1
|
Clairet C, Gay EJ, Porquier A, Blaise F, Marais CL, Balesdent MH, Rouxel T, Soyer JL, Fudal I. Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-player game. THE NEW PHYTOLOGIST 2024; 242:247-261. [PMID: 38358035 DOI: 10.1111/nph.19581] [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: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Effector genes, encoding molecules involved in disease establishment, are concertedly expressed throughout the lifecycle of plant-pathogenic fungi. However, little is known about how effector gene expression is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in their regulation was recently investigated, notably establishing that the repressive histone modification H3K9me3, deposited by KMT1, was involved in several fungal species including Leptosphaeria maculans. Nevertheless, previous data suggest that a second regulatory layer, probably involving a specific transcription factor (TF), might be required. In L. maculans, a Dothideomycete causing stem canker of oilseed rape, we identified the ortholog of Pf2, a TF belonging to the Zn2Cys6 fungal-specific family, and described as essential for pathogenicity and effector gene expression. We investigated its role together with KMT1, by inactivating and over-expressing LmPf2 in a wild-type strain and a ∆kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis and we found a major effect of LmPf2 on the induction of effector gene expression once KMT1 repression is lifted. Our results show, for the first time, a dual control of effector gene expression.
Collapse
Affiliation(s)
- Colin Clairet
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Antoine Porquier
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| |
Collapse
|
2
|
Suarez-Fernandez M, Álvarez-Aragón R, Pastor-Mediavilla A, Maestre-Guillén A, del Olmo I, De Francesco A, Meile L, Sánchez-Vallet A. Sas3-mediated histone acetylation regulates effector gene activation in a fungal plant pathogen. mBio 2023; 14:e0138623. [PMID: 37642412 PMCID: PMC10653901 DOI: 10.1128/mbio.01386-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE Pathogen infections require the production of effectors that enable host colonization. Effectors have diverse functions and are only expressed at certain stages of the infection cycle. Thus, effector genes are tightly regulated by several mechanisms, including chromatin remodeling. Here, we investigate the role of histone acetylation in effector gene activation in the fungal wheat pathogen Zymoseptoria tritici. We demonstrate that lysine acetyltransferases (KATs) are essential for the spatiotemporal regulation of effector genes. We show that the KAT Sas3 is involved in leaf symptom development and pycnidia formation. Importantly, our results indicate that Sas3 controls histone acetylation of effector loci and is a regulator of effector gene activation during stomatal penetration. Overall, our work demonstrates the key role of histone acetylation in regulating gene expression associated with plant infection.
Collapse
Affiliation(s)
- Marta Suarez-Fernandez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
| | - Rocio Álvarez-Aragón
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ana Pastor-Mediavilla
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alejandro Maestre-Guillén
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ivan del Olmo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Agustina De Francesco
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lukas Meile
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Andrea Sánchez-Vallet
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| |
Collapse
|
3
|
Vigneaud J, Kohler A, Sow MD, Delaunay A, Fauchery L, Guinet F, Daviaud C, Barry KW, Keymanesh K, Johnson J, Singan V, Grigoriev I, Fichot R, Conde D, Perales M, Tost J, Martin FM, Allona I, Strauss SH, Veneault-Fourrey C, Maury S. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. THE NEW PHYTOLOGIST 2023; 238:2561-2577. [PMID: 36807327 DOI: 10.1111/nph.18734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.
Collapse
Affiliation(s)
- Julien Vigneaud
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Annegret Kohler
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Mamadou Dia Sow
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Laure Fauchery
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Frederic Guinet
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Kerrie W Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Francis M Martin
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| |
Collapse
|
4
|
Hassanaly-Goulamhoussen R, De Carvalho Augusto R, Marteu-Garello N, Péré A, Favery B, Da Rocha M, Danchin EGJ, Abad P, Grunau C, Perfus-Barbeoch L. Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita. Front Cell Dev Biol 2021; 9:765690. [PMID: 34938734 PMCID: PMC8685519 DOI: 10.3389/fcell.2021.765690] [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: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.
Collapse
Affiliation(s)
| | - Ronaldo De Carvalho Augusto
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | | | - Arthur Péré
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Bruno Favery
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Martine Da Rocha
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | | | - Pierre Abad
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France
| | | |
Collapse
|
5
|
Pimentel D, Amaro R, Erban A, Mauri N, Soares F, Rego C, Martínez-Zapater JM, Mithöfer A, Kopka J, Fortes AM. Transcriptional, hormonal, and metabolic changes in susceptible grape berries under powdery mildew infection. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6544-6569. [PMID: 34106234 DOI: 10.1093/jxb/erab258] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Grapevine (Vitis vinifera) berries are extremely sensitive to infection by the biotrophic pathogen Erysiphe necator, causing powdery mildew disease with deleterious effects on grape and wine quality. The combined analysis of the transcriptome and metabolome associated with this common fungal infection has not been previously carried out in any fruit. In order to identify the molecular, hormonal, and metabolic mechanisms associated with infection, healthy and naturally infected V. vinifera cv. Carignan berries were collected at two developmental stages: late green (EL33) and early véraison (EL35). RNA sequencing combined with GC-electron impact ionization time-of-flight MS, GC-electron impact ionization/quadrupole MS, and LC-tandem MS analyses revealed that powdery mildew-susceptible grape berries were able to activate defensive mechanisms with the involvement of salicylic acid and jasmonates and to accumulate defense-associated metabolites (e.g. phenylpropanoids, fatty acids). The defensive strategies also indicated organ-specific responses, namely the activation of fatty acid biosynthesis. However, defense responses were not enough to restrict fungal growth. The fungal metabolic program during infection involves secretion of effectors related to effector-triggered susceptibility, carbohydrate-active enzymes and activation of sugar, fatty acid, and nitrogen uptake, and could be under epigenetic regulation. This study also identified potential metabolic biomarkers such as gallic, eicosanoic, and docosanoic acids and resveratrol, which can be used to monitor early stages of infection.
Collapse
Affiliation(s)
- Diana Pimentel
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rute Amaro
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Nuria Mauri
- Instituto de Ciencias de la Vid y del Vino, CSIC-UR-Gobierno de La Rioja, Ctra. de Burgos km 6, 26007 Logroño, Spain
| | - Flávio Soares
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Cecília Rego
- Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - José M Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, CSIC-UR-Gobierno de La Rioja, Ctra. de Burgos km 6, 26007 Logroño, Spain
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max-Planck-Institute for Chemical Ecology, 07745 Jena, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Ana Margarida Fortes
- BioISI - Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| |
Collapse
|
6
|
Soyer JL, Clairet C, Gay EJ, Lapalu N, Rouxel T, Stukenbrock EH, Fudal I. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. Chromosome Res 2021; 29:219-236. [PMID: 34018080 PMCID: PMC8159818 DOI: 10.1007/s10577-021-09658-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.
Collapse
Affiliation(s)
- Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Colin Clairet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| |
Collapse
|
7
|
Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T, Balesdent MH. Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. BMC Biol 2021; 19:55. [PMID: 33757516 PMCID: PMC7986464 DOI: 10.1186/s12915-021-00989-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of "two-speed" genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. RESULTS We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. CONCLUSION This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.
Collapse
Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Juliette Linglin
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Levrel
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Jocelyne Lemoine
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Regine Delourme
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
| |
Collapse
|
8
|
Meile L, Peter J, Puccetti G, Alassimone J, McDonald BA, Sánchez-Vallet A. Chromatin Dynamics Contribute to the Spatiotemporal Expression Pattern of Virulence Genes in a Fungal Plant Pathogen. mBio 2020; 11:e02343-20. [PMID: 33024042 PMCID: PMC7542367 DOI: 10.1128/mbio.02343-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022] Open
Abstract
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.IMPORTANCE 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.
Collapse
Affiliation(s)
- Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Jules Peter
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Guido Puccetti
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Julien Alassimone
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón (Madrid), Spain
| |
Collapse
|
9
|
Perrone A, Martinelli F. Plant stress biology in epigenomic era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110376. [PMID: 32234231 DOI: 10.1016/j.plantsci.2019.110376] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/07/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
Recent progress in "omics" methodologies allow us to gain insight into the complex molecular regulatory networks underlying plant responses to environmental stresses. Among the different genome-wide analysis, epigenomics is the most under-investigated "omic" approach requiring more critical and speculative discussion about approaches, methods and experimental designs. Epigenomics allows us to gain insight into the molecular adaptation of plants in response to environmental stresses. The identification of epigenetic marks transmitted during filial generations enables new theories to be developed on the evolution of living organisms in relation to environmental changes. The molecular mechanisms driving the capacity of plants to memorize a stress and to generate stress-resistant progenies are still unclear and scarcely investigated. The elucidation of these cryptic molecular switches will assist breeders in designing crops characterized by minimally compromised productivity in relation to stresses caused by climate change. The aim of this review is to briefly describe the most uptodate epigenomic approaches, update recent progresses in crop epigenomics in plant stress biology, and to stimulate the discussion of new epigenomic methods and approaches in the new era of "omic" sciences.
Collapse
Affiliation(s)
- Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, 90128, Italy.
| | - Federico Martinelli
- Department of Biology, University of Firenze, Sesto Fiorentino, Florence, 50019, Italy.
| |
Collapse
|
10
|
Wang Q, Sun M, Zhang Y, Song Z, Zhang S, Zhang Q, Xu J, Liu H. Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi. MOLECULAR PLANT PATHOLOGY 2020; 21:330-348. [PMID: 31916390 PMCID: PMC7036362 DOI: 10.1111/mpp.12899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/06/2019] [Accepted: 11/28/2019] [Indexed: 05/11/2023]
Abstract
The basal ascomycetes in genus Taphrina have strict host specificity and coevolution with their host plants, making them appealing models for studying the genomic basis of ecological divergence and host adaption. We therefore performed genome sequencing and comparative genomics of different Taphrina species with distinct host ranges to reveal their evolution. We identified frequent chromosomal rearrangements and highly dynamic lineage-specific (LS) genomic regions in Taphrina genomes. The LS regions occur at the flanking regions of chromosomal breakpoints, and are greatly enriched for DNA repeats, non-core genes, and in planta up-regulated genes. Furthermore, we identified hundreds of candidate secreted effector proteins (CSEPs) that are commonly organized in gene clusters that form distinct AT-rich isochore-like regions. Nearly half of the CSEPs constitute two novel superfamilies with modular structures unique to Taphrina. These CSEPs are commonly up-regulated during infection, enriched in the LS regions, evolved faster, and underwent extensive gene gain and loss in different species. In addition to displaying signatures of positive selection, functional characterization of selected CSEP genes confirmed their roles in suppression of plant defence responses. Overall, our results showed that extensive chromosomal rearrangements and rapidly evolving CSEP superfamilies play important roles in speciation and host adaptation in the early-branching ascomycetous fungi.
Collapse
Affiliation(s)
- Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yimei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Zhenzhen Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Qiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jin‐Rong Xu
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Ruud AK, Dieseth JA, Ficke A, Furuki E, Phan HTT, Oliver RP, Tan KC, Lillemo M. Genome-Wide Association Mapping of Resistance to Septoria Nodorum Leaf Blotch in a Nordic Spring Wheat Collection. THE PLANT GENOME 2019; 12:1-15. [PMID: 33016591 DOI: 10.3835/plantgenome2018.12.0105] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/06/2019] [Indexed: 05/12/2023]
Abstract
First genome-wide association mapping of adult plant Septoria nodorum blotch resistance. Some adult plant resistance loci were shared with seedling resistance loci. Other adult plant resistance loci were significant across environments. Resistant haplotypes were identified, which can be used for breeding. Parastagonospora nodorum is the causal agent of Septoria nodorum leaf blotch (SNB) in wheat (Triticum aestivum L.). It is the most important leaf blotch pathogen in Norwegian spring wheat. Several quantitative trait loci (QTL) for SNB susceptibility have been identified. Some of these QTL are the result of underlying gene-for-gene interactions involving necrotrophic effectors (NEs) and corresponding sensitivity (Snn) genes. A collection of diverse spring wheat lines was evaluated for SNB resistance and susceptibility over seven growing seasons in the field. In addition, wheat seedlings were inoculated and infiltrated with culture filtrates (CFs) from four single spore isolates and infiltrated with semipurified NEs (SnToxA, SnTox1, and SnTox3) under greenhouse conditions. In adult plants, the most stable SNB resistance QTL were located on chromosomes 2B, 2D, 4A, 4B, 5A, 6B, 7A, and 7B. The QTL on chromosome 2D was effective most years in the field. At the seedling stage, the most significant QTL after inoculation were located on chromosomes 1A, 1B, 3A, 4B, 5B, 6B, 7A, and 7B. The QTL on chromosomes 3A and 6B were significant both after inoculation and CF infiltration, indicating the presence of novel NE-Snn interactions. The QTL on chromosomes 4B and 7A were significant in both seedlings and adult plants. Correlations between SnToxA sensitivity and disease severity in the field were significant. To our knowledge, this is the first genome-wide association mapping study (GWAS) to investigate SNB resistance at the adult plant stage under field conditions.
Collapse
Affiliation(s)
- Anja Karine Ruud
- Dep. of Plant Sciences, Norwegian Univ. of Life Sciences, Post Box 5003, NO-1432, ÅS, Norway
- Faculty of Science and Technology, Dep. of Molecular Biology and Genetics, Aarhus Univ, 4200, Slagelse, Denmark
| | - Jon Arne Dieseth
- Graminor, AS, Bjørke Gård, Hommelstadvegen 60, NO-2322, Ridabu, Norway
| | - Andrea Ficke
- Division of Biotechnology and Plant Health, Norwegian Inst. of Bioeconomy Research, P.O. Box 115, NO-1431, ÅS, Norway
| | - Eiko Furuki
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Huyen T T Phan
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, Dep. of Environment & Agriculture, Curtin Univ., Bentley, Western Australia, Australia
| | - Morten Lillemo
- Dep. of Plant Sciences, Norwegian Univ. of Life Sciences, Post Box 5003, NO-1432, ÅS, Norway
| |
Collapse
|
13
|
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: 36] [Impact Index Per Article: 7.2] [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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| | | |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
Collapse
|
18
|
Wang Q, Jiang C, Wang C, Chen C, Xu JR, Liu H. Characterization of the Two-Speed Subgenomes of Fusarium graminearum Reveals the Fast-Speed Subgenome Specialized for Adaption and Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:140. [PMID: 28261228 PMCID: PMC5306128 DOI: 10.3389/fpls.2017.00140] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/23/2017] [Indexed: 05/05/2023]
Abstract
Fusarium head blight, caused by Fusarium graminearum, is one of the most severe diseases on wheat and barley worldwide. Although the genomic data of several strains were published, the intragenomic variation of F. graminearum was not well characterized. Here, we sequenced three Chinese strains and conducted genome-wide comparisons. Our data revealed that all the sequenced strains were distinct from each other and over 350 genes were functionally lost in each of them. Variants of each strain were unevenly distributed in a highly conserved pattern along the chromosomes, resulting in a conserved two-speed genome. The fast subgenome has a lower GC content, shorter gene length, and higher variation of exon numbers than the slow subgenome. Genes related to interaction and pathogenicity, under positive selection, and up-regulated in planta were all significantly enriched in the fast subgenome. Furthermore, we found that the fast subgenome coincided with facultative heterochromatin regions that were repressed in vegetative stage but activated during infection as measured by RNA-seq and ChIP-seq data, suggesting that the fast subgenome is epigenetically regulated. Taken together, our data demonstrated that F. graminearum has a highly conserved two-speed genome and the fast subgenome responsible for adaption and infection is under the control of heterochromatin.
Collapse
Affiliation(s)
- Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Chenfang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- Department of Botany and Plant Pathology, Purdue University, West LafayetteIN, USA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Huiquan Liu,
| |
Collapse
|
19
|
Willbanks A, Leary M, Greenshields M, Tyminski C, Heerboth S, Lapinska K, Haskins K, Sarkar S. The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences. GENETICS & EPIGENETICS 2016; 8:25-36. [PMID: 27512339 PMCID: PMC4973776 DOI: 10.4137/geg.s31863] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/03/2016] [Accepted: 07/06/2016] [Indexed: 12/11/2022]
Abstract
The evolution process includes genetic alterations that started with prokaryotes and now continues in humans. A distinct difference between prokaryotic chromosomes and eukaryotic chromosomes involves histones. As evolution progressed, genetic alterations accumulated and a mechanism for gene selection developed. It was as if nature was experimenting to optimally utilize the gene pool without changing individual gene sequences. This mechanism is called epigenetics, as it is above the genome. Curiously, the mechanism of epigenetic regulation in prokaryotes is strikingly different from that in eukaryotes, mainly higher eukaryotes, like mammals. In fact, epigenetics plays a significant role in the conserved process of embryogenesis and human development. Malfunction of epigenetic regulation results in many types of undesirable effects, including cardiovascular disease, metabolic disorders, autoimmune diseases, and cancer. This review provides a comparative analysis and new insights into these aspects.
Collapse
Affiliation(s)
- Amber Willbanks
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Meghan Leary
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Molly Greenshields
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Camila Tyminski
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sarah Heerboth
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Karolina Lapinska
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Kathryn Haskins
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sibaji Sarkar
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.; Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
20
|
Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, Thomma BPHJ. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res 2016; 26:1091-100. [PMID: 27325116 PMCID: PMC4971763 DOI: 10.1101/gr.204974.116] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.
Collapse
Affiliation(s)
- Luigi Faino
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Marc Pauper
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | | | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| |
Collapse
|