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Mejri S, Magnin-Robert M, Randoux B, Ghinet A, Halama P, Siah A, Reignault P. Saccharin Provides Protection and Activates Defense Mechanisms in Wheat Against the Hemibiotrophic Pathogen Zymoseptoria tritici. PLANT DISEASE 2021; 105:780-786. [PMID: 32830594 DOI: 10.1094/pdis-05-20-1106-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plant resistance inducers are among the most promising alternatives to develop sustainable crop protection. Here, we examined the ability of saccharin, a metabolite derived from probenazole, to protect wheat against Zymoseptoria tritici, the most frequently occurring and damaging foliar pathogen on this crop. The experiments were performed in the greenhouse by treating seedlings of the wheat cultivar 'Alixan' with 15 mM of saccharin 2 days before challenge inoculation with the Z. tritici pathogenic strain T02596. Foliar application of saccharin resulted in 77% lower disease severity than in nontreated control plants. In vitro and in planta assays showed that saccharin did not exhibit any direct antifungal effect on spore germination or hyphal growth. Molecular investigations from 2 to 7 days posttreatment (dpt) revealed that saccharin treatment upregulates the expression of genes encoding for lipoxygenase (LOX) at all sampled time points and pathogenesis-related protein 1 (PR1) at 7 dpt, in both noninfectious and infectious contexts, as well as peroxidase (POX2) in noninfectious conditions. However, saccharin did not induce significant change in the expression of PAL gene encoding for phenylalanine ammonia-lyase. Our findings report for the first time the potential of saccharin to confer protection in wheat against Z. tritici through an elicitation and priming of LOX and PR gene-related defense pathways. Additional investigations would provide a better deciphering of defense mechanisms activated by this molecule in wheat against Z. tritici.
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Affiliation(s)
- Samara Mejri
- UMR-Transfrontalière 1158 BioEcoAgro, Junia, Université de Lille, Université d'Artois, ULCO, UPJV, Université de Liège, INRAE, 59000 Lille, France
| | - Maryline Magnin-Robert
- Unité de Chimie Environnementale et Interactions sur le Vivant, Université de Littoral Côte d'Opale, 62228 Calais, France
| | - Beatrice Randoux
- Unité de Chimie Environnementale et Interactions sur le Vivant, Université de Littoral Côte d'Opale, 62228 Calais, France
| | - Alina Ghinet
- Laboratoire de Chimie Durable et Santé, Yncréa Hauts-de-France, Heath & Environment Department, Team Sustainable Chemistry, 59046 Lille, France
- Faculty of Chemistry, University of Iasi, 700506 Iasi, Romania
| | - Patrice Halama
- UMR-Transfrontalière 1158 BioEcoAgro, Junia, Université de Lille, Université d'Artois, ULCO, UPJV, Université de Liège, INRAE, 59000 Lille, France
| | - Ali Siah
- UMR-Transfrontalière 1158 BioEcoAgro, Junia, Université de Lille, Université d'Artois, ULCO, UPJV, Université de Liège, INRAE, 59000 Lille, France
| | - Philippe Reignault
- Unité de Chimie Environnementale et Interactions sur le Vivant, Université de Littoral Côte d'Opale, 62228 Calais, France
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Xie Y, Ravet K, Pearce S. Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.). BMC Genomics 2021; 22:218. [PMID: 33765923 PMCID: PMC7995804 DOI: 10.1186/s12864-021-07475-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bowman-Birk inhibitors (BBI) are a family of serine-type protease inhibitors that modulate endogenous plant proteolytic activities during different phases of development. They also inhibit exogenous proteases as a component of plant defense mechanisms, and their overexpression can confer resistance to phytophagous herbivores and multiple fungal and bacterial pathogens. Dicot BBIs are multifunctional, with a "double-headed" structure containing two separate inhibitory loops that can bind and inhibit trypsin and chymotrypsin proteases simultaneously. By contrast, monocot BBIs have a non-functional chymotrypsin inhibitory loop, although they have undergone internal duplication events giving rise to proteins with multiple BBI domains. RESULTS We used a Hidden Markov Model (HMM) profile-based search to identify 57 BBI genes in the common wheat (Triticum aestivum L.) genome. The BBI genes are unevenly distributed, with large gene clusters in the telomeric regions of homoeologous group 1 and 3 chromosomes that likely arose through a series of tandem gene duplication events. The genomes of wheat progenitors also contain contiguous clusters of BBI genes, suggesting this family underwent expansion before the domestication of common wheat. However, the BBI gene family varied in size among different cultivars, showing this family remains dynamic. Because of these expansions, the BBI gene family is larger in wheat than other monocots such as maize, rice and Brachypodium. We found BBI proteins in common wheat with intragenic homologous duplications of cysteine-rich functional domains, including one protein with four functional BBI domains. This diversification may expand the spectrum of target substrates. Expression profiling suggests that some wheat BBI proteins may be involved in regulating endogenous proteases during grain development, while others were induced in response to biotic and abiotic stresses, suggesting a role in plant defense. CONCLUSIONS Genome-wide characterization reveals that the BBI gene family in wheat is subject to a high rate of homologous tandem duplication and deletion events, giving rise to a diverse set of encoded proteins. This information will facilitate the functional characterization of individual wheat BBI genes to determine their role in wheat development and stress responses, and their potential application in breeding.
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Affiliation(s)
- Yucong Xie
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Karl Ravet
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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Frolova GM, Kotlova ER, Sokornova SV, Senik SV, Shavarda AL, Misharev AD, Berestetskiy AO. Pathogenicity and Lipid Composition of Mycelium of the Fungus Stagonospora cirsii VIZR 1.41 during Submerged Cultivation. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Karki SJ, Reilly A, Zhou B, Mascarello M, Burke J, Doohan F, Douchkov D, Schweizer P, Feechan A. A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 33095257 DOI: 10.5061/dryad.9w0vt4bcx] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
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Affiliation(s)
- Sujit Jung Karki
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Reilly
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Maurizio Mascarello
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 8 32, 3000 Leuven, Belgium
| | - James Burke
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fiona Doohan
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitar Douchkov
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Patrick Schweizer
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Angela Feechan
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Karki SJ, Reilly A, Zhou B, Mascarello M, Burke J, Doohan F, Douchkov D, Schweizer P, Feechan A. A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:733-746. [PMID: 33095257 PMCID: PMC7853600 DOI: 10.1093/jxb/eraa489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/15/2020] [Indexed: 05/05/2023]
Abstract
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
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Affiliation(s)
- Sujit Jung Karki
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Reilly
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Maurizio Mascarello
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 8 32, 3000 Leuven, Belgium
| | - James Burke
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fiona Doohan
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitar Douchkov
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Patrick Schweizer
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Angela Feechan
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Correspondence:
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Reilly A, Karki SJ, Twamley A, Tiley AMM, Kildea S, Feechan A. Isolate-Specific Responses of the Nonhost Grass Brachypodium distachyon to the Fungal Pathogen Zymoseptoria tritici Compared with Wheat. PHYTOPATHOLOGY 2021; 111:356-368. [PMID: 32720875 DOI: 10.1094/phyto-02-20-0041-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: 06/11/2023]
Abstract
Septoria tritici blotch (STB) is an important foliar disease of wheat that is caused by the fungal pathogen Zymoseptoria tritici. The grass Brachypodium distachyon has been used previously as a model system for cereal-pathogen interactions. In this study, we examined the nonhost resistance (NHR) response of B. distachyon to two different Z. tritici isolates in comparison with wheat. These isolates vary in aggressiveness on wheat cultivar Remus, displaying significant differences in disease and pycnidia coverage. Using microscopy, we found that similar isolate-specific responses were observed for hydrogen peroxide accumulation and cell death in both wheat and B. distachyon. Despite this, induction of isolate-specific patterns of defense gene expression by Z. tritici did differ between B. distachyon and wheat. Our results suggest that expression of the phenylalanine ammonia lyase PAL gene may be important for NHR in B. distachyon, while pathogenesis-related PR genes and expression of genes regulating reactive oxygen species may be important to limit disease in wheat. Future studies of the B. distachyon-Z. tritici interaction may allow identification of conserved plant immunity targets that are responsible for the isolate-specific responses observed in both plant species.
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Affiliation(s)
- Aisling Reilly
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sujit Jung Karki
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anthony Twamley
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anna M M Tiley
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven Kildea
- Department of Crop Science, Teagasc Crops Environment and Land Use Programme, Teagasc, Oak Park, County Carlow, Ireland
| | - Angela Feechan
- School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Yang Y, Sossah FL, Li Z, Hyde KD, Li D, Xiao S, Fu Y, Yuan X, Li Y. Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa. Front Microbiol 2021; 11:596719. [PMID: 33505368 PMCID: PMC7829358 DOI: 10.3389/fmicb.2020.596719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/07/2020] [Indexed: 11/18/2022] Open
Abstract
Mycogone perniciosa causes wet bubble disease in Agaricus bisporus and various Agaricomycetes species. In a previous work, we identified 41 GH18 chitinase genes and other pathogenicity-related genes in the genome of M. perniciosa Hp10. Chitinases are enzymes that degrade chitin, and they have diverse functions in nutrition, morphogenesis, and pathogenesis. However, these important genes in M. perniciosa have not been fully characterized, and their functions remain unclear. Here, we performed a genome-wide analysis of M. perniciosa GH18 genes and analyzed the transcriptome profiles and GH18 expression patterns in M. perniciosa during the time course of infection in A. bisporus. Phylogenetic analysis of the 41 GH18 genes with those of 15 other species showed that the genes were clustered into three groups and eight subgroups based on their conserved domains. The GH18 genes clustered in the same group shared different gene structures but had the same protein motifs. All GH18 genes were localized in different organelles, were unevenly distributed on 11 contigs, and had orthologs in the other 13 species. Twelve duplication events were identified, and these had undergone both positive and purifying selection. The transcriptome analyses revealed that numerous genes, including transporters, cell wall degrading enzymes (CWDEs), cytochrome P450, pathogenicity-related genes, secondary metabolites, and transcription factors, were significantly upregulated at different stages of M. perniciosa Hp10 infection of A. bisporus. Twenty-three out of the 41 GH18 genes were differentially expressed. The expression patterns of the 23 GH18 genes were different and were significantly expressed from 3 days post-inoculation of M. perniciosa Hp10 in A. bisporus. Five differentially expressed GH18 genes were selected for RT-PCR and gene cloning to verify RNA-seq data accuracy. The results showed that those genes were successively expressed in different infection stages, consistent with the previous sequencing results. Our study provides a comprehensive analysis of pathogenicity-related and GH18 chitinase genes’ influence on M. perniciosa mycoparasitism of A. bisporus. Our findings may serve as a basis for further studies of M. perniciosa mycoparasitism, and the results have potential value for improving resistance in A. bisporus and developing efficient disease-management strategies to mitigate wet bubble disease.
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Affiliation(s)
- Yang Yang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Guizhou Key Laboratory of Edible Fungi Breeding, Guizhou Academy of Agricultural Sciences, Guiyang, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Frederick Leo Sossah
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Zhuang Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai' an, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Dan Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Guizhou Key Laboratory of Edible Fungi Breeding, Guizhou Academy of Agricultural Sciences, Guiyang, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Shijun Xiao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Xiaohui Yuan
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,College of Plant Protection, Jilin Agricultural University, Changchun, China
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de Borba MC, Velho AC, Maia-Grondard A, Baltenweck R, Magnin-Robert M, Randoux B, Holvoet M, Hilbert JL, Flahaut C, Reignault P, Hugueney P, Stadnik MJ, Siah A. The Algal Polysaccharide Ulvan Induces Resistance in Wheat Against Zymoseptoria tritici Without Major Alteration of Leaf Metabolome. FRONTIERS IN PLANT SCIENCE 2021; 12:703712. [PMID: 34552606 PMCID: PMC8450535 DOI: 10.3389/fpls.2021.703712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 05/22/2023]
Abstract
This study aimed to examine the ability of ulvan, a water-soluble polysaccharide from the green seaweed Ulva fasciata, to provide protection and induce resistance in wheat against the hemibiotrophic fungus Zymoseptoria tritici. Matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS) analysis indicated that ulvan is mainly composed of unsaturated monosaccharides (rhamnose, rhamnose-3-sulfate, and xylose) and numerous uronic acid residues. In the greenhouse, foliar application of ulvan at 10 mg.ml-1 2 days before fungal inoculation reduced disease severity and pycnidium density by 45 and 50%, respectively. Ulvan did not exhibit any direct antifungal activity toward Z. tritici, neither in vitro nor in planta. However, ulvan treatment significantly reduced substomatal colonization and pycnidium formation within the mesophyll of treated leaves. Molecular assays revealed that ulvan spraying elicits, but does not prime, the expression of genes involved in several wheat defense pathways, including pathogenesis-related proteins (β-1,3-endoglucanase and chitinase), reactive oxygen species metabolism (oxalate oxidase), and the octadecanoid pathway (lipoxygenase and allene oxide synthase), while no upregulation was recorded for gene markers of the phenylpropanoid pathway (phenylalanine ammonia-lyase and chalcone synthase). Interestingly, the quantification of 83 metabolites from major chemical families using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) in both non-infectious and infectious conditions showed no substantial changes in wheat metabolome upon ulvan treatment, suggesting a low metabolic cost associated with ulvan-induced resistance. Our findings provide evidence that ulvan confers protection and triggers defense mechanisms in wheat against Z. tritici without major modification of the plant physiology.
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Affiliation(s)
- Marlon C. de Borba
- Laboratory of Plant Pathology, Agricultural Science Center (UFSC-CCA), Federal University of Santa Catarina, Florianópolis, Brazil
- Joint Research Unit N° 1158 BioEcoAgro, ULCO, INRAE, University of Lille, Université Liège, UPJV, University of Artois, Lille, France
| | - Aline C. Velho
- Laboratory of Plant Pathology, Agricultural Science Center (UFSC-CCA), Federal University of Santa Catarina, Florianópolis, Brazil
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d’Opale, Calais, France
| | | | | | - Maryline Magnin-Robert
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d’Opale, Calais, France
| | - Béatrice Randoux
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d’Opale, Calais, France
| | - Maxime Holvoet
- Joint Research Unit N° 1158 BioEcoAgro, ULCO, INRAE, University of Lille, Université Liège, UPJV, University of Artois, Lille, France
| | - Jean-Louis Hilbert
- Joint Research Unit N° 1158 BioEcoAgro, ULCO, INRAE, University of Lille, Université Liège, UPJV, University of Artois, Lille, France
| | - Christophe Flahaut
- Joint Research Unit N° 1158 BioEcoAgro, ULCO, INRAE, University of Lille, Université Liège, UPJV, University of Artois, Lille, France
| | - Philippe Reignault
- Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), Université du Littoral Côte d’Opale, Calais, France
| | | | - Marciel J. Stadnik
- Laboratory of Plant Pathology, Agricultural Science Center (UFSC-CCA), Federal University of Santa Catarina, Florianópolis, Brazil
- Marciel J. Stadnik,
| | - Ali Siah
- Joint Research Unit N° 1158 BioEcoAgro, ULCO, INRAE, University of Lille, Université Liège, UPJV, University of Artois, Lille, France
- *Correspondence: Ali Siah,
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Li Z, Wang Y, Fan Y, Ahmad B, Wang X, Zhang S, Zhu Y, Gao L, Chang P, Wang X. Transcriptome Analysis of the Grape- Elsinoë ampelina Pathosystem Reveals Novel Effectors and a Robust Defense Response. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:110-121. [PMID: 33006532 DOI: 10.1094/mpmi-08-20-0227-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. In this study, a dual RNA-seq analysis was used to simultaneously monitor the fungal genes related to pathogenesis and grape genes related to defense during the interaction at 2, 3, 4, and 5 days postinoculation. Consistent with their potential roles in pathogenicity, genes for carbohydrate-active enzymes, secondary metabolite synthesis, pathogen-host interaction, and those encoding secreted proteins are upregulated during infection. Based on Agrobacterium tumefaciens-mediated transient assays in Nicotiana benthamiana, we further showed that eight and nine candidate effectors, respectively, suppressed BAX- and INF1-mediated programmed cell death. The host response was characterized by the induction of multiple defense systems against E. ampelina, including synthesis of phenylpropanoids, stilbenes, and terpenoid biosynthesis, cell-wall modifications, regulation by phytohormones, and expression of defense-related genes. Together, these findings offer new insights into molecular mechanisms underlying the grape-E. ampelina interaction.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanchun Fan
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bilal Ahmad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianhang Wang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Songlin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanxun Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linlin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pingping Chang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Ma P, Wu L, Xu Y, Xu H, Zhang X, Wang W, Liu C, Wang B. Bulked Segregant RNA-Seq Provides Distinctive Expression Profile Against Powdery Mildew in the Wheat Genotype YD588. FRONTIERS IN PLANT SCIENCE 2021; 12:764978. [PMID: 34925412 PMCID: PMC8677838 DOI: 10.3389/fpls.2021.764978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/03/2021] [Indexed: 05/07/2023]
Abstract
Wheat powdery mildew, caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), is a destructive disease leading to huge yield losses in production. Host resistance can greatly contribute to the control of the disease. To explore potential genes related to the powdery mildew (Pm) resistance, in this study, we used a resistant genotype YD588 to investigate the potential resistance components and profiled its expression in response to powdery mildew infection. Genetic analysis showed that a single dominant gene, tentatively designated PmYD588, conferred resistance to powdery mildew in YD588. Using bulked segregant RNA-Seq (BSR-Seq) and single nucleotide polymorphism (SNP) association analysis, two high-confidence candidate regions were detected in the chromosome arm 2B, spanning 453,752,054-506,356,791 and 584,117,809-664,221,850 bp, respectively. To confirm the candidate region, molecular markers were developed using the BSR-Seq data and mapped PmYD588 to an interval of 4.2 cM by using the markers YTU588-004 and YTU588-008. The physical position was subsequently locked into the interval of 647.1-656.0 Mb, which was different from those of Pm6, Pm33, Pm51, Pm52, Pm63, Pm64, PmQ, PmKN0816, MlZec1, and MlAB10 on the same chromosome arm in its position, suggesting that it is most likely a new Pm gene. To explore the potential regulatory genes of the R gene, 2,973 differentially expressed genes (DEGs) between the parents and bulks were analyzed using gene ontology (GO), clusters of orthologous group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Based on the data, we selected 23 potential regulated genes in the enriched pathway of plant-pathogen interaction and detected their temporal expression patterns using an additional set of wheat samples and time-course analysis postinoculation with Bgt. As a result, six disease-related genes showed distinctive expression profiles after Bgt invasion and can serve as key candidates for the dissection of resistance mechanisms and improvement of durable resistance to wheat powdery mildew.
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Affiliation(s)
- Pengtao Ma
- School of Life Sciences, Yantai University, Yantai, China
- *Correspondence: Pengtao Ma,
| | - Liru Wu
- School of Life Sciences, Yantai University, Yantai, China
| | - Yufei Xu
- School of Life Sciences, Yantai University, Yantai, China
| | - Hongxing Xu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Xu Zhang
- School of Life Sciences, Yantai University, Yantai, China
- School of Life Sciences, Henan University, Kaifeng, China
| | - Wenrui Wang
- School of Life Sciences, Yantai University, Yantai, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- Cheng Liu,
| | - Bo Wang
- School of Life Sciences, Yantai University, Yantai, China
- Bo Wang,
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Fantozzi E, Kilaru S, Cannon S, Schuster M, Gurr SJ, Steinberg G. Conditional promoters to investigate gene function during wheat infection by Zymoseptoria tritici. Fungal Genet Biol 2021; 146:103487. [PMID: 33309991 PMCID: PMC7812376 DOI: 10.1016/j.fgb.2020.103487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 12/27/2022]
Abstract
The fungus Zymoseptoria tritici causes Septoria tritici leaf blotch, which poses a serious threat to temperate-grown wheat. Recently, we described a raft of molecular tools to study the biology of this fungus in vitro. Amongst these are 5 conditional promoters (Pnar1, Pex1A, Picl1, Pgal7, PlaraB), which allow controlled over-expression or repression of target genes in cells grown in liquid culture. However, their use in the host-pathogen interaction in planta was not tested. Here, we investigate the behaviour of these promoters by quantitative live cell imaging of green-fluorescent protein-expressing cells during 6 stages of the plant infection process. We show that Pnar1 and Picl1 are repressed in planta and demonstrate their suitability for studying essential gene expression and function in plant colonisation. The promoters Pgal7 and Pex1A are not fully-repressed in planta, but are induced during pycnidiation. This indicates the presence of inducing galactose or xylose and/or arabinose, released from the plant cell wall by the activity of fungal hydrolases. In contrast, the PlaraB promoter, which normally controls expression of an α-l-arabinofuranosidase B, is strongly induced inside the leaf. This suggests that the fungus is exposed to L-arabinose in the mesophyll apoplast. Taken together, this study establishes 2 repressible promoters (Pnar1 and Picl1) and three inducible promoters (Pgal7, Pex1A, PlaraB) for molecular studies in planta. Moreover, we provide circumstantial evidence for plant cell wall degradation during the biotrophic phase of Z. tritici infection.
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Affiliation(s)
- Elena Fantozzi
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sreedhar Kilaru
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Stuart Cannon
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Martin Schuster
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sarah J Gurr
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK; University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Gero Steinberg
- School of Biosciences, University of Exeter, Exeter EX4 4QD, UK; University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands.
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Asynchronous development of Zymoseptoria tritici infection in wheat. Fungal Genet Biol 2020; 146:103504. [PMID: 33326850 PMCID: PMC7812371 DOI: 10.1016/j.fgb.2020.103504] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Zymoseptoria tritici passes 6 morphologically defined stages during infection. Surface-located spores and hyphae are found for up to 17/18 days. Entry through stomata occurs from 1 to 13 days post infection. Mesophyll apoplast colonisation continuously increases during infection. Up to 5 stages co-exist in infected leaves at a given time.
The fungus Zymoseptoria tritici causes Septoria tritici blotch of wheat. Pathogenicity begins with spore germination, followed by stomata invasion by hyphae, mesophyll colonization and fruiting body formation. It was previously found that entry into the plant via stomata occurs in a non-synchronized way over several days, while later developmental steps, such as early and late fruiting body formation, were reported to follow each other in time. This suggests synchronization of the pathogen population in planta prior to sporulation. Here, we image a fluorescent Z. tritici IPO323-derived strain during infection. We describe 6 morphologically distinct developmental stages, and determine their abundance in infected leaves, with time post inoculation. This demonstrates that 3-5 stages co-exist in infected tissues at any given time. Thus, later stages of pathogen development also occur asynchronously amongst the population of infecting cells. This merits consideration when interpreting transcriptomics or proteomics data gathered from infected plants.
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Fones HN. Presence of ice-nucleating Pseudomonas on wheat leaves promotes Septoria tritici blotch disease (Zymoseptoria tritici) via a mutually beneficial interaction. Sci Rep 2020; 10:17738. [PMID: 33082401 PMCID: PMC7575590 DOI: 10.1038/s41598-020-74615-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 09/09/2020] [Indexed: 11/09/2022] Open
Abstract
Zymoseptoria tritici causes Septoria tritici blotch (STB) of wheat, an economically important disease causing yield losses of up to 10% despite the use of fungicides and resistant cultivars. Z. tritici infection is symptomless for around 10 days, during which time the fungus grows randomly across the leaf surface prior to entry through stomata. Wounded leaves show faster, more extensive STB, suggesting that wounds facilitate fungal entry. Wheat leaves also host epiphytic bacteria; these include ice-nucleating (INA+) bacteria, which induce frost damage at warmer temperatures than it otherwise occurs. Here, STB is shown to be more rapid and severe when wheat is exposed to both INA+ bacteria and sub-zero temperatures. This suggests that ice-nucleation-induced wounding of the wheat leaf provides additional openings for fungal entry. INA+ bacterial populations are shown to benefit from the presence of Z. tritici, indicating that this microbial interaction is mutualistic. Finally, control of INA+ bacteria is shown to reduce STB.
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Affiliation(s)
- Helen N Fones
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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Chromatin Dynamics Contribute to the Spatiotemporal Expression Pattern of Virulence Genes in a Fungal Plant Pathogen. mBio 2020; 11:mBio.02343-20. [PMID: 33024042 PMCID: PMC7542367 DOI: 10.1128/mbio.02343-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fungal plant pathogens possess a large repertoire of genes encoding putative effectors, which are crucial for infection. Many of these genes are expressed at low levels in the absence of the host but are strongly induced at specific stages of the infection. The mechanisms underlying this transcriptional reprogramming remain largely unknown. We investigated the role of the genomic environment and associated chromatin modifications of effector genes in controlling their expression pattern in the fungal wheat pathogen Zymoseptoria tritici. Depending on their genomic location, effector genes are epigenetically repressed in the absence of the host and during the initial stages of infection. Derepression of effector genes occurs mainly during and after penetration of plant leaves and is associated with changes in histone modifications. Our work demonstrates the role of chromatin in shaping the expression of virulence components and, thereby, the interaction between fungal pathogens and their plant hosts. Dynamic changes in transcription profiles are key for the success of pathogens in colonizing their hosts. In many pathogens, genes associated with virulence, such as effector genes, are located in regions of the genome that are rich in transposable elements and heterochromatin. The contribution of chromatin modifications to gene expression in pathogens remains largely unknown. Using a combination of a reporter gene-based approach and chromatin immunoprecipitation, we show that the heterochromatic environment of effector genes in the fungal plant pathogen Zymoseptoria tritici is a key regulator of their specific spatiotemporal expression patterns. Enrichment in trimethylated lysine 27 of histone H3 dictates the repression of effector genes in the absence of the host. Chromatin decondensation during host colonization, featuring a reduction in this repressive modification, indicates a major role for epigenetics in effector gene induction. Our results illustrate that chromatin modifications triggered during host colonization determine the specific expression profile of effector genes at the cellular level and, hence, provide new insights into the regulation of virulence in fungal plant pathogens.
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65
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Hill EH, Solomon PS. Extracellular vesicles from the apoplastic fungal wheat pathogen Zymoseptoria tritici. Fungal Biol Biotechnol 2020; 7:13. [PMID: 32968488 PMCID: PMC7501697 DOI: 10.1186/s40694-020-00103-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The fungal pathogen Zymoseptoria tritici is a significant constraint to wheat production in temperate cropping regions around the world. Despite its agronomic impacts, the mechanisms allowing the pathogen to asymptomatically invade and grow in the apoplast of wheat leaves before causing extensive host cell death remain elusive. Given recent evidence of extracellular vesicles (EVs)-secreted, membrane-bound nanoparticles containing molecular cargo-being implicated in extracellular communication between plants and fungal pathogen, we have initiated an in vitro investigation of EVs from this apoplastic fungal wheat pathogen. We aimed to isolate EVs from Z. tritici broth cultures and examine their protein composition in relation to the soluble protein in the culture filtrate and to existing fungal EV proteomes. RESULTS Zymoseptoria tritici EVs were isolated from broth culture filtrates using differential ultracentrifugation (DUC) and examined with transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Z. tritici EVs were observed as a heterogeneous population of particles, with most between 50 and 250 nm. These particles were found in abundance in the culture filtrates of viable Z. tritici cultures, but not heat-killed cultures incubated for an equivalent time and of comparable biomass. Bottom-up proteomic analysis using LC-MS/MS, followed by stringent filtering revealed 240 Z. tritici EV proteins. These proteins were distinct from soluble proteins identified in Z. tritici culture filtrates, but were similar to proteins identified in EVs from other fungi, based on sequence similarity analyses. Notably, a putative marker protein recently identified in Candida albicans EVs was also consistently detected in Z. tritici EVs. CONCLUSION We have shown EVs can be isolated from the devastating fungal wheat pathogen Z. tritici and are similar to protein composition to previously characterised fungal EVs. EVs from human pathogenic fungi are implicated in virulence, but the role of EVs in the interaction of phytopathogenic fungi and their hosts is unknown. These in vitro analyses provide a basis for expanding investigations of Z. tritici EVs in planta, to examine their involvement in the infection process of this apoplastic wheat pathogen and more broadly, advance understanding of noncanonical secretion in filamentous plant pathogens.
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Affiliation(s)
- Erin H. Hill
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601 Australia
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601 Australia
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66
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Jallet AJ, Le Rouzic A, Genissel A. Evolution and Plasticity of the Transcriptome Under Temperature Fluctuations in the Fungal Plant Pathogen Zymoseptoria tritici. Front Microbiol 2020; 11:573829. [PMID: 33042084 PMCID: PMC7517895 DOI: 10.3389/fmicb.2020.573829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/17/2020] [Indexed: 11/28/2022] Open
Abstract
Most species live in a variable environment in nature. Yet understanding the evolutionary processes underlying molecular adaptation to fluctuations remains a challenge. In this study we investigate the transcriptome of the fungal wheat pathogen Zymoseptoria tritici after experimental evolution under stable or fluctuating temperature, by comparing ancestral and evolved populations simultaneously. We found that temperature regimes could have a large and pervasive effect on the transcriptome evolution, with as much as 38% of the genes being differentially expressed between selection regimes. Although evolved lineages showed different changes of gene expression based on ancestral genotypes, we identified a set of genes responding specifically to fluctuation. We found that transcriptome evolution in fluctuating conditions was repeatable between parallel lineages initiated from the same genotype for about 60% of the differentially expressed genes. Further, we detected several hotspots of significantly differentially expressed genes in the genome, in regions known to be enriched in repetitive elements, including accessory chromosomes. Our findings also evidenced gene expression evolution toward a gain of robustness (loss of phenotypic plasticity) associated with the fluctuating regime, suggesting robustness is adaptive in changing environment. This work provides valuable insight into the role of transcriptional rewiring for rapid adaptation to abiotic changes in filamentous plant pathogens.
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Affiliation(s)
- Arthur J. Jallet
- UMR BIOGER, Université Paris Saclay – INRAE – AgroParisTech, Thiverval-Grignon, France
| | - Arnaud Le Rouzic
- UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay – CNRS – IRD, Gif-sur-Yvette, France
| | - Anne Genissel
- UMR BIOGER, Université Paris Saclay – INRAE – AgroParisTech, Thiverval-Grignon, France
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67
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Benbow HR, Brennan CJ, Zhou B, Christodoulou T, Berry S, Uauy C, Mullins E, Doohan FM. Insights into the resistance of a synthetically-derived wheat to Septoria tritici blotch disease: less is more. BMC PLANT BIOLOGY 2020; 20:407. [PMID: 32883202 PMCID: PMC7469286 DOI: 10.1186/s12870-020-02612-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/18/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Little is known about the initial, symptomless (latent) phase of the devastating wheat disease Septoria tritici blotch. However, speculations as to its impact on fungal success and disease severity in the field have suggested that a long latent phase is beneficial to the host and can reduce inoculum build up in the field over a growing season. The winter wheat cultivar Stigg is derived from a synthetic hexaploid wheat and contains introgressions from wild tetraploid wheat Triticum turgidum subsp. dicoccoides, which contribute to cv. Stigg's exceptional STB resistance, hallmarked by a long latent phase. We compared the early transcriptomic response to Zymoseptoria tritici of cv. Stigg to a susceptible wheat cultivar, to elucidate the mechanisms of and differences in pathogen recognition and disease response in these two hosts. RESULTS The STB-susceptible cultivar Longbow responds to Z. tritici infection with a stress response, including activation of hormone-responsive transcription factors, post translational modifications, and response to oxidative stress. The activation of key genes associated with these pathways in cv. Longbow was independently observed in a second susceptible wheat cultivar based on an independent gene expression study. By comparison, cv. Stigg is apathetic in response to STB, and appears to fail to activate a range of defence pathways that cv. Longbow employs. Stigg also displays some evidence of sub-genome bias in its response to Z. tritici infection, whereas the susceptible cv. Longbow shows even distribution of Z. tritici responsive genes across the three wheat sub-genomes. CONCLUSIONS We identify a suite of disease response genes that are involved in early pathogen response in susceptible wheat cultivars that may ultimately lead to susceptibility. In comparison, we hypothesise that rather than an active defence response to stave off disease progression, cv. Stigg's defence strategy is molecular lethargy, or a lower-amplitude of pathogen recognition that may stem from cv. Stigg's wild wheat-derived ancestry. Overall, we present insights into cv. Stigg's exceptional resistance to STB, and present key biological processes for further characterisation in this pathosystem.
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Affiliation(s)
- Harriet R Benbow
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Ciarán J Brennan
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Thalia Christodoulou
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland
| | - Simon Berry
- Limagrain UK Ltd, Windmill Avenue, Woolpit, Suffolk, IP30 9UP, UK
| | | | - Ewen Mullins
- Teagasc Crops Research, Oak Park, Co. Carlow, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science, University College Dublin, UCD Belfield, Dublin 4, Ireland.
- UCD Earth Institute, University College Dublin, UCD Belfield, Dublin 4, Ireland.
- UCD Centre for Plant Science, University College Dublin, UCD Belfield, Dublin 4, Ireland.
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Dos Santos-Silva CA, Zupin L, Oliveira-Lima M, Vilela LMB, Bezerra-Neto JP, Ferreira-Neto JR, Ferreira JDC, de Oliveira-Silva RL, Pires CDJ, Aburjaile FF, de Oliveira MF, Kido EA, Crovella S, Benko-Iseppon AM. Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. Bioinform Biol Insights 2020; 14:1177932220952739. [PMID: 32952397 PMCID: PMC7476358 DOI: 10.1177/1177932220952739] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.
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Affiliation(s)
| | - Luisa Zupin
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy
| | - Marx Oliveira-Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - José Diogo Cavalcanti Ferreira
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.,Departamento de Genética, Instituto Federal de Pernambuco, Pesqueira, Brazil
| | | | | | | | | | - Ederson Akio Kido
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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Janse van Rensburg HC, Takács Z, Freynschlag F, Toksoy Öner E, Jonak C, Van den Ende W. Fructans Prime ROS Dynamics and Botrytis cinerea Resistance in Arabidopsis. Antioxidants (Basel) 2020; 9:E805. [PMID: 32882794 PMCID: PMC7555011 DOI: 10.3390/antiox9090805] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Naturally derived molecules can be used as priming or defense stimulatory agents to protect against biotic stress. Fructans have gained strong interest due to their ability to induce resistance in a number of crop species. In this study, we set out to establish the role of fructan-induced immunity against the fungal pathogen Botrytis cinerea in Arabidopsis thaliana. We show that both inulin- and levan-type fructans from different sources can enhance Arabidopsis resistance against B. cinerea. We found that inulin from chicory roots and levan oligosaccharides from the exopolysaccharide-producing bacterium Halomonas smyrnensis primed the NADPH-oxidase-mediated reactive oxygen species (ROS) burst in response to the elicitors flg22, derived from the bacterial flagellum, and oligogalacturonides (OGs), derived from the host cell wall. Neither induced a direct ROS burst typical of elicitors. We also found a primed response after infection with B. cinerea for H2O2 accumulation and the activities of ascorbate peroxidase and catalase. Sucrose accumulated as a consequence of fructan priming, and glucose and sucrose levels increased in fructan-treated plants after infection with B. cinerea. This study shows that levan-type fructans, specifically from bacterial origin, can prime plant defenses and that both inulin and levan oligosaccharide-mediated priming is associated with changes in ROS dynamics and sugar metabolism. Establishing fructan-induced immunity in Arabidopsis is an important step to further study the underlying mechanisms since a broad range of biological resources are available for Arabidopsis.
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Affiliation(s)
| | - Zoltan Takács
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria; (Z.T.); (F.F.); (C.J.)
| | - Florentina Freynschlag
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria; (Z.T.); (F.F.); (C.J.)
| | - Ebru Toksoy Öner
- IBSB, Industrial Biotechnology and Systems Biology Research Group, Bioengineering Department, Marmara University, 34722 Istanbul, Turkey;
| | - Claudia Jonak
- AIT Austrian Institute of Technology, Center for Health & Bioresources, Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria; (Z.T.); (F.F.); (C.J.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium;
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70
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Gholizadeh F, Mirzaghaderi G. Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response. PLoS One 2020; 15:e0236226. [PMID: 32866160 PMCID: PMC7458318 DOI: 10.1371/journal.pone.0236226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/08/2020] [Indexed: 11/18/2022] Open
Abstract
Amine oxidases (AOs) including copper containing amine oxidases (CuAOs) and FAD-dependent polyamine oxidases (PAOs) are associated with polyamine catabolism in the peroxisome, apoplast and cytoplasm and play an essential role in growth and developmental processes and response to biotic and abiotic stresses. Here, we identified PAO genes in common wheat (Triticum aestivum), T. urartu and Aegilops tauschii and reported the genome organization, evolutionary features and expression profiles of the wheat PAO genes (TaPAO). Expression analysis using publicly available RNASeq data showed that TaPAO genes are expressed redundantly in various tissues and developmental stages. A large percentage of TaPAOs respond significantly to abiotic stresses, especially temperature (i.e. heat and cold stress). Some TaPAOs were also involved in response to other stresses such as powdery mildew, stripe rust and Fusarium infection. Overall, TaPAOs may have various functions in stress tolerances responses, and play vital roles in different tissues and developmental stages. Our results provided a reference for further functional investigation of TaPAO proteins.
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Affiliation(s)
- Fatemeh Gholizadeh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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Rangel LI, Spanner RE, Ebert MK, Pethybridge SJ, Stukenbrock EH, de Jonge R, Secor GA, Bolton MD. Cercospora beticola: The intoxicating lifestyle of the leaf spot pathogen of sugar beet. MOLECULAR PLANT PATHOLOGY 2020; 21:1020-1041. [PMID: 32681599 PMCID: PMC7368123 DOI: 10.1111/mpp.12962] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 05/07/2023]
Abstract
Cercospora leaf spot, caused by the fungal pathogen Cercospora beticola, is the most destructive foliar disease of sugar beet worldwide. This review discusses C. beticola genetics, genomics, and biology and summarizes our current understanding of the molecular interactions that occur between C. beticola and its sugar beet host. We highlight the known virulence arsenal of C. beticola as well as its ability to overcome currently used disease management strategies. Finally, we discuss future prospects for the study and management of C. beticola infections in the context of newly employed molecular tools to uncover additional information regarding the biology of this pathogen. TAXONOMY Cercospora beticola Sacc.; Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Capnodiales, Family Mycosphaerellaceae, Genus Cercospora. HOST RANGE Well-known pathogen of sugar beet (Beta vulgaris subsp. vulgaris) and most species of the Beta genus. Reported as pathogenic on other members of the Chenopodiaceae (e.g., lamb's quarters, spinach) as well as members of the Acanthaceae (e.g., bear's breeches), Apiaceae (e.g., Apium), Asteraceae (e.g., chrysanthemum, lettuce, safflower), Brassicaceae (e.g., wild mustard), Malvaceae (e.g., Malva), Plumbaginaceae (e.g., Limonium), and Polygonaceae (e.g., broad-leaved dock) families. DISEASE SYMPTOMS Leaves infected with C. beticola exhibit circular lesions that are coloured tan to grey in the centre and are often delimited by tan-brown to reddish-purple rings. As disease progresses, spots can coalesce to form larger necrotic areas, causing severely infected leaves to wither and die. At the centre of these spots are black spore-bearing structures (pseudostromata). Older leaves often show symptoms first and younger leaves become infected as the disease progresses. MANAGEMENT Application of a mixture of fungicides with different modes of action is currently performed although elevated resistance has been documented in most employed fungicide classes. Breeding for high-yielding cultivars with improved host resistance is an ongoing effort and prudent cultural practices, such as crop rotation, weed host management, and cultivation to reduce infested residue levels, are widely used to manage disease. USEFUL WEBSITE: https://www.ncbi.nlm.nih.gov/genome/11237?genome_assembly_id=352037.
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Affiliation(s)
- Lorena I. Rangel
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
| | - Rebecca E. Spanner
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Malaika K. Ebert
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
- Present address:
Department of Plant BiologyMichigan State UniversityEast LansingMIUSA
| | - Sarah J. Pethybridge
- Plant Pathology & Plant‐Microbe Biology SectionSchool of Integrative Plant ScienceCornell AgriTech at The New York State Agricultural Experiment StationCornell UniversityGenevaNYUSA
| | - Eva H. Stukenbrock
- Environmental Genomics GroupMax Planck Institute for Evolutionary BiologyPlönGermany
- Christian‐Albrechts University of KielKielGermany
| | - Ronnie de Jonge
- Department of Plant‐Microbe InteractionsUtrecht UniversityUtrechtNetherlands
| | - Gary A. Secor
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
| | - Melvin D. Bolton
- Northern Crop Science LaboratoryU.S. Department of Agriculture ‐ Agricultural Research ServiceFargoNDUSA
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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Lu Q, Wang Y, Xiong F, Hao X, Zhang X, Li N, Wang L, Zeng J, Yang Y, Wang X. Integrated transcriptomic and metabolomic analyses reveal the effects of callose deposition and multihormone signal transduction pathways on the tea plant-Colletotrichum camelliae interaction. Sci Rep 2020; 10:12858. [PMID: 32733080 PMCID: PMC7393116 DOI: 10.1038/s41598-020-69729-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/17/2020] [Indexed: 12/16/2022] Open
Abstract
Colletotrichum infects diverse hosts, including tea plants, and can lead to crop failure. Numerous studies have reported that biological processes are involved in the resistance of tea plants to Colletotrichum spp. However, the molecular and biochemical responses in the host during this interaction are unclear. Cuttings of the tea cultivar Longjing 43 (LJ43) were inoculated with a conidial suspension of Colletotrichum camelliae, and water-sprayed cuttings were used as controls. In total, 10,592 differentially expressed genes (DEGs) were identified from the transcriptomic data of the tea plants and were significantly enriched in callose deposition and the biosynthesis of various phytohormones. Subsequently, 3,555 mass spectra peaks were obtained by LC-MS detection in the negative ion mode, and 27, 18 and 81 differentially expressed metabolites (DEMs) were identified in the tea leaves at 12 hpi, 24 hpi and 72 hpi, respectively. The metabolomic analysis also revealed that the levels of the precursors and intermediate products of jasmonic acid (JA) and indole-3-acetate (IAA) biosynthesis were significantly increased during the interaction, especially when the symptoms became apparent. In conclusion, we suggest that callose deposition and various phytohormone signaling systems play important roles in the tea plant-C. camelliae interaction.
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Affiliation(s)
- Qinhua Lu
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yuchun Wang
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Xiong
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
- Tea Research Institute, Nanjing Agricultural University, Nanjing, China
| | - Xinyuan Hao
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Xinzhong Zhang
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Nana Li
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lu Wang
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianming Zeng
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yajun Yang
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China.
| | - Xinchao Wang
- Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou, China.
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73
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Septoria Leaf Blotch and Reduced Nitrogen Availability Alter WRKY Transcription Factor Expression in a Codependent Manner. Int J Mol Sci 2020; 21:ijms21114165. [PMID: 32545181 PMCID: PMC7312603 DOI: 10.3390/ijms21114165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 01/03/2023] Open
Abstract
A major cause of yield loss in wheat worldwide is the fungal pathogen Zymoseptoria tritici, a hemibiotrophic fungus which causes Septoria leaf blotch, the most destructive wheat disease in Europe. Resistance in commercial wheat varieties is poor, however, a link between reduced nitrogen availability and increased Septoria tolerance has been observed. We have shown that Septoria load is not affected by nitrogen, whilst the fungus is in its first, symptomless stage of growth. This suggests that a link between nitrogen and Septoria is only present during the necrotrophic phase of Septoria infection. Quantitative real-time PCR data demonstrated that WRKYs, a superfamily of plant-specific transcription factors, are differentially expressed in response to both reduced nitrogen and Septoria. WRKY39 was downregulated over 30-fold in response to necrotrophic stage Septoria, whilst changes in the expression of WRKY68a during the late biotrophic phase were dependent on the concentration of nitrogen under which wheat is grown. WRKY68a may therefore mediate a link between nitrogen and Septoria. The potential remains to identify key regulators in the link between nitrogen and Septoria, and as such, elucidate molecular markers for wheat breeding, or targets for molecular-based breeding approaches.
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74
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Musungu B, Bhatnagar D, Quiniou S, Brown RL, Payne GA, O’Brian G, Fakhoury AM, Geisler M. Use of Dual RNA-seq for Systems Biology Analysis of Zea mays and Aspergillus flavus Interaction. Front Microbiol 2020; 11:853. [PMID: 32582038 PMCID: PMC7285840 DOI: 10.3389/fmicb.2020.00853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/09/2020] [Indexed: 11/18/2022] Open
Abstract
The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore, the authors undertook a systems biology approach involving dual RNA-seq to determine the simultaneous response from the host and the pathogen. What was dramatically highlighted in the analysis is the uniformity in the development patterns of gene expression of the host and the pathogen during infection. This led to the development of a "stage of infection index" that was subsequently used to categorize the samples before down-stream system biology analysis. Additionally, we were able to ascertain that key maize genes in pathways such as the jasmonate, ethylene and ROS pathways, were up-regulated in the study. The stage of infection index used for the transcriptomic analysis revealed that A. flavus produces a relatively limited number of transcripts during the early stages (0 to 12 h) of infection. At later stages, in A. flavus, transcripts and pathways involved in endosomal transport, aflatoxin production, and carbohydrate metabolism were up-regulated. Multiple WRKY genes targeting the activation of the resistance pathways (i.e., jasmonate, phenylpropanoid, and ethylene) were detected using causal inference analysis. This analysis also revealed, for the first time, the activation of Z. mays resistance genes influencing the expression of specific A. flavus genes. Our results show that A. flavus seems to be reacting to a hostile environment resulting from the activation of resistance pathways in Z. mays. This study revealed the dynamic nature of the interaction between the two organisms.
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Affiliation(s)
- Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - Deepak Bhatnagar
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Sylvie Quiniou
- Warm Water Aquaculture Research Unit, USDA-ARS, Stoneville, MS, United States
| | - Robert L. Brown
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, United States
| | - Gary A. Payne
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Greg O’Brian
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Ahmad M. Fakhoury
- Department of Plant Soil and Agriculture Systems, Southern Illinois University, Carbondale, IL, United States
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
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75
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Rahman A, Doohan F, Mullins E. Quantification of In Planta Zymoseptoria tritici Progression Through Different Infection Phases and Related Association with Components of Aggressiveness. PHYTOPATHOLOGY 2020; 110:1208-1215. [PMID: 32133920 DOI: 10.1094/phyto-09-19-0339-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In planta growth of Zymoseptoria tritici, causal agent of Septoria tritici blotch of wheat, during the infection process has remained an understudied topic due to the long symptomless latent period before the emergence of fruiting bodies. In this study, we attempted to understand the relationship between in planta growth of Z. tritici relative to the primary components of aggressiveness, i.e., latent period and pycnidia coverage in regard to contrasting host resistance. We tested isolates collected from Ireland against the susceptible cultivar Gallant and cultivar Stigg, which has strong partial resistance. A clear isolate-host interaction effect (F = 3.018; P = 0.005, and F = 6.008; P < 0.001) for latent period and pycnidia coverage, respectively, was identified. Furthermore, during the early infection phase of latency from 5 to 11 days postinoculation (dpi), in planta growth rate of fungal biomass was significantly (F = 30.06; P < 0.001) more affected by host resistance than isolate specificity (F = 1.27; P = 0.27), indicating the importance of host resistance in the early infection phase. In planta Z. tritici growth rates in cultivar Gallant spiked between 11 and 16 dpi followed by a continuous fall onward, whereas in cultivar Stigg it was slowly progressive in nature. From correlation and regression analysis, we found that the in planta growth rate preceding the average latent period of cultivar Gallant has more influence on latency duration and pycnidia production. Likewise, correlation between component of aggressiveness and in planta growth rate of pathogen supports our understanding of aggressiveness to be driven by the pathogen's multiplication capacity within host tissue.
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Affiliation(s)
- Atikur Rahman
- Crop Science Department, Teagasc, Oakpark, Carlow, R93 XE12, Ireland
- School of Biological and Environmental Sciences, UCD Earth Institute and UCD Institute of Food and Health, University College of Dublin, Dublin, D04 V1W8, Ireland
| | - Fiona Doohan
- School of Biological and Environmental Sciences, UCD Earth Institute and UCD Institute of Food and Health, University College of Dublin, Dublin, D04 V1W8, Ireland
| | - Ewen Mullins
- Crop Science Department, Teagasc, Oakpark, Carlow, R93 XE12, Ireland
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76
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Fedoryshchak RO, Ocasio CA, Strutton B, Mattocks J, Corran AJ, Tate EW. Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism. RSC Chem Biol 2020; 1:68-78. [PMID: 34458749 PMCID: PMC8341946 DOI: 10.1039/d0cb00020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Zymoseptoria tritici is the causative agent of Septoria tritici blotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogen Z. tritici via inhibition of N-myristoyltransferase (NMT). We characterize Z. tritici NMT biochemically for the first time, profile the in vivo Z. tritici myristoylated proteome and identify and validate the first Z. tritici NMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity in Z. tritici through the application of comparative bioinformatics to deconvolute function from the previously largely unannotated Z. tritici proteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studying Z. tritici.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | - Cory A Ocasio
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | | | - Jo Mattocks
- Syngenta AG, Jealott's Hill Research Centre Bracknell UK
| | | | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
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77
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Zhou B, Benbow HR, Brennan CJ, Arunachalam C, Karki SJ, Mullins E, Feechan A, Burke JI, Doohan FM. Wheat Encodes Small, Secreted Proteins That Contribute to Resistance to Septoria Tritici Blotch. Front Genet 2020; 11:469. [PMID: 32477410 PMCID: PMC7235427 DOI: 10.3389/fgene.2020.00469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/16/2020] [Indexed: 11/23/2022] Open
Abstract
During plant-pathogen interactions, pathogens secrete many rapidly evolving, small secreted proteins (SSPs) that can modify plant defense and permit pathogens to colonize plant tissue. The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), one of the most important foliar diseases of wheat, globally. Z. tritici is a strictly apoplastic pathogen that can secrete numerous proteins into the apoplast of wheat leaves to promote infection. We sought to determine if, during STB infection, wheat also secretes small proteins into the apoplast to mediate the recognition of pathogen proteins and/or induce defense responses. To explore this, we developed an SSP-discovery pipeline to identify small, secreted proteins from wheat genomic data. Using this pipeline, we identified 6,998 SSPs, representing 2.3% of all proteins encoded by the wheat genome. We then mined a microarray dataset, detailing a resistant and susceptible host response to STB, and identified 141 Z. tritici- responsive SSPs, representing 4.7% of all proteins encoded by Z. tritici - responsive genes. We demonstrate that a subset of these SSPs have a functional signal peptide and can interact with Z. tritici SSPs. Transiently silencing two of these wheat SSPs using virus-induced gene silencing (VIGS) shows an increase in susceptibility to STB, confirming their role in defense against Z. tritici.
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Affiliation(s)
- Binbin Zhou
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Harriet R. Benbow
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Ciarán J. Brennan
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Chanemougasoundharam Arunachalam
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Sujit J. Karki
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc, Carlow, Ireland
| | - Angela Feechan
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - James I. Burke
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Fiona M. Doohan
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
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Seybold H, Demetrowitsch TJ, Hassani MA, Szymczak S, Reim E, Haueisen J, Lübbers L, Rühlemann M, Franke A, Schwarz K, Stukenbrock EH. A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition. Nat Commun 2020; 11:1910. [PMID: 32313046 PMCID: PMC7171108 DOI: 10.1038/s41467-020-15633-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
Yield losses caused by fungal pathogens represent a major threat to global food production. One of the most devastating fungal wheat pathogens is Zymoseptoria tritici. Despite the importance of this fungus, the underlying mechanisms of plant–pathogen interactions are poorly understood. Here we present a conceptual framework based on coinfection assays, comparative metabolomics, and microbiome profiling to study the interaction of Z. tritici in susceptible and resistant wheat. We demonstrate that Z. tritici suppresses the production of immune-related metabolites in a susceptible cultivar. Remarkably, this fungus-induced immune suppression spreads within the leaf and even to other leaves, a phenomenon that we term “systemic induced susceptibility”. Using a comparative metabolomics approach, we identify defense-related biosynthetic pathways that are suppressed and induced in susceptible and resistant cultivars, respectively. We show that these fungus-induced changes correlate with changes in the wheat leaf microbiome. Our findings suggest that immune suppression by this hemibiotrophic pathogen impacts specialized plant metabolism, alters its associated microbial communities, and renders wheat vulnerable to further infections. The fungal plant pathogen Zymoseptoria tritici is a major threat to wheat yield. Here Seybold et al. show that Z. tritici can suppress immune responses not only in infected tissue but also on other leaves, a phenomenon termed “systemic induced susceptibility” that is correlated with systemic changes in metabolite accumulation.
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Affiliation(s)
- Heike Seybold
- Botanical Institute, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.,Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, 9190401, Israel
| | - Tobias J Demetrowitsch
- Institute of Human Nutrition and Food Science, Kiel University, Heinrich-Hecht-Platz 10, 24118, Kiel, Germany
| | - M Amine Hassani
- Botanical Institute, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig Holstein Campus Kiel, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Ekaterina Reim
- Botanical Institute, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.,Institute of Human Nutrition and Food Science, Kiel University, Heinrich-Hecht-Platz 10, 24118, Kiel, Germany
| | - Janine Haueisen
- Botanical Institute, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Luisa Lübbers
- Botanical Institute, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Am Botanischen Garten 11, 24118, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Am Botanischen Garten 11, 24118, Kiel, Germany
| | - Karin Schwarz
- Institute of Human Nutrition and Food Science, Kiel University, Heinrich-Hecht-Platz 10, 24118, Kiel, Germany
| | - Eva H Stukenbrock
- Botanical Institute, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany. .,Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
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79
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Plant Cells under Attack: Unconventional Endomembrane Trafficking during Plant Defense. PLANTS 2020; 9:plants9030389. [PMID: 32245198 PMCID: PMC7154882 DOI: 10.3390/plants9030389] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022]
Abstract
Since plants lack specialized immune cells, each cell has to defend itself independently against a plethora of different pathogens. Therefore, successful plant defense strongly relies on precise and efficient regulation of intracellular processes in every single cell. Smooth trafficking within the plant endomembrane is a prerequisite for a diverse set of immune responses. Pathogen recognition, signaling into the nucleus, cell wall enforcement, secretion of antimicrobial proteins and compounds, as well as generation of reactive oxygen species, all heavily depend on vesicle transport. In contrast, pathogens have developed a variety of different means to manipulate vesicle trafficking to prevent detection or to inhibit specific plant responses. Intriguingly, the plant endomembrane system exhibits remarkable plasticity upon pathogen attack. Unconventional trafficking pathways such as the formation of endoplasmic reticulum (ER) bodies or fusion of the vacuole with the plasma membrane are initiated and enforced as the counteraction. Here, we review the recent findings on unconventional and defense-induced trafficking pathways as the plant´s measures in response to pathogen attack. In addition, we describe the endomembrane system manipulations by different pathogens, with a focus on tethering and fusion events during vesicle trafficking.
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80
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Human MP, Berger DK, Crampton BG. Time-Course RNAseq Reveals Exserohilum turcicum Effectors and Pathogenicity Determinants. Front Microbiol 2020; 11:360. [PMID: 32265851 PMCID: PMC7099616 DOI: 10.3389/fmicb.2020.00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/18/2020] [Indexed: 11/16/2022] Open
Abstract
Exserohilum turcicum (sexual stage Setosphaeria turcica) is the hemibiotrophic causal agent of northern leaf blight of maize and sorghum. This study aimed to identify the genes involved in host colonization during the biotrophic and necrotrophic phases of infection. It also aimed to identify race-specific differences in gene expression. RNAseq of maize seedlings inoculated with a race 13N or 23N E. turcicum isolate was conducted before inoculation and at 2, 5, 7, and 13 days post-inoculation (dpi). Biological replicates were pooled per time point for each race and sequenced. A bioinformatics pipeline was used to identify candidate effectors, and expression was validated for selected candidates. Fungal biomass was positively correlated with the percentages of E. turcicum reads mapped, which were low at early time points (2-7 dpi) with a significant increase at 13 dpi, indicating a lifestyle switch from biotrophy to necrotrophy between 7 and 13 dpi. AVRHt1 is the putative E. turcicum effector recognized by the maize resistance gene Ht1. Consistent with this, AVRHt1 was expressed in planta by race 23N, but transcripts were absent in race 13N. In addition, specific transposable elements were expressed in 23N only. Genes encoding the virulence-associated peptidases leupeptin-inhibiting protein 1 and fungalysin were expressed in planta. Transcriptional profiles of genes involved in secondary metabolite synthesis or cell wall degradation revealed the importance of these genes during late stages of infection (13 dpi). A total of 346 expressed candidate effectors were identified, including Ecp6 and proteins similar to the secreted in xylem (SIX) effectors common to formae speciales of Fusarium oxysporum, SIX13 and SIX5. Expression profiling of Ecp6 and SIX13-like indicated a peak in expression at 5 and 7 dpi compared to 2 and 13 dpi. Sequencing of SIX13-like from diverse isolates of E. turcicum revealed host-specific polymorphisms that were mostly non-synonymous, resulting in two groups of SIX13-like proteins that corresponded to the maize or sorghum origin of each isolate. This study suggests putative mechanisms whereby E. turcicum causes disease. Identification of the candidate effector SIX13-like is consistent with the infection mode of E. turcicum through the xylem of susceptible hosts.
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Affiliation(s)
| | | | - Bridget Genevieve Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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81
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit ( Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection. Int J Mol Sci 2020; 21:ijms21051789. [PMID: 32150966 PMCID: PMC7084804 DOI: 10.3390/ijms21051789] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 02/08/2023] Open
Abstract
Mulberry sclerotiniose caused by Ciboria shiraiana is a devastating disease of mulberry (Morus alba L.) fruit in Northwest China. At present, no disease-resistant varieties are used in production, as the molecular mechanisms of this disease are not well understood. In this study, to explore new prevention methods and provide direction for molecular breeding, transcriptomic sequencing and un-targeted metabolomics were performed on healthy (CK), early-stage diseased (HB1), and middle-stage diseased (HB2) mulberry fruits. Functional annotation, gene ontology, a Kyoto encyclopedia of genes and genomes (KEGG) analysis, and a Mapman analysis of the differentially expressed genes revealed differential regulation of genes related to plant hormone signal transduction, transcription factors, and phenylpropanoid biosynthesis. A correspondence between the transcript pattern and metabolite profile was observed in the phenylpropanoid biosynthesis pathway. It should be noted that the log2 ratio of eugenol (isoeugenol) in HB1 and HB2 are 85 times and 23 times higher than CK, respectively. Our study shows that phenylpropanoid biosynthesis may play an essential role in response to sclerotiniose pathogen infection and eugenol(isoeugenol) enrichment in mulberry fruit, which may provide a novel method for mulberry sclerotiniose control.
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83
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Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020; 37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity; however, the regulatory mechanisms underlying de-repression are poorly understood. Plant pathogens are excellent models to dissect the impact of stress on TEs. The process of plant infection induces stress for the pathogen, and virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dissect TE de-repression dynamics and contributions to virulence, we analyzed the TE expression landscape of four strains of the major wheat pathogen Zymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including miniature inverted-repeat transposable element and long terminal repeat-Gypsy element, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e., different strains harboring the same TEs) were major predictors of de-repression under stress. Gene expression profiles under stress varied significantly depending on the proximity to the closest TEs and genomic defenses against TEs were largely ineffective to prevent de-repression. Next, we analyzed the locus encoding the Avr3D1 effector. We show that the insertion and subsequent silencing of TEs in close proximity likely contributed to reduced expression and virulence on a specific wheat cultivar. The complexity of TE responsiveness to stress across genetic backgrounds and genomic locations demonstrates substantial intraspecific genetic variation to control TEs with consequences for virulence.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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84
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Précigout PA, Claessen D, Makowski D, Robert C. Does the Latent Period of Leaf Fungal Pathogens Reflect Their Trophic Type? A Meta-Analysis of Biotrophs, Hemibiotrophs, and Necrotrophs. PHYTOPATHOLOGY 2020; 110:345-361. [PMID: 31577162 DOI: 10.1094/phyto-04-19-0144-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We performed a meta-analysis to search for a relation between the trophic type and latent period of fungal pathogens. The pathogen incubation period and the level of resistance of the hosts were also investigated. This ecological knowledge would help us to more efficiently regulate crop epidemics for different types of pathogens. We gathered latent period data from 103 studies dealing with 51 fungal pathogens of the three major trophic types (25 biotrophs, 15 hemibiotrophs, and 11 necrotrophs), representing 2,542 mean latent periods. We show that these three trophic types display significantly different latent periods. Necrotrophs exhibited the shortest latent periods (<100 degree-days [DD]), biotrophs had intermediate ones (between 100 and 200 DD), and hemibiotrophs had the longest latent periods (>200 DD). We argue that this relation between trophic type and latent period points to two opposing host exploitation strategies: necrotrophs mount a rapid destructive attack on the host tissue, whereas biotrophs and hemibiotrophs avoid or delay the damaging phase. We query the definition of hemibiotrophic pathogens and discuss whether the length of the latent period is determined by the physiological limits inherent to each trophic type or by the adaptation of pathogens of different trophic types to the contrasting conditions experienced in their interaction with the host.
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Affiliation(s)
- Pierre-Antoine Précigout
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS-ENS-INSERM UMR8197, Ecole Normale Supérieure, 75005 Paris, France
- UMR EcoSys, Institut National de la Recherche Agronomique (INRA), AgroParisTech, 78850 Thiverval-Grignon, France
| | - David Claessen
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS-ENS-INSERM UMR8197, Ecole Normale Supérieure, 75005 Paris, France
| | - David Makowski
- UMR Agronomie, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Corinne Robert
- UMR EcoSys, Institut National de la Recherche Agronomique (INRA), AgroParisTech, 78850 Thiverval-Grignon, France
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85
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Ma X, Wiedmer J, Palma-Guerrero J. Small RNA Bidirectional Crosstalk During the Interaction Between Wheat and Zymoseptoria tritici. FRONTIERS IN PLANT SCIENCE 2020; 10:1669. [PMID: 31969895 PMCID: PMC6960233 DOI: 10.3389/fpls.2019.01669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/27/2019] [Indexed: 05/21/2023]
Abstract
Cross-kingdom RNA interference (RNAi) has been shown to play important roles during plant-pathogen interactions, and both plants and pathogens can use small RNAs (sRNAs) to silence genes in each other. This bidirectional cross-kingdom RNAi was still unexplored in the wheat-Zymoseptoria tritici pathosystem. Here, we performed a detailed analysis of the sRNA bidirectional crosstalk between wheat and Z. tritici. Using a combination of small RNA sequencing (sRNA-seq) and microRNA sequencing (mRNA-seq), we were able to identify known and novel sRNAs and study their expression and their action on putative targets in both wheat and Z. tritici. We predicted the target genes of all the sRNAs in either wheat or Z. tritici transcriptome and used degradome analysis to validate the cleavage of these gene transcripts. We could not find any clear evidence of a cross-kingdom RNAi acting by mRNA cleavage in this pathosystem. We also found that the fungal sRNA enrichment was lower in planta than during in vitro growth, probably due to the lower expression of the only Dicer gene of the fungus during plant infection. Our results support the recent finding that Z. tritici sRNAs cannot play important roles during wheat infection. However, we also found that the fungal infection induced wheat sRNAs regulating the expression of specific wheat genes, including auxin-related genes, as an immune response. These results indicate a role of sRNAs in the regulation of wheat defenses during Z. tritici infection. Our findings contribute to improve our understanding of the interactions between wheat and Z. tritici.
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Affiliation(s)
- Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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86
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Habig M, Bahena‐Garrido SM, Barkmann F, Haueisen J, Stukenbrock EH. The transcription factor Zt107320 affects the dimorphic switch, growth and virulence of the fungal wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2020; 21:124-138. [PMID: 31702117 PMCID: PMC6913241 DOI: 10.1111/mpp.12886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Zymoseptoria tritici is a filamentous fungus causing Septoria tritici blotch in wheat. The pathogen has a narrow host range and infections of grasses other than susceptible wheat are blocked early after stomatal penetration. During these abortive infections, the fungus shows a markedly different gene expression pattern. However, the underlying mechanisms causing differential gene expression during host and non-host interactions are largely unknown, but likely include transcriptional regulators responsible for the onset of an infection programme in compatible hosts. MoCOD1, a member of the fungal Zn(II)2 Cys6 transcription factor family, has been shown to directly affect pathogenicity in the rice blast pathogen Magnaporthe oryzae. Here, we analyse the role of the putative transcription factor Zt107320, a homologue of MoCOD1, during infection of compatible and incompatible hosts by Z. tritici. We show for the first time that Zt107320 is differentially expressed in host versus non-host infections and that lower expression corresponds to an incompatible infection of non-hosts. Applying reverse genetics approaches, we further show that Zt107320 regulates the dimorphic switch as well as the growth rate of Z. tritici and affects fungal cell wall composition in vitro. Moreover, ∆Zt107320 mutants showed reduced virulence during compatible infections of wheat. We conclude that Zt107320 directly influences pathogen fitness and propose that Zt107320 is involved in the regulation of growth processes and pathogenicity during infection.
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Affiliation(s)
- Michael Habig
- Environmental GenomicsChristian‐Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Sharon Marie Bahena‐Garrido
- Environmental GenomicsChristian‐Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
- Present address:
National Research Institute of Brewing3‐7‐1 KagamiyamaHigashi‐Hiroshima739‐0046Japan
| | - Friederike Barkmann
- Environmental GenomicsChristian‐Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Janine Haueisen
- Environmental GenomicsChristian‐Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Eva Holtgrewe Stukenbrock
- Environmental GenomicsChristian‐Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
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87
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Steinhauer D, Salat M, Frey R, Mosbach A, Luksch T, Balmer D, Hansen R, Widdison S, Logan G, Dietrich RA, Kema GHJ, Bieri S, Sierotzki H, Torriani SFF, Scalliet G. A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici. PLoS Pathog 2019; 15:e1007780. [PMID: 31860693 PMCID: PMC6941823 DOI: 10.1371/journal.ppat.1007780] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 01/03/2020] [Accepted: 11/20/2019] [Indexed: 11/24/2022] Open
Abstract
Succinate dehydrogenase inhibitor (SDHI) fungicides are widely used for the control of a broad range of fungal diseases. This has been the most rapidly expanding fungicide group in terms of new molecules discovered and introduced for agricultural use over the past fifteen years. A particular pattern of differential sensitivity (resistance) to the stretched heterocycle amide SDHIs (SHA-SDHIs), a subclass of chemically-related SDHIs, was observed in naïve Zymoseptoria tritici populations not previously exposed to these chemicals. Subclass-specific resistance was confirmed at the enzyme level but did not correlate with the genotypes of the succinate dehydrogenase (SDH) encoding genes. Mapping and characterization of the molecular mechanisms responsible for standing SHA-SDHI resistance in natural field isolates identified a gene paralog of SDHC, termed ZtSDHC3, which encodes for an alternative C subunit of succinate dehydrogenase, named alt-SDHC. Using reverse genetics, we showed that alt-SDHC associates with the three other SDH subunits, leading to a fully functional enzyme and that a unique Qp-site residue within the alt-SDHC protein confers SHA-SDHI resistance. Enzymatic assays, computational modelling and docking simulations for the two SQR enzymes (altC-SQR, WT_SQR) enabled us to describe enzyme-inhibitor interactions at an atomistic level and to propose rational explanations for differential potency and resistance across SHA-SDHIs. European Z. tritici populations displayed a presence (20–30%) / absence polymorphism of ZtSDHC3, as well as differences in ZtSDHC3 expression levels and splicing efficiency. These polymorphisms have a strong impact on SHA-SDHI resistance phenotypes. Characterization of the ZtSDHC3 promoter in European Z. tritici populations suggests that transposon insertions are associated with the strongest resistance phenotypes. These results establish that a dispensable paralogous gene determines SHA-SDHIs fungicide resistance in natural populations of Z. tritici. This study paves the way to an increased awareness of the role of fungicidal target paralogs in resistance to fungicides and demonstrates the paramount importance of population genomics in fungicide discovery. Zymoseptoria tritici is the causal agent of Septoria tritici leaf blotch (STB) of wheat, the most devastating disease for cereal production in Europe. Multiple succinate dehydrogenase inhibitor (SDHI) fungicides have been developed and introduced for the control of STB. We report the discovery and detailed characterization of a paralog of the C subunit of the SDH enzyme conferring standing resistance towards the SHA-SDHIs, a particular chemical subclass of the SDHIs. The SDHC paralog is characterized by its presence/absence, expression and alternative splicing polymorphisms, which in turn influence resistance levels. The identified mechanisms exemplify the importance of population genomics for the discovery and rational design of the most adapted solutions.
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Affiliation(s)
| | - Marie Salat
- Syngenta Crop Protection AG, Stein, Switzerland
| | - Regula Frey
- Syngenta Crop Protection AG, Stein, Switzerland
| | | | | | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - Rasmus Hansen
- Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, United Kingdom
| | - Stephanie Widdison
- Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, United Kingdom
| | - Grace Logan
- Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, United Kingdom
| | - Robert A. Dietrich
- Syngenta Biotechnology Inc., Research Triangle Park, North Carolina, United States of America
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Wu W, Nemri A, Blackman LM, Catanzariti AM, Sperschneider J, Lawrence GJ, Dodds PN, Jones DA, Hardham AR. Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes. PLoS One 2019; 14:e0226106. [PMID: 31830116 PMCID: PMC6907798 DOI: 10.1371/journal.pone.0226106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
Secreted effectors of fungal pathogens are essential elements for disease development. However, lack of sequence conservation among identified effectors has long been a problem for predicting effector complements in fungi. Here we have explored the expression characteristics of avirulence (Avr) genes and candidate effectors of the flax rust fungus, Melampsora lini. We performed transcriptome sequencing and real-time quantitative PCR (qPCR) on RNA extracted from ungerminated spores, germinated spores, isolated haustoria and flax seedlings inoculated with M. lini isolate CH5 during plant infection. Genes encoding two categories of M. lini proteins, namely Avr proteins and plant cell wall degrading enzymes (CWDEs), were investigated in detail. Analysis of the expression profiles of 623 genes encoding predicted secreted proteins in the M. lini transcriptome shows that the six known Avr genes (i.e. AvrM (avrM), AvrM14, AvrL2, AvrL567, AvrP123 (AvrP) and AvrP4) fall within a group of 64 similarly expressed genes that are induced in planta and show a peak of expression early in infection with a subsequent decline towards sporulation. Other genes within this group include two paralogues of AvrL2, an AvrL567 virulence allele, and a number of genes encoding putative effector proteins. By contrast, M. lini genes encoding CWDEs fall into different expression clusters with their distribution often unrelated to their catalytic activity or substrate targets. These results suggest that synthesis of M. lini Avr proteins may be regulated in a coordinated fashion and that the expression profiling-based analysis has significant predictive power for the identification of candidate Avr genes.
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Affiliation(s)
- Wenjie Wu
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
| | | | - Leila M. Blackman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, the Australian National University, Canberra, Australia
| | | | | | - David A. Jones
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Adrienne R. Hardham
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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Chaudhari Y, Cairns TC, Sidhu Y, Attah V, Thomas G, Csukai M, Talbot NJ, Studholme DJ, Haynes K. The Zymoseptoria tritici ORFeome: A Functional Genomics Community Resource. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1564-1570. [PMID: 31272284 DOI: 10.1094/mpmi-05-19-0123-a] [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: 06/09/2023]
Abstract
Libraries of protein-encoding sequences can be generated by identification of open reading frames (ORFs) from a genome of choice that are then assembled into collections of plasmids termed ORFeome libraries. These represent powerful resources to facilitate functional genomic characterization of genes and their encoded products. Here, we report the generation of an ORFeome for Zymoseptoria tritici, which causes the most serious disease of wheat in temperate regions of the world. We screened the genome of strain IP0323 for high confidence gene models, identifying 4,075 candidates from 10,933 predicted genes. These were amplified from genomic DNA, were cloned into the Gateway entry vector pDONR207, and were sequenced, providing a total of 3,022 quality-controlled plasmids. The ORFeome includes genes predicted to encode effectors (n = 410) and secondary metabolite biosynthetic proteins (n = 171) in addition to genes residing at dispensable chromosomes (n = 122) or those that are preferentially expressed during plant infection (n = 527). The ORFeome plasmid library is compatible with our previously developed suite of Gateway destination vectors, which have various combinations of promoters, selection markers, and epitope tags. The Z. tritici ORFeome constitutes a powerful resource for functional genomics and offers unparalleled opportunities to understand the biology of Z. tritici.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
| | | | | | | | - Graham Thomas
- Biosciences, University of Exeter, Exeter EX4 4QD, U.K
| | - Michael Csukai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, U.K
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR47UH, U.K
| | | | - Ken Haynes
- Biosciences, University of Exeter, Exeter EX4 4QD, U.K
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90
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Cao Z, Li L, Kapoor K, Banniza S. Using a transcriptome sequencing approach to explore candidate resistance genes against stemphylium blight in the wild lentil species Lens ervoides. BMC PLANT BIOLOGY 2019; 19:399. [PMID: 31510924 PMCID: PMC6740027 DOI: 10.1186/s12870-019-2013-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/30/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Stemphylium blight (SB), caused by Stemphylium botryosum, is a devastating disease in lentil production. Although it is known that accessions of Lens ervoides possess superior SB resistance at much higher frequency than the cultivated lentil species, very little is known about the molecular basis regulating SB resistance in L. ervoides. Therefore, a comprehensive molecular study of SB resistance in L. ervoides was needed to exploit this wild resource available at genebanks for use by plant breeders in resistance breeding. RESULTS Microscopic and qPCR quantification of fungal growth revealed that 48, 96, and 144 h post-inoculation (hpi) were interesting time points for disease development in L. ervoides recombinant inbred lines (RILs) LR-66-637 (resistant to SB) and LR-66-577 (susceptible to SB). Results of transcriptome sequencing at 0, 48, 96 and 144 hpi showed that 8810 genes were disease-responsive genes after challenge by S. botryosum. Among them, 7526 genes displayed a similar expression trend in both RILs, and some of them were likely involved in non-host resistance. The remaining 1284 genes were differentially expressed genes (DEGs) between RILs. Of those, 712 DEGs upregulated in LR-66-637 were mostly enriched in 'carbohydrate metabolic process', 'cell wall organization or biogenesis', and 'polysaccharide metabolic process'. In contrast, there were another 572 DEGs that were upregulated in LR-66-577, and some of them were enriched in 'oxidation-reduction process', 'asparagine metabolic process' and 'asparagine biosynthetic process'. After comparing DEGs to genes identified in previously described quantitative trait loci (QTLs) for resistance to SB, nine genes were common and three of them showed differential gene expression between a resistant and a susceptible bulk consisting of five RILs each. Results showed that two genes encoding calcium-transporting ATPase and glutamate receptor3.2 were candidate resistance genes, whereas one gene with unknown function was a candidate susceptibility gene. CONCLUSION This study provides new insights into the mechanisms of resistance and susceptibility in L. ervoides RILs responding to S. botryosum infection. Furthermore, we identified candidate resistance or susceptibility genes which warrant further gene function analyses, and which could be valuable for resistance breeding, if their role in resistance or susceptibility can be confirmed.
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Affiliation(s)
- Zhe Cao
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Li Li
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Karan Kapoor
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Sabine Banniza
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
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91
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Chen F, Ma R, Chen XL. Advances of Metabolomics in Fungal Pathogen-Plant Interactions. Metabolites 2019; 9:metabo9080169. [PMID: 31443304 PMCID: PMC6724083 DOI: 10.3390/metabo9080169] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 01/02/2023] Open
Abstract
Plant disease caused by fungus is one of the major threats to global food security, and understanding fungus-plant interactions is important for plant disease control. Research devoted to revealing the mechanisms of fungal pathogen-plant interactions has been conducted using genomics, transcriptomics, proteomics, and metabolomics. Metabolomics research based on mass spectrometric techniques is an important part of systems biology. In the past decade, the emerging field of metabolomics in plant pathogenic fungi has received wide attention. It not only provides a qualitative and quantitative approach for determining the pathogenesis of pathogenic fungi but also helps to elucidate the defense mechanisms of their host plants. This review focuses on the methods and progress of metabolomics research in fungal pathogen-plant interactions. In addition, the prospects and challenges of metabolomics research in plant pathogenic fungi and their hosts are addressed.
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Affiliation(s)
- Fangfang Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ruijing Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiao-Lin Chen
- The Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in Triticum aestivum. G3-GENES GENOMES GENETICS 2019; 9:2709-2722. [PMID: 31227524 PMCID: PMC6686943 DOI: 10.1534/g3.119.400444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine protease inhibitor (serpin) gene family is the largest family of protease inhibitors. Serine protease inhibitors have an active, but under-characterized, role in grain development and defense against pathogen attack in cereal crops. By exploiting publicly available genomic, transcriptomic and proteomic data for wheat (Triticum aestivum), we have identified and annotated the entire ’serpinome’ of wheat and constructed a high-quality and robust phylogenetic tree of the gene family, identifying paralogous and homeologous clades from the hexaploid wheat genome, including the Serpin-Z group that have been well characterized in barley. Using publicly available RNAseq data (http://www.wheat-expression.com/), expression profiles of the wheat serpins were explored across a variety of tissues from the developing grain, spikelet and spike. We show that the SERPIN-Z clade, among others, are highly expressed during grain development, and that there is homeologous and paralogous functional redundancy in this gene family. Further to their role in grain development, serpins play an important but under-explored role in response to fungal pathogens. Using 13 RNAseq datasets of wheat tissues infected by fungal pathogens, we identified 37 serpins with a significant disease response. The majority of the disease-responsive serpins were upregulated by Fusarium graminearum, a destructive fungal pathogen that attacks the spike and developing grain of wheat. As serpins are ubiquitous in wheat grain, the genes encoding serpins may be linked to grain development, with their disease response a result of pleiotropy.
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93
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Gilbert KB, Holcomb EE, Allscheid RL, Carrington JC. Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes. PLoS One 2019; 14:e0219207. [PMID: 31339899 PMCID: PMC6655640 DOI: 10.1371/journal.pone.0219207] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/18/2019] [Indexed: 11/25/2022] Open
Abstract
The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.
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Affiliation(s)
- Kerrigan B. Gilbert
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Emily E. Holcomb
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Robyn L. Allscheid
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - James C. Carrington
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
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94
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Kettles GJ, Hofinger BJ, Hu P, Bayon C, Rudd JJ, Balmer D, Courbot M, Hammond-Kosack KE, Scalliet G, Kanyuka K. sRNA Profiling Combined With Gene Function Analysis Reveals a Lack of Evidence for Cross-Kingdom RNAi in the Wheat - Zymoseptoria tritici Pathosystem. FRONTIERS IN PLANT SCIENCE 2019; 10:892. [PMID: 31333714 PMCID: PMC6620828 DOI: 10.3389/fpls.2019.00892] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/21/2019] [Indexed: 05/19/2023]
Abstract
Cross-kingdom small RNA (sRNA) silencing has recently emerged as a mechanism facilitating fungal colonization and disease development. Here we characterized RNAi pathways in Zymoseptoria tritici, a major fungal pathogen of wheat, and assessed their contribution to pathogenesis. Computational analysis of fungal sRNA and host mRNA sequencing datasets was used to define the global sRNA populations in Z. tritici and predict their mRNA targets in wheat. 389 in planta-induced sRNA loci were identified. sRNAs generated from some of these loci were predicted to target wheat mRNAs including those potentially involved in pathogen defense. However, molecular approaches failed to validate targeting of selected wheat mRNAs by fungal sRNAs. Mutant strains of Z. tritici carrying deletions of genes encoding key components of RNAi such as Dicer-like (DCL) and Argonaute (AGO) proteins were generated, and virulence bioassays suggested that these are dispensable for full infection of wheat. Nonetheless, our results did suggest the existence of non-canonical DCL-independent pathway(s) for sRNA biogenesis in Z. tritici. dsRNA targeting essential fungal genes applied in vitro or generated from an RNA virus vector in planta in a procedure known as HIGS (Host-Induced Gene Silencing) was ineffective in preventing Z. tritici growth or disease. We also demonstrated that Z. tritici is incapable of dsRNA uptake. Collectively, our data suggest that RNAi approaches for gene function analyses in this fungal species and potentially also as a control measure may not be as effective as has been demonstrated for some other plant pathogenic fungi.
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Affiliation(s)
- Graeme J. Kettles
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Bernhard J. Hofinger
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Pingsha Hu
- Syngenta Biotechnology, Inc., Research Triangle Park, NC, United States
| | - Carlos Bayon
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Jason J. Rudd
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | | | | | | | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
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95
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Collemare J, O'Connell R, Lebrun MH. Nonproteinaceous effectors: the terra incognita of plant-fungal interactions. THE NEW PHYTOLOGIST 2019; 223:590-596. [PMID: 30851201 DOI: 10.1111/nph.15785] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/22/2019] [Indexed: 05/27/2023]
Abstract
Molecular plant-fungal interaction studies have mainly focused on small secreted protein effectors. However, accumulating evidence shows that numerous fungal secondary metabolites are produced at all stages of plant colonization, especially during early asymptomatic/biotrophic phases. The discovery of fungal small RNAs targeting plant transcripts has expanded the fungal repertoire of nonproteinaceous effectors even further. The challenge now is to develop specific functional methods to fully understand the biological roles of these effectors. Studies on fungal extracellular vesicles are also needed because they could be the universal carriers of all kinds of fungal effectors. With this review, we aim to stimulate the nonproteinaceous effector research field to move from descriptive to functional studies, which should bring a paradigm shift in plant-fungal interactions.
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Affiliation(s)
- Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Richard O'Connell
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, F78850, Thiverval-Grignon, France
| | - Marc-Henri Lebrun
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, F78850, Thiverval-Grignon, France
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96
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Kay WT, Fones HN, Gurr SJ. Rapid loss of virulence during submergence of Z. tritici asexual spores. Fungal Genet Biol 2019; 128:14-19. [DOI: 10.1016/j.fgb.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 11/28/2022]
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97
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Möller M, Schotanus K, Soyer JL, Haueisen J, Happ K, Stralucke M, Happel P, Smith KM, Connolly LR, Freitag M, Stukenbrock EH. Destabilization of chromosome structure by histone H3 lysine 27 methylation. PLoS Genet 2019; 15:e1008093. [PMID: 31009462 PMCID: PMC6510446 DOI: 10.1371/journal.pgen.1008093] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 05/10/2019] [Accepted: 03/15/2019] [Indexed: 01/23/2023] Open
Abstract
Chromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in regions considered constitutive heterochromatin. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a "metastable" state for these quasi-essential regions of the genome.
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Affiliation(s)
- Mareike Möller
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Klaas Schotanus
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, United States of America
| | - Jessica L. Soyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Janine Haueisen
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kathrin Happ
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
| | - Maja Stralucke
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
| | - Petra Happel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina M. Smith
- Department of Biology, Oregon State University—Cascades, Bend, OR, United States of America
| | - Lanelle R. Connolly
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States of America
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States of America
| | - Eva H. Stukenbrock
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
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98
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Anasontzis GE, Lebrun MH, Haon M, Champion C, Kohler A, Lenfant N, Martin F, O'Connell RJ, Riley R, Grigoriev IV, Henrissat B, Berrin JG, Rosso MN. Broad-specificity GH131 β-glucanases are a hallmark of fungi and oomycetes that colonize plants. Environ Microbiol 2019; 21:2724-2739. [PMID: 30887618 DOI: 10.1111/1462-2920.14596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/17/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Plant-tissue-colonizing fungi fine-tune the deconstruction of plant-cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant-tissue colonization by saprobic, pathogenic and symbiotic fungi. By searching all the publicly available genomes, we found that GH131-coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but neither other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen or saprobe. We propose that GH131-family expansions and horizontal-gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were upregulated during plant-tissue colonization in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor) and three hemibiotrophic-plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β-1,4, β-1,3 and mixed β-1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonization by symbionts, pathogens and saprobes.
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Affiliation(s)
- George E Anasontzis
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.,CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Marc-Henri Lebrun
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Mireille Haon
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Charlotte Champion
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Annegret Kohler
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Nicolas Lenfant
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Francis Martin
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Richard J O'Connell
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - Bernard Henrissat
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France.,INRA, USC 1408, AFMB, Marseille, France
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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99
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Saia S, Fragasso M, De Vita P, Beleggia R. Metabolomics Provides Valuable Insight for the Study of Durum Wheat: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3069-3085. [PMID: 30829031 DOI: 10.1021/acs.jafc.8b07097] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Metabolomics is increasingly being applied in various fields offering a highly informative tool for high-throughput diagnostics. However, in plant sciences, metabolomics is underused, even though plant studies are relatively easy and cheap when compared to those on humans and animals. Despite their importance for human nutrition, cereals, and especially wheat, remain understudied from a metabolomics point of view. The metabolomics of durum wheat has been essentially neglected, although its genetic structure allows the inference of common mechanisms that can be extended to other wheat and cereal species. This review covers the present achievements in durum wheat metabolomics highlighting the connections with the metabolomics of other cereal species (especially bread wheat). We discuss the metabolomics data from various studies and their relationships to other "-omics" sciences, in terms of wheat genetics, abiotic and biotic stresses, beneficial microbes, and the characterization and use of durum wheat as feed, food, and food ingredient.
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Affiliation(s)
- Sergio Saia
- Council for Agricultural Research and Economics (CREA) , Research Centre for Cereal and Industrial Crops (CREA-CI) , S.S. 673 , Km 25,200, 71122 Foggia , Italy
- Council for Agricultural Research and Economics (CREA) , Research Centre for Cereal and Industrial Crops (CREA-CI) , S.S. 11 per Torino , Km 2,5, 13100 Vercelli , Italy
| | - Mariagiovanna Fragasso
- Council for Agricultural Research and Economics (CREA) , Research Centre for Cereal and Industrial Crops (CREA-CI) , S.S. 673 , Km 25,200, 71122 Foggia , Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA) , Research Centre for Cereal and Industrial Crops (CREA-CI) , S.S. 673 , Km 25,200, 71122 Foggia , Italy
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA) , Research Centre for Cereal and Industrial Crops (CREA-CI) , S.S. 673 , Km 25,200, 71122 Foggia , Italy
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100
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Tarkowski ŁP, Van de Poel B, Höfte M, Van den Ende W. Sweet Immunity: Inulin Boosts Resistance of Lettuce ( Lactuca sativa) against Grey Mold ( Botrytis cinerea) in an Ethylene-Dependent Manner. Int J Mol Sci 2019; 20:E1052. [PMID: 30823420 PMCID: PMC6429215 DOI: 10.3390/ijms20051052] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/12/2019] [Accepted: 02/22/2019] [Indexed: 11/17/2022] Open
Abstract
The concept of "Sweet Immunity" postulates that sugar metabolism and signaling influence plant immune networks. In this study, we tested the potential of commercially available inulin-type fructans to limit disease symptoms caused by Botrytis cinerea in lettuce. Spraying mature lettuce leaves, with inulin-type fructans derived from burdock or chicory was as effective in reducing grey mold disease symptoms caused by Botrytis cinerea as spraying with oligogalacturonides (OGs). OGs are well-known defense elicitors in several plant species. Spraying with inulin and OGs induced accumulation of hydrogen peroxide and levels further increased upon pathogen infection. Inulin and OGs were no longer able to limit Botrytis infection when plants were treated with the ethylene signaling inhibitor 1-methylcyclopropene (1-MCP), indicating that a functional ethylene signaling pathway is needed for the enhanced defense response. Soluble sugars accumulated in leaves primed with OGs, while 1-MCP treatment had an overall negative effect on the sucrose pool. Accumulation of γ-aminobutyric acid (GABA), a stress-associated non-proteinogenic amino acid and possible signaling compound, was observed in inulin-treated samples after infection and negatively affected by the 1-MCP treatment. We have demonstrated for the first time that commercially available inulin-type fructans and OGs can improve the defensive capacity of lettuce, an economically important species. We discuss our results in the context of a possible recognition of fructans as Damage or Microbe Associated Molecular Patterns.
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Affiliation(s)
- Łukasz Paweł Tarkowski
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium.
| | - Bram Van de Poel
- Laboratory of Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium.
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, UGhent, 9000 Ghent, Belgium.
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium.
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