recently that the cercosporin toxin biosynthesis (CTB) gene cluster is present in several other phytopathogenic fungi, prompting the search for biosynthetic gene clusters (BGCs) of structurally similar perylenequinones in other fungi. Here, we report the identification of the elsinochrome and phleichrome BGCs of Elsinoë fawcettii and Cladosporium phlei, respectively, based on gene cluster conservation with the CTB and hypocrellin BGCs. Furthermore, we show that previously reported BGCs for elsinochrome and phleichrome are involved in melanin production. Phylogenetic analysis of the corresponding melanin polyketide synthases (PKSs) and alignment of melanin BGCs revealed high conservation between the established and newly identified C. beticola, E. fawcettii and C. phlei melanin BGCs. Mutagenesis of the identified perylenequinone and melanin PKSs in C. beticola and E. fawcettii coupled with mass spectrometric metabolite analyses confirmed their roles in toxin and melanin production.
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Affiliation(s)
- Malaika K. Ebert
- Red River Valley Agricultural Research CenterUSDA Agricultural Research ServiceFargoNDUSA,Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA,Laboratory of PhytopathologyWageningen UniversityWageningenThe Netherlands
| | - Rebecca E. Spanner
- Red River Valley Agricultural Research CenterUSDA Agricultural Research ServiceFargoNDUSA,Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Ronnie de Jonge
- Plant‐Microbe Interactions, Department of BiologyScience4Life, Utrecht UniversityUtrechtThe Netherlands,Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium,VIB Center for Plant Systems BiologyGhentBelgium
| | - David J. Smith
- Red River Valley Agricultural Research CenterUSDA Agricultural Research ServiceFargoNDUSA
| | - Jason Holthusen
- Red River Valley Agricultural Research CenterUSDA Agricultural Research ServiceFargoNDUSA
| | - Gary A. Secor
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | | | - Melvin D. Bolton
- Red River Valley Agricultural Research CenterUSDA Agricultural Research ServiceFargoNDUSA,Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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29
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Shi-Kunne X, van Kooten M, Depotter JRL, Thomma BPHJ, Seidl MF. The Genome of the Fungal Pathogen Verticillium dahliae Reveals Extensive Bacterial to Fungal Gene Transfer. Genome Biol Evol 2019; 11:855-868. [PMID: 30799497 PMCID: PMC6430987 DOI: 10.1093/gbe/evz040] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2019] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) involves the transmission of genetic material between distinct evolutionary lineages and can be an important source of biological innovation. Reports of interkingdom HGT to eukaryotic microbial pathogens have accumulated over recent years. Verticillium dahliae is a notorious plant pathogen that causes vascular wilt disease on hundreds of plant species, resulting in high economic losses every year. Previously, the effector gene Ave1 and a glucosyltransferase-encoding gene were identified as virulence factor-encoding genes that were proposed to be horizontally acquired from a plant and a bacterial donor, respectively. However, to what extent HGT contributed to the overall genome composition of V. dahliae remained elusive. Here, we systematically searched for evidence of interkingdom HGT events in the genome of V. dahliae and provide evidence for extensive horizontal gene acquisition from bacterial origin.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Mathijs van Kooten
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Cambridge, United Kingdom
- Present address: Botanical Institute, University of Cologne, BioCenter, Cologne, Germany
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Present address: Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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30
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Fiorin GL, Sanchéz-Vallet A, Thomazella DPDT, do Prado PFV, do Nascimento LC, Figueira AVDO, Thomma BPHJ, Pereira GAG, Teixeira PJPL. Suppression of Plant Immunity by Fungal Chitinase-like Effectors. Curr Biol 2018; 28:3023-3030.e5. [PMID: 30220500 DOI: 10.1016/j.cub.2018.07.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/03/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
Crop diseases caused by fungi constitute one of the most important problems in agriculture, posing a serious threat to food security [1]. To establish infection, phytopathogens interfere with plant immune responses [2, 3]. However, strategies to promote virulence employed by fungal pathogens, especially non-model organisms, remain elusive [4], mainly because fungi are more complex and difficult to study when compared to the better-characterized bacterial pathogens. Equally incomplete is our understanding of the birth of microbial virulence effectors. Here, we show that the cacao pathogen Moniliophthora perniciosa evolved an enzymatically inactive chitinase (MpChi) that functions as a putative pathogenicity factor. MpChi is among the most highly expressed fungal genes during the biotrophic interaction with cacao and encodes a chitinase with mutations that abolish its enzymatic activity. Despite the lack of chitinolytic activity, MpChi retains substrate binding specificity and prevents chitin-triggered immunity by sequestering immunogenic chitin fragments. Remarkably, its sister species M. roreri encodes a second non-orthologous catalytically impaired chitinase with equivalent function. Thus, a class of conserved enzymes independently evolved as putative virulence factors in these fungi. In addition to unveiling a strategy of host immune suppression by fungal pathogens, our results demonstrate that the neofunctionalization of enzymes may be an evolutionary pathway for the rise of new virulence factors in fungi. We anticipate that analogous strategies are likely employed by other pathogens.
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Affiliation(s)
- Gabriel Lorencini Fiorin
- Graduate Program in Genetics and Molecular Biology, Instituto de Biologia, Universidade de Estadual de Campinas, Campinas 13083-970, Brazil; Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil
| | - Andrea Sanchéz-Vallet
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 Wageningen, the Netherlands; Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | - Paula Favoretti Vital do Prado
- Graduate Program in Genetics and Molecular Biology, Instituto de Biologia, Universidade de Estadual de Campinas, Campinas 13083-970, Brazil; Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil
| | - Leandro Costa do Nascimento
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil; Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, Campinas 13083-970, Brazil
| | - Antonio Vargas de Oliveira Figueira
- Laboratório de Melhoramento de Plantas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Campus "Luiz de Queiroz," Piracicaba 13400-970, Brazil
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 Wageningen, the Netherlands
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil.
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31
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Abstract
Plants secrete extracellular vesicles to prevent fungal infection
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Affiliation(s)
- Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - David E. Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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32
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Kema GHJ, Mirzadi Gohari A, Aouini L, Gibriel HAY, Ware SB, van den Bosch F, Manning-Smith R, Alonso-Chavez V, Helps J, Ben M'Barek S, Mehrabi R, Diaz-Trujillo C, Zamani E, Schouten HJ, van der Lee TAJ, Waalwijk C, de Waard MA, de Wit PJGM, Verstappen ECP, Thomma BPHJ, Meijer HJG, Seidl MF. Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance. Nat Genet 2018; 50:375-380. [PMID: 29434356 DOI: 10.1038/s41588-018-0052-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/06/2018] [Indexed: 11/09/2022]
Abstract
Host resistance and fungicide treatments are cornerstones of plant-disease control. Here, we show that these treatments allow sex and modulate parenthood in the fungal wheat pathogen Zymoseptoria tritici. We demonstrate that the Z. tritici-wheat interaction complies with the gene-for-gene model by identifying the effector AvrStb6, which is recognized by the wheat resistance protein Stb6. Recognition triggers host resistance, thus implying removal of avirulent strains from pathogen populations. However, Z. tritici crosses on wheat show that sex occurs even with an avirulent parent, and avirulence alleles are thereby retained in subsequent populations. Crossing fungicide-sensitive and fungicide-resistant isolates under fungicide pressure results in a rapid increase in resistance-allele frequency. Isolates under selection always act as male donors, and thus disease control modulates parenthood. Modeling these observations for agricultural and natural environments reveals extended durability of host resistance and rapid emergence of fungicide resistance. Therefore, fungal sex has major implications for disease control.
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Affiliation(s)
- Gerrit H J Kema
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands. .,Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands.
| | - Amir Mirzadi Gohari
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands.,Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Lamia Aouini
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Hesham A Y Gibriel
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Sarah B Ware
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands.,Department of Biological Sciences, Benedictine University, Lisle, IL, USA
| | | | | | | | | | - Sarrah Ben M'Barek
- Laboratory of Molecular Plant Physiology, Biotechnology Center of Borj Cedria (CBBC), Hammam-Lif, Tunisia
| | - Rahim Mehrabi
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Caucasella Diaz-Trujillo
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands.,Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Elham Zamani
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Henk J Schouten
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Theo A J van der Lee
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Maarten A de Waard
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Els C P Verstappen
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Harold J G Meijer
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
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33
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Song Y, Liu L, Wang Y, Valkenburg D, Zhang X, Zhu L, Thomma BPHJ. Transfer of tomato immune receptor Ve1 confers Ave1-dependent Verticillium resistance in tobacco and cotton. Plant Biotechnol J 2018; 16:638-648. [PMID: 28796297 PMCID: PMC5787823 DOI: 10.1111/pbi.12804] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/14/2017] [Accepted: 08/02/2017] [Indexed: 05/24/2023]
Abstract
Verticillium wilts caused by soilborne fungal species of the Verticillium genus are economically important plant diseases that affect a wide range of host plants and are notoriously difficult to combat. Perception of pathogen(-induced) ligands by plant immune receptors is a key component of plant innate immunity. In tomato, race-specific resistance to Verticillium wilt is governed by the cell surface-localized immune receptor Ve1 through recognition of the effector protein Ave1 that is secreted by race 1 strains of Verticillium spp. It was previously demonstrated that transgenic expression of tomato Ve1 in the model plant Arabidopsis thaliana leads to Verticillium wilt resistance. Here, we investigated whether tomato Ve1 can confer Verticillium resistance when expressed in the crop species tobacco (Nicotiana tabcum) and cotton (Gossypium hirsutum). We show that transgenic tobacco and cotton plants constitutively expressing tomato Ve1 exhibit enhanced resistance against Verticillium wilt in an Ave1-dependent manner. Thus, we demonstrate that the functionality of tomato Ve1 in Verticillium wilt resistance through recognition of the Verticillium effector Ave1 is retained after transfer to tobacco and cotton, implying that the Ve1-mediated immune signalling pathway is evolutionary conserved across these plant species. Moreover, our results suggest that transfer of tomato Ve1 across sexually incompatible plant species can be exploited in breeding programmes to engineer Verticillium wilt resistance.
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Affiliation(s)
- Yin Song
- Laboratory of PhytopathologyWageningen UniversityWageningenThe Netherlands
| | - Linlin Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Yidong Wang
- Laboratory of PhytopathologyWageningen UniversityWageningenThe Netherlands
| | | | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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34
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Rodriguez-Moreno L, Ebert MK, Bolton MD, Thomma BPHJ. Tools of the crook- infection strategies of fungal plant pathogens. Plant J 2018; 93:664-674. [PMID: 29277938 DOI: 10.1111/tpj.13810] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 05/14/2023]
Abstract
Fungi represent an ecologically diverse group of microorganisms that includes plant pathogenic species able to cause considerable yield loses in crop production systems worldwide. In order to establish compatible interactions with their hosts, pathogenic fungi rely on the secretion of molecules of diverse nature during host colonization to modulate host physiology, manipulate other environmental factors or provide self-defence. These molecules, collectively known as effectors, are typically small secreted cysteine-rich proteins, but may also comprise secondary metabolites and sRNAs. Here, we discuss the most common strategies that fungal plant pathogens employ to subvert their host plants in order to successfully complete their life cycle and secure the release of abundant viable progeny.
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Affiliation(s)
- Luis Rodriguez-Moreno
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Malaika K Ebert
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Melvin D Bolton
- USDA - Agricultural Research Service, Red River Valley Agricultural Research Center, Fargo, ND, USA
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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35
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Snelders NC, Kettles GJ, Rudd JJ, Thomma BPHJ. Plant pathogen effector proteins as manipulators of host microbiomes? Mol Plant Pathol 2018; 19:257-259. [PMID: 29368817 PMCID: PMC5817402 DOI: 10.1111/mpp.12628] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 05/23/2023]
Affiliation(s)
- Nick C. Snelders
- Laboratory of PhytopathologyWageningen University and Research6708 PB Wageningenthe Netherlands
| | - Graeme J. Kettles
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Jason J. Rudd
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen University and Research6708 PB Wageningenthe Netherlands
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36
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Shi-Kunne X, Faino L, van den Berg GCM, Thomma BPHJ, Seidl MF. Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ Microbiol 2018; 20:1362-1373. [PMID: 29282842 DOI: 10.1111/1462-2920.14037] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 01/09/2023]
Abstract
The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plant pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ∼11 000 genes that are shared at least between two species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than the shared genes.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, Wageningen, The Netherlands 6708 PB
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37
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Song Y, Thomma BPHJ. Host-induced gene silencing compromises Verticillium wilt in tomato and Arabidopsis. Mol Plant Pathol 2018; 19:77-89. [PMID: 27749994 PMCID: PMC6638114 DOI: 10.1111/mpp.12500] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 05/03/2023]
Abstract
Verticillium wilt, caused by soil-borne fungi of the genus Verticillium, is an economically important disease that affects a wide range of host plants. Unfortunately, host resistance against Verticillium wilts is not available for many plant species, and the disease is notoriously difficult to combat. Host-induced gene silencing (HIGS) is an RNA interference (RNAi)-based process in which small RNAs are produced by the host plant to target parasite transcripts. HIGS has emerged as a promising strategy for the improvement of plant resistance against pathogens by silencing genes that are essential for these pathogens. Here, we assessed whether HIGS can be utilized to suppress Verticillium wilt disease by silencing three previously identified virulence genes of V. dahliae (encoding Ave1, Sge1 and NLP1) through the host plants tomato and Arabidopsis. In transient assays, tomato plants were agroinfiltrated with Tobacco rattle virus (TRV) constructs to target V. dahliae transcripts. Subsequent V. dahliae inoculation revealed the suppression of Verticillium wilt disease on treatment with only one of the three TRV constructs. Next, expression of RNAi constructs targeting transcripts of the same three V. dahliae virulence genes was pursued in stable transgenic Arabidopsis thaliana plants. In this host, V. dahliae inoculation revealed reduced Verticillium wilt disease in two of the three targets. Thus, our study suggests that, depending on the target gene chosen, HIGS against V. dahliae is operational in tomato and A. thaliana plants and may be exploited to engineer resistance in Verticillium wilt-susceptible crops.
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Affiliation(s)
- Yin Song
- Laboratory of PhytopathologyWageningen University, Droevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen University, Droevendaalsesteeg 1Wageningen6708 PBthe Netherlands
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38
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Depotter JRL, Rodriguez-Moreno L, Thomma BPHJ, Wood TA. The Emerging British Verticillium longisporum Population Consists of Aggressive Brassica Pathogens. Phytopathology 2017; 107:1399-1405. [PMID: 28653577 DOI: 10.1094/phyto-05-17-0184-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Verticillium longisporum is an economically important fungal pathogen of brassicaceous crops that originated from at least three hybridization events between different Verticillium spp., leading to the hybrid lineages A1/D1, A1/D2, and A1/D3. Isolates of lineage A1/D1 generally cause stem striping on oilseed rape (Brassica napus), which has recently been reported for the first time to occur in the United Kingdom. Intriguingly, the emerging U.K. population is distinct from the north-central European stem striping population. Little is known about the pathogenicity of the newly emerged U.K. population; hence, pathogenicity tests were executed to compare British isolates to previously characterized reference strains. In addition to the model plant Arabidopsis thaliana, the pathogenicity of four British isolates was assessed on four cultivars of three Brassica crop species: oilseed rape (Quartz and Incentive), cauliflower (Clapton), and Chinese cabbage (Hilton). To this end, vascular discoloration of the roots, plant biomass accumulations, and fungal stem colonization upon isolate infection were evaluated. The British isolates appeared to be remarkably aggressive, because plant biomass was significantly affected and severe vascular discoloration was observed. The British isolates were successful stem colonizers and the extent of fungal colonization negatively correlated with plant biomass of cauliflower and Quartz oilseed rape. However, in Quartz, the fungal colonization of A1/D1 isolates was significantly lower than that of the virulent reference isolate from lineage A1/D3, PD589. Moreover, despite levels of stem colonization similar to those of A1/D1 strains, PD589 did not cause significant disease on Incentive. Thus, A1/D1 isolates, including British isolates, are aggressive oilseed rape pathogens despite limited colonization levels in comparison with a virulent A1/D3 isolate.
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Affiliation(s)
- Jasper R L Depotter
- First, second, and third authors: Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; and first and fourth authors: Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, CB3 0LE Cambridge, United Kingdom
| | - Luis Rodriguez-Moreno
- First, second, and third authors: Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; and first and fourth authors: Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, CB3 0LE Cambridge, United Kingdom
| | - Bart P H J Thomma
- First, second, and third authors: Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; and first and fourth authors: Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, CB3 0LE Cambridge, United Kingdom
| | - Thomas A Wood
- First, second, and third authors: Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; and first and fourth authors: Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, CB3 0LE Cambridge, United Kingdom
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Seidl MF, Thomma BPHJ. Transposable Elements Direct The Coevolution between Plants and Microbes. Trends Genet 2017; 33:842-851. [PMID: 28800915 DOI: 10.1016/j.tig.2017.07.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
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Depotter JRL, Seidl MF, van den Berg GCM, Thomma BPHJ, Wood TA. A distinct and genetically diverse lineage of the hybrid fungal pathogen Verticillium longisporum population causes stem striping in British oilseed rape. Environ Microbiol 2017; 19:3997-4009. [PMID: 28523726 DOI: 10.1111/1462-2920.13801] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/11/2017] [Accepted: 05/13/2017] [Indexed: 11/30/2022]
Abstract
Population genetic structures illustrate evolutionary trajectories of organisms adapting to differential environmental conditions. Verticillium stem striping disease on oilseed rape was mainly observed in continental Europe, but has recently emerged in the United Kingdom. The disease is caused by the hybrid fungal species Verticillium longisporum that originates from at least three separate hybridization events, yet hybrids between Verticillium progenitor species A1 and D1 are mainly responsible for Verticillium stem striping. We reveal a hitherto un-described dichotomy within V. longisporum lineage A1/D1 that correlates with the geographic distribution of the isolates with an 'A1/D1 West' and an 'A1/D1 East' cluster. Genome comparison between representatives of the A1/D1 West and East clusters excluded population distinctiveness through separate hybridization events. Remarkably, the A1/D1 West population that is genetically more diverse than the entire A1/D1 East cluster caused the sudden emergence of Verticillium stem striping in the UK, whereas in continental Europe Verticillium stem striping is predominantly caused by the more genetically uniform A1/D1 East population. The observed genetic diversity of the A1/D1 West population argues against a recent introduction of the pathogen into the UK, but rather suggests that the pathogen previously established in the UK and remained latent or unnoticed as oilseed rape pathogen until recently.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.,Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
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Kombrink A, Rovenich H, Shi‐Kunne X, Rojas‐Padilla E, van den Berg GCM, Domazakis E, de Jonge R, Valkenburg D, Sánchez‐Vallet A, Seidl MF, Thomma BPHJ. Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts. Mol Plant Pathol 2017; 18:596-608. [PMID: 27911046 PMCID: PMC6638240 DOI: 10.1111/mpp.12520] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chitin-binding lysin motif (LysM) effectors contribute to the virulence of various plant-pathogenic fungi that are causal agents of foliar diseases. Here, we report the LysM effectors of the soil-borne fungal vascular wilt pathogen Verticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection of V. dahliae strains. Remarkably, and in contrast with the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitored in planta in a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes in V. dahliae strain JR2 did not compromise virulence in infections on Arabidopsis, tomato or Nicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome of V. dahliae strain VdLs17, but not in any other V. dahliae strain sequenced to date. Remarkably, this lineage-specific effector is expressed in planta and contributes to the virulence of V. dahliae strain VdLs17 on tomato, but not on Arabidopsis or N. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast with the core LysM effectors of V. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulence in planta.
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Affiliation(s)
- Anja Kombrink
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Hanna Rovenich
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Xiaoqian Shi‐Kunne
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Eduardo Rojas‐Padilla
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Grardy C. M. van den Berg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Emmanouil Domazakis
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Ronnie de Jonge
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Dirk‐Jan Valkenburg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Andrea Sánchez‐Vallet
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
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Santhanam P, Boshoven JC, Salas O, Bowler K, Islam MT, Saber MK, van den Berg GCM, Bar‐Peled M, Thomma BPHJ. Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae. Mol Plant Pathol 2017; 18:347-362. [PMID: 26996832 PMCID: PMC6638212 DOI: 10.1111/mpp.12401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/17/2016] [Accepted: 03/17/2016] [Indexed: 05/05/2023]
Abstract
The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy-thymidine diphosphate (dTDP)-rhamnose, a precursor of L-rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal-host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)-rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.
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Affiliation(s)
- Parthasarathy Santhanam
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Jordi C. Boshoven
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Omar Salas
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Kyle Bowler
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Md Tohidul Islam
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Mojtaba Keykha Saber
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Grardy C. M. van den Berg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Maor Bar‐Peled
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
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Song Y, Zhang Z, Seidl MF, Majer A, Jakse J, Javornik B, Thomma BPHJ. Broad taxonomic characterization of Verticillium wilt resistance genes reveals an ancient origin of the tomato Ve1 immune receptor. Mol Plant Pathol 2017; 18:195-209. [PMID: 26946045 PMCID: PMC6638226 DOI: 10.1111/mpp.12390] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/12/2016] [Accepted: 03/01/2016] [Indexed: 05/02/2023]
Abstract
Plant-pathogenic microbes secrete effector molecules to establish themselves on their hosts, whereas plants use immune receptors to try and intercept such effectors in order to prevent pathogen colonization. The tomato cell surface-localized receptor Ve1 confers race-specific resistance against race 1 strains of the soil-borne vascular wilt fungus Verticillium dahliae which secrete the Ave1 effector. Here, we describe the cloning and characterization of Ve1 homologues from tobacco (Nicotiana glutinosa), potato (Solanum tuberosum), wild eggplant (Solanum torvum) and hop (Humulus lupulus), and demonstrate that particular Ve1 homologues govern resistance against V. dahliae race 1 strains through the recognition of the Ave1 effector. Phylogenetic analysis shows that Ve1 homologues are widely distributed in land plants. Thus, our study suggests an ancient origin of the Ve1 immune receptor in the plant kingdom.
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Affiliation(s)
- Yin Song
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Zhao Zhang
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Aljaz Majer
- Biotechnical Faculty, Agronomy Department, Centre for Plant Biotechnology and Breeding, University of LjubljanaJamnikarieva 1011000LjubljanaSlovenia
| | - Jernej Jakse
- Biotechnical Faculty, Agronomy Department, Centre for Plant Biotechnology and Breeding, University of LjubljanaJamnikarieva 1011000LjubljanaSlovenia
| | - Branka Javornik
- Biotechnical Faculty, Agronomy Department, Centre for Plant Biotechnology and Breeding, University of LjubljanaJamnikarieva 1011000LjubljanaSlovenia
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
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Rovenich H, Zuccaro A, Thomma BPHJ. Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity. New Phytol 2016; 212:896-901. [PMID: 27329426 DOI: 10.1111/nph.14064] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/12/2016] [Indexed: 05/20/2023]
Abstract
896 I. 896 II. 896 III. 897 IV. 898 V. 899 VI. 899 900 References 900 SUMMARY: All filamentous microbes produce and release a wide range of glycans, which are essential determinants of microbe-microbe and microbe-host interactions. Major cell wall constituents, such as chitin and β-glucans, are elicitors of host immune responses. The widespread capacity for glycan perception in plants has driven the evolution of various strategies that help filamentous microbes to evade detection. Common strategies include structural and chemical modifications of cell wall components as well as the secretion of effector proteins that suppress chitin- and β-glucan-triggered immune responses. Thus, the necessity to avoid glycan-triggered immunity represents a driving force in the convergent evolution of filamentous microbes towards its suppression.
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Affiliation(s)
- Hanna Rovenich
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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Affiliation(s)
- Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University, The Netherlands
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Abstract
Microbial pathogens cause devastating diseases on economically and ecologically important plant species, threatening global food security, and causing billions of dollars of losses annually. During the infection process, pathogens secrete so-called effectors that support host colonization, often by deregulating host immune responses. Over the last decades, much of the research on molecular plant-microbe interactions has focused on the identification and functional characterization of such effectors. The increasing availability of sequenced plant pathogen genomes has enabled genomics-based discovery of effector candidates. Nevertheless, identification of full plant pathogen effector repertoires is often hampered by erroneous gene annotation and the localization effector genes in genomic regions that are notoriously difficult to assemble. Here, we argue that recent advances in genome sequencing technologies, genome assembly, gene annotation, as well as effector identification methods hold promise to disclose complete and correct effector repertoires. This allows to exploit complete effector repertoires, and knowledge of their diversity within pathogen populations, to develop durable and sustainable resistance breeding strategies, disease control, and management of plant pathogens.
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Affiliation(s)
- Hesham A Y Gibriel
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Depotter JRL, Deketelaere S, Inderbitzin P, Tiedemann AV, Höfte M, Subbarao KV, Wood TA, Thomma BPHJ. Verticillium longisporum, the invisible threat to oilseed rape and other brassicaceous plant hosts. Mol Plant Pathol 2016; 17:1004-16. [PMID: 26663851 PMCID: PMC6638321 DOI: 10.1111/mpp.12350] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/03/2015] [Accepted: 12/04/2015] [Indexed: 05/21/2023]
Abstract
INTRODUCTION The causal agents of Verticillium wilts are globally distributed pathogens that cause significant crop losses every year. Most Verticillium wilts are caused by V. dahliae, which is pathogenic on a broad range of plant hosts, whereas other pathogenic Verticillium species have more restricted host ranges. In contrast, V. longisporum appears to prefer brassicaceous plants and poses an increasing problem to oilseed rape production. TAXONOMY Kingdom Fungi; Phylum Ascomycota; Class Sordariomycetes; Subclass Hypocreomycetida; Family Plectosphaerellaceae; genus Verticillium. DISEASE SYMPTOMS Dark unilateral stripes appear on the stems of apparently healthy looking oilseed rape plants at the end of the growing season. Microsclerotia are subsequently formed in the stem cortex beneath the epidermis. GENOME Verticillium longisporum is the only non-haploid species in the Verticillium genus, as it is an amphidiploid hybrid that carries almost twice as much genetic material as the other Verticillium species as a result of interspecific hybridization. DISEASE MANAGEMENT There is no effective fungicide treatment to control Verticillium diseases, and resistance breeding is the preferred strategy for disease management. However, only a few Verticillium wilt resistance genes have been identified, and monogenic resistance against V. longisporum has not yet been found. Quantitative resistance exists mainly in the Brassica C-genome of parental cabbage lines and may be introgressed in oilseed rape breeding lines. COMMON NAME Oilseed rape colonized by V. longisporum does not develop wilting symptoms, and therefore the common name of Verticillium wilt is unsuitable for this crop. Therefore, we propose 'Verticillium stem striping' as the common name for Verticillium infections of oilseed rape.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, the Netherlands
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Silke Deketelaere
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, B-9000, Ghent, Belgium
| | - Patrik Inderbitzin
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Andreas Von Tiedemann
- Department of Crop Sciences, Plant Pathology and Crop Protection Division, Georg-August University Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Monica Höfte
- Laboratory of Phytopathology, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, B-9000, Ghent, Belgium
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, the Netherlands
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Takahara H, Hacquard S, Kombrink A, Hughes HB, Halder V, Robin GP, Hiruma K, Neumann U, Shinya T, Kombrink E, Shibuya N, Thomma BPHJ, O'Connell RJ. Colletotrichum higginsianum extracellular LysM proteins play dual roles in appressorial function and suppression of chitin-triggered plant immunity. New Phytol 2016; 211:1323-37. [PMID: 27174033 DOI: 10.1111/nph.13994] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/21/2016] [Indexed: 05/20/2023]
Abstract
The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large repertoire of candidate-secreted effectors containing LysM domains, but the role of such proteins in the pathogenicity of any Colletotrichum species is unknown. Here, we characterized the function of two effectors, ChELP1 and ChELP2, which are transcriptionally activated during the initial intracellular biotrophic phase of infection. Using immunocytochemistry, we found that ChELP2 is concentrated on the surface of bulbous biotrophic hyphae at the interface with living host cells but is absent from filamentous necrotrophic hyphae. We show that recombinant ChELP1 and ChELP2 bind chitin and chitin oligomers in vitro with high affinity and specificity and that both proteins suppress the chitin-triggered activation of two immune-related plant mitogen-activated protein kinases in the host Arabidopsis. Using RNAi-mediated gene silencing, we found that ChELP1 and ChELP2 are essential for fungal virulence and appressorium-mediated penetration of both Arabidopsis epidermal cells and cellophane membranes in vitro. The findings suggest a dual role for these LysM proteins as effectors for suppressing chitin-triggered immunity and as proteins required for appressorium function.
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Affiliation(s)
- Hiroyuki Takahara
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Anja Kombrink
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - H Bleddyn Hughes
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Vivek Halder
- Chemical Biology Laboratory, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Guillaume P Robin
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Kei Hiruma
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ulla Neumann
- Central Microscopy, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Tomonori Shinya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Erich Kombrink
- Chemical Biology Laboratory, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Naoto Shibuya
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Richard J O'Connell
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, 50829, Cologne, Germany
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
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Hanemian M, Barlet X, Sorin C, Yadeta KA, Keller H, Favery B, Simon R, Thomma BPHJ, Hartmann C, Crespi M, Marco Y, Tremousaygue D, Deslandes L. Arabidopsis CLAVATA1 and CLAVATA2 receptors contribute to Ralstonia solanacearum pathogenicity through a miR169-dependent pathway. New Phytol 2016; 211:502-15. [PMID: 26990325 DOI: 10.1111/nph.13913] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/22/2016] [Indexed: 05/21/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is one of the most destructive bacterial plant diseases. Although many molecular determinants involved in R. solanacearum adaptation to hosts and pathogenesis have been described, host components required for disease establishment remain poorly characterized. Phenotypical analysis of Arabidopsis mutants for leucine-rich repeat (LRR)-receptor-like proteins revealed that mutations in the CLAVATA1 (CLV1) and CLAVATA2 (CLV2) genes confer enhanced disease resistance to bacterial wilt. We further investigated the underlying mechanisms using genetic, transcriptomic and molecular approaches. The enhanced resistance of both clv1 and clv2 mutants to the bacteria did not require the well characterized CLV signalling modules involved in shoot meristem homeostasis, and was conditioned by neither salicylic acid nor ethylene defence-related hormones. Gene expression microarray analysis performed on clv1 and clv2 revealed deregulation of genes encoding nuclear transcription factor Y subunit alpha (NF-YA) transcription factors whose post-transcriptional regulation is known to involve microRNAs from the miR169 family. Both clv mutants showed a defect in miR169 accumulation. Conversely, overexpression of miR169 abrogated the resistance phenotype of clv mutants. We propose that CLV1 and CLV2, two receptors involved in CLV3 perception during plant development, contribute to bacterial wilt through a signalling pathway involving the miR169/NF-YA module.
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Affiliation(s)
- Mathieu Hanemian
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Xavier Barlet
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Céline Sorin
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, UPR2355, 91198, Gif-sur-Yvette, France
| | - Koste A Yadeta
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harald Keller
- INRA, Univ. Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Bruno Favery
- INRA, Univ. Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Rüdiger Simon
- Institut für Entwicklungsgenetik, Heinrich-Heine-Universität, Universitätstr. 1, 40225, Düsseldorf, Germany
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Caroline Hartmann
- Université Paris Diderot, 5 rue Thomas Mann, 75205, Paris Cedex 13, France
| | - Martin Crespi
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, UPR2355, 91198, Gif-sur-Yvette, France
| | - Yves Marco
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Dominique Tremousaygue
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
| | - Laurent Deslandes
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, Chemin de Borde Rouge, F-31326, Castanet-Tolosan, France
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Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, Thomma BPHJ. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res 2016; 26:1091-100. [PMID: 27325116 PMCID: PMC4971763 DOI: 10.1101/gr.204974.116] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.
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Affiliation(s)
- Luigi Faino
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Marc Pauper
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | | | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
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