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Tu T, Ren Y, Gong W, Huang J, Zhu C, Salah M, Zhao L, Xia X, Wang Y. Endoglucanase H from Aspergillus westerdijkiae Plays an Important Role in the Virulence on Pear Fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8415-8422. [PMID: 38573226 DOI: 10.1021/acs.jafc.3c08486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Aspergillus westerdijkiae can infect many agricultural products including cereals, grapes, and pear. Pathogenic fungi secrete diverse effectors as invasive weapons for successful invasion the host plant. During the pathogen-host interaction, 4486 differentially expressed genes were observed in A. westerdijkiae with 2773 up-regulated and 1713 down-regulated, whereas 8456 differentially expressed genes were detected in pear fruits with 4777 up-regulated and 3679 down-regulated. A total of 309 effector candidate genes were identified from the up-regulated genes in A. westerdijkiae. Endoglucanase H (AwEGH) was significantly induced during the pathogen-host interaction. Deletion of AwEGH resulted in altered fungal growth and morphology and reduced conidia production and germination compared to the wild-type. Further experiments demonstrated that AwEGH plays a role in cell wall integrity. Importantly, disruption of AwEGH significantly reduced the fungal virulence on pear fruits, and this defect can be partly explained by the impaired ability of A. westerdijkiae to penetrate host plants.
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Affiliation(s)
- Tingting Tu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yun Ren
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Weifeng Gong
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Juanying Huang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Chenyang Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Mahmoud Salah
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- Department of Environmental Agricultural Science, Faculty of Graduate Studies and Environmental Research, Ain Shams University, Cairo 11566, Egypt
| | - Luning Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaoshuang Xia
- Center of Analysis, Jiangsu University, Zhenjiang 212013, China
| | - Yun Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
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2
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Oliveira-Garcia E, Yan X, Oses-Ruiz M, de Paula S, Talbot NJ. Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae. THE NEW PHYTOLOGIST 2024; 241:1007-1020. [PMID: 38073141 DOI: 10.1111/nph.19446] [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: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024]
Abstract
Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae-host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Miriam Oses-Ruiz
- IMAB, Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Navarra, Spain
| | - Samuel de Paula
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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Hao G, Naumann TA, Chen H, Bai G, McCormick S, Kim HS, Tian B, Trick HN, Naldrett MJ, Proctor R. Fusarium graminearum Effector FgNls1 Targets Plant Nuclei to Induce Wheat Head Blight. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:478-488. [PMID: 36853197 DOI: 10.1094/mpmi-12-22-0254-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium head blight (FHB) caused by Fusarium graminearum is one of the most devastating diseases of wheat and barley worldwide. Effectors suppress host immunity and promote disease development. The genome of F. graminearum contains hundreds of effectors with unknown function. Therefore, investigations of the functions of these effectors will facilitate developing novel strategies to enhance wheat resistance to FHB. We characterized a F. graminearum effector, FgNls1, containing a signal peptide and multiple eukaryotic nuclear localization signals. A fusion protein of green fluorescent protein and FgNls1 accumulated in plant cell nuclei when transiently expressed in Nicotiana benthamiana. FgNls1 suppressed Bax-induced cell death when co-expressed in N. benthamiana. We revealed that the expression of FgNLS1 was induced in wheat spikes infected with F. graminearum. The Fgnls1 mutants significantly reduced initial infection and FHB spread within a spike. The function of FgNLS1 was restored in the Fgnls1-complemented strains. Wheat histone 2B was identified as an interacting protein by FgNls1-affinity chromatography. Furthermore, transgenic wheat plants that silence FgNLS1 expression had significantly lower FHB severity than control plants. This study demonstrates a critical role of FgNls1 in F. graminearum pathogenesis and indicates that host-induced gene silencing targeting F. graminearum effectors is a promising approach to enhance FHB resistance. [Formula: see text] Copyright © 2023 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)
- Guixia Hao
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Hui Chen
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, U.S.A
| | - Susan McCormick
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Bin Tian
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Michael J Naldrett
- Nebraska Center for Biotechnology, Beadle Center, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Robert Proctor
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
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Harris W, Kim S, Vӧlz R, Lee YH. Nuclear effectors of plant pathogens: Distinct strategies to be one step ahead. MOLECULAR PLANT PATHOLOGY 2023; 24:637-650. [PMID: 36942744 DOI: 10.1111/mpp.13315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 02/08/2023] [Indexed: 05/18/2023]
Abstract
Nuclear effector proteins released by bacteria, oomycete, nematode, and fungi burden the global environment and crop yield. Microbial effectors are key weapons in the evolutionary arms race between plants and pathogens, vital in determining the success of pathogenic colonization. Secreted effectors undermine a multitude of host cellular processes depending on their target destination. Effectors are classified by their localization as either extracellular (apoplastic) or intracellular. Intracellular effectors can be further subclassified by their compartment such as the nucleus, cytoplasm or chloroplast. Nuclear effectors bring into question the role of the plant nucleus' intrinsic defence strategies and their vulnerability to effector-based manipulation. Nuclear effectors interfere with multiple nuclear processes including the epigenetic regulation of the host chromatin, the impairment of the trans-kingdom antifungal RNAi machinery, and diverse classes of immunity-associated host proteins. These effector-targeted pathways are widely conserved among different hosts and regulate a broad array of plant cellular processes. Thus, these nuclear sites constitute meaningful targets for effectors to subvert the plant defence system and acquire resources for pathogenic propagation. This review provides an extensive and comparative compilation of diverse plant microbe nuclear effector libraries, thereby highlighting the distinct and conserved mechanisms these effectors employ to modulate plant cellular processes for the pathogen's profit.
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Affiliation(s)
- William Harris
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Ronny Vӧlz
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, 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 Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, South Korea
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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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Singh SK, Shree A, Verma S, Singh K, Kumar K, Srivastava V, Singh R, Saxena S, Singh AP, Pandey A, Verma PK. The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis, increasing host susceptibility. THE PLANT CELL 2023; 35:1134-1159. [PMID: 36585808 PMCID: PMC10015165 DOI: 10.1093/plcell/koac372] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 05/29/2023]
Abstract
Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein Ascochyta rabiei PEXEL-like Effector Candidate 25 (ArPEC25), which is secreted by the necrotroph A. rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaβLIM1a. CaβLIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase (PAL), the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of CaβLIM1a by interfering with its DNA-binding ability, resulting in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions.
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Affiliation(s)
- Shreenivas Kumar Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ankita Shree
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sandhya Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vikas Srivastava
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Samiksha Saxena
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Agam Prasad Singh
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ashutosh Pandey
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Becerra S, Baroncelli R, Boufleur TR, Sukno SA, Thon MR. Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes. Front Microbiol 2023; 14:1129319. [PMID: 37032845 PMCID: PMC10076810 DOI: 10.3389/fmicb.2023.1129319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
The fungal pathogen Colletotrichum graminicola causes the anthracnose of maize (Zea mays) and is responsible for significant yield losses worldwide. The genome of C. graminicola was sequenced in 2012 using Sanger sequencing, 454 pyrosequencing, and an optical map to obtain an assembly of 13 pseudochromosomes. We re-sequenced the genome using a combination of short-read (Illumina) and long-read (PacBio) technologies to obtain a chromosome-level assembly. The new version of the genome sequence has 13 chromosomes with a total length of 57.43 Mb. We detected 66 (23.62 Mb) structural rearrangements in the new assembly with respect to the previous version, consisting of 61 (21.98 Mb) translocations, 1 (1.41 Mb) inversion, and 4 (221 Kb) duplications. We annotated the genome and obtained 15,118 predicted genes and 3,614 new gene models compared to the previous version of the assembly. We show that 25.88% of the new assembly is composed of repetitive DNA elements (13.68% more than the previous assembly version), which are mostly found in gene-sparse regions. We describe genomic compartmentalization consisting of repeat-rich and gene-poor regions vs. repeat-poor and gene-rich regions. A total of 1,140 secreted proteins were found mainly in repeat-rich regions. We also found that ~75% of the three smallest chromosomes (minichromosomes, between 730 and 551 Kb) are strongly affected by repeat-induced point mutation (RIP) compared with 28% of the larger chromosomes. The gene content of the minichromosomes (MCs) comprises 121 genes, of which 83.6% are hypothetical proteins with no predicted function, while the mean percentage of Chr1-Chr10 is 36.5%. No predicted secreted proteins are present in the MCs. Interestingly, only 2% of the genes in Chr11 have homologs in other strains of C. graminicola, while Chr12 and 13 have 58 and 57%, respectively, raising the question as to whether Chrs12 and 13 are dispensable. The core chromosomes (Chr1-Chr10) are very different with respect to the MCs (Chr11-Chr13) in terms of the content and sequence features. We hypothesize that the higher density of repetitive elements and RIPs in the MCs may be linked to the adaptation and/or host co-evolution of this pathogenic fungus.
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Affiliation(s)
- Sioly Becerra
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Thaís R. Boufleur
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- *Correspondence: Serenella A. Sukno
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- Michael R. Thon
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Helm M, Singh R, Hiles R, Jaiswal N, Myers A, Iyer-Pascuzzi AS, Goodwin SB. Candidate Effector Proteins from the Maize Tar Spot Pathogen Phyllachora maydis Localize to Diverse Plant Cell Compartments. PHYTOPATHOLOGY 2022; 112:2538-2548. [PMID: 35815936 DOI: 10.1094/phyto-05-22-0181-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Most fungal pathogens secrete effector proteins into host cells to modulate their immune responses, thereby promoting pathogenesis and fungal growth. One such fungal pathogen is the ascomycete Phyllachora maydis, which causes tar spot disease on leaves of maize (Zea mays). Sequencing of the P. maydis genome revealed 462 putatively secreted proteins, of which 40 contain expected effector-like sequence characteristics. However, the subcellular compartments targeted by P. maydis effector candidate (PmEC) proteins remain unknown, and it will be important to prioritize them for further functional characterization. To test the hypothesis that PmECs target diverse subcellular compartments, cellular locations of super yellow fluorescent protein-tagged PmEC proteins were identified using a Nicotiana benthamiana-based heterologous expression system. Immunoblot analyses showed that most of the PmEC-fluorescent protein fusions accumulated protein in N. benthamiana, indicating that the candidate effectors could be expressed in dicot leaf cells. Laser-scanning confocal microscopy of N. benthamiana epidermal cells revealed that most of the P. maydis putative effectors localized to the nucleus and cytosol. One candidate effector, PmEC01597, localized to multiple subcellular compartments including the nucleus, nucleolus, and plasma membrane, whereas an additional putative effector, PmEC03792, preferentially labelled both the nucleus and nucleolus. Intriguingly, one candidate effector, PmEC04573, consistently localized to the stroma of chloroplasts as well as stroma-containing tubules (stromules). Collectively, these data suggest that effector candidate proteins from P. maydis target diverse cellular organelles and could thus provide valuable insights into their putative functions, as well as host processes potentially manipulated by this fungal pathogen.
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Affiliation(s)
- Matthew Helm
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | - Raksha Singh
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | - Rachel Hiles
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Namrata Jaiswal
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | - Ariana Myers
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
| | | | - Stephen B Goodwin
- Crop Production and Pest Control Research Unit, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), West Lafayette, IN 47907
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Todd JNA, Carreón-Anguiano KG, Islas-Flores I, Canto-Canché B. Fungal Effectoromics: A World in Constant Evolution. Int J Mol Sci 2022; 23:13433. [PMID: 36362218 PMCID: PMC9656242 DOI: 10.3390/ijms232113433] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 10/28/2023] Open
Abstract
Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.
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Affiliation(s)
- Jewel Nicole Anna Todd
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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10
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De Mandal S, Jeon J. Nuclear Effectors in Plant Pathogenic Fungi. MYCOBIOLOGY 2022; 50:259-268. [PMID: 36404902 PMCID: PMC9645283 DOI: 10.1080/12298093.2022.2118928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 05/29/2023]
Abstract
The nuclear import of proteins is a fundamental process in the eukaryotes including plant. It has become evident that such basic process is exploited by nuclear effectors that contain nuclear localization signal (NLS) and are secreted into host cells by fungal pathogens of plants. However, only a handful of nuclear effectors have been known and characterized to date. Here, we first summarize the types of NLSs and prediction tools available, and then delineate examples of fungal nuclear effectors and their roles in pathogenesis. Based on the knowledge on NLSs and what has been gleaned from the known nuclear effectors, we point out the gaps in our understanding of fungal nuclear effectors that need to be filled in the future researches.
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Affiliation(s)
- Surajit De Mandal
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Korea
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
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Ustilaginoidea virens Nuclear Effector SCRE4 Suppresses Rice Immunity via Inhibiting Expression of a Positive Immune Regulator OsARF17. Int J Mol Sci 2022; 23:ijms231810527. [PMID: 36142440 PMCID: PMC9501289 DOI: 10.3390/ijms231810527] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Rice false smut caused by the biotrophic fungal pathogen Ustilaginoidea virens has become one of the most important diseases in rice. The large effector repertory in U. virens plays a crucial role in virulence. However, current knowledge of molecular mechanisms how U. virens effectors target rice immune signaling to promote infection is very limited. In this study, we identified and characterized an essential virulence effector, SCRE4 (Secreted Cysteine-Rich Effector 4), in U. virens. SCRE4 was confirmed as a secreted nuclear effector through yeast secretion, translocation assays and protein subcellular localization, as well as up-regulation during infection. The SCRE4 gene deletion attenuated the virulence of U. virens to rice. Consistently, ectopic expression of SCRE4 in rice inhibited chitin-triggered immunity and enhanced susceptibility to false smut, substantiating that SCRE4 is an essential virulence factor. Furthermore, SCRE4 transcriptionally suppressed the expression of OsARF17, an auxin response factor in rice, which positively regulates rice immune responses and resistance against U. virens. Additionally, the immunosuppressive capacity of SCRE4 depended on its nuclear localization. Therefore, we uncovered a virulence strategy in U. virens that transcriptionally suppresses the expression of the immune positive modulator OsARF17 through nucleus-localized effector SCRE4 to facilitate infection.
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Belisário R, Robertson AE, Vaillancourt LJ. Maize Anthracnose Stalk Rot in the Genomic Era. PLANT DISEASE 2022; 106:2281-2298. [PMID: 35291814 DOI: 10.1094/pdis-10-21-2147-fe] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Anthracnose stalk rot (ASR) of maize results in millions of dollars in losses annually in the United States. ASR, together with anthracnose leaf blight and anthracnose top dieback, is caused by the fungus Colletotrichum graminicola. Current ASR management recommendations emphasize host resistance and reduction of plant stressors (e.g., drought, heat, low fertility, or soil acidity). Stress reduction may be more difficult to achieve in the future due to more high-intensity production protocols and climate change. Moreover, cultural and chemical management practices may conflict with other important goals, including environmental sustainability and maximization of yield potential. Thus, future ASR management may rely more heavily on host resistance, for which there are relatively few highly effective sources. The last comprehensive review of C. graminicola and maize anthracnose was written over two decades ago. The genomic age has brought important new insights into mechanisms governing the host-pathogen interaction from the application of molecular and cytological technologies. This review provides a summary of our current model of maize anthracnose etiology, including how increased knowledge of molecular and cellular events could contribute to better ASR management. Improved understanding of C. graminicola taxonomy has confirmed that the fungus is specific to Zea mays, and that it colonizes living maize tissues via a critical biotrophic phase. Successful biotrophic establishment relies on an array of secreted protein effectors and secondary metabolites produced at different stages of infection and dispersed to multiple locations. These molecules could provide therapeutic targets for the next generation of transgenic or gene-edited ASR-resistant hybrids.
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Affiliation(s)
- Renata Belisário
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY 40546-0312
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, 1344 Advanced Teaching and Research Building, 2213 Pammel Drive, Ames, IA 50011
| | - Lisa J Vaillancourt
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY 40546-0312
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de Oliveira Silva A, Aliyeva-Schnorr L, Wirsel SGR, Deising HB. Fungal Pathogenesis-Related Cell Wall Biogenesis, with Emphasis on the Maize Anthracnose Fungus Colletotrichum graminicola. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070849. [PMID: 35406829 PMCID: PMC9003368 DOI: 10.3390/plants11070849] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 05/25/2023]
Abstract
The genus Colletotrichum harbors many plant pathogenic species, several of which cause significant yield losses in the field and post harvest. Typically, in order to infect their host plants, spores germinate, differentiate a pressurized infection cell, and display a hemibiotrophic lifestyle after plant invasion. Several factors required for virulence or pathogenicity have been identified in different Colletotrichum species, and adaptation of cell wall biogenesis to distinct stages of pathogenesis has been identified as a major pre-requisite for the establishment of a compatible parasitic fungus-plant interaction. Here, we highlight aspects of fungal cell wall biogenesis during plant infection, with emphasis on the maize leaf anthracnose and stalk rot fungus, Colletotrichum graminicola.
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Prediction of effector proteins and their implications in pathogenicity of phytopathogenic filamentous fungi: A review. Int J Biol Macromol 2022; 206:188-202. [PMID: 35227707 DOI: 10.1016/j.ijbiomac.2022.02.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/14/2022]
Abstract
Plant pathogenic fungi encode and secrete effector proteins to promote pathogenesis. In recent years, the important role of effector proteins in fungi and plant host interactions has become increasingly prominent. In this review, the functional characterization and molecular mechanisms by which fungal effector proteins modulate biological processes and suppress the defense of plant hosts are discussed, with an emphasis on cell localization during fungal infection. This paper also provides a comprehensive review of bioinformatic and experimental methods that are currently available for the identification of fungal effector proteins. We additionally summarize the secretion pathways and the methods for verifying the presence effector proteins in plant host cells. For future research, comparative genomic studies of different pathogens with varying life cycles will allow comprehensive and systematic identification of effector proteins. Additionally, functional analysis of effector protein interactions with a wider range of hosts (especially non-model crops) will provide more detailed repertoires of fungal effectors. Identifying effector proteins and verifying their functions will improve our understanding of their role in causing disease and in turn guide future strategies for combatting fungal infections.
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15
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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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Tsushima A, Narusaka M, Gan P, Kumakura N, Hiroyama R, Kato N, Takahashi S, Takano Y, Narusaka Y, Shirasu K. The Conserved Colletotrichum spp. Effector Candidate CEC3 Induces Nuclear Expansion and Cell Death in Plants. Front Microbiol 2021; 12:682155. [PMID: 34539598 PMCID: PMC8446390 DOI: 10.3389/fmicb.2021.682155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/11/2021] [Indexed: 01/25/2023] Open
Abstract
Plant pathogens secrete proteins, known as effectors, that promote infection by manipulating host cells. Members of the phytopathogenic fungal genus Colletotrichum collectively have a broad host range and generally adopt a hemibiotrophic lifestyle that includes an initial biotrophic phase and a later necrotrophic phase. We hypothesized that Colletotrichum fungi use a set of conserved effectors during infection to support the two phases of their hemibiotrophic lifestyle. This study aimed to examine this hypothesis by identifying and characterizing conserved effectors among Colletotrichum fungi. Comparative genomic analyses using genomes of ascomycete fungi with different lifestyles identified seven effector candidates that are conserved across the genus Colletotrichum. Transient expression assays showed that one of these putative conserved effectors, CEC3, induces nuclear expansion and cell death in Nicotiana benthamiana, suggesting that CEC3 is involved in promoting host cell death during infection. Nuclear expansion and cell death induction were commonly observed in CEC3 homologs from four different Colletotrichum species that vary in host specificity. Thus, CEC3 proteins could represent a novel class of core effectors with functional conservation in the genus Colletotrichum.
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Affiliation(s)
- Ayako Tsushima
- Graduate School of Science, The University of Tokyo, Bunkyo, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Mari Narusaka
- Research Institute for Biological Sciences Okayama, Kaga-gun, Japan
| | - Pamela Gan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | | | - Ryoko Hiroyama
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Naoki Kato
- Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | | | | | | | - Ken Shirasu
- Graduate School of Science, The University of Tokyo, Bunkyo, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
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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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18
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Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming. Nat Commun 2020; 11:5845. [PMID: 33203871 PMCID: PMC7672089 DOI: 10.1038/s41467-020-19624-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/20/2020] [Indexed: 02/04/2023] Open
Abstract
Pathogens utilize multiple types of effectors to modulate plant immunity. Although many apoplastic and cytoplasmic effectors have been reported, nuclear effectors have not been well characterized in fungal pathogens. Here, we characterize two nuclear effectors of the rice blast pathogen Magnaporthe oryzae. Both nuclear effectors are secreted via the biotrophic interfacial complex, translocated into the nuclei of initially penetrated and surrounding cells, and reprogram the expression of immunity-associated genes by binding on effector binding elements in rice. Their expression in transgenic rice causes ambivalent immunity: increased susceptibility to M. oryzae and Xanthomonas oryzae pv. oryzae, hemibiotrophic pathogens, but enhanced resistance to Cochliobolus miyabeanus, a necrotrophic pathogen. Our findings help remedy a significant knowledge deficiency in the mechanism of M. oryzae–rice interactions and underscore how effector-mediated manipulation of plant immunity by one pathogen may also affect the disease severity by other pathogens. Plant pathogens secrete various effectors to manipulate host immunity. Here, Kim et al. describe two Magnaporthe oryzae effectors that translocate into the nuclei of infected rice cells and reprogram expression of immunity-associated genes, increasing susceptibility to hemibiotrophic pathogens.
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19
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Madina MH, Rahman MS, Huang X, Zhang Y, Zheng H, Germain H. A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant Susceptibility. BIOLOGY 2020; 9:E294. [PMID: 32947987 PMCID: PMC7564345 DOI: 10.3390/biology9090294] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 11/17/2022]
Abstract
Melampsora larici-populina (Mlp), the causal agent of Populus leaf rust, secretes an array of effectors into the host through the haustorium to gain nutrients and suppress immunity. The precise mechanisms by which these effectors promote virulence remain unclear. To address this question, we developed a transgenic Arabidopsis line expressing a candidate effector, Mlp124357. Constitutive expression of the effector increased plant susceptibility to pathogens. A GxxxG motif present in Mlp124357 is required for its subcellular localization at the vacuolar membrane of the plant cell, as replacement of the glycine residues with alanines led to the delocalization of Mlp124357 to the nucleus and cytoplasm. We used immunoprecipitation and mass spectrometry (MS) to identify Mlp124357 interaction partners. Only one of the putative interaction partners knock-out line caused delocalization of the effector, indicating that Arabidopsis protein disulfide isomerase-11 (AtPDI-11) is required for the effector localization. This interaction was further confirmed by a complementation test, a yeast-two hybrid assay and a molecular modeling experiment. Moreover, localization results and infection assays suggest that AtPDI-11 act as a helper for Mlp124357. In summary, our findings established that one of Mlp effectors resides at the vacuole surface and modulates plant susceptibility.
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Affiliation(s)
- Mst Hur Madina
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boulevard des Forges, Trois-Rivières, QC G9A 5H7, Canada; (M.H.M.); (M.S.R.)
| | - Md Saifur Rahman
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boulevard des Forges, Trois-Rivières, QC G9A 5H7, Canada; (M.H.M.); (M.S.R.)
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; (X.H.); (Y.Z.)
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA; (X.H.); (Y.Z.)
| | - Huanquan Zheng
- Department of Biology, McGill University, 1205 Dr. Penfield Avenue, Montreal, QC H3A 1B1, Canada;
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boulevard des Forges, Trois-Rivières, QC G9A 5H7, Canada; (M.H.M.); (M.S.R.)
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20
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Queiroz CBD, Santana MF. Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia 2020; 112:491-503. [PMID: 32286912 DOI: 10.1080/00275514.2020.1716566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Biologia Molecular, Embrapa Amazônia Ocidental , Rodovia AM 10, km 29, s/n, CEP: 69010-970, Manaus, Amazonas, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia (BIOAGRO), Universidade Federal de Viçosa , CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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21
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Prokchorchik M, Won K, Lee Y, Segonzac C, Sohn KH. Whole Genome Enabled Phylogenetic and Secretome Analyses of Two Venturia nashicola Isolates. THE PLANT PATHOLOGY JOURNAL 2020; 36:98-105. [PMID: 32089665 PMCID: PMC7012575 DOI: 10.5423/ppj.nt.10.2019.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 05/19/2023]
Abstract
Venturia nashicola is a fungal pathogen causing scab disease in Asian pears. It is particularly important in the Northeast Asia region where Asian pears are intensively grown. Venturia nashicola causes disease in Asian pear but not in European pear. Due to the highly restricted host range of Venturia nashicola, it is hypothesized that the small secreted proteins deployed by the pathogen are responsible for the host determination. Here we report the whole genome based phylogenetic analysis and predicted secretomes for V. nashicola isolates. We believe that our data will provide a valuable information for further validation and functional characterization of host determinants in V. nashicola.
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Affiliation(s)
- Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju 58216,
Korea
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Plant Immunity Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673,
Korea
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22
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Eisermann I, Weihmann F, Krijger JJ, Kröling C, Hause G, Menzel M, Pienkny S, Kiesow A, Deising HB, Wirsel SGR. Two genes in a pathogenicity gene cluster encoding secreted proteins are required for appressorial penetration and infection of the maize anthracnose fungus Colletotrichum graminicola. Environ Microbiol 2019; 21:4773-4791. [PMID: 31599055 DOI: 10.1111/1462-2920.14819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/14/2023]
Abstract
To avoid pathogen-associated molecular pattern recognition, the hemibiotrophic maize pathogen Colletotrichum graminicola secretes proteins mediating the establishment of biotrophy. Targeted deletion of 26 individual candidate genes and seven gene clusters comprising 32 genes of C. graminicola identified a pathogenicity cluster (CLU5) of five co-linear genes, all of which, with the exception of CLU5b, encode secreted proteins. Targeted deletion of all genes of CLU5 revealed that CLU5a and CLU5d are required for full appressorial penetration competence, with virulence deficiencies independent of the host genotype and organ inoculated. Cytorrhysis experiments and microscopy showed that Δclu5a mutants form pressurized appressoria, but they are hampered in forming penetration pores and fail to differentiate a penetration peg. Whereas Δclu5d mutants elicited WT-like papillae, albeit at increased frequencies, papillae induced by Δclu5a mutants were much smaller than those elicited by the WT. Synteny of CLU5 is not only conserved in Colletotrichum spp. but also in additional species of Sordariomycetes including insect pathogens and saprophytes suggesting importance of CLU5 for fungal biology. Since CLU5a and CLU5d also occur in non-pathogenic fungi and since they are expressed prior to plant invasion and even in vegetative hyphae, the encoded proteins probably do not act primarily as effectors.
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Affiliation(s)
- Iris Eisermann
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Fabian Weihmann
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Jorrit-Jan Krijger
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Christian Kröling
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany.,Sächsisches Landesamt für Umwelt, Landwirtschaft und Geologie, Abteilung Obst-, Gemüse- und Weinbau, August-Böckstiegel-Str. 1, D-01326, Dresden-Pillnitz, Germany
| | - Gerd Hause
- Biozentrum der Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, D-06120, Halle (Saale), Germany
| | - Matthias Menzel
- Fraunhofer-Institut für Mikrostruktur von Werkstoffen und Systemen, Biologische und makromolekulare Materialien, Walter-Hülse-Str. 1, D-06120, Halle (Saale), Germany
| | - Silke Pienkny
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Andreas Kiesow
- Fraunhofer-Institut für Mikrostruktur von Werkstoffen und Systemen, Biologische und makromolekulare Materialien, Walter-Hülse-Str. 1, D-06120, Halle (Saale), Germany
| | - Holger B Deising
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Stefan G R Wirsel
- Institut für Agrar- und Ernährungswissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
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23
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Fabre F, Vignassa M, Urbach S, Langin T, Bonhomme L. Time-resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism. PLANT, CELL & ENVIRONMENT 2019; 42:2291-2308. [PMID: 30866080 DOI: 10.1111/pce.13549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
Fungal plant diseases are controlled by a complex molecular dialogue that involves pathogen effectors able to manipulate plant susceptibility factors at the earliest stages of the interaction. By probing the wheat-Fusarium graminearum pathosystem, we profiled the coregulations of the fungal and plant proteins shaping the molecular responses of a 96-hr-long infection's dynamics. Although no symptoms were yet detectable, fungal biomass swiftly increased along with an extremely diverse set of secreted proteins and candidate effectors supposed to target key plant organelles. Some showed to be early accumulated during the interaction or already present in spores, otherwise stored in germinating spores and detectable in an in vitro F. graminearum exudate. Wheat responses were swiftly set up and were evidenced before any visible symptom. Significant wheat protein abundance changes co-occurred along with the accumulation of putative secreted fungal proteins and predicted effectors. Regulated wheat proteins were closely connected to basal cellular processes occurring during spikelet ontogeny, and particular coregulation patterns were evidenced between chloroplast proteins and fungal proteins harbouring a predicted chloroplast transit peptide. The described plant and fungal coordinated responses provide a resourceful set of data and expand our understanding of the wheat-F. graminearum interaction.
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Affiliation(s)
- Francis Fabre
- Genetics, Diversity and Ecophysiology of Cereals, UMR 1095, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Manon Vignassa
- Genetics, Diversity and Ecophysiology of Cereals, UMR 1095, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Serge Urbach
- Functional Proteomics Platform (FPP), Institute of Functional Genomics (IGF), CNRS UMR 5203 INSERM U661, Montpellier, France
| | - Thierry Langin
- Genetics, Diversity and Ecophysiology of Cereals, UMR 1095, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ludovic Bonhomme
- Genetics, Diversity and Ecophysiology of Cereals, UMR 1095, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
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van de Vossenberg BTLH, Warris S, Nguyen HDT, van Gent-Pelzer MPE, Joly DL, van de Geest HC, Bonants PJM, Smith DS, Lévesque CA, van der Lee TAJ. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. Sci Rep 2019; 9:8672. [PMID: 31209237 PMCID: PMC6572847 DOI: 10.1038/s41598-019-45128-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/09/2023] Open
Abstract
Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands.
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands.
| | - Sven Warris
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Hai D T Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P E van Gent-Pelzer
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - David L Joly
- Université de Moncton, 18 avenue Antonine-Maillet, Moncton, Canada
| | - Henri C van de Geest
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Donna S Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A J van der Lee
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
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Lelwala RV, Korhonen PK, Young ND, Scott JB, Ades PK, Gasser RB, Taylor PWJ. Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti. PLoS One 2019; 14:e0212248. [PMID: 31150449 PMCID: PMC6544218 DOI: 10.1371/journal.pone.0212248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/02/2019] [Indexed: 01/30/2023] Open
Abstract
Colletotrichum tanaceti is an emerging foliar fungal pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium). Despite being reported consistently from field surveys in Australia, the molecular basis of pathogenicity of C. tanaceti on pyrethrum is unknown. Herein, the genome of C. tanaceti (isolate BRIP57314) was assembled de novo and annotated using transcriptomic evidence. The inferred putative pathogenicity gene suite of C. tanaceti comprised a large array of genes encoding secreted effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its putative pathogenicity gene profiles with those of closely related species suggested that C. tanaceti likely has additional hosts to pyrethrum. The genome of C. tanaceti had a high repeat content and repetitive elements were located significantly closer to genes inferred to influence pathogenicity than other genes. These repeats are likely to have accelerated mutational and transposition rates in the genome, resulting in a rapid evolution of certain CAZyme families in this species. The C. tanaceti genome showed strong signals of Repeat Induced Point (RIP) mutation which likely caused its bipartite nature consisting of distinct gene-sparse, repeat and A-T rich regions. Pathogenicity genes within these RIP affected regions were likely to have a higher evolutionary rate than the rest of the genome. This "two-speed" genome phenomenon in certain Colletotrichum spp. was hypothesized to have caused the clustering of species based on the pathogenicity genes, to deviate from taxonomic relationships. The large repertoire of pathogenicity factors that potentially evolve rapidly due to the plasticity of the genome, indicated that C. tanaceti has a high evolutionary potential. Therefore, C. tanaceti poses a high-risk to the pyrethrum industry. Knowledge of the evolution and diversity of the putative pathogenicity genes will facilitate future research in disease management of C. tanaceti and other Colletotrichum spp.
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Affiliation(s)
- Ruvini V. Lelwala
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jason B. Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia
| | - Peter K. Ades
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul W. J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Hassing B, Winter D, Becker Y, Mesarich CH, Eaton CJ, Scott B. Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne. PLoS One 2019; 14:e0209463. [PMID: 30759164 PMCID: PMC6374014 DOI: 10.1371/journal.pone.0209463] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby maintaining a mutualistic symbiotic interaction. Recent studies have suggested that small secreted proteins, termed effectors, play a vital role in the suppression of host defence responses. To date only a few effectors with important roles in mutualistic interactions have been described. Here we make use of the fully assembled E. festucae genome and EffectorP to generate a suite of 141 effector candidates. These were analysed with respect to their genome location and expression profiles in planta and in several symbiosis-defective mutants. We found an association between effector candidates and a class of transposable elements known as MITEs, but no correlation with other dynamic features of the E. festucae genome, such as transposable element-rich regions. Three effector candidates and a small GPI-anchored protein were chosen for functional analysis based on their high expression in planta compared to in culture and their differential regulation in symbiosis defective E. festucae mutants. All three candidate effector proteins were shown to possess a functional signal peptide and two could be detected in the extracellular medium by western blotting. Localization of the effector candidates in planta suggests that they are not translocated into the plant cell, but rather, are localized in the apoplastic space or are attached to the cell wall. Deletion and overexpression of the effector candidates, as well as the putative GPI-anchored protein, did not affect the plant growth phenotype or restrict growth of E. festucae mutants in planta. These results indicate that these proteins are either not required for the interaction at the observed life stages or that there is redundancy between effectors expressed by E. festucae.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Küehn-Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Carl H. Mesarich
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Carla J. Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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The repertoire of effector candidates in Colletotrichum lindemuthianum reveals important information about Colletotrichum genus lifestyle. Appl Microbiol Biotechnol 2019; 103:2295-2309. [DOI: 10.1007/s00253-019-09639-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/04/2023]
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Ahmed MB, Santos KCGD, Sanchez IB, Petre B, Lorrain C, Plourde MB, Duplessis S, Desgagné-Penix I, Germain H. A rust fungal effector binds plant DNA and modulates transcription. Sci Rep 2018; 8:14718. [PMID: 30283062 PMCID: PMC6170375 DOI: 10.1038/s41598-018-32825-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/21/2018] [Indexed: 02/08/2023] Open
Abstract
The basidiomycete Melampsora larici-populina causes poplar rust disease by invading leaf tissues and secreting effector proteins through specialized infection structures known as haustoria. The mechanisms by which rust effectors promote pathogen virulence are poorly understood. The present study characterized Mlp124478, a candidate effector of M. larici-populina. We used the models Arabidopsis thaliana and Nicotiana benthamiana to investigate the function of Mlp124478 in plant cells. We established that Mlp124478 accumulates in the nucleus and nucleolus, however its nucleolar accumulation is not required to promote growth of the oomycete pathogen Hyaloperonospora arabidopsidis. Stable constitutive expression of Mlp124478 in A. thaliana repressed the expression of genes involved in immune responses, and also altered leaf morphology by increasing the waviness of rosette leaves. Chip-PCR experiments showed that Mlp124478 associats'e with the TGA1a-binding DNA sequence. Our results suggest that Mlp124478 exerts a virulence activity and binds the TGA1a promoter to suppress genes induced in response to pathogen infection.
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Affiliation(s)
- Md Bulbul Ahmed
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Karen Cristine Gonçalves Dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Ingrid Benerice Sanchez
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
- Department of Biotechnology and Engineering in Chemistry, Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Estado de México (ITESM CEM), Margarita Maza de Juárez, 52926, Cd, López Mateos, Mexico
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Faculté des Sciences et Technologies - Campus Aiguillettes, BP, 70239-54506, Vandoeuvre-lès-Nancy, France
| | - Cécile Lorrain
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
| | - Sébastien Duplessis
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
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Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola. BMC Genomics 2018; 19:557. [PMID: 30055574 PMCID: PMC6064131 DOI: 10.1186/s12864-018-4934-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/09/2018] [Indexed: 02/05/2023] Open
Abstract
Background Colletotrichum is a fungal genus in Ascomycota that contain many plant pathogens. Among all Colletotrichum genomes that have been sequenced, C. fructicola contains the largest number of candidate virulence factors, such as plant cell wall degrading enzymes, secondary metabolite (SM) biosynthetic enzymes, secreted proteinases, and small secreted proteins. Systematic analysis of the expressional patterns of these factors would be an important step toward identifying key virulence determinants. Results In this study, we obtained and compared the global transcriptome profiles of four types of infection-related structures: conidia, appressoria, infected apple leaves, and cellophane infectious hyphae (bulbous hyphae spreading inside cellophane) of C. fructicola. We also compared the expression changes of candidate virulence factors among these structures in a systematic manner. A total of 3189 genes were differentially expressed in at least one pairwise comparison. Genes showing in planta-specific expressional upregulations were enriched with small secreted proteins (SSPs), cytochrome P450s, carbohydrate-active enzymes (CAZYs) and secondary metabolite (SM) synthetases, and included homologs of several known candidate effectors and one SM gene cluster specific to the Colletotrichum genus. In conidia, tens of genes functioning in triacylglycerol biosynthesis showed coordinately expressional upregulation, supporting the viewpoint that C. fructicola builds up lipid droplets as energy reserves. Several phosphate starvation responsive genes were coordinately up-regulated during early plant colonization, indicating a phosphate-limited in planta environment immediately faced by biotrophic infectious hyphae. Conclusion This study systematically analyzes the expression patterns of candidate virulence genes, and reveals biological activities related to the development of several infection-related structures of C. fructicola. Our findings lay a foundation for further dissecting infection mechanisms in Colletotrichum and identifying disease control targets. Electronic supplementary material The online version of this article (10.1186/s12864-018-4934-0) contains supplementary material, which is available to authorized users.
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Chang HX, Noel ZA, Sang H, Chilvers MI. Annotation resource of tandem repeat-containing secretory proteins in sixty fungi. Fungal Genet Biol 2018; 119:7-19. [PMID: 30026018 DOI: 10.1016/j.fgb.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/06/2018] [Accepted: 07/15/2018] [Indexed: 11/17/2022]
Abstract
Fungal secretory proteins that interact with host plants are regarded as effectors. Because fungal effectors rarely contain conserved sequence features, identification and annotation of fungal effectors from predicted secretory proteins are difficult using outward comparison methods such as BLAST or hidden Markov model. In desire of more sequence features to prioritize research interests of fungal secretory proteins, this study developed a pipeline to identify tandem repeat (TR) domain within putative secretory proteins and tested a hypothesis that at least one type of TR domain in non-orthologous secretory proteins has emerged from convergent evolution for plant pathogenicity. There were 2804 types of TR domains and a total of 2925 TR-containing secretory proteins found from 60 fungi. There was no conserved type of TR domain shared only by plant pathogens, indicating functional divergence for different types of TR domain and TR-containing secretory proteins. The annotation resource of putative fungal TR-containing secretory proteins provides new sequence features that will be useful for the community interested in fungal effector biology.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Zachary A Noel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Hyunkyu Sang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States.
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Ma LS, Pellegrin C, Kahmann R. Repeat-containing effectors of filamentous pathogens and symbionts. Curr Opin Microbiol 2018; 46:123-130. [PMID: 29929732 DOI: 10.1016/j.mib.2018.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 11/26/2022]
Abstract
Pathogenic and symbiotic filamentous microbes secrete effectors which suppress host immune responses and promote a successful colonization. Pathogen effectors are engaged in the arms race with their hosts and because of this they are subject to intense evolutionary pressure. Effectors particularly prone to rapid evolution display repeat-containing domains which can easily expand or contract and accumulate point mutations without altering their original function. In this review we address the diversity of function in such repeat-containing effectors, focus on new findings and point out avenues for future work.
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32
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Zhang X, Farah N, Rolston L, Ericsson DJ, Catanzariti A, Bernoux M, Ve T, Bendak K, Chen C, Mackay JP, Lawrence GJ, Hardham A, Ellis JG, Williams SJ, Dodds PN, Jones DA, Kobe B. Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P. MOLECULAR PLANT PATHOLOGY 2018; 19:1196-1209. [PMID: 28817232 PMCID: PMC6638141 DOI: 10.1111/mpp.12597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 05/23/2023]
Abstract
The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P-mediated recognition. The first zinc-coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid-binding and chromatin-associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non-conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition.
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Affiliation(s)
- Xiaoxiao Zhang
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Nadya Farah
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Laura Rolston
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Daniel J. Ericsson
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Australian Synchrotron, Macromolecular crystallographyClaytonVictoria 3168Australia
| | - Ann‐Maree Catanzariti
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Thomas Ve
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Institute for Glycomics, Griffith UniversitySouthportQueensland 4222Australia
| | - Katerina Bendak
- School of Molecular BioscienceUniversity of SydneySydneyNew South Wales 2006Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Joel P. Mackay
- School of Molecular BioscienceUniversity of SydneySydneyNew South Wales 2006Australia
| | - Gregory J. Lawrence
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Adrienne Hardham
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Jeffrey G. Ellis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - Simon J. Williams
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation Agriculture and FoodCanberraAustralian Capital Territory 2601Australia
| | - David A. Jones
- Division of Plant SciencesResearch School of Biology, Australian National University, ActonAustralian Capital Territory 2601Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular BiosciencesAustralian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of QueenslandBrisbaneQueensland 4072Australia
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33
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Ma LS, Wang L, Trippel C, Mendoza-Mendoza A, Ullmann S, Moretti M, Carsten A, Kahnt J, Reissmann S, Zechmann B, Bange G, Kahmann R. The Ustilago maydis repetitive effector Rsp3 blocks the antifungal activity of mannose-binding maize proteins. Nat Commun 2018; 9:1711. [PMID: 29703884 PMCID: PMC5923269 DOI: 10.1038/s41467-018-04149-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 04/06/2018] [Indexed: 12/22/2022] Open
Abstract
To cause disease in maize, the biotrophic fungus Ustilago maydis secretes a large arsenal of effector proteins. Here, we functionally characterize the repetitive effector Rsp3 (repetitive secreted protein 3), which shows length polymorphisms in field isolates and is highly expressed during biotrophic stages. Rsp3 is required for virulence and anthocyanin accumulation. During biotrophic growth, Rsp3 decorates the hyphal surface and interacts with at least two secreted maize DUF26-domain family proteins (designated AFP1 and AFP2). AFP1 binds mannose and displays antifungal activity against the rsp3 mutant but not against a strain constitutively expressing rsp3. Maize plants silenced for AFP1 and AFP2 partially rescue the virulence defect of rsp3 mutants, suggesting that blocking the antifungal activity of AFP1 and AFP2 by the Rsp3 effector is an important virulence function. Rsp3 orthologs are present in all sequenced smut fungi, and the ortholog from Sporisorium reilianum can complement the rsp3 mutant of U. maydis, suggesting a novel widespread fungal protection mechanism. The fungus Ustilago maydis secretes many effector proteins to cause disease in maize. Here, Ma et al. show that the repetitive effector Rsp3 is required for virulence by inhibiting the antifungal activity of two mannose-binding proteins that are secreted by the plant cells.
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Affiliation(s)
- Lay-Sun Ma
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Lei Wang
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Department of Pharmacology, Max Planck Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Christine Trippel
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University-Göttingen, 37077, Göttingen, Germany
| | - Artemio Mendoza-Mendoza
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Bio-Protection Research Centre, Lincoln University, PO Box 64, Lincoln, 7647, New Zealand
| | - Steffen Ullmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,, Düsseldorfer Straße 177, 45481, Mülheim an der Ruhr, Germany
| | - Marino Moretti
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Alexander Carsten
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jörg Kahnt
- Mass Spectroscopy Facility, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Stefanie Reissmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Bernd Zechmann
- Center for Microscopy and Imaging (CMI), Baylor University, Waco, Texas, 76798-7046, USA
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
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Pérez-López E, Waldner M, Hossain M, Kusalik AJ, Wei Y, Bonham-Smith PC, Todd CD. Identification of Plasmodiophora brassicae effectors - A challenging goal. Virulence 2018; 9:1344-1353. [PMID: 30146948 PMCID: PMC6177251 DOI: 10.1080/21505594.2018.1504560] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/18/2018] [Indexed: 11/06/2022] Open
Abstract
Clubroot is an economically important disease affecting Brassica plants worldwide. Plasmodiophora brassicae is the protist pathogen associated with the disease, and its soil-borne obligate parasitic nature has impeded studies related to its biology and the mechanisms involved in its infection of the plant host. The identification of effector proteins is key to understanding how the pathogen manipulates the plant's immune response and the genes involved in resistance. After more than 140 years studying clubroot and P. brassicae, very little is known about the effectors playing key roles in the infection process and subsequent disease progression. Here we analyze the information available for identified effectors and suggest several features of effector genes that can be used in the search for others. Based on the information presented in this review, we propose a comprehensive bioinformatics pipeline for effector identification and provide a list of the bioinformatics tools available for such.
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Affiliation(s)
- Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - Matthew Waldner
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Musharaf Hossain
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - Anthony J. Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
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35
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Robin GP, Kleemann J, Neumann U, Cabre L, Dallery JF, Lapalu N, O’Connell RJ. Subcellular Localization Screening of Colletotrichum higginsianum Effector Candidates Identifies Fungal Proteins Targeted to Plant Peroxisomes, Golgi Bodies, and Microtubules. FRONTIERS IN PLANT SCIENCE 2018; 9:562. [PMID: 29770142 PMCID: PMC5942036 DOI: 10.3389/fpls.2018.00562] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/10/2018] [Indexed: 05/20/2023]
Abstract
The genome of the hemibiotrophic anthracnose fungus, Colletotrichum higginsianum, encodes a large inventory of putative secreted effector proteins that are sequentially expressed at different stages of plant infection, namely appressorium-mediated penetration, biotrophy and necrotrophy. However, the destinations to which these proteins are addressed inside plant cells are unknown. In the present study, we selected 61 putative effector genes that are highly induced in appressoria and/or biotrophic hyphae. We then used Agrobacterium-mediated transformation to transiently express them as N-terminal fusions with fluorescent proteins in cells of Nicotiana benthamiana for imaging by confocal microscopy. Plant compartments labeled by the fusion proteins in N. benthamiana were validated by co-localization with specific organelle markers, by transient expression of the proteins in the true host plant, Arabidopsis thaliana, and by transmission electron microscopy-immunogold labeling. Among those proteins for which specific subcellular localizations could be verified, nine were imported into plant nuclei, three were imported into the matrix of peroxisomes, three decorated cortical microtubule arrays and one labeled Golgi stacks. Two peroxisome-targeted proteins harbored canonical C-terminal tripeptide signals for peroxisome import via the PTS1 (peroxisomal targeting signal 1) pathway, and we showed that these signals are essential for their peroxisome localization. Our findings provide valuable information about which host processes are potentially manipulated by this pathogen, and also reveal plant peroxisomes, microtubules, and Golgi as novel targets for fungal effectors.
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Affiliation(s)
- Guillaume P. Robin
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Jochen Kleemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Lisa Cabre
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Jean-Félix Dallery
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Nicolas Lapalu
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Richard J. O’Connell
- UMR BIOGER, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Versailles, France
- *Correspondence: Richard J. O’Connell,
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36
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Lo Presti L, Kahmann R. How filamentous plant pathogen effectors are translocated to host cells. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:19-24. [PMID: 28460240 DOI: 10.1016/j.pbi.2017.04.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
The interaction of microbes with "signature" plants is largely governed by secreted effector proteins, which serve to dampen plant defense responses and modulate host cell processes. Secreted effectors can function either in the apoplast or within plant cell compartments. How oomycetes and fungi translocate their effectors to plant cells is still poorly understood and controversial. While most oomycete effectors share a common 'signature' that was proposed to mediate their uptake via endocytosis, fungal effectors display no conserved motifs at the primary amino acid sequence level. Here we summarize current knowledge in the field of oomycete and fungal effector uptake and highlight emerging themes that may unite rather than set apart these unrelated filamentous pathogens.
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Affiliation(s)
- Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.
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Abstract
Fungi are among the dominant causal agents of plant diseases. To colonize plants and cause disease, pathogenic fungi use diverse strategies. Some fungi kill their hosts and feed on dead material (necrotrophs), while others colonize the living tissue (biotrophs). For successful invasion of plant organs, pathogenic development is tightly regulated and specialized infection structures are formed. To further colonize hosts and establish disease, fungal pathogens deploy a plethora of virulence factors. Depending on the infection strategy, virulence factors perform different functions. While basically all pathogens interfere with primary plant defense, necrotrophs secrete toxins to kill plant tissue. In contrast, biotrophs utilize effector molecules to suppress plant cell death and manipulate plant metabolism in favor of the pathogen. This article provides an overview of plant pathogenic fungal species and the strategies they use to cause disease.
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38
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Derbyshire M, Denton-Giles M, Hegedus D, Seifbarghy S, Rollins J, van Kan J, Seidl MF, Faino L, Mbengue M, Navaud O, Raffaele S, Hammond-Kosack K, Heard S, Oliver R. The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol 2017; 9:593-618. [PMID: 28204478 PMCID: PMC5381539 DOI: 10.1093/gbe/evx030] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/16/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.
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Affiliation(s)
- Mark Derbyshire
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
| | - Dwayne Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | | | - Jeffrey Rollins
- Department of Plant Pathology, University of Florida, Gainesville, FL
| | - Jan van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Malick Mbengue
- LIPM Université de Toulouse INRA CNRS, Castanet-Tolosan, France
| | - Olivier Navaud
- LIPM Université de Toulouse INRA CNRS, Castanet-Tolosan, France
| | | | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Stephanie Heard
- Department of Plant Pathology, University of Florida, Gainesville, FL
- Department of Plant Biology and Crop Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Richard Oliver
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
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Buiate EAS, Xavier KV, Moore N, Torres MF, Farman ML, Schardl CL, Vaillancourt LJ. A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics 2017; 18:67. [PMID: 28073340 PMCID: PMC5225507 DOI: 10.1186/s12864-016-3457-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/22/2016] [Indexed: 01/10/2023] Open
Abstract
Background Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. Results Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. Conclusions Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3457-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E A S Buiate
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Monsanto Company Brazil, Uberlândia, Minas Gerais, Brazil
| | - K V Xavier
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - N Moore
- Department of Computer Science, University of Kentucky, Davis Marksbury Building, 328 Rose Street, Lexington, KY, 40504-0633, USA
| | - M F Torres
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.,Present Address: Functional Genomics Laboratory, Weill Cornell Medicine, Doha, Qatar
| | - M L Farman
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - C L Schardl
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA
| | - L J Vaillancourt
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA.
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40
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Baroncelli R, Amby DB, Zapparata A, Sarrocco S, Vannacci G, Le Floch G, Harrison RJ, Holub E, Sukno SA, Sreenivasaprasad S, Thon MR. Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum. BMC Genomics 2016; 17:555. [PMID: 27496087 PMCID: PMC4974774 DOI: 10.1186/s12864-016-2917-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi. RESULTS We sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc. CONCLUSIONS This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content.
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Affiliation(s)
- Riccardo Baroncelli
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), University of Western Brittany, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frb. C, Copenhagen, Denmark
| | - Antonio Zapparata
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Giovanni Vannacci
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), University of Western Brittany, Technopôle Brest-Iroise, 29280 Plouzané, France
| | | | - Eric Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, Warwickshire CV35 9EF UK
| | - Serenella A. Sukno
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Campus de Villamayor, C/Del Duero, 12, 37185 Villamayor Salamanca, Spain
| | - Surapareddy Sreenivasaprasad
- Institute of Biomedical and Environmental Science and Technology (iBEST), University of Bedfordshire, University Square, Luton, Bedfordshire LU1 3JU UK
| | - Michael R. Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Campus de Villamayor, C/Del Duero, 12, 37185 Villamayor Salamanca, Spain
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Xiong D, Wang Y, Tian L, Tian C. MADS-Box Transcription Factor VdMcm1 Regulates Conidiation, Microsclerotia Formation, Pathogenicity, and Secondary Metabolism of Verticillium dahliae. Front Microbiol 2016; 7:1192. [PMID: 27536281 PMCID: PMC4971026 DOI: 10.3389/fmicb.2016.01192] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/19/2016] [Indexed: 12/02/2022] Open
Abstract
Verticillium dahliae, a notorious phytopathogenic fungus, causes vascular wilt diseases in many plant species resulting in devastating yield losses worldwide. Due to its ability to colonize plant xylem and form microsclerotia, V. dahliae is highly persistent and difficult to control. In this study, we show that the MADS-box transcription factor VdMcm1 is a key regulator of conidiation, microsclerotia formation, virulence, and secondary metabolism of V. dahliae. In addition, our findings suggest that VdMcm1 is involved in cell wall integrity. Finally, comparative RNA-Seq analysis reveals 823 significantly downregulated genes in the VdMcm1 deletion mutant, with diverse biological functions in transcriptional regulation, plant infection, cell adhesion, secondary metabolism, transmembrane transport activity, and cell secretion. When taken together, these data suggest that VdMcm1 performs pleiotropic functions in V. dahliae.
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Affiliation(s)
- Dianguang Xiong
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Yonglin Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Longyan Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
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42
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Oliveira-Garcia E, Deising HB. Attenuation of PAMP-triggered immunity in maize requires down-regulation of the key β-1,6-glucan synthesis genes KRE5 and KRE6 in biotrophic hyphae of Colletotrichum graminicola. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:355-75. [PMID: 27144995 DOI: 10.1111/tpj.13205] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 04/05/2016] [Accepted: 04/27/2016] [Indexed: 05/23/2023]
Abstract
In plants, pathogen defense is initiated by recognition of pathogen-associated molecular patterns (PAMPs) via plasma membrane-localized pattern-recognition receptors (PRRs). Fungal structural cell wall polymers such as branched β-glucans are essential for infection structure rigidity and pathogenicity, but at the same time represent PAMPs. Kre5 and Kre6 are key enzymes in β-1,6-glucan synthesis and formation of branch points of the β-glucan network. In spite of the importance of branched β-glucan for hyphal rigidity and plant-fungus interactions, neither the role of KRE5 and KRE6 in pathogenesis nor mechanisms allowing circumventing branched β-glucan-triggered immune responses are known. We functionally characterized KRE5 and KRE6 of the ascomycete Colletotrichum graminicola, a hemibiotroph that infects maize (Zea mays). After appressorial plant invasion, this fungus sequentially differentiates biotrophic and highly destructive necrotrophic hyphae. RNAi-mediated reduction of KRE5 and KRE6 transcript abundance caused appressoria to burst and swelling of necrotrophic hyphae, indicating that β-1,6-glucosidic bonds are essential in these cells. Live cell imaging employing KRE5:mCherry and KRE6:mCherry knock-in strains and probing of infection structures with a YFP-conjugated β-1,6-glucan-binding protein showed expression of these genes and exposure of β-1,6-glucan in conidia, appressoria and necrotrophic, but not in biotrophic hyphae. Overexpression of KRE5 and KRE6 in biotrophic hyphae led to activation of broad-spectrum plant defense responses, including papilla and H2 O2 formation, as well as transcriptional activation of several defense-related genes. Collectively, our results strongly suggest that down-regulation of synthesis and avoidance of exposure of branched β-1,3-β-1,6-glucan in biotrophic hyphae is required for attenuation of plant immune responses.
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Affiliation(s)
- Ely Oliveira-Garcia
- Martin-Luther-Universität Halle-Wittenberg, Naturwissenschaftliche Fakultät III, Institut für Agrar- und Ernährungswissenschaften, Phytopathologie und Pflanzenschutz, Betty-Heimann-Str. 3., D-06120, Halle/Saale, Germany
| | - Holger B Deising
- Martin-Luther-Universität Halle-Wittenberg, Naturwissenschaftliche Fakultät III, Institut für Agrar- und Ernährungswissenschaften, Phytopathologie und Pflanzenschutz, Betty-Heimann-Str. 3., D-06120, Halle/Saale, Germany.
- Martin-Luther-Universität Halle-Wittenberg, Interdisziplinäres Zentrum für Nutzpflanzenforschung, Betty-Heimann-Str. 3., D-06120, Halle/Saale, Germany.
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