1
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Griebel T, Lapin D, Locci F, Kracher B, Bautor J, Concia L, Benhamed M, Parker JE. Arabidopsis Topless-related 1 mitigates physiological damage and growth penalties of induced immunity. New Phytol 2023. [PMID: 37306028 DOI: 10.1111/nph.19054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
Transcriptional corepressors of the Topless (TPL) family regulate plant hormone and immunity signaling. The lack of a genome-wide profile of their chromatin associations limits understanding of the TPL family roles in transcriptional regulation. Chromatin immunoprecipitation with sequencing (ChIP-Seq) was performed on Arabidopsis thaliana lines expressing GFP-tagged Topless-related 1 (TPR1-GFP) with and without constitutive immunity via Enhanced Disease Susceptibility 1 (EDS1). RNA-Seq profiling of the TPR1-GFP lines and pathogen-infected tpl/tpr mutants, combined with measuring immunity, growth, and physiological parameters was employed to investigate TPL/TPR roles in immunity and defense homeostasis. TPR1 was enriched at promoter regions of c. 1400 genes and c. 10% of the detected binding required EDS1 immunity signaling. In a tpr1 tpl tpr4 (t3) mutant, resistance to bacteria was slightly compromised, and defense-related transcriptional reprogramming was weakly reduced or enhanced, respectively, at early (< 1 h) and late 24 h stages of bacterial infection. The t3 plants challenged with bacteria or pathogen-associated molecular pattern nlp24 displayed photosystem II dysfunctions. Also, t3 plants were hypersensitive to phytocytokine pep1 at the level of root growth inhibition. Transgenic expression of TPR1 rescued these t3 physiological defects. We propose that TPR1 and TPL family proteins function in Arabidopsis to reduce detrimental effects associated with activated transcriptional immunity.
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Affiliation(s)
- Thomas Griebel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Dahlem Centre of Plant Sciences, Plant Physiology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Dmitry Lapin
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Translational Plant Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Federica Locci
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Barbara Kracher
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 91405, Orsay, France
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), 40225, Düsseldorf, Germany
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2
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Hess JA, Eberhard ML, Segura-Lepe M, Grundner-Culemann K, Kracher B, Shryock J, Harrington J, Abraham D. A rodent model for Dirofilaria immitis, canine heartworm: parasite growth, development, and drug sensitivity in NSG mice. Sci Rep 2023; 13:976. [PMID: 36653420 PMCID: PMC9849205 DOI: 10.1038/s41598-023-27537-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
Heartworm disease, caused by Dirofilaria immitis, remains a significant threat to canines and felines. The development of parasites resistant to macrocyclic lactones (ML) has created a significant challenge to the control of the infection. The goal of this study was to determine if mice lacking a functional immune response would be susceptible to D. immitis. Immunodeficient NSG mice were susceptible to the infection, sustaining parasites for at least 15 weeks, with infective third-stage larvae molting and developing into the late fourth-stage larvae. Proteomic analysis of host responses to the infection revealed a complex pattern of changes after infection, with at least some of the responses directed at reducing immune control mechanisms that remain in NSG mice. NSG mice were infected with isolates of D. immitis that were either susceptible or resistant to MLs, as a population. The susceptible isolate was killed by ivermectin whereas the resistant isolate had improved survivability, while both isolates were affected by moxidectin. It was concluded that D. immitis survives in NSG mice for at least 15 weeks. NSG mice provide an ideal model for monitoring host responses to the infection and for testing parasites in vivo for susceptibility to direct chemotherapeutic activity of new agents.
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Affiliation(s)
- Jessica A Hess
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | | | | | | | | | - Jeffrey Shryock
- Boehringer Ingelheim Animal Health USA Inc., 6498 Jade Road, Fulton, MO, USA
| | - John Harrington
- Boehringer Ingelheim Animal Health USA Inc., 1730 Olympic Dr, Athens, GA, USA
| | - David Abraham
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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3
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Bauer S, Yu D, Lawson AW, Saur IML, Frantzeskakis L, Kracher B, Logemann E, Chai J, Maekawa T, Schulze-Lefert P. The leucine-rich repeats in allelic barley MLA immune receptors define specificity towards sequence-unrelated powdery mildew avirulence effectors with a predicted common RNase-like fold. PLoS Pathog 2021; 17:e1009223. [PMID: 33534797 PMCID: PMC7857584 DOI: 10.1371/journal.ppat.1009223] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/07/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleotide-binding domain leucine-rich repeat-containing receptors (NLRs) in plants can detect avirulence (AVR) effectors of pathogenic microbes. The Mildew locus a (Mla) NLR gene has been shown to confer resistance against diverse fungal pathogens in cereal crops. In barley, Mla has undergone allelic diversification in the host population and confers isolate-specific immunity against the powdery mildew-causing fungal pathogen Blumeria graminis forma specialis hordei (Bgh). We previously isolated the Bgh effectors AVRA1, AVRA7, AVRA9, AVRA13, and allelic AVRA10/AVRA22, which are recognized by matching MLA1, MLA7, MLA9, MLA13, MLA10 and MLA22, respectively. Here, we extend our knowledge of the Bgh effector repertoire by isolating the AVRA6 effector, which belongs to the family of catalytically inactive RNase-Like Proteins expressed in Haustoria (RALPHs). Using structural prediction, we also identified RNase-like folds in AVRA1, AVRA7, AVRA10/AVRA22, and AVRA13, suggesting that allelic MLA recognition specificities could detect structurally related avirulence effectors. To better understand the mechanism underlying the recognition of effectors by MLAs, we deployed chimeric MLA1 and MLA6, as well as chimeric MLA10 and MLA22 receptors in plant co-expression assays, which showed that the recognition specificity for AVRA1 and AVRA6 as well as allelic AVRA10 and AVRA22 is largely determined by the receptors' C-terminal leucine-rich repeats (LRRs). The design of avirulence effector hybrids allowed us to identify four specific AVRA10 and five specific AVRA22 aa residues that are necessary to confer MLA10- and MLA22-specific recognition, respectively. This suggests that the MLA LRR mediates isolate-specific recognition of structurally related AVRA effectors. Thus, functional diversification of multi-allelic MLA receptors may be driven by a common structural effector scaffold, which could be facilitated by proliferation of the RALPH effector family in the pathogen genome.
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Affiliation(s)
- Saskia Bauer
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dongli Yu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne at Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aaron W. Lawson
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Isabel M. L. Saur
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Elke Logemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jijie Chai
- Institute of Biochemistry, University of Cologne at Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Takaki Maekawa
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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4
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Saur IML, Bauer S, Kracher B, Lu X, Franzeskakis L, Müller MC, Sabelleck B, Kümmel F, Panstruga R, Maekawa T, Schulze-Lefert P. Multiple pairs of allelic MLA immune receptor-powdery mildew AVR A effectors argue for a direct recognition mechanism. eLife 2019; 8:e44471. [PMID: 30777147 PMCID: PMC6414202 DOI: 10.7554/elife.44471] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 01/03/2023] Open
Abstract
Nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins in plants and animals mediate intracellular pathogen sensing. Plant NLRs typically detect strain-specific pathogen effectors and trigger immune responses often linked to localized host cell death. The barley Mla disease resistance locus has undergone extensive functional diversification in the host population and encodes numerous allelic NLRs each detecting a matching isolate-specific avirulence effector (AVRA) of the fungal pathogen Blumeria graminis f. sp. hordei (Bgh). We report here the isolation of Bgh AVRa7, AVRa9, AVRa10, and AVRa22, which encode small secreted proteins recognized by allelic MLA7, MLA9, MLA10, and MLA22 receptors, respectively. These effectors are sequence-unrelated, except for allelic AVRa10 and AVRa22 that are co-maintained in pathogen populations in the form of a balanced polymorphism. Contrary to numerous examples of indirect recognition of bacterial effectors by plant NLRs, co-expression experiments with matching Mla-AVRa pairs indicate direct detection of the sequence-unrelated fungal effectors by MLA receptors.
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Affiliation(s)
- Isabel ML Saur
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Saskia Bauer
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Barbara Kracher
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Xunli Lu
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lamprinos Franzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Marion C Müller
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Björn Sabelleck
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Takaki Maekawa
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Paul Schulze-Lefert
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant SciencesDüsseldorfGermany
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5
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Groß A, Kracher B, Kraus JM, Kühlwein SD, Pfister AS, Wiese S, Luckert K, Pötz O, Joos T, Van Daele D, De Raedt L, Kühl M, Kestler HA. Representing dynamic biological networks with multi-scale probabilistic models. Commun Biol 2019; 2:21. [PMID: 30675519 PMCID: PMC6336720 DOI: 10.1038/s42003-018-0268-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 12/07/2018] [Indexed: 12/26/2022] Open
Abstract
Dynamic models analyzing gene regulation and metabolism face challenges when adapted to modeling signal transduction networks. During signal transduction, molecular reactions and mechanisms occur in different spatial and temporal frames and involve feedbacks. This impedes the straight-forward use of methods based on Boolean networks, Bayesian approaches, and differential equations. We propose a new approach, ProbRules, that combines probabilities and logical rules to represent the dynamics of a system across multiple scales. We demonstrate that ProbRules models can represent various network motifs of biological systems. As an example of a comprehensive model of signal transduction, we provide a Wnt network that shows remarkable robustness under a range of phenotypical and pathological conditions. Its simulation allows the clarification of controversially discussed molecular mechanisms of Wnt signaling by predicting wet-lab measurements. ProbRules provides an avenue in current computational modeling by enabling systems biologists to integrate vast amounts of available data on different scales.
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Affiliation(s)
- Alexander Groß
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Barbara Kracher
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Silke D. Kühlwein
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Astrid S. Pfister
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Katrin Luckert
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Pötz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Thomas Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Dries Van Daele
- Department of Computer Science, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Luc De Raedt
- Department of Computer Science, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
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6
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Maekawa T, Kracher B, Saur IML, Yoshikawa-Maekawa M, Kellner R, Pankin A, von Korff M, Schulze-Lefert P. Subfamily-Specific Specialization of RGH1/MLA Immune Receptors in Wild Barley. Mol Plant Microbe Interact 2019; 32:107-119. [PMID: 30295580 DOI: 10.1094/mpmi-07-18-0186-fi] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The barley disease resistance (R) gene locus mildew locus A (Mla) provides isolate-specific resistance against the powdery mildew fungus Blumeria graminis hordei and has been introgressed into modern cultivars from diverse germplasms, including the wild relative Hordeum spontaneum. Known Mla disease resistance specificities to B. graminis hordei appear to encode allelic variants of the R gene homolog 1 (RGH1) family of nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Here, we sequenced and assembled the transcriptomes of 50 H. spontaneum accessions representing nine populations distributed throughout the Fertile Crescent. The assembled Mla transcripts exhibited rich sequence diversity, linked neither to geographic origin nor population structure, and could be grouped into two similar-sized subfamilies based on two major N-terminal coiled-coil (CC) signaling domains that are both capable of eliciting cell death. The presence of positively selected sites located mainly in the C-terminal leucine-rich repeats of both MLA subfamilies, together with the fact that both CC signaling domains mediate cell death, implies that the two subfamilies are actively maintained in the population. Unexpectedly, known MLA receptor variants that confer B. graminis hordei resistance belong exclusively to one subfamily. Thus, signaling domain divergence, potentially as adaptation to distinct pathogen populations, is an evolutionary signature of functional diversification of an immune receptor. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Affiliation(s)
- Takaki Maekawa
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Barbara Kracher
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Isabel M L Saur
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | | | - Ronny Kellner
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
| | - Artem Pankin
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
- 2 Institute of Plant Genetics, Heinrich-Heine-University and Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Maria von Korff
- 1 Max Planck Institute for Plant Breeding Research, Cologne, Germany; and
- 2 Institute of Plant Genetics, Heinrich-Heine-University and Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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7
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Birkenbihl RP, Kracher B, Ross A, Kramer K, Finkemeier I, Somssich IE. Principles and characteristics of the Arabidopsis WRKY regulatory network during early MAMP-triggered immunity. Plant J 2018; 96:487-502. [PMID: 30044528 DOI: 10.1111/tpj.14043] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 05/04/2023]
Abstract
During microbe-associated molecular pattern-triggered immunity more than 5000 Arabidopsis genes are significantly altered in their expression, and the question arises, how such an enormous reprogramming of the transcriptome can be regulated in a safe and robust manner? For the WRKY transcription factors (TFs), which are important regulators of numerous defense responses, it appears that they act in a complex regulatory sub-network rather than in a linear fashion, which would be much more vulnerable to gene function loss either by pathogen-derived effectors or by mutations. In this study we employed RNA-seq, mass spectrometry and chromatin immunoprecipitation-seq to find evidence for and uncover principles and characteristics of this network. Upon flg22-treatment, one can distinguish between two sets of WRKY genes: constitutively expressed and induced WRKY genes. Prior to elicitation the induced WRKY genes appear to be maintained in a repressed state mainly by the constitutively expressed WRKY factors, which themselves appear to be regulated by non-WRKY TFs. Upon elicitation, induced WRKYs rapidly bind to induced WRKY gene promoters and by auto- and cross-regulation build up the regulatory network. Maintenance of this flg22-induced network appears highly robust as removal of three key WRKY factors can be physically and functionally compensated for by other WRKY family members.
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Affiliation(s)
- Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Annegret Ross
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Katharina Kramer
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg10, 50829, Cologne, Germany
| | - Iris Finkemeier
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg10, 50829, Cologne, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
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8
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Halder V, Oeljeklaus J, Heilmann G, Krahn JH, Liu Y, Xiong Y, Schlicht M, Schillinger J, Kracher B, Ehrmann M, Kombrink E, Kaschani F, Kaiser M. Identification of the Natural Product Rotihibin A as a TOR Kinase Signaling Inhibitor by Unbiased Transcriptional Profiling. Chemistry 2018; 24:12500-12504. [DOI: 10.1002/chem.201802647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Vivek Halder
- Chemical Biology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
- Chemical Biology Laboratory; Max-Planck-Institute for Plant Breeding Research; Carl-von-Linnè-Weg 10 50829 Köln Germany
| | - Julian Oeljeklaus
- Chemical Biology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
| | - Geronimo Heilmann
- Chemical Biology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
| | - Jan H. Krahn
- Chemical Biology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
| | - Yanlin Liu
- Basic Forestry and Proteomics Research Center; Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University; Fujian Province 350002 P.R. China
| | - Yan Xiong
- Basic Forestry and Proteomics Research Center; Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University; Fujian Province 350002 P.R. China
| | - Markus Schlicht
- Chemical Biology Laboratory; Max-Planck-Institute for Plant Breeding Research; Carl-von-Linnè-Weg 10 50829 Köln Germany
| | - Jasmin Schillinger
- Microbiology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
| | - Barbara Kracher
- Bioinformatics, Department of Plant Microbe Interactions; Max-Planck-Institute for Plant Breeding Research; Carl-von-Linnè-Weg 10 50829 Köln Germany
| | - Michael Ehrmann
- Microbiology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
| | - Erich Kombrink
- Chemical Biology Laboratory; Max-Planck-Institute for Plant Breeding Research; Carl-von-Linnè-Weg 10 50829 Köln Germany
| | - Farnusch Kaschani
- Chemical Biology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
| | - Markus Kaiser
- Chemical Biology, Zentrum für Medizinische Biotechnologie; Universität Duisburg-Essen; Universitätsstrasse 2 45117 Essen Germany
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9
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Mine A, Seyfferth C, Kracher B, Berens ML, Becker D, Tsuda K. The Defense Phytohormone Signaling Network Enables Rapid, High-Amplitude Transcriptional Reprogramming during Effector-Triggered Immunity. Plant Cell 2018; 30:1199-1219. [PMID: 29794063 PMCID: PMC6048782 DOI: 10.1105/tpc.17.00970] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 05/22/2018] [Indexed: 05/18/2023]
Abstract
The phytohormone network consisting of jasmonate, ethylene, PHYTOALEXIN-DEFICIENT4, and salicylic acid signaling is required for the two modes of plant immunity, pattern-triggered immunity (PTI), and effector-triggered immunity (ETI). A previous study showed that during PTI, the transcriptional responses of over 5000 genes qualitatively depend on complex interactions between the network components. However, the role of the network in transcriptional reprogramming during ETI and whether it differs between PTI and ETI remain elusive. Here, we generated time-series RNA-sequencing data of Arabidopsis thaliana wild-type and combinatorial mutant plants deficient in components of the network upon challenge with virulent or ETI-triggering avirulent strains of the foliar bacterial pathogen Pseudomonas syringae Resistant plants such as the wild type achieved high-amplitude transcriptional reprogramming 4 h after challenge with avirulent strains and sustained this transcriptome response. Strikingly, susceptible plants including the quadruple network mutant showed almost identical transcriptome responses to resistant plants but with several hours delay. Furthermore, gene coexpression network structure was highly conserved between the wild type and quadruple mutant. Thus, in contrast to PTI, the phytohormone network is required only for achieving high-amplitude transcriptional reprogramming within the early time window of ETI against this bacterial pathogen.
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Affiliation(s)
- Akira Mine
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Center for Gene Research, Nagoya University, Aichi 464-8602, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Shiga 525-8577, Japan
- JST, PRESTO, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Carolin Seyfferth
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Matthias L Berens
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Dieter Becker
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
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10
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Frantzeskakis L, Kracher B, Kusch S, Yoshikawa-Maekawa M, Bauer S, Pedersen C, Spanu PD, Maekawa T, Schulze-Lefert P, Panstruga R. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 2018; 19:381. [PMID: 29788921 PMCID: PMC5964911 DOI: 10.1186/s12864-018-4750-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
Background Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). Results The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. Conclusions The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens. Electronic supplementary material The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lamprinos Frantzeskakis
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Barbara Kracher
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stefan Kusch
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Makoto Yoshikawa-Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Saskia Bauer
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Pietro D Spanu
- Imperial College, Department of Life Sciences, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Takaki Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
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11
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Jacob F, Kracher B, Mine A, Seyfferth C, Blanvillain‐Baufumé S, Parker JE, Tsuda K, Schulze‐Lefert P, Maekawa T. A dominant-interfering camta3 mutation compromises primary transcriptional outputs mediated by both cell surface and intracellular immune receptors in Arabidopsis thaliana. New Phytol 2018; 217:1667-1680. [PMID: 29226970 PMCID: PMC5873390 DOI: 10.1111/nph.14943] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/08/2017] [Indexed: 05/15/2023]
Abstract
Pattern recognition receptors (PRRs) and nucleotide-binding domain and leucine-rich repeat (LRR)-containing proteins (NLRs) initiate pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), respectively, each associated with the activation of an overlapping set of defence genes. The regulatory mechanism behind this convergence of PTI- and ETI-mediated defence gene induction remains elusive. We generated transgenic Arabidopsis plants that enable conditional NLR activation without pathogen infection to dissect NLR- and PRR-mediated transcriptional signals. A comparative analysis of over 40 transcriptome datasets linked calmodulin-binding transcription activators (CAMTAs) to the activation of overlapping defence genes in PTI and ETI. We used a dominant camta3 mutant (camta3-D) to assess CAMTA functions in the corresponding transcriptional regulation. Transcriptional regulation by NLRs, although highly similar to PTI responses, can be established independently of pathogen-associated molecular pattern (PAMP) perception, defence phytohormones and host cell death. Conditional expression of the N-terminal coiled-coil domain of the barley MLA (Mildew resistance locus A) NLR is sufficient to trigger similar transcriptional reprogramming as full-length NLRs. CAMTA-binding motifs are overrepresented in the 5' regulatory regions of the identified primary immune response genes, consistent with their altered expression and disease resistance responses in camta3-D plants. We propose that CAMTA-mediated transcriptional regulation defines an early convergence point in NLR- and PRR-mediated signalling.
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Affiliation(s)
- Florence Jacob
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
- Institute of Plant Sciences Paris‐SaclayCentre National de la Recherche ScientifiqueInstitut National de la Recherche AgronomiqueUniversité Paris‐SudUniversité d'EvryUniversité Paris‐DiderotSorbonne Paris‐CitéUniversité Paris‐Saclay91405OrsayFrance
| | - Barbara Kracher
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Akira Mine
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Carolin Seyfferth
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | | | - Jane E. Parker
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Kenichi Tsuda
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Paul Schulze‐Lefert
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Takaki Maekawa
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
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12
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de Montaigu A, Oeljeklaus J, Krahn JH, Suliman MN, Halder V, de Ansorena E, Nickel S, Schlicht M, Plíhal O, Kubiasová K, Radová L, Kracher B, Tóth R, Kaschani F, Coupland G, Kombrink E, Kaiser M. The Root Growth-Regulating Brevicompanine Natural Products Modulate the Plant Circadian Clock. ACS Chem Biol 2017; 12:1466-1471. [PMID: 28379676 PMCID: PMC5477000 DOI: 10.1021/acschembio.6b00978] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Plant
growth regulating properties of brevicompanines (Brvs), natural
products of the fungus Penicillium brevicompactum, have been known for several years, but further investigations into
the molecular mechanism of their bioactivity have not been performed.
Following chemical synthesis of brevicompanine derivatives, we studied
their activity in the model plant Arabidopsis by
a combination of plant growth assays, transcriptional profiling, and
numerous additional bioassays. These studies demonstrated that brevicompanines
cause transcriptional misregulation of core components of the circadian
clock, whereas other biological read-outs were not affected. Brevicompanines
thus represent promising chemical tools for investigating the regulation
of the plant circadian clock. In addition, our study also illustrates
the potential of an unbiased -omics-based characterization of bioactive
compounds for identifying the often cryptic modes of action of small
molecules.
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Affiliation(s)
- Amaury de Montaigu
- Department
of Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Julian Oeljeklaus
- Department
of Chemical Biology, Universität Duisburg-Essen, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany
| | - Jan H. Krahn
- Department
of Chemical Biology, Universität Duisburg-Essen, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany
| | - Mohamed N.S. Suliman
- Chemical
Biology Laboratory, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829 Köln, Germany
| | - Vivek Halder
- Department
of Chemical Biology, Universität Duisburg-Essen, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany
- Chemical
Biology Laboratory, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829 Köln, Germany
| | - Elisa de Ansorena
- Department
of Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Sabrina Nickel
- Department
of Chemical Biology, Universität Duisburg-Essen, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany
| | - Markus Schlicht
- Chemical
Biology Laboratory, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829 Köln, Germany
| | - Ondřej Plíhal
- Department
of Molecular Biology, Centre of the Region Haná for Biotechnological
and Agricultural Research, Palacký University, Šlechtitelů
241/27, 78371 Olomouc, Czech Republic
| | - Karolina Kubiasová
- Department
of Molecular Biology, Centre of the Region Haná for Biotechnological
and Agricultural Research, Palacký University, Šlechtitelů
241/27, 78371 Olomouc, Czech Republic
| | - Lenka Radová
- Center
of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Barbara Kracher
- Bioinformatics,
Department of Plant Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829 Köln, Germany
| | - Réka Tóth
- Department
of Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Farnusch Kaschani
- Department
of Chemical Biology, Universität Duisburg-Essen, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany
| | - George Coupland
- Department
of Developmental Biology, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Erich Kombrink
- Chemical
Biology Laboratory, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829 Köln, Germany
| | - Markus Kaiser
- Department
of Chemical Biology, Universität Duisburg-Essen, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany
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13
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Cui H, Gobbato E, Kracher B, Qiu J, Bautor J, Parker JE. A core function of EDS1 with PAD4 is to protect the salicylic acid defense sector in Arabidopsis immunity. New Phytol 2017; 213:1802-1817. [PMID: 27861989 DOI: 10.1111/nph.14302] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/23/2016] [Indexed: 05/19/2023]
Abstract
Plant defenses induced by salicylic acid (SA) are vital for resistance against biotrophic pathogens. In basal and receptor-triggered immunity, SA accumulation is promoted by Enhanced Disease Susceptibility1 with its co-regulator Phytoalexin Deficient4 (EDS1/PAD4). Current models position EDS1/PAD4 upstream of SA but their functional relationship remains unclear. In a genetic and transcriptomic analysis of Arabidopsis autoimmunity caused by constitutive or conditional EDS1/PAD4 overexpression, intrinsic EDS1/PAD4 signaling properties and their relation to SA were uncovered. A core EDS1/PAD4 pathway works in parallel with SA in basal and effector-triggered bacterial immunity. It protects against disabled SA-regulated gene expression and pathogen resistance, and is distinct from a known SA-compensatory route involving MAPK signaling. Results help to explain previously identified EDS1/PAD4 regulated SA-dependent and SA-independent gene expression sectors. Plants have evolved an alternative route for preserving SA-regulated defenses against pathogen or genetic perturbations. In a proposed signaling framework, EDS1 with PAD4, besides promoting SA biosynthesis, maintains important SA-related resistance programs, thereby increasing robustness of the innate immune system.
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Affiliation(s)
- Haitao Cui
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Enrico Gobbato
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Barbara Kracher
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Jingde Qiu
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
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14
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Birkenbihl RP, Kracher B, Roccaro M, Somssich IE. Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity. Plant Cell 2017; 29:20-38. [PMID: 28011690 PMCID: PMC5304350 DOI: 10.1105/tpc.16.00681] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/28/2016] [Accepted: 12/16/2016] [Indexed: 05/19/2023]
Abstract
During microbial-associated molecular pattern-triggered immunity (MTI), molecules derived from microbes are perceived by cell surface receptors and upon signaling to the nucleus initiate a massive transcriptional reprogramming critical to mount an appropriate host defense response. WRKY transcription factors play an important role in regulating these transcriptional processes. Here, we determined on a genome-wide scale the flg22-induced in vivo DNA binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40, and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Binding occurred mainly in the 500-bp promoter regions of these genes. Many of the targeted genes are involved in signal perception and transduction not only during MTI but also upon damage-associated molecular pattern-triggered immunity, providing a mechanistic link between these functionally interconnected basal defense pathways. Among the additional targets were genes involved in the production of indolic secondary metabolites and in modulating distinct plant hormone pathways. Importantly, among the targeted genes were numerous transcription factors, encoding predominantly ethylene response factors, active during early MTI, and WRKY factors, supporting the previously hypothesized existence of a WRKY subregulatory network. Transcriptional analysis revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes often to prevent exaggerated defense responses.
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Affiliation(s)
- Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Koeln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Koeln, Germany
| | | | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Koeln, Germany
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15
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Hacquard S, Kracher B, Hiruma K, Münch PC, Garrido-Oter R, Thon MR, Weimann A, Damm U, Dallery JF, Hainaut M, Henrissat B, Lespinet O, Sacristán S, van Themaat EVL, Kemen E, McHardy AC, Schulze-Lefert P, O'Connell RJ. Erratum: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nat Commun 2016; 7:13072. [PMID: 27681013 PMCID: PMC5056416 DOI: 10.1038/ncomms13072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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16
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Hacquard S, Kracher B, Hiruma K, Münch PC, Garrido-Oter R, Thon MR, Weimann A, Damm U, Dallery JF, Hainaut M, Henrissat B, Lespinet O, Sacristán S, Ver Loren van Themaat E, Kemen E, McHardy AC, Schulze-Lefert P, O'Connell RJ. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nat Commun 2016. [PMID: 27150427 DOI: 10.1016/j.disc.2013.08.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses.
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Affiliation(s)
- Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kei Hiruma
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Philipp C Münch
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
- Max-von-Pettenkofer Institute, LMU Munich, German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Michael R Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, 37185 Villamayor, Spain
| | - Aaron Weimann
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Ulrike Damm
- CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, The Netherlands
| | - Jean-Félix Dallery
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Matthieu Hainaut
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91405 Orsay, France
- Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, 91405 Orsay, France
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid Campus de Montegancedo, 28223 Madrid, Spain
| | - Emiel Ver Loren van Themaat
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Eric Kemen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
- Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Richard J O'Connell
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
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17
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Hiruma K, Gerlach N, Sacristán S, Nakano RT, Hacquard S, Kracher B, Neumann U, Ramírez D, Bucher M, O'Connell RJ, Schulze-Lefert P. Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent. Cell 2016. [PMID: 26997485 DOI: 10.1016/j.cell.2016.02.028s0092-8674(16)30130-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A staggering diversity of endophytic fungi associate with healthy plants in nature, but it is usually unclear whether these represent stochastic encounters or provide host fitness benefits. Although most characterized species of the fungal genus Colletotrichum are destructive pathogens, we show here that C. tofieldiae (Ct) is an endemic endophyte in natural Arabidopsis thaliana populations in central Spain. Colonization by Ct initiates in roots but can also spread systemically into shoots. Ct transfers the macronutrient phosphorus to shoots, promotes plant growth, and increases fertility only under phosphorus-deficient conditions, a nutrient status that might have facilitated the transition from pathogenic to beneficial lifestyles. The host's phosphate starvation response (PSR) system controls Ct root colonization and is needed for plant growth promotion (PGP). PGP also requires PEN2-dependent indole glucosinolate metabolism, a component of innate immune responses, indicating a functional link between innate immunity and the PSR system during beneficial interactions with Ct.
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Affiliation(s)
- Kei Hiruma
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Department of Biological Sciences, Nara Institute of Science and Technology, 630-0192 Nara, Japan
| | - Nina Gerlach
- Botanical Institute, Cologne Biocenter, University of Cologne, 50931 Cologne, Germany
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Ryohei Thomas Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50931 Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ulla Neumann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Diana Ramírez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Marcel Bucher
- Botanical Institute, Cologne Biocenter, University of Cologne, 50931 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50931 Cologne, Germany
| | - Richard J O'Connell
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50931 Cologne, Germany.
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18
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Hiruma K, Gerlach N, Sacristán S, Nakano RT, Hacquard S, Kracher B, Neumann U, Ramírez D, Bucher M, O'Connell RJ, Schulze-Lefert P. Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent. Cell 2016; 165:464-74. [PMID: 26997485 PMCID: PMC4826447 DOI: 10.1016/j.cell.2016.02.028] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/15/2015] [Accepted: 02/10/2016] [Indexed: 01/06/2023]
Abstract
A staggering diversity of endophytic fungi associate with healthy plants in nature, but it is usually unclear whether these represent stochastic encounters or provide host fitness benefits. Although most characterized species of the fungal genus Colletotrichum are destructive pathogens, we show here that C. tofieldiae (Ct) is an endemic endophyte in natural Arabidopsis thaliana populations in central Spain. Colonization by Ct initiates in roots but can also spread systemically into shoots. Ct transfers the macronutrient phosphorus to shoots, promotes plant growth, and increases fertility only under phosphorus-deficient conditions, a nutrient status that might have facilitated the transition from pathogenic to beneficial lifestyles. The host’s phosphate starvation response (PSR) system controls Ct root colonization and is needed for plant growth promotion (PGP). PGP also requires PEN2-dependent indole glucosinolate metabolism, a component of innate immune responses, indicating a functional link between innate immunity and the PSR system during beneficial interactions with Ct. Colletotrichum tofieldiae (Ct) is a fungal root endophyte of Arabidopsis Ct transfers the macronutrient phosphorus to Arabidopsis shoots Ct-mediated plant growth promotion needs an intact phosphate starvation response A branch of the plant innate immune system is essential for beneficial Ct activities
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Affiliation(s)
- Kei Hiruma
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Department of Biological Sciences, Nara Institute of Science and Technology, 630-0192 Nara, Japan
| | - Nina Gerlach
- Botanical Institute, Cologne Biocenter, University of Cologne, 50931 Cologne, Germany
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Ryohei Thomas Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50931 Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ulla Neumann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Diana Ramírez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Marcel Bucher
- Botanical Institute, Cologne Biocenter, University of Cologne, 50931 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50931 Cologne, Germany
| | - Richard J O'Connell
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50931 Cologne, Germany.
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Liu S, Kracher B, Ziegler J, Birkenbihl RP, Somssich IE. Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. eLife 2015. [PMID: 26076231 DOI: 10.7554/elife.07295.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.
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Affiliation(s)
- Shouan Liu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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Liu S, Kracher B, Ziegler J, Birkenbihl RP, Somssich IE. Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. eLife 2015. [PMID: 26076231 DOI: 10.7554/elife.07295.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.
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Affiliation(s)
- Shouan Liu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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Liu S, Kracher B, Ziegler J, Birkenbihl RP, Somssich IE. Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100. eLife 2015; 4:e07295. [PMID: 26076231 PMCID: PMC4487144 DOI: 10.7554/elife.07295] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/13/2015] [Indexed: 02/07/2023] Open
Abstract
The Arabidopsis mutant wrky33 is highly susceptible to Botrytis cinerea. We identified >1680 Botrytis-induced WRKY33 binding sites associated with 1576 Arabidopsis genes. Transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. Comparative analyses revealed that WRKY33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. We confirmed known WRKY33 targets involved in hormone signaling and phytoalexin biosynthesis, but also uncovered a novel negative role of abscisic acid (ABA) in resistance towards B. cinerea 2100. The ABA biosynthesis genes NCED3 and NCED5 were identified as direct targets required for WRKY33-mediated resistance. Loss-of-WRKY33 function resulted in elevated ABA levels and genetic studies confirmed that WRKY33 acts upstream of NCED3/NCED5 to negatively regulate ABA biosynthesis. This study provides the first detailed view of the genome-wide contribution of a specific plant transcription factor in modulating the transcriptional network associated with plant immunity.
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Affiliation(s)
- Shouan Liu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jörg Ziegler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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Hacquard S, Kracher B, Maekawa T, Vernaldi S, Schulze-Lefert P, Ver Loren van Themaat E. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc Natl Acad Sci U S A 2013; 110:E2219-28. [PMID: 23696672 PMCID: PMC3683789 DOI: 10.1073/pnas.1306807110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barley powdery mildew, Blumeria graminis f. sp. hordei (Bgh), is an obligate biotrophic ascomycete fungal pathogen that can grow and reproduce only on living cells of wild or domesticated barley (Hordeum sp.). Domestication and deployment of resistant barley cultivars by humans selected for amplification of Bgh isolates with different virulence combinations. We sequenced the genomes of two European Bgh isolates, A6 and K1, for comparative analysis with the reference genome of isolate DH14. This revealed a mosaic genome structure consisting of large isolate-specific DNA blocks with either high or low SNP densities. Some of the highly polymorphic blocks likely accumulated SNPs for over 10,000 years, well before the domestication of barley. These isolate-specific blocks of alternating monomorphic and polymorphic regions imply an exceptionally large standing genetic variation in the Bgh population and might be generated and maintained by rare outbreeding and frequent clonal reproduction. RNA-sequencing experiments with isolates A6 and K1 during four early stages of compatible and incompatible interactions on leaves of partially immunocompromised Arabidopsis mutants revealed a conserved Bgh transcriptional program during pathogenesis compared with the natural host barley despite ~200 million years of reproductive isolation of these hosts. Transcripts encoding candidate-secreted effector proteins are massively induced in successive waves. A specific decrease in candidate-secreted effector protein transcript abundance in the incompatible interaction follows extensive transcriptional reprogramming of the host transcriptome and coincides with the onset of localized host cell death, suggesting a host-inducible defense mechanism that targets fungal effector secretion or production.
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Affiliation(s)
| | | | - Takaki Maekawa
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Saskia Vernaldi
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman MA, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun MH, Lee YH, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, Ver Loren van Themaat E, Ma LJ, Vaillancourt LJ. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 2012; 44:1060-5. [PMID: 22885923 DOI: 10.1038/ng.2372] [Citation(s) in RCA: 561] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 07/05/2012] [Indexed: 11/09/2022]
Abstract
Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
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Affiliation(s)
- Richard J O'Connell
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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Abstract
MOTIVATION Accurate, context-specific regulation of gene expression is essential for all organisms. Accordingly, it is very important to understand the complex relations within cellular gene regulatory networks. A tool to describe and analyze the behavior of such networks are Boolean models. The reconstruction of a Boolean network from biological data requires identification of dependencies within the network. This task becomes increasingly computationally demanding with large amounts of data created by recent high-throughput technologies. Thus, we developed a method that is especially suited for network structure reconstruction from large-scale data. In our approach, we took advantage of the fact that a specific transcription factor often will consistently either activate or inhibit a specific target gene, and this kind of regulatory behavior can be modeled using monotone functions. RESULTS To detect regulatory dependencies in a network, we examined how the expression of different genes correlates to successive network states. For this purpose, we used Pearson correlation as an elementary correlation measure. Given a Boolean network containing only monotone Boolean functions, we prove that the correlation of successive states can identify the dependencies in the network. This method not only finds dependencies in randomly created artificial networks to very high percentage, but also reconstructed large fractions of both a published Escherichia coli regulatory network from simulated data and a yeast cell cycle network from real microarray data.
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Affiliation(s)
- Markus Maucher
- Research group Bioinformatics and Systems Biology, Clinic for Internal Medicine I, University Medical Center Ulm, Ulm, Germany
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