1
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van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E, Chavarro-Carrero E, Meijer HJG, Feurtey A, Maryani N, Ordóñez N, Schneiders H, Nijbroek K, Wittenberg AHJ, Hofstede R, García-Bastidas F, Sørensen A, Swennen R, Drenth A, Stukenbrock EH, Kema GHJ, Seidl MF. Segmental duplications drive the evolution of accessory regions in a major crop pathogen. THE NEW PHYTOLOGIST 2024; 242:610-625. [PMID: 38402521 DOI: 10.1111/nph.19604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Abstract
Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.
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Affiliation(s)
- Anouk C van Westerhoven
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Carolina Aguilera-Galvez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Giuliana Nakasato-Tagami
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Einar Martinez de la Parte
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Edgar Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department Biointeractions and Plant Health, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Alice Feurtey
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
- Plant Pathology, Eidgenössische Technische Hochschule Zürich, Rämistrasse 101, 8092, Zürich, Switzerland
| | - Nani Maryani
- Biology Education, Universitas Sultan Ageng Tirtayasa, Jalan Raya Palka No.Km 3, 42163, Banten, Indonesia
| | - Nadia Ordóñez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harrie Schneiders
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Koen Nijbroek
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Rene Hofstede
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Anker Sørensen
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Ronny Swennen
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Catholic University of Leuven, Oude Markt 13, 3000, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15 Naguru E Rd, Kampala, PO Box 7878, Uganda
| | - Andre Drenth
- The University of Queensland, St Lucia, 4072, Brisbane, Queensland, Australia
| | - Eva H Stukenbrock
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Michael F Seidl
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
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2
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Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
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Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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3
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Bazzicalupo A. Local adaptation in fungi. FEMS Microbiol Rev 2022; 46:6604384. [PMID: 35675293 DOI: 10.1093/femsre/fuac026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
In this review, I explore the pervasive but underappreciated role of local adaptation in fungi. It has been difficult historically to study local adaptation in fungi because of the limited understanding of fungal species and their traits, but new hope has been offered with technological advances in sequencing. The filamentous nature of fungi invalidates some assumptions made in evolution because of their ability to exist as multinucleate entities with genetically different nuclei sharing the same cytoplasm. Many insights on local adaptation have come from studying fungi, and much of the empirical evidence gathered about local adaptation in the context of host-pathogen interactions comes from studying fungal virulence genes, drug resistance, and environmental adaptation. Together, these insights paint a picture of the variety of processes involved in fungal local adaptation and their connections to the unusual cell biology of Fungi (multinucleate, filamentous habit), but there is much that remains unknown, with major gaps in our knowledge of fungal species, their phenotypes, and the ways by which they adapt to local conditions.
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Affiliation(s)
- Anna Bazzicalupo
- Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., Vancouver V6T 1Z4, Canada
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4
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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5
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Kashiwa T, Suzuki T. High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii. G3 (BETHESDA, MD.) 2021; 11:jkab277. [PMID: 34568928 PMCID: PMC8496228 DOI: 10.1093/g3journal/jkab277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022]
Abstract
Plant diseases caused by the Cercospora genus of ascomycete fungi are a major concern for commercial agricultural practices. Several Cercospora species can affect soybeans, such as Cercospora kikuchii which causes soybean leaf blight. Speciation in Cercospora on soybean has not been adequately studied. Some cryptic groups of Cercospora also cause diseases on soybean. Moreover, it has been known C. kikuchii population genetic structure is different between countries. Consequently, further genomic information could help to elucidate the covert differentiation of Cercospora diseases in soybean. Here, we report for the first time, a chromosome-level genome assembly for C. kikuchii. The genome assembly of 9 contigs was 34.44 Mb and the N50 was 4.19 Mb. Based on ab initio gene prediction, several candidates for pathogenicity-related genes, including 242 genes for putative effectors, 55 secondary metabolite gene clusters, and 399 carbohydrate-active enzyme genes were identified. The genome sequence and the features described in this study provide a solid foundation for comparative and evolutionary genomic analysis for Cercospora species that cause soybean diseases worldwide.
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Affiliation(s)
- Takeshi Kashiwa
- Biological Resources and Post-harvest Division, Japan International Research
Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686,
Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya
University, Utsunomiya, Tochigi 321-8505, Japan
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6
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Torres DE, Thomma BPHJ, Seidl MF. Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae. Genome Biol Evol 2021; 13:evab135. [PMID: 34100895 PMCID: PMC8290119 DOI: 10.1093/gbe/evab135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, University of Cologne, Germany
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
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7
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Zhu Q, Chen L, Chen T, Xu Q, He T, Wang Y, Deng X, Zhang S, Pan Y, Jin A. Integrated transcriptome and metabolome analyses of biochar-induced pathways in response to Fusarium wilt infestation in pepper. Genomics 2021; 113:2085-2095. [PMID: 33895283 DOI: 10.1016/j.ygeno.2021.04.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/13/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022]
Abstract
The present study used soils contaminated with Fusarium oxysporum f. sp. capsici (CCS) and CCS amended with bamboo biochar (CCS + BC) to grow the pepper variety Qujiao No.1. The physiological performance, and transcriptome and metabolome profiling in leaf (L) and fruit (F) of Qujiao No.1 were conducted. Application of biochar improved soil properties, pepper plant nutrition and increased activities of enzymes related to pest/disease resistance, leading to superior physiological performance and lesser F. wilt disease incidence than plants from CCS. Most of the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were involved in protein processing in endoplasmic reticulum (fruit), plant pathogen interaction (fruit), photosynthesis (leaf), phenylpropanoid biosynthesis (both tissues) and metabolic pathways (both tissues). Biochar improved plant photosynthesis, enhanced the immune system, energy production and increased stress signaling pathways. Overall, our results provide evidence of a number of pathways induced by biochar in pepper regulating its response to F. wilt disease.
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Affiliation(s)
- Qianggen Zhu
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Limin Chen
- Integrated Plant Protection Center, Lishui Academy of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui, Zhejiang 323000, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agricultural and Forestry University, Fuzhou 350002, China
| | - Tingting Chen
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Qian Xu
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Tianjun He
- Integrated Plant Protection Center, Lishui Academy of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui, Zhejiang 323000, China
| | - Yikun Wang
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Xianjun Deng
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Sihai Zhang
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China
| | - Yiming Pan
- Integrated Plant Protection Center, Lishui Academy of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui, Zhejiang 323000, China
| | - Aiwu Jin
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China; Integrated Plant Protection Center, Lishui Academy of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui, Zhejiang 323000, China.
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8
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Local Rather than Global H3K27me3 Dynamics Are Associated with Differential Gene Expression in Verticillium dahliae. mBio 2021; 13:e0356621. [PMID: 35130723 PMCID: PMC8822345 DOI: 10.1128/mbio.03566-21] [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] [Indexed: 01/16/2023] Open
Abstract
Differential growth conditions typically trigger global transcriptional responses in filamentous fungi. Such fungal responses to environmental cues involve epigenetic regulation, including chemical histone modifications. It has been proposed that conditionally expressed genes, such as those that encode secondary metabolites but also effectors in pathogenic species, are often associated with a specific histone modification, lysine27 methylation of H3 (H3K27me3). However, thus far, no analyses on the global H3K27me3 profiles have been reported under differential growth conditions in order to assess if H3K27me3 dynamics govern differential transcription. Using chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing data from the plant-pathogenic fungus Verticillium dahliae grown in three in vitro cultivation media, we now show that a substantial number of the identified H3K27me3 domains globally display stable profiles among these growth conditions. However, we observe local quantitative differences in H3K27me3 ChIP-seq signals that are associated with a subset of differentially transcribed genes between media. Comparing the in vitro results to expression during plant infection suggests that in planta-induced genes may require chromatin remodeling to achieve expression. Overall, our results demonstrate that some loci display H3K27me3 dynamics associated with concomitant transcriptional variation, but many differentially expressed genes are associated with stable H3K27me3 domains. Thus, we conclude that while H3K27me3 is required for transcriptional repression, it does not appear that transcriptional activation requires the global erasure of H3K27me3. We propose that the H3K27me3 domains that do not undergo dynamic methylation may contribute to transcription through other mechanisms or may serve additional genomic regulatory functions. IMPORTANCE In many organisms, including filamentous fungi, epigenetic mechanisms that involve chemical and physical modifications of DNA without changing the genetic sequence have been implicated in transcriptional responses upon developmental or environmental cues. In fungi, facultative heterochromatin that can decondense to allow transcription in response to developmental changes or environmental stimuli is characterized by the trimethylation of lysine 27 on histone H3 (H3K27me3), and H3K27me3 has been implicated in transcriptional regulation, although the precise mechanisms and functions remain enigmatic. Based on ChIP and RNA sequencing data, we show for the soilborne broad-host-range vascular wilt plant-pathogenic fungus Verticillium dahliae that although some loci display H3K27me3 dynamics that can contribute to transcriptional variation, other loci do not show such a dependence. Thus, although we recognize that H3K27me3 is required for transcriptional repression, we also conclude that this mark is not a conditionally responsive global regulator of differential transcription upon responses to environmental cues.
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9
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Zhang W, Huang J, Cook DE. Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae. PLoS Genet 2021; 17:e1009376. [PMID: 33534835 PMCID: PMC7886369 DOI: 10.1371/journal.pgen.1009376] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/16/2021] [Accepted: 01/22/2021] [Indexed: 12/03/2022] Open
Abstract
Transcriptional dynamic in response to environmental and developmental cues are fundamental to biology, yet many mechanistic aspects are poorly understood. One such example is fungal plant pathogens, which use secreted proteins and small molecules, termed effectors, to suppress host immunity and promote colonization. Effectors are highly expressed in planta but remain transcriptionally repressed ex planta, but our mechanistic understanding of these transcriptional dynamics remains limited. We tested the hypothesis that repressive histone modification at H3-Lys27 underlies transcriptional silencing ex planta, and that exchange for an active chemical modification contributes to transcription of in planta induced genes. Using genetics, chromatin immunoprecipitation and sequencing and RNA-sequencing, we determined that H3K27me3 provides significant local transcriptional repression. We detail how regions that lose H3K27me3 gain H3K27ac, and these changes are associated with increased transcription. Importantly, we observed that many in planta induced genes were marked by H3K27me3 during axenic growth, and detail how altered H3K27 modification influences transcription. ChIP-qPCR during in planta growth suggests that H3K27 modifications are generally stable, but can undergo dynamics at specific genomic locations. Our results support the hypothesis that dynamic histone modifications at H3K27 contributes to fungal genome regulation and specifically contributes to regulation of genes important during host infection. Fungal pathogens of crops and humans pose annual threats to our food and health. There are many steps to the host infection process, during which fungal pathogens display unique growth, and use specific genes to cause disease. Despite this knowledge, many aspects of how pathogens regulate their genome to enact this process remain unknown. Here, we demonstrate how chemical modification of lysine residues on the histone H3, which helps organize and control DNA usage, play an important regulatory role in the model fungal pathogen causing rice blast disease. Our analysis shows a significant association between genes important for host infection and H3 lysine 27 methylation. We show that by experimentally changing histone modifications, many fungal genes normally used during plant infection are turned on outside of the host. Furthermore, we detail how histone modifications can change naturally in the fungus during plant infection. These findings help broaden our knowledge of genome regulation for these pathogens, and advances the goal of a more comprehensive understanding of the infection process.
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Affiliation(s)
- Wei Zhang
- Kansas State University, Department of Plant Pathology, Manhattan, Kansas, United States of America
| | - Jun Huang
- Kansas State University, Department of Plant Pathology, Manhattan, Kansas, United States of America
| | - David E. Cook
- Kansas State University, Department of Plant Pathology, Manhattan, Kansas, United States of America
- * E-mail:
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10
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Chen H, Raffaele S, Dong S. Silent control: microbial plant pathogens evade host immunity without coding sequence changes. FEMS Microbiol Rev 2021; 45:6095737. [PMID: 33440001 DOI: 10.1093/femsre/fuab002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Both animals and plants have evolved a robust immune system to surveil and defeat invading pathogenic microbes. Evasion of host immune surveillance is the key for pathogens to initiate successful infection. To evade the host immunity, plant pathogens evolved a variety of strategies such as masking themselves from host immune recognitions, blocking immune signaling transductions, reprogramming immune responses and adapting to immune microenvironmental changes. Gain of new virulence genes, sequence and structural variations enables plant pathogens to evade host immunity through changes in the genetic code. However, recent discoveries demonstrated that variations at the transcriptional, post-transcriptional, post-translational and glycome level enable pathogens to cope with the host immune system without coding sequence changes. The biochemical modification of pathogen associated molecular patterns and silencing of effector genes emerged as potent ways for pathogens to hide from host recognition. Altered processing in mRNA activities provide pathogens with resilience to microenvironment changes. Importantly, these hiding variants are directly or indirectly modulated by catalytic enzymes or enzymatic complexes and cannot be revealed by classical genomics alone. Unveiling these novel host evasion mechanisms in plant pathogens enables us to better understand the nature of plant disease and pinpoints strategies for rational diseases management in global food protection.
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Affiliation(s)
- Han Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, 24 Chemin de Borde Rouge - Auzeville, CS52627, F31326 Castanet Tolosan Cedex, France
| | - Suomeng Dong
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
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11
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Cook DE, Kramer HM, Torres DE, Seidl MF, Thomma BPHJ. A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen. eLife 2020; 9:e62208. [PMID: 33337321 PMCID: PMC7781603 DOI: 10.7554/elife.62208] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Genomes store information at scales beyond the linear nucleotide sequence, which impacts genome function at the level of an individual, while influences on populations and long-term genome function remains unclear. Here, we addressed how physical and chemical DNA characteristics influence genome evolution in the plant pathogenic fungus Verticillium dahliae. We identified incomplete DNA methylation of repetitive elements, associated with specific genomic compartments originally defined as Lineage-Specific (LS) regions that contain genes involved in host adaptation. Further chromatin characterization revealed associations with features such as H3 Lys-27 methylated histones (H3K27me3) and accessible DNA. Machine learning trained on chromatin data identified twice as much LS DNA as previously recognized, which was validated through orthogonal analysis, and we propose to refer to this DNA as adaptive genomic regions. Our results provide evidence that specific chromatin profiles define adaptive genomic regions, and highlight how different epigenetic factors contribute to the organization of these regions.
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Affiliation(s)
- David E Cook
- Department of Plant Pathology, Kansas State UniversityManhattanUnited States
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
| | - David E Torres
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht UniversityUtrechtNetherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht UniversityUtrechtNetherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & ResearchWageningenNetherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
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12
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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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Torres DE, Oggenfuss U, Croll D, Seidl MF. Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Leonard M, Kühn A, Harting R, Maurus I, Nagel A, Starke J, Kusch H, Valerius O, Feussner K, Feussner I, Kaever A, Landesfeind M, Morgenstern B, Becher D, Hecker M, Braus-Stromeyer SA, Kronstad JW, Braus GH. Verticillium longisporum Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments. Front Microbiol 2020; 11:1876. [PMID: 32849460 PMCID: PMC7423881 DOI: 10.3389/fmicb.2020.01876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Verticillia cause a vascular wilt disease affecting a broad range of economically valuable crops. The fungus enters its host plants through the roots and colonizes the vascular system. It requires extracellular proteins for a successful plant colonization. The exoproteomes of the allodiploid Verticillium longisporum upon cultivation in different media or xylem sap extracted from its host plant Brassica napus were compared. Secreted fungal proteins were identified by label free liquid chromatography-tandem mass spectrometry screening. V. longisporum induced two main secretion patterns. One response pattern was elicited in various non-plant related environments. The second pattern includes the exoprotein responses to the plant-related media, pectin-rich simulated xylem medium and pure xylem sap, which exhibited similar but additional distinct features. These exoproteomes include a shared core set of 221 secreted and similarly enriched fungal proteins. The pectin-rich medium significantly induced the secretion of 143 proteins including a number of pectin degrading enzymes, whereas xylem sap triggered a smaller but unique fungal exoproteome pattern with 32 enriched proteins. The latter pattern included proteins with domains of known pathogenicity factors, metallopeptidases and carbohydrate-active enzymes. The most abundant proteins of these different groups are the necrosis and ethylene inducing-like proteins Nlp2 and Nlp3, the cerato-platanin proteins Cp1 and Cp2, the metallopeptidases Mep1 and Mep2 and the carbohydrate-active enzymes Gla1, Amy1 and Cbd1. Their pathogenicity contribution was analyzed in the haploid parental strain V. dahliae. Deletion of the majority of the corresponding genes caused no phenotypic changes during ex planta growth or invasion and colonization of tomato plants. However, we discovered that the MEP1, NLP2, and NLP3 deletion strains were compromised in plant infections. Overall, our exoproteome approach revealed that the fungus induces specific secretion responses in different environments. The fungus has a general response to non-plant related media whereas it is able to fine-tune its exoproteome in the presence of plant material. Importantly, the xylem sap-specific exoproteome pinpointed Nlp2 and Nlp3 as single effectors required for successful V. dahliae colonization.
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Affiliation(s)
- Miriam Leonard
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anika Kühn
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rebekka Harting
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Isabel Maurus
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Alexandra Nagel
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Jessica Starke
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Kirstin Feussner
- Department for Plant Biochemistry, Göttingen Center for Molecular Biosciences, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Ivo Feussner
- Department for Plant Biochemistry, Göttingen Center for Molecular Biosciences, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Alexander Kaever
- Department of Bioinformatics, Göttingen Center for Molecular Biosciences, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Manuel Landesfeind
- Department of Bioinformatics, Göttingen Center for Molecular Biosciences, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Burkhard Morgenstern
- Department of Bioinformatics, Göttingen Center for Molecular Biosciences, Institute for Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Dörte Becher
- Department Microbial Proteomics, Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Michael Hecker
- Department of Microbial Physiology, Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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Depotter JRL, Shi-Kunne X, Missonnier H, Liu T, Faino L, van den Berg GCM, Wood TA, Zhang B, Jacques A, Seidl MF, Thomma BPHJ. Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation. Mol Ecol 2019; 28:3482-3495. [PMID: 31282048 PMCID: PMC6771948 DOI: 10.1111/mec.15168] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/23/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two‐speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so‐called lineage‐specific regions, that are enriched in in planta‐induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage‐specific regions and the core genome. Unanticipated, lineage‐specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage‐specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage‐specific regions of V. dahliae.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands.,Department of Crops and Agronomy, National Institute of Agricultural Botany, Cambridge, UK
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hélène Missonnier
- Département des Sciences Agronomiques et Agroalimentaires, Equipe Agrophysiologie et Agromolécules, Institut National Polytechnique de Toulouse - Ecole d'Ingénieurs de Purpan, Université de Toulouse, Toulouse, France
| | - Tingli Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Cambridge, UK
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Alban Jacques
- Département des Sciences Agronomiques et Agroalimentaires, Equipe Agrophysiologie et Agromolécules, Institut National Polytechnique de Toulouse - Ecole d'Ingénieurs de Purpan, Université de Toulouse, Toulouse, France
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
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Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens. Int J Mol Sci 2019; 20:ijms20143597. [PMID: 31340492 PMCID: PMC6679389 DOI: 10.3390/ijms20143597] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/18/2019] [Accepted: 06/25/2019] [Indexed: 01/08/2023] Open
Abstract
Transposable elements (TEs) are agents of genetic variability in phytopathogens as they are a source of adaptive evolution through genome diversification. Although many studies have uncovered information on TEs, the exact mechanism behind TE-induced changes within the genome remains poorly understood. Furthermore, convergent trends towards bigger genomes, emergence of novel genes and gain or loss of genes implicate a TE-regulated genome plasticity of fungal phytopathogens. TEs are able to alter gene expression by revamping the cis-regulatory elements or recruiting epigenetic control. Recent findings show that TEs recruit epigenetic control on the expression of effector genes as part of the coordinated infection strategy. In addition to genome plasticity and diversity, fungal pathogenicity is an area of economic concern. A survey of TE distribution suggests that their proximity to pathogenicity genes TEs may act as sites for emergence of novel pathogenicity factors via nucleotide changes and expansion or reduction of the gene family. Through a systematic survey of literature, we were able to conclude that the role of TEs in fungi is wide: ranging from genome plasticity, pathogenicity to adaptive behavior in evolution. This review also identifies the gaps in knowledge that requires further elucidation for a better understanding of TEs' contribution to genome architecture and versatility.
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Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
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Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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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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Kuźnicki D, Meller B, Arasimowicz-Jelonek M, Braszewska-Zalewska A, Drozda A, Floryszak-Wieczorek J. BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2019; 10:650. [PMID: 31214209 PMCID: PMC6554679 DOI: 10.3389/fpls.2019.00650] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC-mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network.
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Affiliation(s)
- Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Agnieszka Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Andżelika Drozda
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Jolanta Floryszak-Wieczorek
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
- *Correspondence: Jolanta Floryszak-Wieczorek,
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Chen H, Shu H, Wang L, Zhang F, Li X, Ochola SO, Mao F, Ma H, Ye W, Gu T, Jiang L, Wu Y, Wang Y, Kamoun S, Dong S. Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions. Genome Biol 2018; 19:181. [PMID: 30382931 PMCID: PMC6211444 DOI: 10.1186/s13059-018-1564-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Filamentous plant pathogen genomes often display a bipartite architecture with gene-sparse, repeat-rich compartments serving as a cradle for adaptive evolution. The extent to which this two-speed genome architecture is associated with genome-wide DNA modifications is unknown. RESULTS We show that the oomycetes Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine could not be detected in these species. Methylated DNA IP sequencing (MeDIP-seq) of each species reveals 6mA is depleted around the transcription start sites (TSSs) and is associated with lowly expressed genes, particularly transposable elements. Genes occupying the gene-sparse regions have higher levels of 6mA in both genomes, possibly implicating the methylome in adaptive evolution. All six putative adenine methyltransferases from P. infestans and P. sojae, except PsDAMT2, display robust enzymatic activities. Surprisingly, single knockouts in P. sojae significantly reduce in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the psdamt3 mutant reveals uneven 6mA methylation reduction across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Furthermore, transposable elements such as DNA elements are more active in the psdamt3 mutant. A large number of genes, particularly those from the adaptive genomic compartment, are differentially expressed. CONCLUSIONS Our findings provide evidence that 6mA modification is potentially an epigenetic mark in Phytophthora genomes, and complex patterns of 6mA methylation may be associated with adaptive evolution in these important plant pathogens.
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Affiliation(s)
- Han Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haidong Shu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liyuan Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fan Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | | | - Fei Mao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongyu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwu Ye
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Gu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lubin Jiang
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yufeng Wu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Suomeng Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
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Rao S, Sharda S, Oddi V, Nandineni MR. The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum. Front Microbiol 2018; 9:2367. [PMID: 30337918 PMCID: PMC6180176 DOI: 10.3389/fmicb.2018.02367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Saphy Sharda
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Möller M, Habig M, Freitag M, Stukenbrock EH. Extraordinary Genome Instability and Widespread Chromosome Rearrangements During Vegetative Growth. Genetics 2018; 210:517-529. [PMID: 30072376 PMCID: PMC6216587 DOI: 10.1534/genetics.118.301050] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/18/2018] [Indexed: 12/27/2022] Open
Abstract
The haploid genome of the pathogenic fungus Zymoseptoria tritici is contained on "core" and "accessory" chromosomes. While 13 core chromosomes are found in all strains, as many as eight accessory chromosomes show presence/absence variation and rearrangements among field isolates. The factors influencing these presence/absence polymorphisms are so far unknown. We investigated chromosome stability using experimental evolution, karyotyping, and genome sequencing. We report extremely high and variable rates of accessory chromosome loss during mitotic propagation in vitro and in planta Spontaneous chromosome loss was observed in 2 to >50% of cells during 4 weeks of incubation. Similar rates of chromosome loss in the closely related Zymoseptoria ardabiliae suggest that this extreme chromosome dynamic is a conserved phenomenon in the genus. Elevating the incubation temperature greatly increases instability of accessory and even core chromosomes, causing severe rearrangements involving telomere fusion and chromosome breakage. Chromosome losses do not affect the fitness of Zymoseptoria tritici in vitro, but some lead to increased virulence, suggesting an adaptive role of this extraordinary chromosome instability.
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Affiliation(s)
- Mareike Möller
- Environmental Genomics, Christian-Albrechts University, D-24118 Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, D-24306 Plön, Germany
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University, D-24118 Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, D-24306 Plön, Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, D-24118 Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, D-24306 Plön, Germany
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23
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Sánchez-Vallet A, Fouché S, Fudal I, Hartmann FE, Soyer JL, Tellier A, Croll D. The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:21-40. [PMID: 29768136 DOI: 10.1146/annurev-phyto-080516-035303] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification. The expression of many effectors converges on an epigenetic control mediated by the presence of repetitive elements. Population genomics analyses showed that rapidly evolving pathogens show high rates of turnover at effector loci and display a mosaic in effector presence-absence polymorphism among strains. We conclude that effective pathogen containment strategies require a thorough understanding of the effector genome biology and the pathogen's potential for rapid adaptation.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, AgroParisTech, Université Paris-Sud, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Jessica L Soyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, 85354 Freising, Germany
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland;
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24
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Krishnan P, Meile L, Plissonneau C, Ma X, Hartmann FE, Croll D, McDonald BA, Sánchez-Vallet A. Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat. BMC Biol 2018; 16:78. [PMID: 30012138 PMCID: PMC6047131 DOI: 10.1186/s12915-018-0543-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However, very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements, which can potentially contribute to gene expression regulation. In this work, we elucidated how transposable elements contribute to variation in melanin accumulation, a quantitative trait in fungi that affects survival under stressful conditions. RESULTS We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1, which controls expression of the genes in the melanin biosynthetic gene cluster, is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably, independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression, contributing to variation in melanin accumulation. CONCLUSIONS Our studies identified two levels of transcriptional control that regulate the synthesis of melanin. We propose that these regulatory mechanisms evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments.
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Affiliation(s)
- Parvathy Krishnan
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris Saclay, Orsay, France
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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25
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Rodriguez-Moreno L, Ebert MK, Bolton MD, Thomma BPHJ. Tools of the crook- infection strategies of fungal plant pathogens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:664-674. [PMID: 29277938 DOI: 10.1111/tpj.13810] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 05/14/2023]
Abstract
Fungi represent an ecologically diverse group of microorganisms that includes plant pathogenic species able to cause considerable yield loses in crop production systems worldwide. In order to establish compatible interactions with their hosts, pathogenic fungi rely on the secretion of molecules of diverse nature during host colonization to modulate host physiology, manipulate other environmental factors or provide self-defence. These molecules, collectively known as effectors, are typically small secreted cysteine-rich proteins, but may also comprise secondary metabolites and sRNAs. Here, we discuss the most common strategies that fungal plant pathogens employ to subvert their host plants in order to successfully complete their life cycle and secure the release of abundant viable progeny.
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Affiliation(s)
- Luis Rodriguez-Moreno
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Malaika K Ebert
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Melvin D Bolton
- USDA - Agricultural Research Service, Red River Valley Agricultural Research Center, Fargo, ND, USA
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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26
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Seidl MF, Thomma BPHJ. Transposable Elements Direct The Coevolution between Plants and Microbes. Trends Genet 2017; 33:842-851. [PMID: 28800915 DOI: 10.1016/j.tig.2017.07.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022]
Abstract
Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as 'selfish' genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host-microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a 'two-speed' genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Both authors contributed equally.
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27
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Oliva R, Quibod IL. Immunity and starvation: new opportunities to elevate disease resistance in crops. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:84-91. [PMID: 28505583 DOI: 10.1016/j.pbi.2017.04.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/27/2017] [Accepted: 04/30/2017] [Indexed: 05/18/2023]
Abstract
Plants use multiple mechanisms to defend themselves against invading microbes. Besides using their immune system to surveil and eliminate pathogens, plants actively block the pathogens' access to nutrients as an alternative way to prevent colonization. In this review, we focus on immunity and starvation as major obstacles for pathogens' adaptation. We summarize the key mechanisms employed by pathogens to modulate host immunity and to guarantee sugar uptake. In contrast to genes that deal with the immune system and show high levels of plasticity, pathogen genes involved in sugar acquisition are highly conserved, and may not have adapted to co-evolving interactions with the host. We propose a model to assess the durability of different control strategies based on the ability of pathogens to deal with host immunity or starvation. This analysis opens new opportunities to elevate disease resistance in crops by reducing the likelihood of pathogen adaptation.
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Affiliation(s)
- Ricardo Oliva
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.
| | - Ian Lorenzo Quibod
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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