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Liu L, Li J, Wang Z, Zhou H, Wang Y, Qin W, Duan H, Zhao H, Ge X. Suppression of plant immunity by Verticillium dahliae effector Vd6317 through AtNAC53 association. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1767-1781. [PMID: 38924284 DOI: 10.1111/tpj.16883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/24/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Verticillium dahliae, a soil-borne fungal pathogen, compromises host innate immunity by secreting a plethora of effectors, thereby facilitating host colonization and causing substantial yield and quality losses. The mechanisms underlying the modulation of cotton immunity by V. dahliae effectors are predominantly unexplored. In this study, we identified that the V. dahliae effector Vd6317 inhibits plant cell death triggered by Vd424Y and enhances PVX viral infection in Nicotiana benthamiana. Attenuation of Vd6317 significantly decreased the virulence of V. dahliae, whereas ectopic expression of Vd6317 in Arabidopsis and cotton enhanced susceptibility to V. dahliae infection, underscoring Vd6317's critical role in pathogenicity. We observed that Vd6317 targeted the Arabidopsis immune regulator AtNAC53, thereby impeding its transcriptional activity on the defense-associated gene AtUGT74E2. Arabidopsis nac53 and ugt74e2 mutants exhibited heightened sensitivity to V. dahliae compared to wild-type plants. A mutation at the conserved residue 193L of Vd6317 abrogated its interaction with AtNAC53 and reduced the virulence of V. dahliae, which was partially attributable to a reduction in Vd6317 protein stability. Our findings unveil a hitherto unrecognized regulatory mechanism by which the V. dahliae effector Vd6317 directly inhibits the plant transcription factor AtNAC53 activity to suppress the expression of AtUGT74E2 and plant defense.
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Affiliation(s)
- Lisen Liu
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jianing Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaohan Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Haodan Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongying Duan
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
| | - Hang Zhao
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xiaoyang Ge
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
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Bucknell AH, McDonald MC. That's no moon, it's a Starship: Giant transposons driving fungal horizontal gene transfer. Mol Microbiol 2023; 120:555-563. [PMID: 37434470 DOI: 10.1111/mmi.15118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023]
Abstract
To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II-like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host-beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine-recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship-mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom.
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Affiliation(s)
- Angus H Bucknell
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Megan C McDonald
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Lee S, Völz R, Lim YJ, Harris W, Kim S, Lee YH. The nuclear effector MoHTR3 of Magnaporthe oryzae modulates host defence signalling in the biotrophic stage of rice infection. MOLECULAR PLANT PATHOLOGY 2023; 24:602-615. [PMID: 36977203 DOI: 10.1111/mpp.13326] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 05/18/2023]
Abstract
Fungal effectors play a pivotal role in suppressing the host defence system, and their evolution is highly dynamic. By comparative sequence analysis of plant-pathogenic fungi and Magnaporthe oryzae, we identified the small secreted C2 H2 zinc finger protein MoHTR3. MoHTR3 exhibited high conservation in M. oryzae strains but low conservation among other plant-pathogenic fungi, suggesting an emerging evolutionary selection process. MoHTR3 is exclusively expressed in the biotrophic stage of fungal invasion, and the encoded protein localizes to the biotrophic interfacial complex (BIC) and the host cell nucleus. The signal peptide crucial for MoHTR3' secretion to the BIC and the protein section required for its translocation to the nucleus were both identified by a functional protein domain study. The host-nuclear localization of MoHTR3 suggests a function as a transcriptional modulator of host defence gene induction. After ΔMohtr3 infection, the expression of jasmonic acid- and ethylene-associated genes was diminished in rice, in contrast to when the MoHTR3-overexpressing strain (MoHTR3ox) was applied. The transcript levels of salicylic acid- and defence-related genes were also affected after ΔMohtr3 and MoHTR3ox application. In pathogenicity assays, ΔMohtr3 was indistinguishable from the wild type. However, MoHTR3ox-infected plants showed diminished lesion formation and hydrogen peroxide accumulation, accompanied by a decrease in susceptibility, suggesting that the MoHTR3-induced manipulation of host cells affects host-pathogen interaction. MoHTR3 emphasizes the role of the host nucleus as a critical target for the pathogen-driven manipulation of host defence mechanisms and underscores the ongoing evolution of rice blast's arms race.
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Affiliation(s)
- Sehee Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Ronny Völz
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - You-Jin Lim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - William Harris
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, South Korea
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4
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Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Guo Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. MOLECULAR PLANT PATHOLOGY 2023; 24:474-494. [PMID: 36790136 PMCID: PMC10098069 DOI: 10.1111/mpp.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.
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Affiliation(s)
- Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ellie L Bradley
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Yanan Guo
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | | | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hannah M McCarthy
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Christiaan R Schol
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Rosie E Bradshaw
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
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Verticillium dahliae Effector VdCE11 Contributes to Virulence by Promoting Accumulation and Activity of the Aspartic Protease GhAP1 from Cotton. Microbiol Spectr 2023; 11:e0354722. [PMID: 36656049 PMCID: PMC9927275 DOI: 10.1128/spectrum.03547-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Verticillium dahliae is a soilborne plant fungal pathogen that causes Verticillium wilt, a disease that reduces the yields of many economically important crops. Despite its worldwide distribution and harmful impacts, much remains unknown regarding how the numerous effectors of V. dahliae modulate plant immunity. Here, we identified the intracellular effector VdCE11 that induces cell death and defense responses in Nicotiana benthamiana to counter leaf pathogens such as Sclerotinia sclerotiorum and Botrytis cinerea. VdCE11 also contributes to the virulence of V. dahliae in cotton and Arabidopsis. Yeast two-hybrid library screening and immunoprecipitation revealed that VdCE11 interacts physically with the cotton aspartic protease GhAP1. GhAP1 and its Arabidopsis homolog AtAP1 are negative regulators of plant immunity, since disruption of either increased the resistance of cotton or Arabidopsis to V. dahliae. Further, VdCE11 plays a role in promoting the accumulation of the AP1 proteins and increasing its hydrolase activity. Taken together, these results indicate a novel mechanism regulating virulence whereby the secreted effector VdCE11 increases cotton susceptibility to V. dahliae by promoting the accumulation and activity of GhAP1. IMPORTANCE Verticclium dahliae is a plant fungal pathogen that causes a destructive vascular disease on a large number of plant hosts, resulting in great threat to agricultural production. In this study, we identified a V. dahliae effector VdCE11 that induces cell death and defense responses in Nicotiana benthamiana. Meanwhile, VdCE11 contributes to the virulence of V. dahliae in cotton and Arabidopsis. Yeast two-hybrid library screening and immunoprecipitation revealed that VdCE11 interacts physically with the cotton aspartic protease GhAP1. GhAP1 and its Arabidopsis homolog AtAP1 are negative regulators of plant immunity since disruption of either increased the resistance of cotton or Arabidopsis to V. dahliae. Further research showed that VdCE11 plays a role in promoting the accumulation of the AP1 proteins and increasing its hydrolase activity. These results suggested that a novel mechanism regulating virulence whereby VdCE11 increases susceptibility to V. dahliae by promoting the accumulation and activity of GhAP1 in the host.
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Arifin AR, Phillips RD, Linde CC. Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids. J Evol Biol 2023; 36:221-237. [PMID: 36309962 PMCID: PMC10091943 DOI: 10.1111/jeb.14107] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 01/11/2023]
Abstract
The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host-switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually deceptive orchids that consists of approximately 66 species. In this study, we investigated the evolutionary relationships between representatives of all six Drakaeinae orchid genera (39 species) and their mycorrhizal fungi. We used an exome capture dataset to generate the first well-resolved phylogeny of the Drakaeinae genera. A total of 10 closely related Tulasnella Operational Taxonomic Units (OTUs) and previously described species were associated with the Drakaeinae orchids. Three of them were shared among orchid genera, with each genus associating with 1-6 Tulasnella lineages. Cophylogenetic analyses show Drakaeinae orchids and their Tulasnella associates exhibit significant congruence (p < 0.001) in the topology of their phylogenetic trees. An event-based method also revealed significant congruence in Drakaeinae-Tulasnella relationships, with duplications (35), losses (25), and failure to diverge (9) the most frequent events, with minimal evidence for cospeciation (1) and host-switches (2). The high number of duplications suggests that the orchids speciate independently from the fungi, and the fungal species association of the ancestral orchid species is typically maintained in the daughter species. For the Drakaeinae-Tulasnella interaction, a pattern of phylogenetic niche conservatism rather than coevolution likely explains the observed phylogenetic congruency in orchid and fungal phylogenies. Given that many orchid genera are characterized by sharing of fungal species between closely related orchid species, we predict that these findings may apply to a wide range of orchid lineages.
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Affiliation(s)
- Arild R Arifin
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,Department of Plant Pathology, Washington State University Tree Fruit Research and Extension Center, Wenatchee, Washington, USA
| | - Ryan D Phillips
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,Department of Ecology, Environment & Evolution, La Trobe University, Bundoora, Victoria, Australia.,Department of Biodiversity, Conservation and Attractions, Kings Park Science, Perth, Western Australia, Australia.,Royal Botanic Gardens Victoria, Victoria, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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Waheed A, Haxim Y, Islam W, Kahar G, Liu X, Zhang D. Role of pathogen's effectors in understanding host-pathogen interaction. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119347. [PMID: 36055522 DOI: 10.1016/j.bbamcr.2022.119347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Pathogens can pose challenges to plant growth and development at various stages of their life cycle. Two interconnected defense strategies prevent the growth of pathogens in plants, i.e., molecular patterns triggered immunity (PTI) and pathogenic effector-triggered immunity (ETI) that often provides resistance when PTI no longer functions as a result of pathogenic effectors. Plants may trigger an ETI defense response by directly or indirectly detecting pathogen effectors via their resistance proteins. A typical resistance protein is a nucleotide-binding receptor with leucine-rich sequences (NLRs) that undergo structural changes as they recognize their effectors and form associations with other NLRs. As a result of dimerization or oligomerization, downstream components activate "helper" NLRs, resulting in a response to ETI. It was thought that ETI is highly dependent on PTI. However, recent studies have found that ETI and PTI have symbiotic crosstalk, and both work together to create a robust system of plant defense. In this article, we have summarized the recent advances in understanding the plant's early immune response, its components, and how they cooperate in innate defense mechanisms. Moreover, we have provided the current perspective on engineering strategies for crop protection based on up-to-date knowledge.
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Affiliation(s)
- Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi 830011, China; Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Xiaojie Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology & Geography, Chinese Academy of Sciences, Urumqi 830011, China; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China.
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Quintanilha-Peixoto G, Marone MP, Raya FT, José J, Oliveira A, Fonseca PLC, Tomé LMR, Bortolini DE, Kato RB, Araújo DS, De-Paula RB, Cuesta-Astroz Y, Duarte EAA, Badotti F, de Carvalho Azevedo VA, Brenig B, Soares ACF, Carazzolle MF, Pereira GAG, Aguiar ERGR, Góes-Neto A. Phylogenomics and gene selection in Aspergillus welwitschiae: Possible implications in the pathogenicity in Agave sisalana. Genomics 2022; 114:110517. [PMID: 36306958 DOI: 10.1016/j.ygeno.2022.110517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
Abstract
Aspergillus welwitschiae causes bole rot disease in sisal (Agave sisalana and related species) which affects the production of natural fibers in Brazil, the main worldwide producer of sisal fibers. This fungus is a saprotroph with a broad host range. Previous research established A. welwitschiae as the only causative agent of bole rot in the field, but little is known about the evolution of this species and its strains. In this work, we performed a comparative genomics analysis of 40 Aspergillus strains. We show the conflicting molecular identity of this species, with one sisal-infecting strain sharing its last common ancestor with Aspergillus niger, having diverged only 833 thousand years ago. Furthermore, our analysis of positive selection reveals sites under selection in genes coding for siderophore transporters, Sodium‑calcium exchangers, and Phosphatidylethanolamine-binding proteins (PEBPs). Herein, we discuss the possible impacts of these gene functions on the pathogenicity in sisal.
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Affiliation(s)
| | - Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Fábio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Juliana José
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Adriele Oliveira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Dener Eduardo Bortolini
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, United States
| | - Ruth B De-Paula
- Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Yesid Cuesta-Astroz
- Instituto Colombiano de Medicina Tropical, Universidad CES, Medellín, Colombia
| | - Elizabeth A A Duarte
- Centro Universitário Maria Milza, Cruz das Almas, Brazil; Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Federal Center of Technological Education of Minas Gerais, Belo Horizonte, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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9
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Tarallo M, McDougal RL, Chen Z, Wang Y, Bradshaw RE, Mesarich CH. Characterization of two conserved cell death elicitor families from the Dothideomycete fungal pathogens Dothistroma septosporum and Fulvia fulva (syn. Cladosporium fulvum). Front Microbiol 2022; 13:964851. [PMID: 36160260 PMCID: PMC9493481 DOI: 10.3389/fmicb.2022.964851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Dothistroma septosporum (Ds) and Fulvia fulva (Ff; previously called Cladosporium fulvum) are two closely related Dothideomycete fungal species that cause Dothistroma needle blight in pine and leaf mold in tomato, respectively. During host colonization, these pathogens secrete virulence factors termed effectors to promote infection. In the presence of corresponding host immune receptors, however, these effectors activate plant defenses, including a localized cell death response that halts pathogen growth. We identified two apoplastic effector protein families, Ecp20 and Ecp32, which are conserved between the two pathogens. The Ecp20 family has four paralogues in both species, while the Ecp32 family has four paralogues in D. septosporum and five in F. fulva. Both families have members that are highly expressed during host infection. Members of the Ecp20 family have predicted structural similarity to proteins with a β-barrel fold, including the Alt a 1 allergen from Alternaria alternata, while members of the Ecp32 family have predicted structural similarity to proteins with a β-trefoil fold, such as trypsin inhibitors and lectins. Using Agrobacterium tumefaciens-mediated transient transformation assays, each family member was assessed for its ability to trigger cell death in leaves of the non-host species Nicotiana benthamiana and N. tabacum. Using this approach, FfEcp20-2, DsEcp20-3, and FfEcp20-3 from the Ecp20 family, and all members from the Ecp32 family, except for the Ds/FfEcp32-4 pair, triggered cell death in both species. This cell death was dependent on secretion of the effectors to the apoplast. In line with recognition by an extracellular immune receptor, cell death triggered by Ds/FfEcp20-3 and FfEcp32-3 was compromised in N. benthamiana silenced for BAK1 or SOBIR1, which encode extracellular co-receptors involved in transducing defense response signals following apoplastic effector recognition. We then investigated whether DsEcp20-3 and DsEcp20-4 triggered cell death in the host species Pinus radiata by directly infiltrating purified protein into pine needles. Strikingly, as in the non-host species, DsEcp20-3 triggered cell death, while DsEcp20-4 did not. Collectively, our study describes two new candidate effector families with cell death-eliciting activity from D. septosporum and F. fulva and provides evidence that members of these families are recognized by plant immune receptors.
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Affiliation(s)
- Mariana Tarallo
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Zhiyuan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
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10
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Chang Y, Wang Y, Mondo S, Ahrendt S, Andreopoulos W, Barry K, Beard J, Benny GL, Blankenship S, Bonito G, Cuomo C, Desiro A, Gervers KA, Hundley H, Kuo A, LaButti K, Lang BF, Lipzen A, O’Donnell K, Pangilinan J, Reynolds N, Sandor L, Smith ME, Tsang A, Grigoriev IV, Stajich JE, Spatafora JW. Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies. iScience 2022; 25:104840. [PMID: 35996588 PMCID: PMC9391592 DOI: 10.1016/j.isci.2022.104840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/09/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Fungi survive in diverse ecological niches by secreting proteins and other molecules into the environment to acquire food and interact with various biotic and abiotic stressors. Fungal secretome content is, therefore, believed to be tightly linked to fungal ecologies. We sampled 132 genomes from the early-diverging terrestrial fungal lineage zygomycetes (Mucoromycota and Zoopagomycota) and characterized their secretome composition. Our analyses revealed that phylogeny played an important role in shaping the secretome composition of zygomycete fungi with trophic mode contributing a smaller amount. Reconstruction of the evolution of secreted digestive enzymes revealed lineage-specific expansions, indicating that Mucoromycota and Zoopagomycota followed different trajectories early in their evolutionary history. We identified the presence of multiple pathogenicity-related proteins in the lineages known as saprotrophs, suggesting that either the ecologies of these fungi are incompletely known, and/or that these pathogenicity-related proteins have important functions associated with saprotrophic ecologies, both of which invite further investigation.
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Affiliation(s)
- Ying Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Stephen Mondo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Steven Ahrendt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Jeff Beard
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Gerald L. Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Sabrina Blankenship
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Gregory Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Christina Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
| | - Alessandro Desiro
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Kyle A. Gervers
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Hope Hundley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - B. Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Kerry O’Donnell
- National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Nicole Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Laura Sandor
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Matthew E. Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC H4B 1R6, Canada
| | - Igor V. Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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11
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Buijs VA, Groenewald JZ, Haridas S, LaButti KM, Lipzen A, Martin FM, Barry K, Grigoriev IV, Crous PW, Seidl MF. Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis. G3 (BETHESDA, MD.) 2022; 12:jkac061. [PMID: 35311955 PMCID: PMC9073689 DOI: 10.1093/g3journal/jkac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/02/2022] [Indexed: 11/14/2022]
Abstract
Members of the fungal genus Phyllosticta can colonize a variety of plant hosts, including several Citrus species such as Citrus sinensis (orange), Citrus limon (lemon), and Citrus maxima (pomelo). Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. Furthermore, the lifestyle of Phyllosticta citrichinaensis is ambiguous, as it has been described as a weak pathogen but Koch's postulates may not have been established and the presence of this species was never reported to cause any crop or economic losses. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or endophytes. We also observed that species, based on their carbohydrate active enzymes, group independent of their phylogenetic association, and this clustering correlated with trophy prediction. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. We thus present the first genomic comparison of multiple citrus-colonizing pathogens and endophytes of the genus Phyllosticta, and therefore provide the basis for further comparative studies into the lifestyle adaptations within this genus.
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Affiliation(s)
- Valerie A Buijs
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Johannes Z Groenewald
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt M LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Francis M Martin
- Department of Biology, Institut National de la Recherche Agronomique, UMR INRA-Université de Lorraine “Interaction Arbres/Microorganismes”, Champenoux F-54280, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Pedro W Crous
- Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, The Netherlands
- Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht 3584 CH, The Netherlands
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12
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Rajput M, Kumar M, Pareek N. Myco-chitinases as versatile biocatalysts for translation of coastal residual resources to eco-competent chito-bioactives. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Chaudhary A, Singh D. In-silico analysis of the regulatory region of effector protein genes in Verticillium dahliae. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Wilkerson DG, Crowell CR, Carlson CH, McMullen PW, Smart CD, Smart LB. Comparative transcriptomics and eQTL mapping of response to Melampsora americana in selected Salix purpurea F2 progeny. BMC Genomics 2022; 23:71. [PMID: 35065596 PMCID: PMC8783449 DOI: 10.1186/s12864-021-08254-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Background Melampsora spp. rusts are the greatest pathogen threat to shrub willow (Salix spp.) bioenergy crops. Genetic resistance is key to limit the effects of these foliar diseases on host response and biomass yield, however, the genetic basis of host resistance has not been characterized. The addition of new genomic resources for Salix provides greater power to investigate the interaction between S. purpurea and M. americana, species commonly found in the Northeast US. Here, we utilize 3′ RNA-seq to investigate host-pathogen interactions following controlled inoculations of M. americana on resistant and susceptible F2S. purpurea genotypes identified in a recent QTL mapping study. Differential gene expression, network analysis, and eQTL mapping were used to contrast the response to inoculation and to identify associated candidate genes. Results Controlled inoculation in a replicated greenhouse study identified 19 and 105 differentially expressed genes between resistant and susceptible genotypes at 42 and 66 HPI, respectively. Defense response gene networks were activated in both resistant and susceptible genotypes and enriched for many of the same defense response genes, yet the hub genes of these common response modules showed greater mean expression among the resistant plants. Further, eight and six eQTL hotspots were identified at 42 and 66 HPI, respectively. The combined results of three analyses highlight 124 candidate genes in the host for further analysis while analysis of pathogen RNA showed differential expression of 22 genes, two of which are candidate pathogen effectors. Conclusions We identified two differentially expressed M. americana transcripts and 124 S. purpurea genes that are good candidates for future studies to confirm their role in conferring resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08254-1.
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15
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Huang Z, Li H, Zhou Y, Bao Y, Duan Z, Wang C, Powell CA, Chen B, Zhang M, Yao W. Predication of the Effector Proteins Secreted by Fusarium sacchari Using Genomic Analysis and Heterogenous Expression. J Fungi (Basel) 2022; 8:jof8010059. [PMID: 35049998 PMCID: PMC8780550 DOI: 10.3390/jof8010059] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 01/01/2023] Open
Abstract
One of the causative agents of pokkah boeng disease (PBD), which affects sugarcane crops globally, is the fungus Fusarium sacchari. These fungal infections reduce sugar quality and yield, resulting in severe economic losses. Effector proteins play important roles in the interactions between pathogenic fungi and plants. Here, we used bioinformatic prediction approaches to identify 316 candidate secreted effector proteins (CSEPs) in the complete genome of F. sacchari. In total, 95 CSEPs contained known conserved structures, representing 40 superfamilies and 18 domains, while an additional 91 CSEPs contained seven known motifs. Of the 130 CSEPs containing no known domains or motifs, 14 contained one of four novel motifs. A heterogeneous expression system in Nicotiana benthamiana was used to investigate the functions of 163 CSEPs. Seven CSEPs suppressed BAX-triggered programmed cell death in N. benthamiana, while four caused cell death in N. benthamiana. The expression profiles of these eleven CSEPs during F. sacchari infection suggested that they may be involved in sugarcane-F. sacchari interaction. Our results establish a basis for further studies of the role of effector molecules in pathogen–sugarcane interactions, and provide a framework for future predictions of pathogen effector molecules.
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Affiliation(s)
- Zhen Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Huixue Li
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Yuming Zhou
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Yixue Bao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Zhenzhen Duan
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Caixia Wang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | | | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
- IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA;
- Correspondence: (M.Z.); (W.Y.)
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
- IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA;
- Correspondence: (M.Z.); (W.Y.)
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16
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Boufleur TR, Massola Júnior NS, Tikami Í, Sukno SA, Thon MR, Baroncelli R. Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean. Pathogens 2021; 10:pathogens10111520. [PMID: 34832675 PMCID: PMC8625359 DOI: 10.3390/pathogens10111520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Colletotrichum is one of the most important plant pathogenic genus of fungi due to its scientific and economic impact. A wide range of hosts can be infected by Colletotrichum spp., which causes losses in crops of major importance worldwide, such as soybean. Soybean anthracnose is mainly caused by C. truncatum, but other species have been identified at an increasing rate during the last decade, becoming one of the most important limiting factors to soybean production in several regions. To gain a better understanding of the evolutionary origin of soybean anthracnose, we compared the repertoire of effector candidates of four Colletotrichum species pathogenic to soybean and eight species not pathogenic. Our results show that the four species infecting soybean belong to two lineages and do not share any effector candidates. These results strongly suggest that two Colletotrichum lineages have acquired the capability to infect soybean independently. This study also provides, for each lineage, a set of candidate effectors encoding genes that may have important roles in pathogenicity towards soybean offering a new resource useful for further research on soybean anthracnose management.
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Affiliation(s)
- Thaís R. Boufleur
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
- Correspondence: (T.R.B.); (R.B.)
| | - Nelson S. Massola Júnior
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
| | - Ísis Tikami
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 44, 40126 Bologna, Italy
- Correspondence: (T.R.B.); (R.B.)
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17
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Seong K, Krasileva KV. Computational Structural Genomics Unravels Common Folds and Novel Families in the Secretome of Fungal Phytopathogen Magnaporthe oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1267-1280. [PMID: 34415195 PMCID: PMC9447291 DOI: 10.1094/mpmi-03-21-0071-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Structural biology has the potential to illuminate the evolution of pathogen effectors and their commonalities that cannot be readily detected at the primary sequence level. Recent breakthroughs in protein structure modeling have demonstrated the feasibility to predict the protein folds without depending on homologous templates. These advances enabled a genome-wide computational structural biology approach to help understand proteins based on their predicted folds. In this study, we employed structure prediction methods on the secretome of the destructive fungal pathogen Magnaporthe oryzae. Out of 1,854 secreted proteins, we predicted the folds of 1,295 proteins (70%). We showed that template-free modeling by TrRosetta captured 514 folds missed by homology modeling, including many known effectors and virulence factors, and that TrRosetta generally produced higher quality models for secreted proteins. Along with sensitive homology search, we employed structure-based clustering, defining not only homologous groups with divergent members but also sequence-unrelated structurally analogous groups. We demonstrate that this approach can reveal new putative members of structurally similar MAX effectors and novel analogous effector families present in M. oryzae and possibly in other phytopathogens. We also investigated the evolution of expanded putative ADP-ribose transferases with predicted structures. We suggest that the loss of catalytic activities of the enzymes might have led them to new evolutionary trajectories to be specialized as protein binders. Collectively, we propose that computational structural genomics approaches can be an integral part of studying effector biology and provide valuable resources that were inaccessible before the advent of machine learning-based structure prediction.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Ksenia V. Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
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18
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Jones DAB, Moolhuijzen PM, Hane JK. Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi. Microb Genom 2021; 7. [PMID: 34468307 PMCID: PMC8715435 DOI: 10.1099/mgen.0.000637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between 'effector' molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.
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Affiliation(s)
- Darcy A B Jones
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - Paula M Moolhuijzen
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia.,Curtin Institute for Computation, Curtin University, Perth, Australia
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Liu L, Wang Z, Li J, Wang Y, Yuan J, Zhan J, Wang P, Lin Y, Li F, Ge X. Verticillium dahliae secreted protein Vd424Y is required for full virulence, targets the nucleus of plant cells, and induces cell death. MOLECULAR PLANT PATHOLOGY 2021; 22:1109-1120. [PMID: 34233072 PMCID: PMC8358993 DOI: 10.1111/mpp.13100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/09/2021] [Accepted: 05/27/2021] [Indexed: 05/26/2023]
Abstract
Fungal pathogens secrete effector proteins that regulate host immunity and can suppress basal defence mechanisms against colonization in plants. Verticillium dahliae is a widespread and destructive soilborne fungus that can cause vascular wilt disease and reduces plant yields. However, little is currently known about how the effectors secreted by V. dahliae function. In this study, we analysed and identified 34 candidate effectors in the V. dahliae secretome and found that Vd424Y, a glycoside hydrolase family 11 protein, was highly upregulated during the early stages of V. dahliae infection in cotton plants. This protein was located in the nucleus and its deletion compromised the virulence of the fungus. The transient expression of Vd424Y in Nicotiana benthamiana induced BAK1- and SOBIR1-dependent cell death and activated both salicylic acid and jasmonic acid signalling. This enhanced its resistance to the oomycetes Phytophthora capsici in a way that depended on its nuclear localization signal and signal peptides. Our results demonstrate that Vd424Y is an important effector protein targeting the host nucleus to regulate and activate effector-triggered immunity in plants.
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Affiliation(s)
- Lisen Liu
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Zhaohan Wang
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Jianing Li
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Ye Wang
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Jiachen Yuan
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural SciencesZhengzhou UniversityZhengzhouChina
| | - Jingjing Zhan
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Peng Wang
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fuguang Li
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
| | - Xiaoyang Ge
- Institute of Cotton ResearchHenan Normal University Research Base of State Key Laboratory of Cotton BiologyHenanChina
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural SciencesZhengzhou UniversityZhengzhouChina
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Goughenour KD, Whalin J, Slot JC, Rappleye CA. Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum. Mol Biol Evol 2021; 38:1339-1355. [PMID: 33185664 PMCID: PMC8042737 DOI: 10.1093/molbev/msaa293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chitinases enzymatically hydrolyze chitin, a highly abundant and utilized polymer of N-acetyl-glucosamine. Fungi are a rich source of chitinases; however, the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C) as chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin-binding domains (including the LysM domain) do not define specific clades, but instead are found more broadly across clades of chitinases. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade, one B clade, and one formerly classified C clade chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. These results suggest chitinase activity is variable even within subclades and that predictions of functionality require more sophisticated models.
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Affiliation(s)
| | - Janice Whalin
- Department of Microbiology, Ohio State University, Columbus, OH
| | - Jason C Slot
- Department of Plant Pathology, Ohio State University, Columbus, OH
| | - Chad A Rappleye
- Department of Microbiology, Ohio State University, Columbus, OH
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Qiao M, Zheng H, Lv R, Yu Z. Neodactylariales, Neodactylariaceae (Dothideomycetes, Ascomycota): new order and family, with a new species from China. MycoKeys 2020; 73:69-85. [PMID: 32994703 PMCID: PMC7501314 DOI: 10.3897/mycokeys.73.54054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/21/2020] [Indexed: 12/28/2022] Open
Abstract
During a mycological survey of aquatic hyphomycetes on submerged decaying leaves in southwest China, a distinct new fungus was collected. The collection was cultured and sequenced and a BLAST search of its ITS and LSU sequence against data in GenBank revealed a dothideomycetous affiliation, with the closest related taxa in the genus Neodactylaria. Phylogenetic analyses of a multigene matrix containing sequences from four genes (LSU, SSU, rpb2, and tef1), representing broad groups of Dothideomycetes, revealed its placement within Dothideomycetes, but without a supported familial or ordinal affiliation. Based on further phylogenetic analyses and morphological investigations, the new fungus is described here as a new species of Neodactylaria, N.simaoensissp. nov., and placed in a new family Neodactylariaceaefam. nov. and a new order Neodactylarialesord. nov.
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Affiliation(s)
- Min Qiao
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China Yunnan University Kunming China
| | - Hua Zheng
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China Yunnan University Kunming China
| | - Ruili Lv
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China Yunnan University Kunming China
| | - Zefen Yu
- Laboratory for Conservation and Utilization of Bio-resources, Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China Yunnan University Kunming China
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Li J, Gao M, Gabriel DW, Liang W, Song L. Secretome-Wide Analysis of Lysine Acetylation in Fusarium oxysporum f. sp. lycopersici Provides Novel Insights Into Infection-Related Proteins. Front Microbiol 2020; 11:559440. [PMID: 33013791 PMCID: PMC7506082 DOI: 10.3389/fmicb.2020.559440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 01/13/2023] Open
Abstract
Fusarium oxysporum f. sp. lycopersici (Fol) is the causal agent of Fusarium wilt disease in tomato. Proteins secreted by this pathogen during initial host colonization largely determine the outcome of pathogen-host interactions. Lysine acetylation (Kac) plays a vital role in the functions of many proteins, but little is known about Kac in Fol secreted proteins. In this study, we analyzed lysine acetylation of the entire Fol secretome. Using high affinity enrichment of Kac peptides and LC-MS/MS analysis, 50 potentially secreted Fol proteins were identified and acetylation sites determined. Bioinformatics analysis revealed 32 proteins with canonical N-terminal signal peptide leaders, and most of them were predicted to be enzymes involved in a variety of biological processes and metabolic pathways. Remarkably, all 32 predicted secreted proteins were novel and encoded on the core chromosomes rather than on the previously identified LS pathogenicity chromosomes. Homolog scanning of the secreted proteins among 40 different species revealed 4 proteins that were species specific, 3 proteins that were class-specific in the Ascomycota phylum, and 25 proteins that were more widely conserved genes. These secreted proteins provide a starting resource for investigating putative novel pathogenic genes, with 26 up-regulated genes encoding Kac proteins that may play an important role during initial symptomless infection stages.
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Affiliation(s)
- Jingtao Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mingming Gao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Dean W Gabriel
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Wenxing Liang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Limin Song
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Zhang Y, Zhang J, Vanderpool D, Smith JA, Rollins JA. Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis. BMC Genomics 2020; 21:570. [PMID: 32819276 PMCID: PMC7441637 DOI: 10.1186/s12864-020-06988-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/13/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Laurel wilt caused by Raffaelea lauricola is a lethal vascular disease of North American members of the Lauraceae plant family. This fungus and its primary ambrosia beetle vector Xyleborus glabratus originated from Asia; however, there is no report of laurel wilt causing widespread mortality on native Lauraceae trees in Asia. To gain insight into why R. lauricola is a tree-killing plant pathogen in North America, we generated and compared high quality draft genome assemblies of R. lauricola and its closely related non-pathogenic species R. aguacate. RESULTS Relative to R. aguacate, the R. lauricola genome uniquely encodes several small-secreted proteins that are associated with virulence in other pathogens and is enriched in secondary metabolite biosynthetic clusters, particularly polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and PKS-NRPS anchored gene clusters. The two species also exhibit significant differences in secreted proteins including CAZymes that are associated with polysaccharide binding including the chitin binding CBM50 (LysM) domain. Transcriptomic comparisons of inoculated redbay trees and in vitro-grown fungal cultures further revealed a number of secreted protein genes, secondary metabolite clusters and alternative sulfur uptake and assimilation pathways that are coordinately up-regulated during infection. CONCLUSIONS Through these comparative analyses we have identified potential adaptations of R. lauricola that may enable it to colonize and cause disease on susceptible hosts. How these adaptations have interacted with co-evolved hosts in Asia, where little to no disease occurs, and non-co-evolved hosts in North America, where lethal wilt occurs, requires additional functional analysis of genes and pathways.
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Affiliation(s)
- Yucheng Zhang
- Department of Plant Pathology, University of Florida, 1453 Fifield Hall, Gainesville, FL, 32611-0680, USA
| | - Junli Zhang
- Department of Plant Pathology, University of Florida, 1453 Fifield Hall, Gainesville, FL, 32611-0680, USA.,School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611-0410, USA
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, MT, USA.,Present address: Department of Biology and Department of Computer Science, Indiana University, 1001 E. 3rd Street, Bloomington, IN, 47405, USA
| | - Jason A Smith
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611-0410, USA
| | - Jeffrey A Rollins
- Department of Plant Pathology, University of Florida, 1453 Fifield Hall, Gainesville, FL, 32611-0680, USA.
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25
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Sudhagar A, El-Matbouli M, Kumar G. Identification and Expression Profiling of Toll-Like Receptors of Brown Trout ( Salmo trutta) during Proliferative Kidney Disease. Int J Mol Sci 2020; 21:E3755. [PMID: 32466538 PMCID: PMC7312180 DOI: 10.3390/ijms21113755] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/14/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022] Open
Abstract
Proliferative kidney disease is an emerging disease among salmonids in Europe and North America caused by the myxozoan parasite Tetracapsuloides bryosalmonae. The decline of endemic brown trout (Salmo trutta) in the Alpine streams of Europe is fostered by T. bryosalmonae infection. Toll-like receptors (TLRs) are a family of pattern recognition receptors that acts as sentinels of the immune system against the invading pathogens. However, little is known about the TLRs' response in salmonids against the myxozoan infection. In the present study, we identified and evaluated TLR1, TLR19, and TLR13-like genes of brown trout using data-mining and phylogenetic analysis. The expression pattern of TLRs was examined in the posterior kidney of brown trout infected with T. bryosalmonae at various time points. Typical Toll/interleukin-1 receptor protein domain was found in all tested TLRs. However, TLR13-like chr2 had a short amino acid sequence with no LRR domain. Phylogenetic analysis illustrated that TLR orthologs are conserved across vertebrates. Similarly, a conserved synteny gene block arrangement was observed in the case of TLR1 and TLR19 across fish species. Interestingly, all tested TLRs showed their maximal relative expression from 6 to 10 weeks post-exposure to the parasite. Our results suggest that these TLRs may play an important role in the innate defense mechanism of brown trout against the invading T. bryosalmonae.
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Affiliation(s)
- Arun Sudhagar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210 Vienna, Austria; (A.S.); (M.E.-M.)
- Central Institute of Fisheries Education, Rohtak Centre, Haryana 124411, India
| | - Mansour El-Matbouli
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210 Vienna, Austria; (A.S.); (M.E.-M.)
| | - Gokhlesh Kumar
- Clinical Division of Fish Medicine, University of Veterinary Medicine, 1210 Vienna, Austria; (A.S.); (M.E.-M.)
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Denton‐Giles M, McCarthy H, Sehrish T, Dijkwel Y, Mesarich CH, Bradshaw RE, Cox MP, Dijkwel PP. Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae. MOLECULAR PLANT PATHOLOGY 2020; 21:512-526. [PMID: 32061186 PMCID: PMC7060139 DOI: 10.1111/mpp.12913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 05/02/2023]
Abstract
Fungal effector proteins facilitate host-plant colonization and have generally been characterized as small secreted proteins (SSPs). We classified and functionally tested SSPs from the secretomes of three closely related necrotrophic phytopathogens: Ciborinia camelliae, Botrytis cinerea, and Sclerotinia sclerotiorum. Alignment of predicted SSPs identified a large protein family that share greater than 41% amino acid identity and that have key characteristics of previously described microbe-associated molecular patterns (MAMPs). Strikingly, 73 of the 75 SSP family members were predicted within the secretome of the host-specialist C. camelliae with single-copy homologs identified in the secretomes of the host generalists S. sclerotiorum and B. cinerea. To explore the potential function of this family of SSPs, 10 of the 73 C. camelliae proteins, together with the single-copy homologs from S. sclerotiorum (SsSSP3) and B. cinerea (BcSSP2), were cloned and expressed as recombinant proteins. Infiltration of SsSSP3 and BcSSP2 into host tissue induced rapid necrosis. In contrast, only one of the 10 tested C. camelliae SSPs was able to induce a limited amount of necrosis. Analysis of chimeric proteins consisting of domains from both a necrosis-inducing and a non-necrosis-inducing SSP demonstrated that the C-terminus of the S. sclerotiorum SSP is essential for necrosis-inducing function. Deletion of the BcSSP2 homolog from B. cinerea did not affect growth or pathogenesis. Thus, this research uncovered a family of highly conserved SSPs present in diverse ascomycetes that exhibit contrasting necrosis-inducing functions.
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Affiliation(s)
- Matthew Denton‐Giles
- Centre for Crop and Disease ManagementCurtin UniversityPerthAustralia
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Hannah McCarthy
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Tina Sehrish
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Yasmin Dijkwel
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Carl H. Mesarich
- School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Rosie E. Bradshaw
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Murray P. Cox
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Paul P. Dijkwel
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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Guo Y, Hunziker L, Mesarich CH, Chettri P, Dupont PY, Ganley RJ, McDougal RL, Barnes I, Bradshaw RE. DsEcp2-1 is a polymorphic effector that restricts growth of Dothistroma septosporum in pine. Fungal Genet Biol 2020; 135:103300. [PMID: 31730909 DOI: 10.1016/j.fgb.2019.103300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022]
Abstract
The detrimental effect of fungal pathogens on forest trees is an increasingly important problem that has implications for the health of our planet. Despite this, the study of molecular plant-microbe interactions in forest trees is in its infancy, and very little is known about the roles of effector molecules from forest pathogens. Dothistroma septosporum causes a devastating needle blight disease of pines, and intriguingly, is closely related to Cladosporium fulvum, a tomato pathogen in which pioneering effector biology studies have been carried out. Here, we studied D. septosporum effectors that are shared with C. fulvum, by comparing gene sequences from global isolates of D. septosporum and assessing effector function in both host and non-host plants. Many of the effectors were predicted to be non-functional in D. septosporum due to their pseudogenization or low expression in planta, suggesting adaptation to lifestyle and host. Effector sequences were polymorphic among a global collection of D. septosporum isolates, but there was no evidence for positive selection. The DsEcp2-1 effector elicited cell death in the non-host plant Nicotiana tabacum, whilst D. septosporum DsEcp2-1 mutants showed increased colonization of pine needles. Together these results suggest that DsEcp2-1 might be recognized by an immune receptor in both angiosperm and gymnosperm plants. This work may lead to the identification of plant targets for DsEcp2-1 that will provide much needed information on the molecular basis of gymnosperm-pathogen interactions in forests, and may also lead to novel methods of disease control.
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Affiliation(s)
- Yanan Guo
- Bio-Protection Research Centre, School of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand.
| | - Lukas Hunziker
- Bio-Protection Research Centre, School of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand
| | - Carl H Mesarich
- Bio-Protection Research Centre, School of Agriculture and Environment, Massey University, Palmerston North 4474, New Zealand
| | - Pranav Chettri
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Pierre-Yves Dupont
- Institute of Environmental Science and Research, Christchurch 8041, New Zealand
| | - Rebecca J Ganley
- The New Zealand Institute for Plant & Food Research Limited, Te Puke, New Zealand
| | - Rebecca L McDougal
- Scion, New Zealand Forest Research Institute Ltd, Rotorua 3010, New Zealand
| | - Irene Barnes
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Rosie E Bradshaw
- Bio-Protection Research Centre, School of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand
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Pandaranayaka EP, Frenkel O, Elad Y, Prusky D, Harel A. Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens. BMC Genomics 2019; 20:1020. [PMID: 31878885 PMCID: PMC6933724 DOI: 10.1186/s12864-019-6409-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Background Genomic studies demonstrate that components of virulence mechanisms in filamentous eukaryotic pathogens (FEPs, fungi and oomycetes) of plants are often highly conserved, or found in gene families that include secreted hydrolytic enzymes (e.g., cellulases and proteases) and secondary metabolites (e.g., toxins), central to the pathogenicity process. However, very few large-scale genomic comparisons have utilized complete proteomes from dozens of FEPs to reveal lifestyle-associated virulence mechanisms. Providing a powerful means for exploration, and the discovery of trends in large-scale datasets, network analysis has been used to identify core functions of the primordial cyanobacteria, and ancient evolutionary signatures in oxidoreductases. Results We used a sequence-similarity network to study components of virulence mechanisms of major pathogenic lifestyles (necrotroph (ic), N; biotroph (ic), B; hemibiotroph (ic), H) in complete pan-proteomes of 65 FEPs and 17 saprobes. Our comparative analysis highlights approximately 190 core functions found in 70% of the genomes of these pathogenic lifestyles. Core functions were found mainly in: transport (in H, N, B cores); carbohydrate metabolism, secondary metabolite synthesis, and protease (H and N cores); nucleic acid metabolism and signal transduction (B core); and amino acid metabolism (H core). Taken together, the necrotrophic core contains functions such as cell wall-associated degrading enzymes, toxin metabolism, and transport, which are likely to support their lifestyle of killing prior to feeding. The biotrophic stealth growth on living tissues is potentially controlled by a core of regulatory functions, such as: small G-protein family of GTPases, RNA modification, and cryptochrome-based light sensing. Regulatory mechanisms found in the hemibiotrophic core contain light- and CO2-sensing functions that could mediate important roles of this group, such as transition between lifestyles. Conclusions The selected set of enriched core functions identified in our work can facilitate future studies aimed at controlling FEPs. One interesting example would be to facilitate the identification of the pathogenic potential of samples analyzed by metagenomics. Finally, our analysis offers potential evolutionary scenarios, suggesting that an early-branching saprobe (identified in previous studies) has probably evolved a necrotrophic lifestyle as illustrated by the highest number of shared gene families between saprobes and necrotrophs.
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Affiliation(s)
- Eswari Pj Pandaranayaka
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Dov Prusky
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Arye Harel
- Department of Vegetable and Field Crops, Institute of Plant Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel.
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Noar RD, Thomas E, Xie DY, Carter ME, Ma D, Daub ME. A polyketide synthase gene cluster associated with the sexual reproductive cycle of the banana pathogen, Pseudocercospora fijiensis. PLoS One 2019; 14:e0220319. [PMID: 31344104 PMCID: PMC6657885 DOI: 10.1371/journal.pone.0220319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/12/2019] [Indexed: 11/19/2022] Open
Abstract
Disease spread of Pseudocercospora fijiensis, causal agent of the black Sigatoka disease of banana, depends on ascospores produced through the sexual reproductive cycle. We used phylogenetic analysis to identify P. fijiensis homologs (PKS8-4 and Hybrid8-3) to the PKS4 polyketide synthases (PKS) from Neurospora crassa and Sordaria macrospora involved in sexual reproduction. These sequences also formed a clade with lovastatin, compactin, and betaenone-producing PKS sequences. Transcriptome analysis showed that both the P. fijiensis Hybrid8-3 and PKS8-4 genes have higher expression in infected leaf tissue compared to in culture. Domain analysis showed that PKS8-4 is more similar than Hybrid8-3 to PKS4. pPKS8-4:GFP transcriptional fusion transformants showed expression of GFP in flask-shaped structures in mycelial cultures as well as in crosses between compatible and incompatible mating types. Confocal microscopy confirmed expression in spermagonia in leaf substomatal cavities, consistent with a role in sexual reproduction. A disruption mutant of pks8-4 retained normal pathogenicity on banana, and no differences were observed in growth, conidial production, and spermagonia production. GC-MS profiling of the mutant and wild type did not identify differences in polyketide metabolites, but did identify changes in saturated fatty acid methyl esters and alkene and alkane derivatives. To our knowledge, this is the first report of a polyketide synthase pathway associated with spermagonia.
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Affiliation(s)
- Roslyn D. Noar
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America
| | - Elizabeth Thomas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Morgan E. Carter
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Dongming Ma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Margaret E. Daub
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
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Zhang M, Xie S, Zhao Y, Meng X, Song L, Feng H, Huang L. Hce2 domain-containing effectors contribute to the full virulence of Valsa mali in a redundant manner. MOLECULAR PLANT PATHOLOGY 2019; 20:843-856. [PMID: 30912612 PMCID: PMC6637899 DOI: 10.1111/mpp.12796] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Valsa mali is the causal agent of apple Valsa canker, a destructive disease in East Asia. Effector proteins play important roles in the virulence of phytopathogenic fungi, and we identified five Hce2 domain-containing effectors (VmHEP1, VmHEP2, VmHEP3, VmHEP4 and VmHEP5) from the V. mali genome. Amongst these, VmHEP1 and VmHEP2 were found to be up-regulated during the early infection stage and VmHEP1 was also identified as a cell death inducer through its transient expression in Nicotiana benthamiana. Although the deletion of each single VmHEP gene did not lead to a reduction in virulence, the double-deletion of VmHEP1 and VmHEP2 notably attenuated V. mali virulence in both apple twigs and leaves. An evolutionary analysis revealed that VmHEP1 and VmHEP2 are two paralogues, under purifying selection. VmHEP1 and VmHEP2 are located next to each other on chromosome 11 as tandem genes with only a 604 bp physical distance. Interestingly, the deletion of VmHEP1 promoted the expression of VmHEP2 and, vice versa, the deletion of VmHEP2 promoted the expression of VmHEP1. The present results provide insights into the functions of Hce2 domain-containing effectors acting as virulence factors of V. mali, and provide a new perspective regarding the contribution of tandem genes to the virulence of phytopathogenic fungi.
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Affiliation(s)
- Mian Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shichang Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yuhuan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Xiang Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Linlin Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Hao Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environ Microbiol 2019; 21:2677-2695. [PMID: 30838748 DOI: 10.1111/1462-2920.14583] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/28/2023]
Abstract
Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Killer toxin-like chitinases in filamentous fungi: Structure, regulation and potential roles in fungal biology. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Noar RD, Thomas E, Daub ME. A novel polyketide synthase gene cluster in the plant pathogenic fungus Pseudocercospora fijiensis. PLoS One 2019; 14:e0212229. [PMID: 30735556 PMCID: PMC6368318 DOI: 10.1371/journal.pone.0212229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/29/2019] [Indexed: 12/30/2022] Open
Abstract
Pseudocercospora fijiensis, causal agent of black Sigatoka of banana, produces polyketide synthase (PKS) pathways shown to be important in disease development by related Dothideomycete fungi. Genome analysis of the P. fijiensis PKS8-1 gene identified it as part of a gene cluster including genes encoding two transcription factors, a regulatory protein, a glyoxylase/beta-lactamase-like protein, an MFS transporter, a cytochrome P450, two aldo/keto reductases, a dehydrogenase, and a decarboxylase. Genome analysis of the related pathogens Pseudocercospora musae, Pseudocercospora eumusae, and Pseudocercospora pini-densiflorae, identified orthologous clusters containing a nearly identical combination of genes. Phylogenetic analysis of PKS8-1 identified homology to PKS proteins in the monodictyphenone and cladofulvin pathways in Aspergillus nidulans and Cladosporium fulvum, respectively. Analysis of clustered genes showed that the PKS8-1 cluster shares genes for enzymes involved in the production of the emodin intermediate in the monodictyphenone and cladofulvin pathways, but differs in many genes, suggesting production of a different metabolic product. Time course analysis of gene expression in infected banana showed up-regulation of PKS8-1 and four of eight clustered genes as early as 2 weeks post-inoculation and remaining high through 9 weeks. Overexpression of the pathway through constitutive expression of an aflR-like transcription factor gene in the cluster resulted in increased expression in culture of PKS8-1 as well as the four clustered genes that are up-regulated in infected plants. No differences were seen in timing or severity of disease symptoms with the overexpression strains relative to controls, however gene expression analysis showed no difference in expression in planta by an overexpression strain relative to controls. Thus constitutive expression of the aflR-like gene is not sufficient to upregulate the pathway above normal expression in planta. Pathway expression during all phases of disease development and conservation of the pathway in related Pseudocercospora species support a role for this pathway in disease.
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Affiliation(s)
- Roslyn D. Noar
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States of America
| | - Elizabeth Thomas
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
| | - Margaret E. Daub
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States of America
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Neu E, Debener T. Prediction of the Diplocarpon rosae secretome reveals candidate genes for effectors and virulence factors. Fungal Biol 2018; 123:231-239. [PMID: 30798878 DOI: 10.1016/j.funbio.2018.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 01/01/2023]
Abstract
Rose black spot is one of the most severe diseases of field-grown roses. Though R-genes have been characterised, little information is known about the molecular details of the interaction between pathogen and host. Based on the recently published genome sequence of the black spot fungus, we analysed gene models with various bioinformatic tools utilising the expression data of infected host tissues, which led to the prediction of 827 secreted proteins. A significant proportion of the predicted secretome comprises enzymes for the degradation of cell wall components, several of which were highly expressed during the first infection stages. As the secretome comprises major factors determining the ability of the fungus to colonise its host, we focused our further analyses on predicted effector candidates. In total, 52 sequences of 251 effector candidates matched several bioinformatic criteria of effectors, contained a Y/F/WxC motif, and did not match annotated proteins from other fungi. Additional sequences were identified based on their high expression levels during the penetration/haustorium formation phase and/or by matching known effectors from other fungi. Several host genotypes that are resistant to the sequenced isolate but differ in the R-genes responsible for this resistance are available. The combination of these genotypes with functional studies of the identified candidate effectors will allow the mechanisms of the rose black spot interaction to be dissected.
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Affiliation(s)
- Enzo Neu
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhaeuser Str. 2, Hannover 30419, Germany
| | - Thomas Debener
- Department of Molecular Plant Breeding, Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhaeuser Str. 2, Hannover 30419, Germany.
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Boulain H, Legeai F, Guy E, Morlière S, Douglas NE, Oh J, Murugan M, Smith M, Jaquiéry J, Peccoud J, White FF, Carolan JC, Simon JC, Sugio A. Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants. Genome Biol Evol 2018; 10:1554-1572. [PMID: 29788052 PMCID: PMC6012102 DOI: 10.1093/gbe/evy097] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2018] [Indexed: 12/31/2022] Open
Abstract
Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization. With this aim in mind, we assembled catalogues of putative effectors in the legume specialist aphid, Acyrthosiphon pisum, using transcriptomics and proteomics approaches. We identified 3,603 candidate effector genes predicted to be expressed in A. pisum salivary glands (SGs), and 740 of which displayed up-regulated expression in SGs in comparison to the alimentary tract. A search for orthologs in 17 arthropod genomes revealed that SG-up-regulated effector candidates of A. pisum are enriched in aphid-specific genes and tend to evolve faster compared with the whole gene set. We also found that a large fraction of proteins detected in the A. pisum saliva belonged to three gene families, of which certain members show evidence consistent with positive selection. Overall, this comprehensive analysis suggests that the large repertoire of effector candidates in A. pisum constitutes a source of novelties promoting plant adaptation to legumes.
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Affiliation(s)
- Hélène Boulain
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France.,Inria/IRISA GenScale, Campus de Beaulieu, Rennes, France
| | - Endrick Guy
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Stéphanie Morlière
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Nadine E Douglas
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,UCD School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas
| | - Marimuthu Murugan
- Community Science College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Michael Smith
- Department of Entomology, Kansas State University, Manhattan, Kansas
| | - Julie Jaquiéry
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean Peccoud
- UMR CNRS 7267 Ecologie et Biologie des Interactions, équipe Ecologie Evolution Symbiose, Université de Poitiers, Poitiers, France
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, Florida
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Jean-Christophe Simon
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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Marton K, Flajšman M, Radišek S, Košmelj K, Jakše J, Javornik B, Berne S. Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PLoS One 2018; 13:e0198971. [PMID: 29894496 PMCID: PMC5997321 DOI: 10.1371/journal.pone.0198971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/28/2018] [Indexed: 12/22/2022] Open
Abstract
The vascular plant pathogen Verticillium nonalfalfae causes Verticillium wilt in several important crops. VnaSSP4.2 was recently discovered as a V. nonalfalfae virulence effector protein in the xylem sap of infected hop. Here, we expanded our search for candidate secreted effector proteins (CSEPs) in the V. nonalfalfae predicted secretome using a bioinformatic pipeline built on V. nonalfalfae genome data, RNA-Seq and proteomic studies of the interaction with hop. The secretome, rich in carbohydrate active enzymes, proteases, redox proteins and proteins involved in secondary metabolism, cellular processing and signaling, includes 263 CSEPs. Several homologs of known fungal effectors (LysM, NLPs, Hce2, Cerato-platanins, Cyanovirin-N lectins, hydrophobins and CFEM domain containing proteins) and avirulence determinants in the PHI database (Avr-Pita1 and MgSM1) were found. The majority of CSEPs were non-annotated and were narrowed down to 44 top priority candidates based on their likelihood of being effectors. These were examined by spatio-temporal gene expression profiling of infected hop. Among the highest in planta expressed CSEPs, five deletion mutants were tested in pathogenicity assays. A deletion mutant of VnaUn.279, a lethal pathotype specific gene with sequence similarity to SAM-dependent methyltransferase (LaeA), had lower infectivity and showed highly reduced virulence, but no changes in morphology, fungal growth or conidiation were observed. Several putative secreted effector proteins that probably contribute to V. nonalfalfae colonization of hop were identified in this study. Among them, LaeA gene homolog was found to act as a potential novel virulence effector of V. nonalfalfae. The combined results will serve for future characterization of V. nonalfalfae effectors, which will advance our understanding of Verticillium wilt disease.
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Affiliation(s)
- Kristina Marton
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Flajšman
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Katarina Košmelj
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Kelly AC, Ward TJ. Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen. PLoS One 2018; 13:e0194616. [PMID: 29584736 PMCID: PMC5870968 DOI: 10.1371/journal.pone.0194616] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/06/2018] [Indexed: 12/30/2022] Open
Abstract
The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi.
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Affiliation(s)
- Amy C. Kelly
- United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois, United States of America
| | - Todd J. Ward
- United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois, United States of America
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Adam A, Deimel S, Pardo-Medina J, García-Martínez J, Konte T, Limón MC, Avalos J, Terpitz U. Protein Activity of the Fusarium fujikuroi Rhodopsins CarO and OpsA and Their Relation to Fungus-Plant Interaction. Int J Mol Sci 2018; 19:ijms19010215. [PMID: 29324661 PMCID: PMC5796164 DOI: 10.3390/ijms19010215] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 01/25/2023] Open
Abstract
Fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. The biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. The rice plant pathogen Fusarium fujikuroi exhibits two different rhodopsins, CarO and OpsA. CarO was previously characterized as a light-driven proton pump. We further analyzed the pumping behavior of CarO by patch-clamp experiments. Our data show that CarO pumping activity is strongly augmented in the presence of the plant hormone indole-3-acetic acid and in sodium acetate, in a dose-dependent manner under slightly acidic conditions. By contrast, under these and other tested conditions, the Neurospora rhodopsin (NR)-like rhodopsin OpsA did not exhibit any pump activity. Basic local alignment search tool (BLAST) searches in the genomes of ascomycetes revealed the occurrence of rhodopsin-encoding genes mainly in phyto-associated or phytopathogenic fungi, suggesting a possible correlation of the presence of rhodopsins with fungal ecology. In accordance, rice plants infected with a CarO-deficient F. fujikuroi strain showed more severe bakanae symptoms than the reference strain, indicating a potential role of the CarO rhodopsin in the regulation of plant infection by this fungus.
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Affiliation(s)
- Alexander Adam
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, D-97074 Würzburg, Germany; (A.A.); (S.D.)
| | - Stephan Deimel
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, D-97074 Würzburg, Germany; (A.A.); (S.D.)
| | - Javier Pardo-Medina
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Jorge García-Martínez
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Tilen Konte
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Sl-1000 Ljubljana, Slovenia;
| | - M. Carmen Limón
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Javier Avalos
- Department of Genetics, Faculty of Biology, University of Seville, E-41012 Seville, Spain; (J.P.-M.); (J.G.-M.); (M.C.L.); (J.A.)
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, D-97074 Würzburg, Germany; (A.A.); (S.D.)
- Correspondence: ; Tel.: +49-931-31-84226
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Mesarich CH, Ӧkmen B, Rovenich H, Griffiths SA, Wang C, Karimi Jashni M, Mihajlovski A, Collemare J, Hunziker L, Deng CH, van der Burgt A, Beenen HG, Templeton MD, Bradshaw RE, de Wit PJGM. Specific Hypersensitive Response-Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:145-162. [PMID: 29144204 DOI: 10.1094/mpmi-05-17-0114-fi] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged. To combat these strains, new Cf genes are required. An effectoromics approach was employed to identify wild tomato accessions carrying new Cf genes. Proteomics and transcriptome sequencing were first used to identify 70 apoplastic in planta-induced C. fulvum SSPs. Based on sequence homology, 61 of these SSPs were novel or lacked known functional domains. Seven, however, had predicted structural homology to antimicrobial proteins, suggesting a possible role in mediating antagonistic microbe-microbe interactions in planta. Wild tomato accessions were then screened for HR-associated recognition of 41 SSPs, using the Potato virus X-based transient expression system. Nine SSPs were recognized by one or more accessions, suggesting that these plants carry new Cf genes available for incorporation into cultivated tomato.
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Affiliation(s)
- Carl H Mesarich
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- 2 Laboratory of Molecular Plant Pathology, Institute of Agriculture & Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
- 3 Bio-Protection Research Centre, New Zealand
| | - Bilal Ӧkmen
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hanna Rovenich
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Scott A Griffiths
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Changchun Wang
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- 4 College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, People's Republic of China
| | - Mansoor Karimi Jashni
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- 5 Department of Plant Pathology, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, P.O. Box 19395‒1454, Tehran, Iran
| | - Aleksandar Mihajlovski
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jérôme Collemare
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Lukas Hunziker
- 3 Bio-Protection Research Centre, New Zealand
- 6 Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Cecilia H Deng
- 7 Breeding & Genomics/Bioprotection Portfolio, the New Zealand Institute for Plant & Food Research Limited, Mount Albert Research Centre, Auckland 1025, New Zealand; and
| | - Ate van der Burgt
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Henriek G Beenen
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Matthew D Templeton
- 3 Bio-Protection Research Centre, New Zealand
- 7 Breeding & Genomics/Bioprotection Portfolio, the New Zealand Institute for Plant & Food Research Limited, Mount Albert Research Centre, Auckland 1025, New Zealand; and
| | - Rosie E Bradshaw
- 3 Bio-Protection Research Centre, New Zealand
- 6 Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Pierre J G M de Wit
- 1 Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- 8 Centre for BioSystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
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Zhang L, Ni H, Du X, Wang S, Ma XW, Nürnberger T, Guo HS, Hua C. The Verticillium-specific protein VdSCP7 localizes to the plant nucleus and modulates immunity to fungal infections. THE NEW PHYTOLOGIST 2017; 215:368-381. [PMID: 28407259 DOI: 10.1111/nph.14537] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/21/2017] [Indexed: 05/05/2023]
Abstract
Fungal pathogens secrete effector proteins to suppress plant basal defense for successful colonization. Resistant plants, however, can recognize effectors by cognate R proteins to induce effector-triggered immunity (ETI). By analyzing secretomes of the vascular fungal pathogen Verticillium dahliae, we identified a novel secreted protein VdSCP7 that targets the plant nucleus. The green fluorescent protein (GFP)-tagged VdSCP7 gene with either a mutated nuclear localization signal motif or with additional nuclear export signal was transiently expressed in Nicotiana benthamiana, and investigated for induction of plant immunity. The role of VdSCP7 in V. dahliae pathogenicity was characterized by gene knockout and complementation, and GFP labeling. Expression of the VdSCP7 gene in N. benthamiana activated both salicylic acid and jasmonate signaling, and altered the plant's susceptibility to the pathogens Botrytis cinerea and Phytophthora capsici. The immune response activated by VdSCP7 was highly dependent on its initial extracellular secretion and subsequent nuclear localization in plants. Knockout of the VdSCP7 gene significantly enhanced V. dahliae aggressiveness on cotton. GFP-labeled VdSCP7 is secreted by V. dahliae and accumulates in the plant nucleus. We conclude that VdSCP7 is a novel effector protein that targets the host nucleus to modulate plant immunity, and suggest that plants can recognize VdSCP7 to activate ETI during fungal infection.
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Affiliation(s)
- Lisha Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, D-72076, Germany
| | - Hao Ni
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Du
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Wei Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, D-72076, Germany
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenlei Hua
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Tübingen, D-72076, Germany
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Franceschetti M, Maqbool A, Jiménez-Dalmaroni MJ, Pennington HG, Kamoun S, Banfield MJ. Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity. Microbiol Mol Biol Rev 2017; 81:e00066-16. [PMID: 28356329 PMCID: PMC5485802 DOI: 10.1128/mmbr.00066-16] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.
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Affiliation(s)
- Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Helen G Pennington
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Chang TC, Salvucci A, Crous PW, Stergiopoulos I. Comparative Genomics of the Sigatoka Disease Complex on Banana Suggests a Link between Parallel Evolutionary Changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and Increased Virulence on the Banana Host. PLoS Genet 2016; 12:e1005904. [PMID: 27513322 PMCID: PMC4981473 DOI: 10.1371/journal.pgen.1005904] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 02/05/2016] [Indexed: 01/05/2023] Open
Abstract
The Sigatoka disease complex, caused by the closely-related Dothideomycete fungi Pseudocercospora musae (yellow sigatoka), Pseudocercospora eumusae (eumusae leaf spot), and Pseudocercospora fijiensis (black sigatoka), is currently the most devastating disease on banana worldwide. The three species emerged on bananas from a recent common ancestor and show clear differences in virulence, with P. eumusae and P. fijiensis considered the most aggressive. In order to understand the genomic modifications associated with shifts in the species virulence spectra after speciation, and to identify their pathogenic core that can be exploited in disease management programs, we have sequenced and analyzed the genomes of P. eumusae and P. musae and compared them with the available genome sequence of P. fijiensis. Comparative analysis of genome architectures revealed significant differences in genome size, mainly due to different rates of LTR retrotransposon proliferation. Still, gene counts remained relatively equal and in the range of other Dothideomycetes. Phylogenetic reconstruction based on a set of 46 conserved single-copy genes strongly supported an earlier evolutionary radiation of P. fijiensis from P. musae and P. eumusae. However, pairwise analyses of gene content indicated that the more virulent P. eumusae and P. fijiensis share complementary patterns of expansions and contractions in core gene families related to metabolism and enzymatic degradation of plant cell walls, suggesting that the evolution of virulence in these two pathogens has, to some extent, been facilitated by convergent changes in metabolic pathways associated with nutrient acquisition and assimilation. In spite of their common ancestry and shared host-specificity, the three species retain fairly dissimilar repertoires of effector proteins, suggesting that they likely evolved different strategies for manipulating the host immune system. Finally, 234 gene families, including seven putative effectors, were exclusively present in the three Sigatoka species, and could thus be related to adaptation to the banana host. Understanding the evolutionary and genomic changes involved in the emergence of new pathogens and shifts in virulence spectra is vital for deciphering the biological process of disease emergence and for designing new and effective disease control methods. In this study, we employed comparative genomics in order to examine the nature, diversity, and extent of genomic modifications associated with changes in virulence among Pseudocercospora musae, Pseudocercospora eumusae, and Pseudocercospora fijiensis, the main constituents of the Sigatoka disease complex on banana, currently one of the most destructive diseases on banana worldwide. Our comparative genome analyses have highlighted the role of pathoadaptive changes in virulence associated genes, such as those encoding for effectors, in shaping the underlying differences in virulence spectra among the three species, and also revealed that changes in the size of gene families associated with nutrient acquisition and assimilation are more respectful of the species virulence profiles rather than their evolutionary relationships. Thus, we posit that next to species-specific evolutionary adaptations in virulence-associated genes, the increase in virulence of P. eumusae and P. fijiensis has been driven by convergent evolution in metabolic pathways that likely facilitate a higher efficiency of nutrient acquisition, uptake, and utilization.
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Affiliation(s)
- Ti-Cheng Chang
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Anthony Salvucci
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Pedro W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Cell biology of Zymoseptoria tritici: Pathogen cell organization and wheat infection. Fungal Genet Biol 2016; 79:17-23. [PMID: 26092785 PMCID: PMC4502449 DOI: 10.1016/j.fgb.2015.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/27/2015] [Accepted: 04/02/2015] [Indexed: 01/26/2023]
Abstract
Cell biology of the infection begins to shed light on the host–pathogen interaction. The cell biology of the fungal pathogen is highly understudied. Intensified cell biology research promises new fungicide targets and will help mode-of-action studies.
Cell biological research in the wheat pathogen Zymoseptoria tritici (formerly Mycosphaerella graminicola) has led to a good understanding of the histology of the infection process. Expression profiling and bioinformatic approaches, combined with molecular studies on signaling pathways, effectors and potential necrosis factors provides first insight into the complex interplay between the host and the pathogen. Cell biological studies will help to further our understanding of the infection strategy of the fungus. The cellular organization and intracellular dynamics of the fungus itself is largely unexplored. Insight into essential cellular processes within the pathogen will expand our knowledge of the basic biology of Z. tritici, thereby providing putative new anti-fungal targets.
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Shcherbakova LA, Odintsova TI, Stakheev AA, Fravel DR, Zavriev SK. Identification of a Novel Small Cysteine-Rich Protein in the Fraction from the Biocontrol Fusarium oxysporum Strain CS-20 that Mitigates Fusarium Wilt Symptoms and Triggers Defense Responses in Tomato. FRONTIERS IN PLANT SCIENCE 2016; 6:1207. [PMID: 26779237 PMCID: PMC4703993 DOI: 10.3389/fpls.2015.01207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/15/2015] [Indexed: 05/06/2023]
Abstract
The biocontrol effect of the non-pathogenic Fusarium oxysporum strain CS-20 against the tomato wilt pathogen F. oxysporum f. sp. lycopersici (FOL) has been previously reported to be primarily plant-mediated. This study shows that CS-20 produces proteins, which elicit defense responses in tomato plants. Three protein-containing fractions were isolated from CS-20 biomass using size exclusion chromatography. Exposure of seedling roots to one of these fractions prior to inoculation with pathogenic FOL strains significantly reduced wilt severity. This fraction initiated an ion exchange response in cultured tomato cells resulting in a reversible alteration of extracellular pH; increased tomato chitinase activity, and induced systemic resistance by enhancing PR-1 expression in tomato leaves. Two other protein fractions were inactive in seedling protection. The main polypeptide (designated CS20EP), which was specifically present in the defense-inducing fraction and was not detected in inactive protein fractions, was identified. The nucleotide sequence encoding this protein was determined, and its complete amino acid sequence was deduced from direct Edman degradation (25 N-terminal amino acid residues) and DNA sequencing. The CS20EP was found to be a small basic cysteine-rich protein with a pI of 9.87 and 23.43% of hydrophobic amino acid residues. BLAST search in the NCBI database showed that the protein is new; however, it displays 48% sequence similarity with a hypothetical protein FGSG_10784 from F. graminearum strain PH-1. The contribution of CS20EP to elicitation of tomato defense responses resulting in wilt mitigating is discussed.
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Affiliation(s)
- Larisa A. Shcherbakova
- Laboratory of Physiological Plant Pathology, All-Russian Research Institute of PhytopathologyMoscow, Russia
| | - Tatyana I. Odintsova
- Laboratory of Molecular-Genetic Bases of Plant Immunity, Vavilov Institute of General GeneticsMoscow, Russia
| | - Alexander A. Stakheev
- Laboratory of Molecular Diagnostic, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of SciencesMoscow, Russia
| | - Deborah R. Fravel
- Crop Production and Protection, United States Department of Agriculture, Agricultural Research ServiceBeltsville, MD, USA
| | - Sergey K. Zavriev
- Laboratory of Molecular Diagnostic, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of SciencesMoscow, Russia
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Kim KT, Jeon J, Choi J, Cheong K, Song H, Choi G, Kang S, Lee YH. Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association. FRONTIERS IN PLANT SCIENCE 2016; 7:186. [PMID: 26925088 PMCID: PMC4759460 DOI: 10.3389/fpls.2016.00186] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 02/03/2016] [Indexed: 05/18/2023]
Abstract
Fungal secretome consists of various functional groups of proteins, many of which participate in nutrient acquisition, self-protection, or manipulation of the environment and neighboring organisms. The least characterized component of the secretome is small secreted proteins (SSPs). Some SSPs have been reported to function as effectors, but most remain to be characterized. The composition of major secretome components, such as carbohydrate-active enzymes, proteases, lipases, and oxidoreductases, appear to reflect the lifestyle and ecological niche of individual species. We hypothesize that many SSPs participate in manipulating plants as effectors. Obligate biotrophs likely encode more and diverse effector-like SSPs to suppress host defense compared to necrotrophs, which generally use cell wall degrading enzymes and phytotoxins to kill hosts. Because different secretome prediction workflows have been used in different studies, available secretome data are difficult to integrate for comprehensive comparative studies to test this hypothesis. In this study, SSPs encoded by 136 fungal species were identified from data archived in Fungal Secretome Database (FSD) via a refined secretome workflow. Subsequently, compositions of SSPs and other secretome components were compared in light of taxa and lifestyles. Those species that are intimately associated with host cells, such as biotrophs and symbionts, usually have higher proportion of species-specific SSPs (SSSPs) than hemibiotrophs and necrotrophs, but the latter groups displayed higher proportions of secreted enzymes. Results from our study established a foundation for functional studies on SSPs and will also help understand genomic changes potentially underpinning different fungal lifestyles.
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Affiliation(s)
- Ki-Tae Kim
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Department of Agricultural Biotechnology, Seoul National UniversitySeoul, South Korea
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Jaeyoung Choi
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National UniversitySeoul, South Korea
- Department of Agricultural Biotechnology, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National UniversitySeoul, South Korea
- Center for Fungal Genetic Resources, Center for Fungal Pathogenesis, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
- *Correspondence: Yong-Hwan Lee
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Wanasinghe DN, Jones EG, Camporesi E, Mortimer PE, Xu J, Bahkali AH, Hyde KD. The GenusMurispora. CRYPTOGAMIE MYCOL 2015. [DOI: 10.7872/crym/v36.iss4.2015.419] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mirzadi Gohari A, Ware SB, Wittenberg AHJ, Mehrabi R, Ben M'Barek S, Verstappen ECP, van der Lee TAJ, Robert O, Schouten HJ, de Wit PPJGM, Kema GHJ. Effector discovery in the fungal wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2015; 16:931-45. [PMID: 25727413 PMCID: PMC6638447 DOI: 10.1111/mpp.12251] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Fungal plant pathogens, such as Zymoseptoria tritici (formerly known as Mycosphaerella graminicola), secrete repertoires of effectors to facilitate infection or trigger host defence mechanisms. The discovery and functional characterization of effectors provides valuable knowledge that can contribute to the design of new and effective disease management strategies. Here, we combined bioinformatics approaches with expression profiling during pathogenesis to identify candidate effectors of Z. tritici. In addition, a genetic approach was conducted to map quantitative trait loci (QTLs) carrying putative effectors, enabling the validation of both complementary strategies for effector discovery. In planta expression profiling revealed that candidate effectors were up-regulated in successive waves corresponding to consecutive stages of pathogenesis, contrary to candidates identified by QTL mapping that were, overall, expressed at low levels. Functional analyses of two top candidate effectors (SSP15 and SSP18) showed their dispensability for Z. tritici pathogenesis. These analyses reveal that generally adopted criteria, such as protein size, cysteine residues and expression during pathogenesis, may preclude an unbiased effector discovery. Indeed, genetic mapping of genomic regions involved in specificity render alternative effector candidates that do not match the aforementioned criteria, but should nevertheless be considered as promising new leads for effectors that are crucial for the Z. tritici-wheat pathosystem.
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Affiliation(s)
- Amir Mirzadi Gohari
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Department of Plant Protection, College of Agriculture, University of Tehran, Plant Pathology Building, Karaj, Iran
| | - Sarah B Ware
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Alexander H J Wittenberg
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Rahim Mehrabi
- Cereal Research Department, Seed and Plant Improvement Institute, PO Box 31585-4119, Karaj, Iran
| | - Sarrah Ben M'Barek
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif, 2050, Tunisia
| | - Els C P Verstappen
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Theo A J van der Lee
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Olivier Robert
- Bioplante, Florimond Desprez, BP41, 59242, Cappelle-en-Pévèle, France
| | - Henk J Schouten
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Pierre P J G M de Wit
- Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Gert H J Kema
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
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Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi. PLoS Pathog 2015; 11:e1005228. [PMID: 26506000 PMCID: PMC4624222 DOI: 10.1371/journal.ppat.1005228] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/24/2015] [Indexed: 01/13/2023] Open
Abstract
Phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown. To get a deeper understanding of fungal effectors, we determined by NMR spectroscopy the 3-dimensional structures of the Magnaporthe oryzae effectors AVR1-CO39 and AVR-Pia. Despite a lack of sequence similarity, both proteins have very similar 6 β-sandwich structures that are stabilized in both cases by a disulfide bridge between 2 conserved cysteins located in similar positions of the proteins. Structural similarity searches revealed that AvrPiz-t, another effector from M. oryzae, and ToxB, an effector of the wheat tan spot pathogen Pyrenophora tritici-repentis have the same structures suggesting the existence of a family of sequence-unrelated but structurally conserved fungal effectors that we named MAX-effectors (MagnaportheAvrs and ToxB like). Structure-informed pattern searches strengthened this hypothesis by identifying MAX-effector candidates in a broad range of ascomycete phytopathogens. Strong expansion of the MAX-effector family was detected in M. oryzae and M. grisea where they seem to be particularly important since they account for 5–10% of the effector repertoire and 50% of the cloned avirulence effectors. Expression analysis indicated that the majority of M. oryzae MAX-effectors are expressed specifically during early infection suggesting important functions during biotrophic host colonization. We hypothesize that the scenario observed for MAX-effectors can serve as a paradigm for ascomycete effector diversity and that the enormous number of sequence-unrelated ascomycete effectors may in fact belong to a restricted set of structurally conserved effector families. Fungal plant pathogens are of outstanding economic and ecological importance and cause destructive diseases on many cultivated and wild plants. Effector proteins that are secreted during infection to manipulate the host and to promote disease are a key element in fungal virulence. Phytopathogenic fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The molecular functions of this most important class of fungal effectors and the evolutionary mechanisms that generate this tremendous numbers of apparently unrelated proteins are largely unknown. By investigating the 3-dimensional structures of effectors from the rice blast fungus M. oryzae, we discovered an effector family comprising structurally conserved but sequence-unrelated effectors from M. oryzae and the phylogenetically distant wheat pathogen Pyrenophora tritici-repentis that we named MAX-effectors (M. oryzaeAvrs and ToxB). Structure-informed searches of whole genome sequence databases suggest that MAX-effectors are present at low frequencies and with a patchy phylogenetic distribution in many ascomycete phytopathogens. They underwent strong lineage-specific expansion in fungi of the Pyriculariae family that contains M. oryzae where they seem particularly important during biotrophic plant colonization and account for 50% of the cloned Avr effectors and 5–10% of the effector repertoire. Based on our results on the MAX-effectors and the widely accepted concept that fungal effectors evolve according to a birth-and-death model we propose the hypothesis that the majority of the immense numbers of different ascomycete effectors could in fact belong to a limited set of structurally defined families whose members are phylogenetically related.
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Cheeseman K, Ropars J, Renault P, Dupont J, Gouzy J, Branca A, Abraham AL, Ceppi M, Conseiller E, Debuchy R, Malagnac F, Goarin A, Silar P, Lacoste S, Sallet E, Bensimon A, Giraud T, Brygoo Y. Multiple recent horizontal transfers of a large genomic region in cheese making fungi. Nat Commun 2015; 5:2876. [PMID: 24407037 PMCID: PMC3896755 DOI: 10.1038/ncomms3876] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/06/2013] [Indexed: 02/01/2023] Open
Abstract
While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought by many to be anecdotal. Here we report multiple recent transfers of a huge genomic island between Penicillium spp. found in the food environment. Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti, and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti—called Wallaby—present as identical fragments at non-homologous loci in P. camemberti and P. rubens. Wallaby is detected in Penicillium collections exclusively in strains from food environments. Wallaby encompasses about 250 predicted genes, some of which are probably involved in competition with microorganisms. The occurrence of multiple recent eukaryotic transfers in the food environment provides strong evidence for the importance of this understudied and probably underestimated phenomenon in eukaryotes. Horizontal gene transfers are known to play an important role in prokaryote evolution but their impact and prevalence in eukaryotes is less clear. Here, the authors sequence the genomes of cheese making fungi P. roqueforti and P. camemberti, and provide evidence for recent horizontal transfers of a large genomic region.
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Affiliation(s)
- Kevin Cheeseman
- INRA, UMR1319 Micalis, F-78352 Jouy-en-Josas, France; Genomic Vision, 80-84 rue des Meuniers, 92220 Bagneux, France; AgroParisTech, UMR Micalis, F-78352 Jouy-en-Josas, France
| | - Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France; Univ Paris-Sud, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France; CNRS, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France
| | - Pierre Renault
- INRA, UMR1319 Micalis, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78352 Jouy-en-Josas, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Jérôme Gouzy
- LIMP Toulouse, INRA/CNRS, INRA, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France; INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France
| | - Antoine Branca
- Univ Paris-Sud, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France; CNRS, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France
| | - Anne-Laure Abraham
- INRA, UMR1319 Micalis, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78352 Jouy-en-Josas, France
| | - Maurizio Ceppi
- Genomic Vision, 80-84 rue des Meuniers, 92220 Bagneux, France
| | | | - Robert Debuchy
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France; CNRS, Institut de Génétique et Microbiologie UMR8621, 91405 Orsay, France
| | - Fabienne Malagnac
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France; Univ Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), 75205 Paris, France
| | - Anne Goarin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France
| | - Philippe Silar
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, 91405 Orsay, France; Univ Paris Diderot, Sorbonne Paris Cité, Institut des Energies de Demain (IED), 75205 Paris, France
| | - Sandrine Lacoste
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Erika Sallet
- LIMP Toulouse, INRA/CNRS, INRA, 24 Chemin de Borde Rouge-Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France; INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France
| | - Aaron Bensimon
- Genomic Vision, 80-84 rue des Meuniers, 92220 Bagneux, France
| | - Tatiana Giraud
- Univ Paris-Sud, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France; CNRS, Ecologie, Systématique et Evolution, UMR8079, 91405 Orsay, France
| | - Yves Brygoo
- 13 ruelle d'Aigrefoin 78470 St Rémy-lès-Chevreuse
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50
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Weßling R, Epple P, Altmann S, He Y, Yang L, Henz SR, McDonald N, Wiley K, Bader KC, Gläßer C, Mukhtar MS, Haigis S, Ghamsari L, Stephens AE, Ecker JR, Vidal M, Jones JDG, Mayer KFX, Ver Loren van Themaat E, Weigel D, Schulze-Lefert P, Dangl JL, Panstruga R, Braun P. Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe 2015; 16:364-75. [PMID: 25211078 DOI: 10.1016/j.chom.2014.08.004] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 06/27/2014] [Accepted: 08/14/2014] [Indexed: 01/31/2023]
Abstract
While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.
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Affiliation(s)
- Ralf Weßling
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Petra Epple
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefan Altmann
- Technische Universität München (TUM), Center for Life and Food Sciences Weihenstephan, Department for Plant Systems Biology, D-85354 Freising, Germany
| | - Yijian He
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Yang
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefan R Henz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Nathan McDonald
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristin Wiley
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kai Christian Bader
- Plant Genome and Systems Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Christine Gläßer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - M Shahid Mukhtar
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, University of Alabama Birmingham, Birmingham, AL 35294, USA
| | - Sabine Haigis
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana Farber Cancer Institute, and Harvard Medical School, Department of Genetics, Boston, MA 02215, USA
| | - Amber E Stephens
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Joseph R Ecker
- Howard Hughes Medical Institute and Salk Institute for Biological Studies, Plant Biology Lab, La Jolla, CA 92037, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana Farber Cancer Institute, and Harvard Medical School, Department of Genetics, Boston, MA 02215, USA
| | - Jonathan D G Jones
- The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Jeffery L Dangl
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Center for Genome Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Ralph Panstruga
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany; Rheinisch Westfälische Technische Hochschule (RWTH) Aachen University, Institute for Biology I, Unit of Plant Molecular Cell Biology, D-52074 Aachen, Germany.
| | - Pascal Braun
- Technische Universität München (TUM), Center for Life and Food Sciences Weihenstephan, Department for Plant Systems Biology, D-85354 Freising, Germany.
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