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Escaray FJ, Felipo-Benavent A, Antonelli CJ, Balaguer B, Lopez-Gresa MP, Vera P. Plant triterpenoid saponins function as susceptibility factors to promote the pathogenicity of Botrytis cinerea. MOLECULAR PLANT 2024; 17:1073-1089. [PMID: 38807367 DOI: 10.1016/j.molp.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/12/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024]
Abstract
The gray mold fungus Botrytis cinerea is a necrotrophic pathogen that causes diseases in hundreds of plant species, including high-value crops. Its polyxenous nature and pathogenic success are due to its ability to perceive host signals in its favor. In this study, we found that laticifer cells of Euphorbia lathyris are a source of susceptibility factors required by B. cinerea to cause disease. Consequently, poor-in-latex (pil) mutants, which lack laticifer cells, show full resistance to this pathogen, whereas lot-of-latex mutants, which produce more laticifer cells, are hypersusceptible. These S factors are triterpenoid saponins, which are widely distributed natural products of vast structural diversity. The downregulation of laticifer-specific oxydosqualene cyclase genes, which encode the first committed step enzymes for triterpene and, therefore, saponin biosynthesis, conferred disease resistance to B. cinerea. Likewise, the Medicago truncatula lha-1 mutant, compromised in triterpenoid saponin biosynthesis, showed enhanced resistance. Interestingly, the application of different purified triterpenoid saponins pharmacologically complemented the disease-resistant phenotype of pil and hla-1 mutants and enhanced disease susceptibility in different plant species. We found that triterpenoid saponins function as plant cues that signal transcriptional reprogramming in B. cinerea, leading to a change in its growth habit and infection strategy, culminating in the abundant formation of infection cushions, the multicellular appressoria apparatus dedicated to plant penetration and biomass destruction in B. cinerea. Taken together, these results provide an explanation for how plant triterpenoid saponins function as disease susceptibility factors to promote B. cinerea pathogenicity.
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Affiliation(s)
- Francisco J Escaray
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, acceso G, Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain
| | - Amelia Felipo-Benavent
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, acceso G, Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain
| | - Cristian J Antonelli
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, acceso G, Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain
| | - Begoña Balaguer
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, acceso G, Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain
| | - Maria Pilar Lopez-Gresa
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, acceso G, Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain
| | - Pablo Vera
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Ciudad Politécnica de la Innovación, Edificio 8E, acceso G, Ingeniero Fausto Elio, s/n, 46022 Valencia, Spain.
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Suárez I, Collado IG, Garrido C. Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites. Int J Mol Sci 2024; 25:5900. [PMID: 38892087 PMCID: PMC11173184 DOI: 10.3390/ijms25115900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.
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Affiliation(s)
- Ivonne Suárez
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain;
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª planta, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª planta, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Carlos Garrido
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain;
- Instituto de Investigación Vitivinícola y Agroalimentaria (IVAGRO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
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3
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Coca-Ruiz V, Suárez I, Aleu J, Cantoral JM, González C, Garrido C, Brito N, Collado IG. Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Lifecycle of Botrytis cinerea. Int J Mol Sci 2024; 25:5125. [PMID: 38791163 PMCID: PMC11120764 DOI: 10.3390/ijms25105125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The genome sequencing of Botrytis cinerea supplies a general overview of the map of genes involved in secondary metabolite synthesis. B. cinerea genomic data reveals that this phytopathogenic fungus has seven sesquiterpene cyclase (Bcstc) genes that encode proteins involved in the farnesyl diphosphate cyclization. Three sesquiterpene cyclases (BcStc1, BcStc5 and BcStc7) are characterized, related to the biosynthesis of botrydial, abscisic acid and (+)-4-epi-eremophilenol, respectively. However, the role of the other four sesquiterpene cyclases (BcStc2, BcStc3, BcStc4 and BcStc6) remains unknown. BcStc3 is a well-conserved protein with homologues in many fungal species, and here, we undertake its functional characterization in the lifecycle of the fungus. A null mutant ΔBcstc3 and an overexpressed-Bcstc3 transformant (OvBcstc3) are generated, and both strains show the deregulation of those other sesquiterpene cyclase-encoding genes (Bcstc1, Bcstc5 and Bcstc7). These results suggest a co-regulation of the expression of the sesquiterpene cyclase gene family in B. cinerea. The phenotypic characterization of both transformants reveals that BcStc3 is involved in oxidative stress tolerance, the production of reactive oxygen species and virulence. The metabolomic analysis allows the isolation of characteristic polyketides and eremophilenols from the secondary metabolism of B. cinerea, although no sesquiterpenes different from those already described are identified.
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Affiliation(s)
- Víctor Coca-Ruiz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Ivonne Suárez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (J.M.C.); (C.G.)
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Jesús M. Cantoral
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (J.M.C.); (C.G.)
- Instituto de Investigación Vitivinícola y Agroalimentaria (IVAGRO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Celedonio González
- Área de Bioquímica y Biología Molecular, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Tenerife, Spain;
| | - Carlos Garrido
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (J.M.C.); (C.G.)
- Instituto de Investigación Vitivinícola y Agroalimentaria (IVAGRO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Nélida Brito
- Área de Bioquímica y Biología Molecular, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Tenerife, Spain;
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
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Singh R, Caseys C, Kliebenstein DJ. Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2024; 25:e13404. [PMID: 38037862 PMCID: PMC10788480 DOI: 10.1111/mpp.13404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Botrytis cinerea Pers. Fr. (teleomorph: Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity of B. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combat B. cinerea. TAXONOMY Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus: Botrytis, species: cinerea. HOST RANGE B. cinerea infects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts of B. cinerea. GENETIC DIVERSITY This polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PATHOGENICITY Genetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. DISEASE CONTROL STRATEGIES Efforts to control B. cinerea, being a high-diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology.
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Affiliation(s)
- Ritu Singh
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
| | - Celine Caseys
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
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Hiruma K, Aoki S, Takino J, Higa T, Utami YD, Shiina A, Okamoto M, Nakamura M, Kawamura N, Ohmori Y, Sugita R, Tanoi K, Sato T, Oikawa H, Minami A, Iwasaki W, Saijo Y. A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae. Nat Commun 2023; 14:5288. [PMID: 37673872 PMCID: PMC10482981 DOI: 10.1038/s41467-023-40867-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Plant-associated fungi show diverse lifestyles from pathogenic to mutualistic to the host; however, the principles and mechanisms through which they shift the lifestyles require elucidation. The root fungus Colletotrichum tofieldiae (Ct) promotes Arabidopsis thaliana growth under phosphate limiting conditions. Here we describe a Ct strain, designated Ct3, that severely inhibits plant growth. Ct3 pathogenesis occurs through activation of host abscisic acid pathways via a fungal secondary metabolism gene cluster related to the biosynthesis of sesquiterpene metabolites, including botrydial. Cluster activation during root infection suppresses host nutrient uptake-related genes and changes mineral contents, suggesting a role in manipulating host nutrition state. Conversely, disruption or environmental suppression of the cluster renders Ct3 beneficial for plant growth, in a manner dependent on host phosphate starvation response regulators. Our findings indicate that a fungal metabolism cluster provides a means by which infectious fungi modulate lifestyles along the parasitic-mutualistic continuum in fluctuating environments.
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Affiliation(s)
- Kei Hiruma
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
- Department of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Seishiro Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-0882, Japan
| | - Junya Takino
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Takeshi Higa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yuniar Devi Utami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Akito Shiina
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-cho, Utsunomiya, Tochigi, 321-8505, Japan
| | - Masami Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Nanami Kawamura
- Department of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Yoshihiro Ohmori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryohei Sugita
- Radioisotope Research Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Keitaro Tanoi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Toyozo Sato
- Genetic Resources Center, National Agriculture and Food Research Organization, Ibaraki, 305-8602, Japan
| | - Hideaki Oikawa
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong, 529020, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-0882, Japan
| | - Yusuke Saijo
- Department of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan
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Qin S, Veloso J, Puccetti G, van Kan JAL. Molecular characterization of cross-kingdom RNA interference in Botrytis cinerea by tomato small RNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1107888. [PMID: 36968352 PMCID: PMC10031073 DOI: 10.3389/fpls.2023.1107888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Previous studies have suggested that plants can modulate gene expression in pathogenic fungi by producing small RNAs (sRNAs) that can be translocated into the fungus and mediate gene silencing, which may interfere with the infection mechanism of the intruder. We sequenced sRNAs and mRNAs in early phases of the Solanum lycopersicum (tomato)-Botrytis cinerea interaction and examined the potential of plant sRNAs to silence their predicted mRNA targets in the fungus. Almost a million unique plant sRNAs were identified that could potentially target 97% of all fungal genes. We selected three fungal genes for detailed RT-qPCR analysis of the correlation between the abundance of specific plant sRNAs and their target mRNAs in the fungus. The fungal Bcspl1 gene, which had been reported to be important for the fungal virulence, showed transient down-regulation around 20 hours post inoculation and contained a unique target site for a single plant sRNA that was present at high levels. In order to study the functionality of this plant sRNA in reducing the Bcspl1 transcript level, we generated a fungal mutant that contained a 5-nucleotide substitution that would abolish the interaction between the transcript and the sRNA without changing the encoded protein sequence. The level of the mutant Bcspl1 transcript showed a transient decrease similar to wild type transcript, indicating that the tomato sRNA was not responsible for the downregulation of the Bcspl1 transcript. The virulence of the Bcspl1 target site mutant was identical to the wild type fungus.
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Affiliation(s)
- Si Qin
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Javier Veloso
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
- Departamento de Biología Funcional, Escuela Politécnica Superior de Ingeniería, Universidad de Santiago de Compostela, Lugo, Spain
| | - Guido Puccetti
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
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Wildhagen M, Pudenz T, Nguyen T, Kirschning A, Beutel S. Biokatalytische Ganzzellproduktion des Sesquiterpens Presilphiperfolan‐8β‐ol in stoffwechseloptimierten
Escherichia coli. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Maik Wildhagen
- Leibniz Universität Hannover Institut für Technische Chemie Callinstraße 5 30167 Hannover Deutschland
| | - Tabea Pudenz
- Leibniz Universität Hannover Institut für Technische Chemie Callinstraße 5 30167 Hannover Deutschland
| | - Trang Nguyen
- Leibniz Universität Hannover Institut für Organische Chemie Schneiderberg 1 B 30167 Hannover Deutschland
| | - Andreas Kirschning
- Leibniz Universität Hannover Institut für Organische Chemie Schneiderberg 1 B 30167 Hannover Deutschland
| | - Sascha Beutel
- Leibniz Universität Hannover Institut für Technische Chemie Callinstraße 5 30167 Hannover Deutschland
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da Silva Ripardo-Filho H, Coca Ruíz V, Suárez I, Moraga J, Aleu J, Collado IG. From Genes to Molecules, Secondary Metabolism in Botrytis cinerea: New Insights into Anamorphic and Teleomorphic Stages. PLANTS (BASEL, SWITZERLAND) 2023; 12:553. [PMID: 36771642 PMCID: PMC9920419 DOI: 10.3390/plants12030553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The ascomycete Botrytis cinerea Pers. Fr., classified within the family Sclerotiniaceae, is the agent that causes grey mould disease which infects at least 1400 plant species, including crops of economic importance such as grapes and strawberries. The life cycle of B. cinerea consists of two phases: asexual (anamorph, Botrytis cinerea Pers. Fr.) and sexual (teleomorph, Botryotinia fuckeliana (de Bary) Wetzel). During the XVI International Symposium dedicated to the Botrytis fungus, which was held in Bari in June 2013, the scientific community unanimously decided to assign the most widely used name of the asexual form, Botrytis, to this genus of fungi. However, in the literature, we continue to find articles referring to both morphic stages. In this review, we take stock of the genes and metabolites reported for both morphic forms of B. cinerea between January 2015 and October 2022.
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Affiliation(s)
| | - Víctor Coca Ruíz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Ivonne Suárez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Javier Moraga
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
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9
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The Botrytis cinerea Gene Expression Browser. J Fungi (Basel) 2023; 9:jof9010084. [PMID: 36675905 PMCID: PMC9861337 DOI: 10.3390/jof9010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023] Open
Abstract
For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays.
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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11
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Wei Z, Shu D, Sun Q, Chen DB, Li ZM, Luo D, Yang J, Tan H. The BcLAE1 is involved in the regulation of ABA biosynthesis in Botrytis cinerea TB-31. Front Microbiol 2022; 13:969499. [PMID: 35992717 PMCID: PMC9386520 DOI: 10.3389/fmicb.2022.969499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Abscisic acid (ABA), as a classic plant hormone, is a key factor in balancing the metabolism of endogenous plant hormones, and plays an important role in regulating the activation of mammalian innate immune cells and glucose homeostasis. Currently, Botrytis cinerea has been used for fermentation to produce ABA. However, the mechanism of the regulation of ABA biosynthesis in B. cinerea is still not fully understood. The putative methyltransferase LaeA/LAE1 is a global regulator involved in the biosynthesis of a variety of secondary metabolites in filamentous fungi. In this study, we demonstrated that BcLAE1 plays an important role in the regulation of ABA biosynthesis in B. cinerea TB-31 by knockout experiment. The deletion of Bclae1 caused a 95% reduction in ABA yields, accompanied by a decrease of the transcriptional level of the ABA synthesis gene cluster Bcaba1-4. Further RNA-seq analysis indicated that deletion of Bclae1 also affected the expression level of key enzymes of BOA and BOT in secondary metabolism, and accompanied by clustering regulatory features. Meanwhile, we found that BcLAE1 is involved in epigenetic regulation as a methyltransferase, with enhanced H3K9me3 modification and attenuated H3K4me2 modification in ΔBclae1 mutant, and this may be a strategy for BcLAE1 to regulate ABA synthesis.
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Affiliation(s)
- Zhao Wei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Key Laboratory of Bio-Resources and Eco-Environment Ministry of the Education, College of Life Sciences, Sichuan University, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dan Shu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- *Correspondence: Dan Shu,
| | - Qun Sun
- Key Laboratory of Bio-Resources and Eco-Environment Ministry of the Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dong-bo Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhe-min Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Di Luo
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jie Yang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hong Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Hong Tan,
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12
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Chen H, He S, Zhang S, A R, Li W, Liu S. The Necrotroph Botrytis cinerea BcSpd1 Plays a Key Role in Modulating Both Fungal Pathogenic Factors and Plant Disease Development. FRONTIERS IN PLANT SCIENCE 2022; 13:820767. [PMID: 35845699 PMCID: PMC9280406 DOI: 10.3389/fpls.2022.820767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Botrytis cinerea is a necrotrophic microbe that causes gray mold disease in a broad range of hosts. In the present study, we conducted molecular microbiology and transcriptomic analyses of the host-B. cinerea interaction to investigate the plant defense response and fungal pathogenicity. Upon B. cinerea infection, plant defense responses changed from activation to repression; thus, the expression of many defense genes decreased in Arabidopsis thaliana. B. cinerea Zn(II)2Cys6 transcription factor BcSpd1 was involved in the suppression of plant defense as ΔBcSpd1 altered wild-type B05.10 virulence by recovering part of the defense responses at the early infection stage. BcSpd1 affected genes involved in the fungal sclerotium development, infection cushion formation, biosynthesis of melanin, and change in environmental pH values, which were reported to influence fungal virulence. Specifically, BcSpd1 bound to the promoter of the gene encoding quercetin dioxygenase (BcQdo) and positively affected the gene expression, which was involved in catalyzing antifungal flavonoid degradation. This study indicates BcSpd1 plays a key role in the necrotrophic microbe B. cinerea virulence toward plants by regulating pathogenicity-related compounds and thereby suppressing early plant defense.
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Affiliation(s)
| | | | | | | | | | - Shouan Liu
- Laboratory of Molecular Plant Pathology, Jilin University, Changchun, China
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13
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Zhang T, Pang X, Zhao J, Guo Z, He W, Cai G, Su J, Cen S, Yu L. Discovery and Activation of the Cryptic Cluster from Aspergillus sp. CPCC 400735 for Asperphenalenone Biosynthesis. ACS Chem Biol 2022; 17:1524-1533. [PMID: 35616995 DOI: 10.1021/acschembio.2c00204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Postgenomic analysis manifested that filamentous fungi contain numerous natural product biosynthetic gene clusters in their genome, yet most clusters remain cryptic or down-regulated. Herein, we report the successful manipulation of strain Aspergillus sp. CPCC 400735 that enables its genetic engineering via targeted overexpression of pathway-specific transcriptional regulator AspE. The down-regulated metabolic pathway encoded by the biosynthetic gene cluster asp was successfully up-activated. Analyses of mutant Ai-OE::aspE extracts led to isolation and characterization of 13 asperphenalenone derivatives, of which 11 of them are new compounds. All of the asperphenalenones exhibited conspicuous anti-influenza A virus effects with IC50 values of 0.45-2.22 μM. Additionally, their identification provided insight into biosynthesis of asperphenalenones and might benefit studies of downstream combinatorial biosynthesis. Our study further demonstrates the effective application of targeted overexpressing pathway-specific activator and novel metabolite discovery in microorganisms. These will accelerate the exploitation of the untapped resources and biosynthetic capability in filamentous fungi.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xu Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhe Guo
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenni He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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14
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De Miccolis Angelini RM, Landi L, Raguseo C, Pollastro S, Faretra F, Romanazzi G. Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa. Front Microbiol 2022; 13:854852. [PMID: 35356516 PMCID: PMC8959702 DOI: 10.3389/fmicb.2022.854852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
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Affiliation(s)
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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15
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Olivares-Yañez C, Sánchez E, Pérez-Lara G, Seguel A, Camejo PY, Larrondo LF, Vidal EA, Canessa P. A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride. Comput Struct Biotechnol J 2021; 19:6212-6228. [PMID: 34900134 PMCID: PMC8637145 DOI: 10.1016/j.csbj.2021.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms' transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizing available sequence motifs describing DNA-binding specificity and global gene expression data. As a proof of concept of the usefulness of this resource to pinpoint key transcriptional regulators, we employed publicly available transcriptomics data and a newly generated dual RNA-seq dataset to build context-specific Botrytis and Trichoderma GRNs under two different biological paradigms: exposure to continuous light and Botrytis-Trichoderma confrontation assays. Network analysis of fungal responses to constant light revealed striking differences in the transcriptional landscape of both fungi. On the other hand, we found that the confrontation of both microorganisms elicited a distinct set of differentially expressed genes with changes in T. atroviride exceeding those in B. cinerea. Using our regulatory network data, we were able to determine, in both fungi, central TFs involved in this interaction response, including TFs controlling a large set of extracellular peptidases in the biocontrol agent T. atroviride. In summary, our work provides a comprehensive catalog of transcription factors and regulatory interactions for both organisms. This catalog can now serve as a basis for generating novel hypotheses on transcriptional regulatory circuits in different experimental contexts.
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Affiliation(s)
- Consuelo Olivares-Yañez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Biotecnologia Vegetal, Universidad Andres Bello, Republica 330, Santiago, Chile
| | - Evelyn Sánchez
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Genomica y Bioinformatica, Facultad de Ciencias, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago, Chile
| | - Gabriel Pérez-Lara
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Biotecnologia Vegetal, Universidad Andres Bello, Republica 330, Santiago, Chile
| | - Aldo Seguel
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Pamela Y Camejo
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile
| | - Elena A Vidal
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Genomica y Bioinformatica, Facultad de Ciencias, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago, Chile.,Escuela de Biotecnologia, Facultad de Ciencias, Universidad Mayor, Camino la Pirámide 5750, Huechuraba, Santiago, Chile
| | - Paulo Canessa
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Avda. Libertador Bernardo O'Higgins 340, Santiago, Chile.,Centro de Biotecnologia Vegetal, Universidad Andres Bello, Republica 330, Santiago, Chile
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16
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Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. PHYTOPATHOLOGY 2021; 111:2355-2366. [PMID: 33829853 DOI: 10.1094/phyto-07-20-0302-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help to prevent the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the gray mold pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host of origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and nonsynonymous sites, and analyses of presence and absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.
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Affiliation(s)
- Alex Mercier
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
- Université Paris-Saclay, Orsay, France
| | - Adeline Simon
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Marc Bardin
- UR0407 Pathologie Végétale, INRAE, 84143 Montfavet, France
| | - Anne-Sophie Walker
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Muriel Viaud
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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17
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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18
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Porquier A, Tisserant C, Salinas F, Glassl C, Wange L, Enard W, Hauser A, Hahn M, Weiberg A. Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea. Genome Biol 2021; 22:225. [PMID: 34399815 PMCID: PMC8365987 DOI: 10.1186/s13059-021-02446-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/26/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Retrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons can become temporarily active during epigenetic reprogramming and cellular stress response, which may accelerate host genome evolution. In fungal pathogens, a positive role has been attributed to retrotransposons when shaping genome architecture and expression of genes encoding pathogenicity factors; thus, retrotransposons are known to influence pathogenicity. RESULTS We uncover a hitherto unknown role of fungal retrotransposons as being pathogenicity factors, themselves. The aggressive fungal plant pathogen, Botrytis cinerea, is known to deliver some long-terminal repeat (LTR) deriving regulatory trans-species small RNAs (BcsRNAs) into plant cells to suppress host gene expression for infection. We find that naturally occurring, less aggressive B. cinerea strains possess considerably lower copy numbers of LTR retrotransposons and had lost retrotransposon BcsRNA production. Using a transgenic proof-of-concept approach, we reconstitute retrotransposon expression in a BcsRNA-lacking B. cinerea strain, which results in enhanced aggressiveness in a retrotransposon and BcsRNA expression-dependent manner. Moreover, retrotransposon expression in B. cinerea leads to suppression of plant defence-related genes during infection. CONCLUSIONS We propose that retrotransposons are pathogenicity factors that manipulate host plant gene expression by encoding trans-species BcsRNAs. Taken together, the novelty that retrotransposons are pathogenicity factors will have a broad impact on studies of host-microbe interactions and pathology.
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Affiliation(s)
| | | | | | - Carla Glassl
- Faculty of Biology, Genetics, LMU Munich, Martinsried, Germany
| | - Lucas Wange
- Faculty of Biology, Anthropology & Human Genomics, LMU Munich, Martinsried, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology & Human Genomics, LMU Munich, Martinsried, Germany
| | - Andreas Hauser
- Gene Center, Laboratory for Functional Genome Analysis, LMU Munich, Martinsried, Germany
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, LMU Munich, Martinsried, Germany.
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19
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Zhang Z, Jia H, Liu N, Li H, Meng Q, Wu N, Cao Z, Dong J. The zinc finger protein StMR1 affects the pathogenicity and melanin synthesis of Setosphaeria turcica and directly regulates the expression of DHN melanin synthesis pathway genes. Mol Microbiol 2021; 117:261-273. [PMID: 34278632 DOI: 10.1111/mmi.14786] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/28/2022]
Abstract
The infection and colonization of pathogenic fungi are often regulated by transcription factors. In our previous study, the zinc finger protein-encoding gene StMR1 was found to be highly expressed during the infection process of Setosphaeria turcica, the pathogen causing northern corn leaf blight. Evolutionary tree analysis showed that this gene was associated with regulatory factors of melanin synthesis. However, the regulatory mechanism of melanin synthesis and its effect on pathogenicity remain unclear. In this study, the function of StMR1 was analyzed by gene knockout. When the expression level of StMR1 in the mutants was significantly reduced, the colony color became lighter, the mycelia were curved and transparent, and the mutant showed a significant loss of pathogenicity. In addition, compared with wild-type, the accumulation of melanin decreased significantly in △Stmr1. RNA-seq analysis revealed 1,981 differentially expressed genes between the wild-type and knockout mutant, among which 39 genes were involved in melanin metabolism. qPCR revealed that the expression levels of 6 key genes in the melanin synthesis pathway were significantly reduced. ChIP-PCR and yeast one-hybrid assays confirmed that StMR1 directly binds to the promoters of St3HNR, St4HNR, StPKS, and StLAC2 in the DHN melanin synthesis pathway and regulates gene expression. The C2H2-type zinc fingers and Zn(Ⅱ)2Cys6 binuclear cluster in StMR1 was important for the binding to targets.
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Affiliation(s)
- Zexue Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Hui Jia
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Ning Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Haixiao Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Qingjiang Meng
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Nan Wu
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Zhiyan Cao
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, 071001, P.R.China
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Acosta Morel W, Anta Fernández F, Baroncelli R, Becerra S, Thon MR, van Kan JAL, Díaz-Mínguez JM, Benito EP. A Major Effect Gene Controlling Development and Pathogenicity in Botrytis cinerea Identified Through Genetic Analysis of Natural Mycelial Non-pathogenic Isolates. FRONTIERS IN PLANT SCIENCE 2021; 12:663870. [PMID: 33936154 PMCID: PMC8079791 DOI: 10.3389/fpls.2021.663870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Botrytis cinerea is a necrotrophic plant pathogenic fungus with a wide host range. Its natural populations are phenotypically and genetically very diverse. A survey of B. cinerea isolates causing gray mold in the vineyards of Castilla y León, Spain, was carried out and as a result eight non-pathogenic natural variants were identified. Phenotypically these isolates belong to two groups. The first group consists of seven isolates displaying a characteristic mycelial morphotype, which do not sporulate and is unable to produce sclerotia. The second group includes one isolate, which sporulates profusely and does not produce sclerotia. All of them are unresponsive to light. Crosses between a representative mycelial non-pathogenic isolate and a highly aggressive field isolate revealed that the phenotypic differences regarding pathogenicity, sporulation and production of sclerotia cosegregated in the progeny and are determined by a single genetic locus. By applying a bulked segregant analysis strategy based on the comparison of the two parental genomes the locus was mapped to a 110 kb region in chromosome 4. Subcloning and transformation experiments revealed that the polymorphism is an SNP affecting gene Bcin04g03490 in the reference genome of B. cinerea. Genetic complementation analysis and sequencing of the Bcin04g03490 alleles demonstrated that the mutations in the mycelial isolates are allelic and informed about the nature of the alterations causing the phenotypes observed. Integration of the allele of the pathogenic isolate into the non-pathogenic isolate fully restored the ability to infect, to sporulate and to produce sclerotia. Therefore, it is concluded that a major effect gene controlling differentiation and developmental processes as well as pathogenicity has been identified in B. cinerea. It encodes a protein with a GAL4-like Zn(II)2Cys6 binuclear cluster DNA binding domain and an acetyltransferase domain, suggesting a role in regulation of gene expression through a mechanism involving acetylation of specific substrates.
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Affiliation(s)
- Wilson Acosta Morel
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Francisco Anta Fernández
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Riccardo Baroncelli
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Sioly Becerra
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Michael R. Thon
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - José María Díaz-Mínguez
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Ernesto Pérez Benito
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
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21
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Moraga J, Izquierdo-Bueno Reina I, Pinedo C, Hernández-Galán R, Viaud M, Collado IG. Impairment of botrydial production in Botrytis cinerea allows the isolation of undescribed polyketides and reveals new insights into the botcinins biosynthetic pathway. PHYTOCHEMISTRY 2021; 183:112627. [PMID: 33429353 DOI: 10.1016/j.phytochem.2020.112627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Botrytis cinerea is a necrotrophic fungal pathogen that affects a total of 586 genera representing approximately 1400 plant species. This pathogen produces two families of phytotoxins involved in its infection process i.e. botrydial and its relatives, and botcinic and botcineric acids and their relatives, botcinins. The botrydial biosynthetic cluster consists of seven genes, where the gene BcBOT4 encodes a cytochrome P450 monooxygenase that was shown to catalyse regio- and stereospecific hydroxylation at position C-4 of the presilphiperfolan-8-β-ol skeleton. The null mutant bcbot4Δ halted the production of botrydial and its derivatives, and instead accumulated tricyclic presilphiperfolane alcohol and overproduced a significant number of polyketides. A detailed study of the bcbot4Δ mutant led us to the isolation and characterization of five undescribed polyketides, three derived from botcinic and botcineric acids (botcinins H, I, J), one derived from the initial pentaketide (botcinin K), and one cinbotolide derivative (cinbotolide D). Botcinins are tetra-methylated tetraketides biosynthesized by the sequential assembly of a pentaketide (C10) based on an acetate primer unit which is lost through a retro-Claisen type C-C bond cleavage. The structural characterization of botcinin K showed a basic chemical structure corresponding to a botcinin (C14) derivative obtained directly from the original per-methylated pentaketide leading to the biosynthesis of botrylactone and other botcinins, confirming the previously proposed biosynthetic route.
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Affiliation(s)
- Javier Moraga
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain
| | - Inmaculada Izquierdo-Bueno Reina
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain
| | - Cristina Pinedo
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain
| | - Rosario Hernández-Galán
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain
| | - Muriel Viaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Avenue Lucien Brétignières, 78850, Thiverval-Grignon, France
| | - Isidro G Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4a planta, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain.
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22
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Reboledo G, Agorio A, Vignale L, Batista-García RA, Ponce De León I. Botrytis cinerea Transcriptome during the Infection Process of the Bryophyte Physcomitrium patens and Angiosperms. J Fungi (Basel) 2020; 7:11. [PMID: 33379257 PMCID: PMC7824268 DOI: 10.3390/jof7010011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
Botrytis cinerea is a necrotrophic pathogen that causes grey mold in many plant species, including crops and model plants of angiosperms. B. cinerea also infects and colonizes the bryophyte Physcomitrium patens (previously Physcomitrella patens), which perceives the pathogen and activates defense mechanisms. However, these defenses are not sufficient to stop fungal invasion, leading finally to plant decay. To gain more insights into B. cinerea infection and virulence strategies displayed during moss colonization, we performed genome wide transcriptional profiling of B. cinerea during different infection stages. We show that, in total, 1015 B. cinerea genes were differentially expressed in moss tissues. Expression patterns of upregulated genes and gene ontology enrichment analysis revealed that infection of P. patens tissues by B. cinerea depends on reactive oxygen species generation and detoxification, transporter activities, plant cell wall degradation and modification, toxin production and probable plant defense evasion by effector proteins. Moreover, a comparison with available RNAseq data during angiosperm infection, including Arabidopsis thaliana, Solanum lycopersicum and Lactuca sativa, suggests that B. cinerea has virulence and infection functions used in all hosts, while others are more specific to P. patens or angiosperms.
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Affiliation(s)
- Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
| | - Astrid Agorio
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
| | - Lucía Vignale
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico;
| | - Inés Ponce De León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay; (G.R.); (A.A.); (L.V.)
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23
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Pinedo-Rivilla C, Moraga J, Pérez-Sasián G, Peña-Hernández A, G. Collado I, Aleu J. Biocatalytic Preparation of Chloroindanol Derivatives. Antifungal Activity and Detoxification by the Phytopathogenic Fungus Botrytis cinerea. PLANTS 2020; 9:plants9121648. [PMID: 33255810 PMCID: PMC7759767 DOI: 10.3390/plants9121648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022]
Abstract
Indanols are a family of chemical compounds that have been widely studied due to their broad range of biological activity. They are also important intermediates used as synthetic precursors to other products with important applications in pharmacology. Enantiomerically pure chloroindanol derivatives exhibiting antifungal activity against the phytopathogenic fungus Botrytis cinerea were prepared using biocatalytic methods. As a result of the biotransformation of racemic 6-chloroindanol (1) and 5-chloroindanol (2) by the fungus B. cinerea, the compounds anti-(+)-6-chloroindan-1,2-diol (anti-(+)-7), anti-(+)-5-chloroindan-1,3-diol (anti-(+)-8), syn-(+)-5-chloroindan-1,3-diol (syn-(+)-8), syn-(-)-5-chloroindan-1,3-diol (syn-(-)-8), and anti-(+)-5-chloroindan-1,2-diol (anti-(+)-9) were isolated for the first time. These products were characterized by spectroscopic techniques and their enantiomeric excesses studied by chromatographic techniques. The results obtained in the biotransformation seem to suggest that the fungus B. cinerea uses oxidation reactions as a detoxification mechanism.
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Affiliation(s)
- Cristina Pinedo-Rivilla
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (C.P.-R.); (J.M.); (G.P.-S.); (A.P.-H.); (I.G.C.)
| | - Javier Moraga
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (C.P.-R.); (J.M.); (G.P.-S.); (A.P.-H.); (I.G.C.)
- Departamento de Biomedicina, Biotecnología y Salud Pública, Área de Microbiología, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - Guillermo Pérez-Sasián
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (C.P.-R.); (J.M.); (G.P.-S.); (A.P.-H.); (I.G.C.)
| | - Alba Peña-Hernández
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (C.P.-R.); (J.M.); (G.P.-S.); (A.P.-H.); (I.G.C.)
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (C.P.-R.); (J.M.); (G.P.-S.); (A.P.-H.); (I.G.C.)
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (C.P.-R.); (J.M.); (G.P.-S.); (A.P.-H.); (I.G.C.)
- Correspondence: ; Tel.: +34-956-012747
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24
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Valero-Jiménez CA, Steentjes MBF, Slot JC, Shi-Kunne X, Scholten OE, van Kan JAL. Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis. Genome Biol Evol 2020; 12:2491-2507. [PMID: 33283866 PMCID: PMC7719232 DOI: 10.1093/gbe/evaa218] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2020] [Indexed: 02/05/2023] Open
Abstract
Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.
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Affiliation(s)
| | | | - Jason C Slot
- Department of Plant Pathology, The Ohio State University
| | | | - Olga E Scholten
- Plant Breeding, Wageningen University & Research, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
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25
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Soltis NE, Caseys C, Zhang W, Corwin JA, Atwell S, Kliebenstein DJ. Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana - Botrytis cinerea Pathosystem. Genetics 2020; 215:253-266. [PMID: 32165442 PMCID: PMC7198280 DOI: 10.1534/genetics.120.303070] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/11/2020] [Indexed: 01/12/2023] Open
Abstract
In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described, whereas little is known about how the pathogen genetic variation modulates both organisms' transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Arabidopsis thaliana-Botrytis cinerea pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide association (eGWA) for each of 23,947 measurable transcripts in Arabidopsis (host), and 9267 measurable transcripts in B. cinerea (pathogen). Unlike other eGWA studies, we detected a relative absence of locally acting expression quantitative trait loci (cis-eQTL), partly caused by structural variants and allelic heterogeneity hindering their identification. This study identified several distantly acting trans-eQTL linked to eQTL hotspots dispersed across Botrytis genome that altered only Botrytis transcripts, only Arabidopsis transcripts, or transcripts from both species. Gene membership in the trans-eQTL hotspots suggests links between gene expression regulation and both known and novel virulence mechanisms in this pathosystem. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist necrotrophic pathogen.
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Affiliation(s)
- Nicole E Soltis
- Department of Plant Sciences, University of California, Davis, California 95616
- Plant Biology Graduate Group, University of California, Davis, California 95616
| | - Celine Caseys
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Wei Zhang
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Jason A Corwin
- Department of Ecology and Evolution Biology, University of Colorado, Boulder, Colorado 80309-0334
| | - Susanna Atwell
- Plant Biology Graduate Group, University of California, Davis, California 95616
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, California 95616
- Plant Biology Graduate Group, University of California, Davis, California 95616
- DynaMo Center of Excellence, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
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26
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Lee RC, Farfan-Caceres LM, Debler JW, Syme RA. Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean ( Vicia faba L.). Front Microbiol 2020; 11:217. [PMID: 32132988 PMCID: PMC7040437 DOI: 10.3389/fmicb.2020.00217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/30/2020] [Indexed: 11/13/2022] Open
Abstract
Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, Botrytis fabae. B. fabae is also implicated in botrytis gray mold disease in lentils, along with B. cinerea. Here we have isolated and characterized two B. fabae isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, B. fabae was more aggressive than B. cinerea and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward B. fabae. In contrast, the plant response to B. cinerea was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of B. fabae, we produced genome assemblies for both B. fabae isolates using Illumina sequencing. Genome sequencing coverage and assembly size for B. fabae isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for B. fabae, and using the same selection criteria for B. cinerea, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from B. fabae and B. cinerea was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in B. fabae. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the B. cinerea phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from B. fabae. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in B. fabae was double that of B. cinerea.
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Affiliation(s)
- Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Lina M Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Robert A Syme
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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27
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Botrydial confers Botrytis cinerea the ability to antagonize soil and phyllospheric bacteria. Fungal Biol 2020; 124:54-64. [DOI: 10.1016/j.funbio.2019.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 11/21/2022]
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28
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Bidirectional histone-gene promoters in Aspergillus: characterization and application for multi-gene expression. Fungal Biol Biotechnol 2019; 6:24. [PMID: 31867115 PMCID: PMC6900853 DOI: 10.1186/s40694-019-0088-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/23/2019] [Indexed: 02/01/2023] Open
Abstract
Background Filamentous fungi are important producers of enzymes and bioactive secondary metabolites and are exploited for industrial purposes. Expression and characterization of biosynthetic pathways requires stable expression of multiple genes in the production host. Fungal promoters are indispensable for the accomplishment of this task, and libraries of promoters that show functionality across diverse fungal species facilitate synthetic biology approaches, pathway expression, and cell-factory construction. Results In this study, we characterized the intergenic region between the genes encoding histones H4.1 and H3, from five phylogenetically diverse species of Aspergillus, as bidirectional promoters (Ph4h3). By expression of the genes encoding fluorescent proteins mRFP1 and mCitrine, we show at the translational and transcriptional level that this region from diverse species is applicable as strong and constitutive bidirectional promoters in Aspergillus nidulans. Bioinformatic analysis showed that the divergent gene orientation of h4.1 and h3 appears maintained among fungi, and that the Ph4h3 display conserved DNA motifs among the investigated 85 Aspergilli. Two of the heterologous Ph4h3s were utilized for single-locus expression of four genes from the putative malformin producing pathway from Aspergillus brasiliensis in A. nidulans. Strikingly, heterologous expression of mlfA encoding the non-ribosomal peptide synthetase is sufficient for biosynthesis of malformins in A. nidulans, which indicates an iterative use of one adenylation domain in the enzyme. However, this resulted in highly stressed colonies, which was reverted to a healthy phenotype by co-expressing the residual four genes from the putative biosynthetic gene cluster. Conclusions Our study has documented that Ph4h3 is a strong constitutive bidirectional promoter and a valuable new addition to the genetic toolbox of at least the genus Aspergillus.
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29
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Zhang W, Corwin JA, Copeland DH, Feusier J, Eshbaugh R, Cook DE, Atwell S, Kliebenstein DJ. Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield. eLife 2019; 8:e44279. [PMID: 31081752 PMCID: PMC6557632 DOI: 10.7554/elife.44279] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/08/2019] [Indexed: 12/27/2022] Open
Abstract
A central goal of studying host-pathogen interaction is to understand how host and pathogen manipulate each other to promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection and provide a systematic map of the cross-kingdom communication between two species. Here we used the Arabidopsis-B. cinerea pathosystem to test how plant host and fungal pathogen interact at the transcriptomic level. We assessed the impact of genetic diversity in pathogen and host by utilization of a collection of 96 isolates infection on Arabidopsis wild-type and two mutants with jasmonate or salicylic acid compromised immunities. We identified ten B. cinereagene co-expression networks (GCNs) that encode known or novel virulence mechanisms. Construction of a dual interaction network by combining four host- and ten pathogen-GCNs revealed potential connections between the fungal and plant GCNs. These co-transcriptome data shed lights on the potential mechanisms underlying host-pathogen interaction.
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Affiliation(s)
- Wei Zhang
- Department of Plant PathologyKansas State UniversityManhattanUnited States
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Jason A Corwin
- Department of Ecology and Evolution BiologyUniversity of ColoradoBoulderUnited States
| | | | - Julie Feusier
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Robert Eshbaugh
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - David E Cook
- Department of Plant PathologyKansas State UniversityManhattanUnited States
| | - Suzi Atwell
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Daniel J Kliebenstein
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
- DynaMo Center of ExcellenceUniversity of CopenhagenFrederiksbergDenmark
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30
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Kumar A, Kumar V, Kumar A. Functional characterization of host toxic EcdB transcription factor protein of echinocandin B biosynthetic gene cluster. Biotechnol Appl Biochem 2019; 66:626-633. [PMID: 31069846 DOI: 10.1002/bab.1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022]
Abstract
The ecdB is a transcription factor, located in the echinocandin B biosynthetic gene cluster of Emericella rugulosa NRRL11440. Here, we validated the ecdB mRNA sequence for functional expression and to explore the role of EcdB protein in the echinocandin B regulation. The sequence alignment study revealed that the ecdB coding sequence was found 75 bp shorter than the reference mRNA sequence. This coding sequence encodes for EcdB protein and comprises three conserved domains; DNA binding domain (DBD), coiled-coil domain, and signature middle homology region. The full-length and DBD (truncated) DNA sequences were expressed in Escherichia coli BL21(DE3) under different tested conditions. The expression of EcdB protein was found to be toxic, which curbs the cell growth. In contrast to truncated protein (GST:EcdB1-54), the full-length (GST:EcdB) protein was expressed at very low titer and not detectable in SDS-PAGE under the varying isopropyl β-d-1-thiogalactopyranoside (IPTG), temperature, and media conditions. However, GST:EcdB1-54 was successfully purified under standard conditions (0.5 mM IPTG at 0.5OD) with 33 kDa expected size. The functionality of GST:EcdB1-54 was attained by electrophoretic mobility shift assay study as a clear band shifting showed with ecdA promoter. Taken together, we conclude that EcdB interacts with the ecdA promoter that reflected to require for echinocandin B regulation.
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Affiliation(s)
- Arvind Kumar
- Department of Biotechnology, Central University of South Bihar, Panchanpur, Gaya, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Antresh Kumar
- Department of Biotechnology, Central University of South Bihar, Panchanpur, Gaya, India
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Botcinic acid biosynthesis in Botrytis cinerea relies on a subtelomeric gene cluster surrounded by relics of transposons and is regulated by the Zn2Cys6 transcription factor BcBoa13. Curr Genet 2019; 65:965-980. [DOI: 10.1007/s00294-019-00952-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 01/11/2023]
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Cys 2His 2 Zinc Finger Transcription Factor BcabaR1 Positively Regulates Abscisic Acid Production in Botrytis cinerea. Appl Environ Microbiol 2018; 84:AEM.00920-18. [PMID: 29959241 DOI: 10.1128/aem.00920-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/11/2018] [Indexed: 01/03/2023] Open
Abstract
Abscisic acid (ABA) is one of the five classical phytohormones involved in increasing the tolerance of plants for various kinds of stresses caused by abiotic or biotic factors, and it also plays important roles in regulating the activation of innate immune cells and glucose homeostasis in mammals. For these reasons, as a "stress hormone," ABA has recently received attention as a candidate drug for agriculture and biomedical applications, prompting significant development of ABA synthesis. Some plant-pathogenic fungi can synthesize natural ABA. The fungus Botrytis cinerea has been used for biotechnological production of ABA. Identification of the transcription factors (TFs) involved in regulation of ABA biosynthesis in B. cinerea would provide new clues to understand how ABA is synthesized and regulated. In this study, we defined a novel Cys2His2 TF, BcabaR1, that regulates the transcriptional levels of ABA synthase genes (bcaba1, bcaba2, bcaba3, and bcaba4) in an ABA-overproducing mutant, B. cinerea TBC-A. Electrophoretic mobility shift assays revealed that recombinant BcabaR1 can bind specifically to both a 14-nucleotide sequence motif and a 39-nucleotide sequence motif in the promoter region of bcaba1 to -4 genes in vitro A decreased transcriptional level of the bcabaR1 gene in B. cinerea led to significantly decreased ABA production and downregulated transcription of bcaba1 to -4 When bcabaR1 was overexpressed in B. cinerea, ABA production was significantly increased, with upregulated transcription of bcaba1 to -4 Thus, in this study, we found that BcabaR1 acts as a positive regulator of ABA biosynthesis in B. cinereaIMPORTANCE Abscisic acid (ABA) could make a potentially important contribution to theoretical research and applications in agriculture and medicine. Botrytis cinerea is a plant-pathogenic fungus that was found to produce ABA. There has been a view that ABA is related to the interaction between pathogenic fungi and plants. Identification of regulatory genes involved in ABA biosynthesis may facilitate an understanding of the underlying molecular mechanisms of ABA biosynthesis and the pathogenesis of B. cinerea Here, we present a positive regulator, BcabaR1, of ABA biosynthesis in B. cinerea that can affect the transcriptional level of the ABA biosynthesis gene cluster, bcaba1 to -4, by directly binding to the conserved sequence elements in the promoter of the bcaba1 to -4 genes. This TF was found to be specifically involved in regulation of ABA biosynthesis. This work provides new clues for finding other ABA biosynthesis genes and improving ABA yield in B. cinerea.
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Izquierdo-Bueno I, González-Rodríguez VE, Simon A, Dalmais B, Pradier JM, Le Pêcheur P, Mercier A, Walker AS, Garrido C, Collado IG, Viaud M. Biosynthesis of abscisic acid in fungi: identification of a sesquiterpene cyclase as the key enzyme in Botrytis cinerea. Environ Microbiol 2018; 20:2469-2482. [PMID: 29708647 DOI: 10.1111/1462-2920.14258] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/25/2022]
Abstract
While abscisic acid (ABA) is known as a hormone produced by plants through the carotenoid pathway, a small number of phytopathogenic fungi are also able to produce this sesquiterpene but they use a distinct pathway that starts with the cyclization of farnesyl diphosphate (FPP) into 2Z,4E-α-ionylideneethane which is then subjected to several oxidation steps. To identify the sesquiterpene cyclase (STC) responsible for the biosynthesis of ABA in fungi, we conducted a genomic approach in Botrytis cinerea. The genome of the ABA-overproducing strain ATCC58025 was fully sequenced and five STC-coding genes were identified. Among them, Bcstc5 exhibits an expression profile concomitant with ABA production. Gene inactivation, complementation and chemical analysis demonstrated that BcStc5/BcAba5 is the key enzyme responsible for the key step of ABA biosynthesis in fungi. Unlike what is observed for most of the fungal secondary metabolism genes, the key enzyme-coding gene Bcstc5/Bcaba5 is not clustered with the other biosynthetic genes, i.e., Bcaba1 to Bcaba4 that are responsible for the oxidative transformation of 2Z,4E-α-ionylideneethane. Finally, our study revealed that the presence of the Bcaba genes among Botrytis species is rare and that the majority of them do not possess the ability to produce ABA.
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Affiliation(s)
- Inmaculada Izquierdo-Bueno
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Cádiz, 11510 Puerto Real, Spain
| | - Victoria E González-Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias de Mar y Ambientales, Universidad de Cádiz, Puerto Real, Cádiz 11510, Spain
| | - Adeline Simon
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Bérengère Dalmais
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Jean-Marc Pradier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Pascal Le Pêcheur
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Alex Mercier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France.,Université Paris-Sud, 91405 Orsay, France
| | - Anne-Sophie Walker
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Carlos Garrido
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias de Mar y Ambientales, Universidad de Cádiz, Puerto Real, Cádiz 11510, Spain
| | - Isidro González Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Cádiz, 11510 Puerto Real, Spain
| | - Muriel Viaud
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
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Wiemann P, Soukup AA, Folz JS, Wang PM, Noack A, Keller NP. CoIN: co-inducible nitrate expression system for secondary metabolites in Aspergillus nidulans. Fungal Biol Biotechnol 2018; 5:6. [PMID: 29564145 PMCID: PMC5851313 DOI: 10.1186/s40694-018-0049-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequencing of fungal species has demonstrated the existence of thousands of putative secondary metabolite gene clusters, the majority of them harboring a unique set of genes thought to participate in production of distinct small molecules. Despite the ready identification of key enzymes and potential cluster genes by bioinformatics techniques in sequenced genomes, the expression and identification of fungal secondary metabolites in the native host is often hampered as the genes might not be expressed under laboratory conditions and the species might not be amenable to genetic manipulation. To overcome these restrictions, we developed an inducible expression system in the genetic model Aspergillus nidulans. RESULTS We genetically engineered a strain of A. nidulans devoid of producing eight of the most abundant endogenous secondary metabolites to express the sterigmatocystin Zn(II)2Cys6 transcription factor-encoding gene aflR and its cofactor aflS under control of the nitrate inducible niiA/niaD promoter. Furthermore, we identified a subset of promoters from the sterigmatocystin gene cluster that are under nitrate-inducible AflR/S control in our production strain in order to yield coordinated expression without the risks from reusing a single inducible promoter. As proof of concept, we used this system to produce β-carotene from the carotenoid gene cluster of Fusarium fujikuroi. CONCLUSION Utilizing one-step yeast recombinational cloning, we developed an inducible expression system in the genetic model A. nidulans and show that it can be successfully used to produce commercially valuable metabolites.
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Affiliation(s)
- Philipp Wiemann
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Hexagon Bio, Menlo Park, CA 94025 USA
| | - Alexandra A. Soukup
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53705 USA
| | - Jacob S. Folz
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Davis Genome Center – Metabolomics, University of California, 451 Health Science Drive, Davis, CA 95616 USA
| | - Pin-Mei Wang
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Present Address: Ocean College, Zhejiang University, Hangzhou, 310058 Zhejiang Province People’s Republic of China
| | - Andreas Noack
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706 USA
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706 USA
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35
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Khalid S, Baccile JA, Spraker JE, Tannous J, Imran M, Schroeder FC, Keller NP. NRPS-Derived Isoquinolines and Lipopetides Mediate Antagonism between Plant Pathogenic Fungi and Bacteria. ACS Chem Biol 2018; 13:171-179. [PMID: 29182847 DOI: 10.1021/acschembio.7b00731] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacterial-fungal interactions are presumed to be mediated chiefly by small-molecule signals; however, little is known about the signaling networks that regulate antagonistic relationships between pathogens. Here, we show that the ralstonins, lipopeptides produced by the plant pathogenic bacteria Ralstonia solanacearum, interfere with germination of the plant-pathogenic fungus Aspergillus flavus by down-regulating expression of a cryptic biosynthetic gene cluster (BGC), named imq. Comparative metabolomic analysis of overexpression strains of the transcription factor ImqK revealed imq-dependent production of a family of tripeptide-derived alkaloids, the imizoquins. These alkaloids are produced via a nonribosomal peptide synthetase- (NRPS-)derived tripeptide and contain an unprecedented tricyclic imidazo[2,1-a]isoquinoline ring system. We show that the imizoquins serve a protective role against oxidative stress that is essential for normal A. flavus germination. Supplementation of purified imizoquins restored wildtype germination to a ΔimqK A. flavus strain and protected the fungus from ROS damage. Whereas the bacterial ralstonins retarded A. flavus germination and suppressed expression of the imq cluster, the fungal imizoquins in turn suppressed growth of R. solanacearum. We suggest such reciprocal small-molecule-mediated antagonism is a common feature in microbial encounters affecting pathogenicity and survival of the involved species.
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Affiliation(s)
- Saima Khalid
- Departments
of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
- Department
of Microbiology, Qauid-i-Azam University, Islamabad, Pakistan
| | - Joshua A. Baccile
- Boyce
Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Joseph E. Spraker
- Department
of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | - Joanna Tannous
- Departments
of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
| | - Muhammad Imran
- Department
of Microbiology, Qauid-i-Azam University, Islamabad, Pakistan
| | - Frank C. Schroeder
- Boyce
Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States
| | - Nancy P. Keller
- Departments
of Bacteriology, Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, United States
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36
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Dallery JF, Lapalu N, Zampounis A, Pigné S, Luyten I, Amselem J, Wittenberg AHJ, Zhou S, de Queiroz MV, Robin GP, Auger A, Hainaut M, Henrissat B, Kim KT, Lee YH, Lespinet O, Schwartz DC, Thon MR, O'Connell RJ. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics 2017; 18:667. [PMID: 28851275 PMCID: PMC5576322 DOI: 10.1186/s12864-017-4083-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/21/2017] [Indexed: 11/11/2022] Open
Abstract
Background The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Results Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. Conclusion The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen. Electronic supplementary material The online version of this article (10.1186/s12864-017-4083-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-Félix Dallery
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Nicolas Lapalu
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Antonios Zampounis
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,Present Address: Department of Deciduous Fruit Trees, Institute of Plant Breeding and Plant Genetic Resources, Hellenic Agricultural Organization 'Demeter', Naoussa, Greece
| | - Sandrine Pigné
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | | | | | | | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marisa V de Queiroz
- Laboratório de Genética Molecular de Fungos, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Guillaume P Robin
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Matthieu Hainaut
- CNRS UMR 7257, Aix-Marseille University, Marseille, France.,INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France.,INRA, USC 1408 AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Olivier Lespinet
- Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, Orsay, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Orsay, France
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael R Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Richard J O'Connell
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.
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37
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van der Does HC, Rep M. Adaptation to the Host Environment by Plant-Pathogenic Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:427-450. [PMID: 28645233 DOI: 10.1146/annurev-phyto-080516-035551] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Many fungi can live both saprophytically and as endophyte or pathogen inside a living plant. In both environments, complex organic polymers are used as sources of nutrients. Propagation inside a living host also requires the ability to respond to immune responses of the host. We review current knowledge of how plant-pathogenic fungi do this. First, we look at how fungi change their global gene expression upon recognition of the host environment, leading to secretion of effectors, enzymes, and secondary metabolites; changes in metabolism; and defense against toxic compounds. Second, we look at what is known about the various cues that enable fungi to sense the presence of living plant cells. Finally, we review literature on transcription factors that participate in gene expression in planta or are suspected to be involved in that process because they are required for the ability to cause disease.
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Affiliation(s)
| | - Martijn Rep
- Molecular Plant Pathology, University of Amsterdam, 1098XH Amsterdam, The Netherlands;
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38
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Collado IG, Hanson JR, Sanchez AJM. The botryane sesquiterpenoid metabolism of the fungus Botrytis cinerea. JOURNAL OF CHEMICAL RESEARCH 2017. [DOI: 10.3184/174751917x14993374065962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The evidence is reviewed for the biosynthesis of the phytotoxic sesquiterpenoid botryane metabolites of Botrytis cinerea and its genetic regulation. The use of this information in the development of a novel strategy for the selective control of this fungus is reviewed.
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Affiliation(s)
- Isidro Gonzalez Collado
- Departamento de Quimica Organica, Facultad de Ciencias, Universidad de Cadiz, Apdo.40, 11510 Puerto Real, Cadiz, Spain
| | - James R. Hanson
- Department of Chemistry, University of Sussex, Brighton, Sussex BN1 9QJ, UK
| | - Antonio Jose Macias Sanchez
- Departamento de Quimica Organica, Facultad de Ciencias, Universidad de Cadiz, Apdo.40, 11510 Puerto Real, Cadiz, Spain
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39
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Franco dos Santos G, Moraga J, Takahashi JA, Viaud M, Hanson JR, Hernández Galán R, Collado IG. The formation of sesquiterpenoid presilphiperfolane and cameroonane metabolites in the Bcbot4 null mutant of Botrytis cinerea. Org Biomol Chem 2017; 15:5357-5363. [DOI: 10.1039/c7ob01088e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metabolic fate of presilphiperfolan-8-ol yielded new derivatives and cameroonanes. These results have shed light on the involved rearrangement.
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Affiliation(s)
| | - Javier Moraga
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Cádiz
- Cádiz
- Spain
| | - Jacqueline A. Takahashi
- Departamento de Química
- Instituto de Ciências Exatas
- Universidade Federal de Minas Gerais
- Belo Horizonte
- Brazil
| | - Muriel Viaud
- UMR BIOGER
- INRA
- AgroParisTech
- Université Paris-Saclay
- 78850 Thiverval-Grignon
| | - James R. Hanson
- Department of Organic Chemistry
- University of Sussex
- Brighton
- UK
| | | | - Isidro G. Collado
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Cádiz
- Cádiz
- Spain
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