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Lambou K, Tag A, Lassagne A, Collemare J, Clergeot PH, Barbisan C, Perret P, Tharreau D, Millazo J, Chartier E, De Vries RP, Hirsch J, Morel JB, Beffa R, Kroj T, Thomas T, Lebrun MH. The bZIP transcription factor BIP1 of the rice blast fungus is essential for infection and regulates a specific set of appressorium genes. PLoS Pathog 2024; 20:e1011945. [PMID: 38252628 PMCID: PMC10833574 DOI: 10.1371/journal.ppat.1011945] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 02/01/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The rice blast fungus Magnaporthe oryzae differentiates specialized cells called appressoria that are required for fungal penetration into host leaves. In this study, we identified the novel basic leucine zipper (bZIP) transcription factor BIP1 (B-ZIP Involved in Pathogenesis-1) that is essential for pathogenicity. BIP1 is required for the infection of plant leaves, even if they are wounded, but not for appressorium-mediated penetration of artificial cellophane membranes. This phenotype suggests that BIP1 is not implicated in the differentiation of the penetration peg but is necessary for the initial establishment of the fungus within plant cells. BIP1 expression was restricted to the appressorium by both transcriptional and post-transcriptional control. Genome-wide transcriptome analysis showed that 40 genes were down regulated in a BIP1 deletion mutant. Most of these genes were specifically expressed in the appressorium. They encode proteins with pathogenesis-related functions such as enzymes involved in secondary metabolism including those encoded by the ACE1 gene cluster, small secreted proteins such as SLP2, BAS2, BAS3, and AVR-Pi9 effectors, as well as plant cuticle and cell wall degrading enzymes. Interestingly, this BIP1 network is different from other known infection-related regulatory networks, highlighting the complexity of gene expression control during plant-fungal interactions. Promoters of BIP1-regulated genes shared a GCN4/bZIP-binding DNA motif (TGACTC) binding in vitro to BIP1. Mutation of this motif in the promoter of MGG_08381.7 from the ACE1 gene cluster abolished its appressorium-specific expression, showing that BIP1 behaves as a transcriptional activator. In summary, our findings demonstrate that BIP1 is critical for the expression of early invasion-related genes in appressoria. These genes are likely needed for biotrophic invasion of the first infected host cell, but not for the penetration process itself. Through these mechanisms, the blast fungus strategically anticipates the host plant environment and responses during appressorium-mediated penetration.
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Affiliation(s)
- Karine Lambou
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Andrew Tag
- Department of Biology, Texas A&M University. College Station, Texas, United States of America
| | - Alexandre Lassagne
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jérôme Collemare
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Pierre-Henri Clergeot
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- ASP Bourgogne Franche-Comté, Dijon, France
| | | | - Philippe Perret
- Biochemistry Department, Bayer Crop Science SAS, Lyon, France
- Bayer S.A.S. Crop Science Division Global Toxicology- Sophia Antipolis Cedex, France
| | - Didier Tharreau
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Joelle Millazo
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Elia Chartier
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Ronald P. De Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Judith Hirsch
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Pathologie Végétale, INRAE, Montfavet, France
| | - Jean-Benoit Morel
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Roland Beffa
- Biochemistry Department, Bayer Crop Science SAS, Lyon, France
| | - Thomas Kroj
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Terry Thomas
- Department of Biology, Texas A&M University. College Station, Texas, United States of America
| | - Marc-Henri Lebrun
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- Université Paris-Saclay, INRAE, UR 1290 BIOGER, Palaiseau, France
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Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP. Expression-based clustering of CAZyme-encoding genes of Aspergillus niger. BMC Genomics 2017; 18:900. [PMID: 29169319 PMCID: PMC5701360 DOI: 10.1186/s12864-017-4164-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 03/28/2017] [Accepted: 10/05/2017] [Indexed: 11/29/2022] Open
Abstract
Background The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. Results The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Conclusions Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4164-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Birgit S Gruben
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: ATGM, Avans University of Applied Sciences, Lovensdijkstraat 61-63, 4818, AJ, Breda, The Netherlands
| | - Isabelle Benoit-Gelber
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.,Current affiliation: Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Ronald P De Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. .,Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands. .,Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
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Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CMM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RHY, Johnson J, Krajaejun T, Lin H, Meijer HJG, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol 2010; 11:R73. [PMID: 20626842 PMCID: PMC2926784 DOI: 10.1186/gb-2010-11-7-r73] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [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: 02/17/2010] [Revised: 05/02/2010] [Accepted: 07/13/2010] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. RESULTS The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. CONCLUSIONS Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
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Affiliation(s)
- C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Henk Brouwer
- CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | | | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Carson Holt
- Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA
| | | | | | - Gregg P Robideau
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Marco Thines
- Biodiversity and Climate Research Centre, Georg-Voigt-Str 14-16, D-60325, Frankfurt, Germany
- Department of Biological Sciences, Insitute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University, Siesmayerstr. 70, D-60323 Frankfurt, Germany
| | - Joe Win
- The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Marcelo M Zerillo
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Gordon W Beakes
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jeffrey L Boore
- Genome Project Solutions, 1024 Promenade Street, Hercules, CA 94547, USA
| | - Dana Busam
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Bernard Dumas
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR5546 CNRS-Université de Toulouse, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
| | - Steve Ferriera
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | | | | | - Elodie Gaulin
- Surfaces Cellulaires et Signalisation chez les Végétaux, UMR5546 CNRS-Université de Toulouse, 24 chemin de Borde Rouge, BP42617, Auzeville, Castanet-Tolosan, F-31326, France
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, NL-1-6708 PB, Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), PO Box 98, 6700 AB Wageningen, The Netherlands
| | - Laura Grenville-Briggs
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Neil Horner
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Jessica Hostetler
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Rays HY Jiang
- The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Justin Johnson
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Theerapong Krajaejun
- Department of Pathology, Faculty of Medicine-Ramathibodi Hospital, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Haining Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Harold JG Meijer
- Laboratory of Phytopathology, Wageningen University, NL-1-6708 PB, Wageningen, The Netherlands
| | - Barry Moore
- Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA
| | - Paul Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Vipaporn Phuntmart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Daniela Puiu
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Jyoti Shetty
- J Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Jason E Stajich
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061-0477, USA
| | - Stephan Wawra
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Pieter van West
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Brett R Whitty
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS, Univ. Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolecules Biologiques, UMR6098, CNRS, Univ. Aix-Marseille I & II, 163 Avenue de Luminy, 13288 Marseille, France
| | - Frank Martin
- USDA-ARS, 1636 East Alisal St, Salinias, CA, 93905, USA
| | - Paul D Thomas
- Evolutionary Systems Biology, SRI International, Room AE207, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061-0477, USA
| | - Ronald P De Vries
- CBS-KNAW, Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | | | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Room 2100, Salt Lake City, UT 84112-5330, USA
| | - Ned Tisserat
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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