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Shi L, Wang Z, Chen JH, Qiu H, Liu WD, Zhang XY, Martin FM, Zhao MW. LbSakA-mediated phosphorylation of the scaffolding protein LbNoxR in the ectomycorrhizal basidiomycete Laccaria bicolor regulates NADPH oxidase activity, ROS accumulation and symbiosis development. THE NEW PHYTOLOGIST 2024; 243:381-397. [PMID: 38741469 DOI: 10.1111/nph.19813] [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: 03/04/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Ectomycorrhizal symbiosis, which involves mutually beneficial interactions between soil fungi and tree roots, is essential for promoting tree growth. To establish this symbiotic relationship, fungal symbionts must initiate and sustain mutualistic interactions with host plants while avoiding host defense responses. This study investigated the role of reactive oxygen species (ROS) generated by fungal NADPH oxidase (Nox) in the development of Laccaria bicolor/Populus tremula × alba symbiosis. Our findings revealed that L. bicolor LbNox expression was significantly higher in ectomycorrhizal roots than in free-living mycelia. RNAi was used to silence LbNox, which resulted in decreased ROS signaling, limited formation of the Hartig net, and a lower mycorrhizal formation rate. Using Y2H library screening, BiFC and Co-IP, we demonstrated an interaction between the mitogen-activated protein kinase LbSakA and LbNoxR. LbSakA-mediated phosphorylation of LbNoxR at T409, T477 and T480 positively modulates LbNox activity, ROS accumulation and upregulation of symbiosis-related genes involved in dampening host defense reactions. These results demonstrate that regulation of fungal ROS metabolism is critical for maintaining the mutualistic interaction between L. bicolor and P. tremula × alba. Our findings also highlight a novel and complex regulatory mechanism governing the development of symbiosis, involving both transcriptional and posttranslational regulation of gene networks.
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Affiliation(s)
- Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zi Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ju Hong Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Hao Qiu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wei Dong Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiao Yan Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, INRAE Grand Est-Nancy, Champenoux, 54280, France
| | - Ming Wen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. THE NEW PHYTOLOGIST 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [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: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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3
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Furtado ANM, de Farias ST, Maia MDS. Structural analyzes suggest that MiSSP13 and MiSSP16.5 may act as proteases inhibitors during ectomycorrhiza establishment in Laccaria bicolor. Biosystems 2024; 238:105194. [PMID: 38513884 DOI: 10.1016/j.biosystems.2024.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/29/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
•The signaling process during mycorrhiza establishment involves intense molecular communication between symbionts. It has been suggested that a group of protein effectors, the so-called MiSSPs, plays a broader function in the symbiosis metabolism, however, many of these remain uncharacterized structurally and functionally. •Herein we used three-dimensional protein structure modeling methods, ligand analysis, and molecular docking to structurally characterize and describe two protein effectors, MiSSP13 and MiSSP16.5, with enhanced expression during the mycorrhizal process in Laccaria bicolor. •MiSSP13 and MiSSP16.5 show structural homology with the cysteine and aspartate protease inhibitor, cocaprin (CCP1). Through structural analysis, it was observed that MiSSP13 and MiSSP16.5 have an active site similar to that observed in CCP1. The protein-protein docking data showed that MiSSP13 and MiSSP16.5 interact with the papain and pepsin proteases at sites that are near to where CCP1 interacts with these same targets, suggesting a function as inhibitor of cysteine and aspartate proteases. The interaction of MiSSP13 with papain and MiSSP16.5 with pepsin was stronger than the interaction of CCP1 with these proteases, suggesting that the MiSSPs had a greater activity in inhibiting these classes of proteases. Based on the data supplied, a model is proposed for the function of MiSSPs 13 and 16.5 during the symbiosis establishment. Our findings, while derived from in silico analyses, enable us formulate intriguing hypothesis on the function of MiSSPs in ectomycorrhization, which will require experimental validation.
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Affiliation(s)
- Ariadne N M Furtado
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil.
| | - Sávio Torres de Farias
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil; Network of Researchers on Chemical Emergence of Life (NoRCEL), Leeds, LS7 3RB, UK
| | - Mayara Dos Santos Maia
- Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, 58051-900, Brazil
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Kahar G, Haxim Y, Waheed A, Bozorov TA, Liu X, Wen X, Zhao M, Zhang D. Multi-Omics Approaches Provide New Insights into the Identification of Putative Fungal Effectors from Valsa mali. Microorganisms 2024; 12:655. [PMID: 38674600 PMCID: PMC11051974 DOI: 10.3390/microorganisms12040655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogenic fungi secrete numerous effectors into host cells to manipulate plants' defense mechanisms. Valsa mali, a necrotrophic fungus, severely impacts apple production in China due to the occurrence of Valsa canker. Here, we predicted 210 candidate effector protein (CEP)-encoding genes from V. mali. The transcriptome analysis revealed that 146 CEP-encoding genes were differentially expressed during the infection of the host, Malus sieversii. Proteome analysis showed that 27 CEPs were differentially regulated during the infection stages. Overall, 25 of the 146 differentially expressed CEP-encoding genes were randomly selected to be transiently expressed in Nicotiana benthamiana. Pathogenicity analysis showed that the transient expression of VM1G-05058 suppressed BAX-triggered cell death while the expression of VM1G-10148 and VM1G-00140 caused cell death in N. benthamiana. In conclusion, by using multi-omics analysis, we identified potential effector candidates for further evaluation in vivo. Our results will provide new insights into the investigation of virulent mechanisms of V. mali.
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Affiliation(s)
- Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yakupjan Haxim
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Abdul Waheed
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Tohir A. Bozorov
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Laboratory of Molecular and Biochemical Genetics, Institute of Genetics and Plants Experimental Biology, Uzbek Academy of Sciences, Yukori-Yuz, Kibray 111226, Tashkent Region, Uzbekistan
| | - Xiaojie Liu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Xuejing Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Mingqi Zhao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (G.K.); (Y.H.); (A.W.); (X.L.); (X.W.); (M.Z.)
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
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5
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Tao Y, Li C, Liu Y, Xu C, Okabe S, Matsushita N, Lian C. Identification of microRNAs involved in ectomycorrhizal formation in Populus tomentosa. TREE PHYSIOLOGY 2023; 43:2012-2030. [PMID: 37777191 DOI: 10.1093/treephys/tpad102] [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: 01/29/2023] [Accepted: 08/17/2023] [Indexed: 10/02/2023]
Abstract
The majority of woody plants are able to form ectomycorrhizal (ECM) symbioses with fungi. During symbiotic development, plants undergo a complex re-programming process involving a series of physiological and morphological changes. MicroRNAs (miRNAs) are important components of the regulatory network underlying symbiotic development. To elucidate the mechanisms of miRNAs and miRNA-mediated mRNA cleavage during symbiotic development, we conducted high-throughput sequencing of small RNAs and degradome tags from roots of Populus tomentosa inoculated with Cenococcum geophilum. This process led to the annotation of 51 differentially expressed miRNAs between non-mycorrhizal and mycorrhizal roots of P. tomentosa, including 13 novel miRNAs. Increased or decreased accumulation of several novel and conserved miRNAs in ECM roots, including miR162, miR164, miR319, miR396, miR397, miR398, novel-miR44 and novel-miR47, suggests essential roles for these miRNAs in ECM formation. The degradome analysis identified root transcripts as miRNA-mediated mRNA cleavage targets, which was confirmed using real-time quantitative PCR. Several of the identified miRNAs and corresponding targets are involved in arbuscular mycorrhizal symbioses. In summary, increased or decreased accumulation of specific miRNAs and miRNA-mediated cleavage of symbiosis-related genes indicate that miRNAs play important roles in the regulatory network underlying symbiotic development.
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Affiliation(s)
- Yuanxun Tao
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Chaofeng Li
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
- Maize Research Institute, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715 China
| | - Ying Liu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715 China
| | - Shin Okabe
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
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Vigneaud J, Kohler A, Sow MD, Delaunay A, Fauchery L, Guinet F, Daviaud C, Barry KW, Keymanesh K, Johnson J, Singan V, Grigoriev I, Fichot R, Conde D, Perales M, Tost J, Martin FM, Allona I, Strauss SH, Veneault-Fourrey C, Maury S. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. THE NEW PHYTOLOGIST 2023; 238:2561-2577. [PMID: 36807327 DOI: 10.1111/nph.18734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/21/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.
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Affiliation(s)
- Julien Vigneaud
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Annegret Kohler
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Mamadou Dia Sow
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Laure Fauchery
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Frederic Guinet
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Kerrie W Barry
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jenifer Johnson
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Igor Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91000, France
| | - Francis M Martin
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres-Microorganismes, Centre INRAE Grand Est-Nancy, INRAE, Université de Lorraine, Champenoux, 54280, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orleans, EA 1207 USC 1328, Orléans, 45067, France
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7
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Feng W, Sun X, Ding G. Morphological and Transcriptional Characteristics of the Symbiotic Interaction between Pinus massoniana and Suillus bovinus. J Fungi (Basel) 2022; 8:1162. [PMID: 36354929 PMCID: PMC9699607 DOI: 10.3390/jof8111162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 09/08/2023] Open
Abstract
Ectomycorrhiza (ECM) function has been well studied; however, there is little detailed information regarding the establishment of ECM symbioses. We investigated the morphological and transcriptional changes that occur during the establishment of the Pinus massoniana-Suillus bovinus ECM. S. bovinus promoted the growth of P. massoniana via the release of volatile organic compounds and exudates during the pre-symbiotic stage. Exudate-induced effects showed host plant specificity. At seven days post-inoculation (dpi), the mycelium started to penetrate P. massoniana roots. At 28 dpi, the Hartig net and mantle formed. At the pre-symbiotic stage, most differentially expressed genes in P. massoniana roots were mapped to the biosynthesis of secondary metabolites, signal transduction, and carbohydrate metabolism. At the symbiotic stage, S. bovinus colonization induced the reprogramming of pathways involved in genetic information processing in P. massoniana, particularly at the Hartig net and mantle formation stage. Phenylpropanoid biosynthesis was present at all stages and was regulated via S. bovinus colonization. Enzyme inhibitor tests suggested that hydroxycinnamoyl-CoA shikimate/quinate transferase is involved in the development of the Hartig net. Our findings outline the mechanism involved in the P. massoniana-S. bovinus ECM. Further studies are needed to clarify the role of phenylpropanoid biosynthesis in ECM formation.
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Affiliation(s)
- Wanyan Feng
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang 550025, China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Xueguang Sun
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang 550025, China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Guijie Ding
- Institute for Forest Resources & Environment of Guizhou, Guizhou University, Guiyang 550025, China
- Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Guizhou University, Guiyang 550025, China
- College of Forestry, Guizhou University, Guiyang 550025, China
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8
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Todd JNA, Carreón-Anguiano KG, Islas-Flores I, Canto-Canché B. Fungal Effectoromics: A World in Constant Evolution. Int J Mol Sci 2022; 23:13433. [PMID: 36362218 PMCID: PMC9656242 DOI: 10.3390/ijms232113433] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 10/28/2023] Open
Abstract
Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.
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Affiliation(s)
- Jewel Nicole Anna Todd
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom ( Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication. Genes (Basel) 2022; 13:genes13091628. [PMID: 36140797 PMCID: PMC9498453 DOI: 10.3390/genes13091628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Gomphus purpuraceus (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting body are unclear. To obtain a comprehensive overview of genetic features, whole-genome and comparative genomics analyses of G. purpuraceus were performed. High-quality DNA was extracted from the mycelium, which was isolated from a fresh fruiting body of G. purpuraceus. The DNA sample was subjected to sequencing using Illumina and Oxford Nanopore sequencing platforms. A genome assembly totaling 40.15 Mb in 50 contigs with an N50 length of 2.06 Mb was generated, and 8705 putative predicted genes were found. Subsequently, phylogenetic analysis revealed a close evolutionary relationship between G. purpuraceus and Gomphus bonarii. Moreover, a total of 403 carbohydrate-active enzymes (CAZymes) were identified in G. purpuraceus, which included 147 glycoside hydrolases (GHs), 85 glycosyl transferases (GTs), 8 polysaccharide lyases (PLs), 76 carbohydrate esterases (CEs), 57 auxiliary activities (AAs) and 30 carbohydrate-binding modules (CBMs). Compared with the other 13 fungi (Laccaria bicolor, Russula virescens, Boletus edulis, etc.), the number and distribution of CAZymes in G. purpuraceus were similar to other mycorrhizal fungi. Furthermore, the optimization of culture medium for G. purpuraceus showed the efficient utilization of disaccharides such as sucrose and maltose. The genome of G. purpuraceus provides new insights into its niche, food applications and potential artificial domestication.
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10
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Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. Proc Natl Acad Sci U S A 2022; 119:e2118852119. [PMID: 35727987 PMCID: PMC9245616 DOI: 10.1073/pnas.2118852119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Advances in DNA sequencing have provided an unprecedented view of the complex microbial communities that populate global ecosystems. We present a metatranscriptomic analysis of samples from the boreal forest—the largest terrestrial carbon store—capturing the seasonally resolved transcriptomes of Norway spruce roots and more than 350 root-associated fungal species. Our findings link the functional response of host-trees to increased nutrient availability, with profound perturbations in the fungal community. Notably, we observed an exchange in prevalence and host-coordination of specialist ectomycorrhizal species critical for enzymatic cycling of recalcitrant carbon, to metabolically versatile species with resilient melanized cell walls. This research unites kingdom-spanning taxonomic and functional details of the boreal root microbiome, contributing a missing perspective toward modeling global carbon cycling. Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.
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11
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Hillary VE, Ceasar SA. Prime editing in plants and mammalian cells: Mechanism, achievements, limitations, and future prospects. Bioessays 2022; 44:e2200032. [PMID: 35750651 DOI: 10.1002/bies.202200032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/06/2023]
Abstract
Clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system has revolutionized genetic research in the life sciences. Four classes of CRISPR/Cas-derived genome editing agents, such as nuclease, base editor, recombinase, and prime editor have been introduced for engineering the genomes of diverse organisms. The recently introduced prime editing system offers precise editing without many off-target effects than traditional CRISPR-based systems. Many researchers have successfully applied this gene-editing toolbox in diverse systems for various genome-editing applications. This review presents the mechanism of prime editing and summarizes the details of the prime editing system applied in plants and mammalian cells for precise genome editing. We also discuss the advantages, limitations, and potential future applications of prime editing in these systems. This review enables the researcher to gain knowledge on prime editing tools and their potential applications in plants and mammalian cells.
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Affiliation(s)
- V Edwin Hillary
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, India
| | - S Antony Ceasar
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, India
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12
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Villalobos Solis MI, Engle NL, Spangler MK, Cottaz S, Fort S, Maeda J, Ané JM, Tschaplinski TJ, Labbé JL, Hettich RL, Abraham PE, Rush TA. Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:808578. [PMID: 37746234 PMCID: PMC10512320 DOI: 10.3389/ffunb.2022.808578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 09/26/2023]
Abstract
The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO4), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.
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Affiliation(s)
| | - Nancy L. Engle
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Margaret K. Spangler
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sylvain Cottaz
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Sébastien Fort
- Université Grenoble Alpes, CNRS, CERMAV, Grenoble, France
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Jesse L. Labbé
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Paul E. Abraham
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Tomás A. Rush
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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13
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The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis. Proc Natl Acad Sci U S A 2022; 119:2103527119. [PMID: 35012977 PMCID: PMC8784151 DOI: 10.1073/pnas.2103527119] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Abstract
Plant genomes encode hundreds of genes controlling the detection, signaling pathways, and immune responses necessary to defend against pathogens. Pathogens, in turn, continually evolve to evade these defenses. Small RNAs, such as microRNAs (miRNAs), are one mechanism used by pathogens to overcome plant defenses and facilitate plant colonization. Mounting evidence would suggest that beneficial microbes, likewise, use miRNAs to facilitate symbiosis. Here, we demonstrate that the beneficial fungus Pisolithus microcarpus encodes a miRNA that enters plant cells and stabilizes the symbiotic interaction. These results demonstrate that beneficial fungi may regulate host gene expression through the use of miRNAs and sheds light on how beneficial microbes have evolved mechanisms to colonize plant tissues. Small RNAs (sRNAs) are known to regulate pathogenic plant–microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we characterized miRNAs encoded by the ectomycorrhizal fungus Pisolithus microcarpus and investigated their expression during mutualistic interaction with Eucalyptus grandis. Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA, Pmic_miR-8, was found to be transported into E. grandis roots after interaction with P. microcarpus. Further characterization experiments demonstrate that inhibition of Pmic_miR-8 negatively impacts the maintenance of mycorrhizal roots in E. grandis, while supplementation of Pmic_miR-8 led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that Pmic_miR-8 may target the host NB-ARC domain containing transcripts, suggesting a potential role for this miRNA in subverting host signaling to stabilize the symbiotic interaction. Altogether, we provide evidence of previously undescribed cross-kingdom sRNA transfer from ectomycorrhizal fungi to plant roots, shedding light onto the involvement of miRNAs during the developmental process of mutualistic symbioses.
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14
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Huang Z, Li H, Zhou Y, Bao Y, Duan Z, Wang C, Powell CA, Chen B, Zhang M, Yao W. Predication of the Effector Proteins Secreted by Fusarium sacchari Using Genomic Analysis and Heterogenous Expression. J Fungi (Basel) 2022; 8:jof8010059. [PMID: 35049998 PMCID: PMC8780550 DOI: 10.3390/jof8010059] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 01/01/2023] Open
Abstract
One of the causative agents of pokkah boeng disease (PBD), which affects sugarcane crops globally, is the fungus Fusarium sacchari. These fungal infections reduce sugar quality and yield, resulting in severe economic losses. Effector proteins play important roles in the interactions between pathogenic fungi and plants. Here, we used bioinformatic prediction approaches to identify 316 candidate secreted effector proteins (CSEPs) in the complete genome of F. sacchari. In total, 95 CSEPs contained known conserved structures, representing 40 superfamilies and 18 domains, while an additional 91 CSEPs contained seven known motifs. Of the 130 CSEPs containing no known domains or motifs, 14 contained one of four novel motifs. A heterogeneous expression system in Nicotiana benthamiana was used to investigate the functions of 163 CSEPs. Seven CSEPs suppressed BAX-triggered programmed cell death in N. benthamiana, while four caused cell death in N. benthamiana. The expression profiles of these eleven CSEPs during F. sacchari infection suggested that they may be involved in sugarcane-F. sacchari interaction. Our results establish a basis for further studies of the role of effector molecules in pathogen–sugarcane interactions, and provide a framework for future predictions of pathogen effector molecules.
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Affiliation(s)
- Zhen Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Huixue Li
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Yuming Zhou
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Yixue Bao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Zhenzhen Duan
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Caixia Wang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | | | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
- IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA;
- Correspondence: (M.Z.); (W.Y.)
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning 530005, China; (Z.H.); (H.L.); (Y.Z.); (Y.B.); (Z.D.); (C.W.); (B.C.)
- IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA;
- Correspondence: (M.Z.); (W.Y.)
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15
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A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor. Microorganisms 2021; 9:microorganisms9122612. [PMID: 34946213 PMCID: PMC8708209 DOI: 10.3390/microorganisms9122612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 02/05/2023] Open
Abstract
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.
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16
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Gupta GD, Bansal R, Mistry H, Pandey B, Mukherjee PK. Structure-function analysis reveals Trichoderma virens Tsp1 to be a novel fungal effector protein modulating plant defence. Int J Biol Macromol 2021; 191:267-276. [PMID: 34547313 DOI: 10.1016/j.ijbiomac.2021.09.085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022]
Abstract
Trichoderma virens colonizes roots and develops a symbiotic relationship with plants where the fungal partner derives nutrients from plants and offers defence, in return. Tsp1, a small secreted cysteine-rich protein, was earlier found to be upregulated in co-cultivation of T. virens with maize roots. Tsp1 is well conserved in Ascomycota division of fungi, but none of its homologs have been studied yet. We have expressed and purified recombinant Tsp1, and resolved its structure to 1.25 Å resolutions, from two crystal forms, using Se-SAD methods. The Tsp1 adopts a β barrel fold and forms dimer in structure as well as in solution form. DALI based structure analysis revealed the structure similarity with two known fungal effector proteins: Alt a1 and PevD1. Structure and evolutionary analysis suggested that Tsp1 belongs to a novel effector protein family. Tsp1 acted as an inducer of salicylic acid mediated susceptibility in plants, rendering maize plants more susceptible to a necrotrophic pathogen Cochliobolus heterostrophus, as observed using plant defence assay and RT-qPCR analysis.
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Affiliation(s)
- Gagan D Gupta
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India.
| | - Ravindra Bansal
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Hiral Mistry
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
| | - Bharati Pandey
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Prasun K Mukherjee
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India; Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India.
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17
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Lebreton A, Zeng Q, Miyauchi S, Kohler A, Dai YC, Martin FM. Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012021-114902] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current understanding of the limits and future potential of using genomics to understand the ecological roles of these forest fungi. Comparative genomics unraveled the molecular machineries involved in lignocellulose decomposition in wood decayers, soil and litter saprotrophs, and mycorrhizal symbionts. They also showed that transitions from saprotrophy to mutualism entailed widespread losses of lignocellulose-degrading enzymes; diversification of novel, lineage-specific symbiosis-induced genes; and convergent evolution of genetic innovations that facilitate the accommodationof mutualistic symbionts within their plant hosts. We also identify the major questions that remain unanswered and propose new avenues of genome-based research to understand the role of soil fungi in sustainable forest ecosystems.
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Affiliation(s)
- Annie Lebreton
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Qingchao Zeng
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, Köln, Germany, D-50829
| | - Annegret Kohler
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
| | - Yu-Cheng Dai
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
| | - Francis M. Martin
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Beijing, China 100083
- Université de Lorraine, Unité Mixte de Recherche (UMR) Interactions Arbres/Microorganismes, Centre INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement) Grand Est-Nancy, INRAE, 54280 Champenoux, France
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18
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Novel Microdialysis Technique Reveals a Dramatic Shift in Metabolite Secretion during the Early Stages of the Interaction between the Ectomycorrhizal Fungus Pisolithus microcarpus and Its Host Eucalyptus grandis. Microorganisms 2021; 9:microorganisms9091817. [PMID: 34576712 PMCID: PMC8465077 DOI: 10.3390/microorganisms9091817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/28/2022] Open
Abstract
The colonisation of tree roots by ectomycorrhizal (ECM) fungi is the result of numerous signalling exchanges between organisms, many of which occur before physical contact. However, information is lacking about these exchanges and the compounds that are secreted by each organism before contact. This is in part due to a lack of low disturbance sampling methods with sufficient temporal and spatial resolution to capture these exchanges. Using a novel in situ microdialysis approach, we sampled metabolites released from Eucalyptus grandis and Pisolithus microcarpus independently and during indirect contact over a 48-h time-course using UPLC-MS. A total of 560 and 1530 molecular features (MFs; ESI- and ESI+ respectively) were identified with significant differential abundance from control treatments. We observed that indirect contact between organisms altered the secretion of MFs to produce a distinct metabolomic profile compared to either organism independently. Many of these MFs were produced within the first hour of contact and included several phenylpropanoids, fatty acids and organic acids. These findings show that the secreted metabolome, particularly of the ECM fungus, can rapidly shift during the early stages of pre-symbiotic contact and highlight the importance of observing these early interactions in greater detail. We present microdialysis as a useful tool for examining plant–fungal signalling with high temporal resolution and with minimal experimental disturbance.
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Tang N, Lebreton A, Xu W, Dai Y, Yu F, Martin FM. Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius-Pinus Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:714393. [PMID: 34490014 PMCID: PMC8417538 DOI: 10.3389/fpls.2021.714393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Ectomycorrhizal fungi establish a mutualistic symbiosis in roots of most woody plants. The molecular underpinning of ectomycorrhizal development was only explored in a few lineages. Here, we characterized the symbiotic transcriptomes of several milkcap species (Lactarius, Russulales) in association with different pine hosts. A time-course study of changes in gene expression during the development of L. deliciosus-Pinus taeda symbiosis identified 6 to 594 differentially expressed fungal genes at various developmental stages. Up- or down-regulated genes are involved in signaling pathways, nutrient transport, cell wall modifications, and plant defenses. A high number of genes coding for secreted proteases, especially sedolisins, were induced during root colonization. In contrast, only a few genes encoding mycorrhiza-induced small secreted proteins were identified. This feature was confirmed in several other Lactarius species in association with various pines. Further comparison among all these species revealed that each Lactarius species encodes a highly specific symbiotic gene repertoire, a feature possibly related to their host-specificity. This study provides insights on the genetic basis of symbiosis in an ectomycorrhizal order, the Russulales, which was not investigated so far.
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Affiliation(s)
- Nianwu Tang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Wenjun Xu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Fuqiang Yu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Centre INRAE-GrandEst Nancy, INRAE, UMR Interactions Arbres/Microorganismes, Université de Lorraine, Champenoux, France
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20
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R. Cope K, B. Irving T, Chakraborty S, Ané JM. Perception of lipo-chitooligosaccharides by the bioenergy crop Populus. PLANT SIGNALING & BEHAVIOR 2021; 16:1903758. [PMID: 33794743 PMCID: PMC8143229 DOI: 10.1080/15592324.2021.1903758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Populus sp. is a developing feedstock for second-generation biofuel production. To ensure its success as a sustainable biofuel source, it is essential to capitalize on the ability of Populus sp. to associate with beneficial plant-associated microbes (e.g., mycorrhizal fungi) and engineer Populus sp. to associate with non-native symbionts (e.g., rhizobia). Here, we review recent research into the molecular mechanisms that control ectomycorrhizal associations in Populus sp. with particular emphasis on the discovery that ectomycorrhizal fungi produce lipochitooligosaccharides capable of activating the common symbiosis pathway. We also present new evidence that lipo-chitooligosaccharides produced by both ectomycorrhizal fungi and various species of rhizobia that do not associate with Populus sp. can induce nuclear calcium spiking in the roots of Populus sp. Thus, we argue Populus sp. already possesses the molecular machinery necessary for perceiving rhizobia, and the next step in engineering symbiosis with rhizobia should be focused on inducing bacterial accommodation and nodule organogenesis. The gene Nodule INception is central to these processes, and several putative orthologs are present in Populus sp. Manipulating the promoters of these genes to match that of plants in the nitrogen-fixing clade may be sufficient to introduce nodulation in Populus sp.
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Affiliation(s)
- Kevin R. Cope
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, WI,United States
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, WI,United States
| | - Thomas B. Irving
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, WI,United States
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, WI,United States
| | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, WI,United States
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, WI,United States
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, WI,United States
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, WI,United States
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21
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Marqués‐Gálvez JE, Miyauchi S, Paolocci F, Navarro‐Ródenas A, Arenas F, Pérez‐Gilabert M, Morin E, Auer L, Barry KW, Kuo A, Grigoriev IV, Martin FM, Kohler A, Morte A. Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle. THE NEW PHYTOLOGIST 2021; 229:2917-2932. [PMID: 33118170 PMCID: PMC7898904 DOI: 10.1111/nph.17044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 10/09/2020] [Indexed: 06/11/2023]
Abstract
Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Transcriptomes of T. claveryi × Helianthemum almeriense mycorrhiza from well-watered and drought-stressed plants, when intracellular colonizations is promoted, were investigated. We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-specific small secreted proteins differentially regulated in symbiosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence-related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions.
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Affiliation(s)
- José Eduardo Marqués‐Gálvez
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Shingo Miyauchi
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Francesco Paolocci
- CNR‐IBBRIstituto di Bioscienze e BiorisorseUOS di PerugiaPerugia06128Italy
| | - Alfonso Navarro‐Ródenas
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Francisco Arenas
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Manuela Pérez‐Gilabert
- Departamento de Bioquímica y Biología Molecular‐AUniversidad de MurciaCampus de EspinardoMurcia30100Spain
| | - Emmanuelle Morin
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Lucas Auer
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Kerrie W. Barry
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
| | - Alan Kuo
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCA94598USA
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCA94598USA
| | - Francis M. Martin
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Annegret Kohler
- INRAEUMR 1136Interactions Arbres/Microorganismes (IAM)Centre INRAE GrandEst ‐ NancyUniversité de LorraineChampenoux54280France
| | - Asunción Morte
- Departamento de Biología Vegetal (Botánica)Facultad de BiologíaUniversidad de MurciaCampus de EspinardoMurcia30100Spain
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22
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Dreischhoff S, Das IS, Jakobi M, Kasper K, Polle A. Local Responses and Systemic Induced Resistance Mediated by Ectomycorrhizal Fungi. FRONTIERS IN PLANT SCIENCE 2020; 11:590063. [PMID: 33381131 PMCID: PMC7767828 DOI: 10.3389/fpls.2020.590063] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/10/2020] [Indexed: 05/13/2023]
Abstract
Ectomycorrhizal fungi (EMF) grow as saprotrophs in soil and interact with plants, forming mutualistic associations with roots of many economically and ecologically important forest tree genera. EMF ensheath the root tips and produce an extensive extramatrical mycelium for nutrient uptake from the soil. In contrast to other mycorrhizal fungal symbioses, EMF do not invade plant cells but form an interface for nutrient exchange adjacent to the cortex cells. The interaction of roots and EMF affects host stress resistance but uncovering the underlying molecular mechanisms is an emerging topic. Here, we focused on local and systemic effects of EMF modulating defenses against insects or pathogens in aboveground tissues in comparison with arbuscular mycorrhizal induced systemic resistance. Molecular studies indicate a role of chitin in defense activation by EMF in local tissues and an immune response that is induced by yet unknown signals in aboveground tissues. Volatile organic compounds may be involved in long-distance communication between below- and aboveground tissues, in addition to metabolite signals in the xylem or phloem. In leaves of EMF-colonized plants, jasmonate signaling is involved in transcriptional re-wiring, leading to metabolic shifts in the secondary and nitrogen-based defense metabolism but cross talk with salicylate-related signaling is likely. Ectomycorrhizal-induced plant immunity shares commonalities with systemic acquired resistance and induced systemic resistance. We highlight novel developments and provide a guide to future research directions in EMF-induced resistance.
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Affiliation(s)
| | | | | | | | - Andrea Polle
- Forest Botany and Tree Physiology, University of Göttingen, Göttingen, Germany
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23
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Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits. Nat Commun 2020; 11:5125. [PMID: 33046698 PMCID: PMC7550596 DOI: 10.1038/s41467-020-18795-w] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022] Open
Abstract
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.
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24
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Villalobos Solis MI, Poudel S, Bonnot C, Shrestha HK, Hettich RL, Veneault-Fourrey C, Martin F, Abraham PE. A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1177-1188. [PMID: 32597696 DOI: 10.1094/mpmi-04-20-0082-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry-based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo-assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar Populus × canescens 717-1B4 in interaction with the ectomycorrhizal basidiomycete Laccaria bicolor. In total, we identified 1,660 and 2,870 Populus and L. bicolor unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of L. bicolor. These PCPs mapped to 64 Populus proteins and 69 L. bicolor proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.
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Affiliation(s)
- Manuel I Villalobos Solis
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
- Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A
| | - Suresh Poudel
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Clemence Bonnot
- UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France
| | - Him K Shrestha
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
- Department of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, U.S.A
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
| | - Claire Veneault-Fourrey
- UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France
| | - Francis Martin
- UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Microorganismes', Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux, France
| | - Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A
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25
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Plett JM, Plett KL, Wong-Bajracharya J, de Freitas Pereira M, Costa MD, Kohler A, Martin F, Anderson IC. Mycorrhizal effector PaMiSSP10b alters polyamine biosynthesis in Eucalyptus root cells and promotes root colonization. THE NEW PHYTOLOGIST 2020; 228:712-727. [PMID: 32562507 DOI: 10.1111/nph.16759] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Pathogenic microbes are known to manipulate the defences of their hosts through the production of secreted effector proteins. More recently, mutualistic mycorrhizal fungi have also been described as using these secreted effectors to promote host colonization. Here we characterize a mycorrhiza-induced small secreted effector protein of 10 kDa produced by the ectomycorrhizal fungus Pisolithus albus, PaMiSSP10b. We demonstrate that PaMiSSP10b is secreted from fungal hyphae, enters the cells of its host, Eucalyptus grandis, and interacts with an S-adenosyl methionine decarboxylase (AdoMetDC) in the polyamine pathway. Plant polyamines are regulatory molecules integral to the plant immune system during microbial challenge. Using biochemical and transgenic approaches we show that expression of PaMiSSP10b influences levels of polyamines in the plant roots as it enhances the enzymatic activity of AdoMetDC and increases the biosynthesis of higher polyamines. This ultimately favours the colonization success of P. albus. These results identify a new mechanism by which mutualistic microbes are able to manipulate the host´s enzymatic pathways to favour colonization.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Johanna Wong-Bajracharya
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Maíra de Freitas Pereira
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA GrandEst Nancy, Université de Lorraine, Champenoux, 54280, France
- Bolsista do CNPq, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maurício Dutra Costa
- Bolsista do CNPq, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Annegret Kohler
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA GrandEst Nancy, Université de Lorraine, Champenoux, 54280, France
| | - Francis Martin
- INRAE, UMR Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA GrandEst Nancy, Université de Lorraine, Champenoux, 54280, France
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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26
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Hassan MM, Yuan G, Chen JG, Tuskan GA, Yang X. Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. BIODESIGN RESEARCH 2020; 2020:9350905. [PMID: 37849904 PMCID: PMC10530660 DOI: 10.34133/2020/9350905] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 10/19/2023] Open
Abstract
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
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Affiliation(s)
- Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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27
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Bouffaud ML, Herrmann S, Tarkka MT, Bönn M, Feldhahn L, Buscot F. Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi. BMC Genomics 2020; 21:399. [PMID: 32532205 PMCID: PMC7291512 DOI: 10.1186/s12864-020-06806-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis. RESULTS The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed. CONCLUSIONS Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.
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Affiliation(s)
- Marie-Lara Bouffaud
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - Sylvie Herrmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany.
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany.
| | - Mika T Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - Markus Bönn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - Lasse Feldhahn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
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