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de Carvalho-Niebel F, Fournier J, Becker A, Marín Arancibia M. Cellular insights into legume root infection by rhizobia. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102597. [PMID: 39067084 DOI: 10.1016/j.pbi.2024.102597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 07/30/2024]
Abstract
Legume plants establish an endosymbiosis with nitrogen-fixing rhizobia bacteria, which are taken up from the environment anew by each host generation. This requires a dedicated genetic program on the host side to control microbe invasion, involving coordinated reprogramming of host cells to create infection structures that facilitate inward movement of the symbiont. Infection initiates in the epidermis, with different legumes utilizing distinct strategies for crossing this cell layer, either between cells (intercellular infection) or transcellularly (infection thread infection). Recent discoveries on the plant side using fluorescent-based imaging approaches have illuminated the spatiotemporal dynamics of infection, underscoring the importance of investigating this process at the dynamic single-cell level. Extending fluorescence-based live-dynamic approaches to the bacterial partner opens the exciting prospect of learning how individual rhizobia reprogram from rhizospheric to a host-confined state during early root infection.
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Affiliation(s)
| | - Joëlle Fournier
- LIPME, INRAE, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032, Marburg, Germany; Department of Biology, Philipps-Universität Marburg, D-35032, Marburg, Germany
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2
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Zhang Y, Fu Y, Xian W, Li X, Feng Y, Bu F, Shi Y, Chen S, van Velzen R, Battenberg K, Berry AM, Salgado MG, Liu H, Yi T, Fournier P, Alloisio N, Pujic P, Boubakri H, Schranz ME, Delaux PM, Wong GKS, Hocher V, Svistoonoff S, Gherbi H, Wang E, Kohlen W, Wall LG, Parniske M, Pawlowski K, Normand P, Doyle JJ, Cheng S. Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis. PLANT COMMUNICATIONS 2024; 5:100671. [PMID: 37553834 PMCID: PMC10811378 DOI: 10.1016/j.xplc.2023.100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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Affiliation(s)
- Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuan Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Robin van Velzen
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Marco G Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Valerie Hocher
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Hassen Gherbi
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Luis G Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Jeffrey J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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3
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Su C. Pectin modifications at the symbiotic interface. THE NEW PHYTOLOGIST 2023; 238:25-32. [PMID: 36565041 DOI: 10.1111/nph.18705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Plant cells are surrounded by a structured cell wall, which not only defines cell shape but also provides a structural barrier for protection against pathogen infection. However, the presence of this barrier does not impede the establishment of mutualistic symbioses between plants and several microbes (e.g. ectomycorrhizal fungi, arbuscular mycorrhizal fungi, and rhizobia). To establish such beneficial associations, symbiotic microbes need to colonize the plant tissues via intercellular and/or intracellular infection, a process that requires cell wall modifications. Although cell wall composition and changes during this process have interested researchers for years, the functional characterization of the molecular players involved is still limited. In this viewpoint, based on several new studies, I discuss how the PME-PL/PG pathway mediates cell wall pectin modifications at the symbiotic interface and highlight further research directions which can broaden our understanding of how beneficial root symbioses are established.
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Affiliation(s)
- Chao Su
- Plant Cell Biology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
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4
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Gasser M, Alloisio N, Fournier P, Balmand S, Kharrat O, Tulumello J, Carro L, Heddi A, Da Silva P, Normand P, Pujic P, Boubakri H. A Nonspecific Lipid Transfer Protein with Potential Functions in Infection and Nodulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1096-1108. [PMID: 36102948 DOI: 10.1094/mpmi-06-22-0131-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The response of Alnus glutinosa to Frankia alni ACN14a is driven by several sequential physiological events from calcium spiking and root-hair deformation to the development of the nodule. Early stages of actinorhizal symbiosis were monitored at the transcriptional level to observe plant host responses to Frankia alni. Forty-two genes were significantly upregulated in inoculated compared with noninoculated roots. Most of these genes encode proteins involved in biological processes induced during microbial infection, such as oxidative stress or response to stimuli, but a large number of them are not differentially modulated or downregulated later in the process of nodulation. In contrast, several of them remained upregulated in mature nodules, and this included the gene most upregulated, which encodes a nonspecific lipid transfer protein (nsLTP). Classified as an antimicrobial peptide, this nsLTP was immunolocalized on the deformed root-hair surfaces that are points of contact for Frankia spp. during infection. Later in nodules, it binds to the surface of F. alni ACN14a vesicles, which are the specialized cells for nitrogen fixation. This nsLTP, named AgLTP24, was biologically produced in a heterologous host and purified for assay on F. alni ACN14a to identify physiological effects. Thus, the activation of the plant immunity response occurs upon first contact, while the recognition of F. alni ACN14a genes switches off part of the defense system during nodulation. AgLTP24 constitutes a part of the defense system that is maintained all along the symbiosis, with potential functions such as the formation of infection threads or nodule primordia to the control of F. alni proliferation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mélanie Gasser
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Severine Balmand
- INSA-Lyon, INRAE, UMR203 BF2i, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Ons Kharrat
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Joris Tulumello
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Lorena Carro
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Abdelaziz Heddi
- INSA-Lyon, INRAE, UMR203 BF2i, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Pedro Da Silva
- INSA-Lyon, INRAE, UMR203 BF2i, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
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5
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Chetri SPK, Rahman Z, Thomas L, Lal R, Gour T, Agarwal LK, Vashishtha A, Kumar S, Kumar G, Kumar R, Sharma K. Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives. J Basic Microbiol 2022; 62:764-778. [PMID: 35638879 DOI: 10.1002/jobm.202200043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/17/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
Abstract
Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N2 ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N2 ) accessible and bioavailable in the form of ammonium (NH4 + ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.
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Affiliation(s)
| | - Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, New Delhi, Delhi, India
| | - Ratan Lal
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Tripti Gour
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Akanksha Vashishtha
- Department of Plant Protection, CCS University, Meerut, Uttar Pradesh, India
| | - Sachin Kumar
- Department of Botany, Shri Venkateshwara College, University of Delhi, New Delhi, Delhi, India
| | - Gaurav Kumar
- Department of Environmental Studies, PGDAV College, University of Delhi, New Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Botany, Hindu College, University of Delhi, New Delhi, Delhi, India
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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6
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Li FW, Nishiyama T, Waller M, Frangedakis E, Keller J, Li Z, Fernandez-Pozo N, Barker MS, Bennett T, Blázquez MA, Cheng S, Cuming AC, de Vries J, de Vries S, Delaux PM, Diop IS, Harrison CJ, Hauser D, Hernández-García J, Kirbis A, Meeks JC, Monte I, Mutte SK, Neubauer A, Quandt D, Robison T, Shimamura M, Rensing SA, Villarreal JC, Weijers D, Wicke S, Wong GKS, Sakakibara K, Szövényi P. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. NATURE PLANTS 2020; 6:259-272. [PMID: 32170292 PMCID: PMC8075897 DOI: 10.1038/s41477-020-0618-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/11/2020] [Indexed: 05/12/2023]
Abstract
Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.
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Affiliation(s)
- Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Ishikawa, Japan
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Tom Bennett
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Andrew C Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Jan de Vries
- Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Georg-August University Göttingen, Göttingen, Germany
| | - Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Pierre-Marc Delaux
- LRSV, Université de Toulouse, CNRS, UPS Castanet-Tolosan, Toulouse, France
| | - Issa S Diop
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Isabel Monte
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Sumanth K Mutte
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Tanner Robison
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Stefan A Rensing
- Faculty of Biology, Philipps University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, Canada
- Smithsonian Tropical Research Institute, Balboa, Panamá
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, the Netherlands
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Münster, Germany
| | - Gane K-S Wong
- Department of Biological Sciences, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Shenzhen, China
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
- Zurich-Basel Plant Science Center, Zurich, Switzerland.
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7
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Chabaud M, Fournier J, Brichet L, Abdou-Pavy I, Imanishi L, Brottier L, Pirolles E, Hocher V, Franche C, Bogusz D, Wall LG, Svistoonoff S, Gherbi H, Barker DG. Chitotetraose activates the fungal-dependent endosymbiotic signaling pathway in actinorhizal plant species. PLoS One 2019; 14:e0223149. [PMID: 31600251 PMCID: PMC6786586 DOI: 10.1371/journal.pone.0223149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/13/2019] [Indexed: 01/17/2023] Open
Abstract
Mutualistic plant-microbe associations are widespread in natural ecosystems and have made major contributions throughout the evolutionary history of terrestrial plants. Amongst the most remarkable of these are the so-called root endosymbioses, resulting from the intracellular colonization of host tissues by either arbuscular mycorrhizal (AM) fungi or nitrogen-fixing bacteria that both provide key nutrients to the host in exchange for energy-rich photosynthates. Actinorhizal host plants, members of the Eurosid 1 clade, are able to associate with both AM fungi and nitrogen-fixing actinomycetes known as Frankia. Currently, little is known about the molecular signaling that allows these plants to recognize their fungal and bacterial partners. In this article, we describe the use of an in vivo Ca2+ reporter to identify symbiotic signaling responses to AM fungi in roots of both Casuarina glauca and Discaria trinervis, actinorhizal species with contrasting modes of Frankia colonization. This approach has revealed that, for both actinorhizal hosts, the short-chain chitin oligomer chitotetraose is able to mimic AM fungal exudates in activating the conserved symbiosis signaling pathway (CSSP) in epidermal root cells targeted by AM fungi. These results mirror findings in other AM host plants including legumes and the monocot rice. In addition, we show that chitotetraose is a more efficient elicitor of CSSP activation compared to AM fungal lipo-chitooligosaccharides. These findings reinforce the likely role of short-chain chitin oligomers during the initial stages of the AM association, and are discussed in relation to both our current knowledge about molecular signaling during Frankia recognition as well as the different microsymbiont root colonization mechanisms employed by actinorhizal hosts.
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Affiliation(s)
- Mireille Chabaud
- Laboratory of Plant-Microbe Interactions (INRA/CNRS/University of Toulouse), Castanet-Tolosan, France
| | - Joëlle Fournier
- Laboratory of Plant-Microbe Interactions (INRA/CNRS/University of Toulouse), Castanet-Tolosan, France
| | - Lukas Brichet
- Laboratory of Plant-Microbe Interactions (INRA/CNRS/University of Toulouse), Castanet-Tolosan, France
| | - Iltaf Abdou-Pavy
- Laboratory of Plant-Microbe Interactions (INRA/CNRS/University of Toulouse), Castanet-Tolosan, France
| | - Leandro Imanishi
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Laurent Brottier
- Laboratory of Tropical and Mediterranean Symbioses (IRD/INRA/CIRAD/University of Montpellier/Supagro), Montpellier, France
| | - Elodie Pirolles
- Laboratory of Tropical and Mediterranean Symbioses (IRD/INRA/CIRAD/University of Montpellier/Supagro), Montpellier, France
| | - Valérie Hocher
- Laboratory of Tropical and Mediterranean Symbioses (IRD/INRA/CIRAD/University of Montpellier/Supagro), Montpellier, France
| | - Claudine Franche
- Plant Diversity, Adaptation and Development (IRD/University of Montpellier), Montpellier, France
| | - Didier Bogusz
- Plant Diversity, Adaptation and Development (IRD/University of Montpellier), Montpellier, France
| | - Luis G. Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Sergio Svistoonoff
- Laboratory of Tropical and Mediterranean Symbioses (IRD/INRA/CIRAD/University of Montpellier/Supagro), Montpellier, France
| | - Hassen Gherbi
- Laboratory of Tropical and Mediterranean Symbioses (IRD/INRA/CIRAD/University of Montpellier/Supagro), Montpellier, France
| | - David G. Barker
- Laboratory of Plant-Microbe Interactions (INRA/CNRS/University of Toulouse), Castanet-Tolosan, France
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8
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Salgado MG, van Velzen R, Nguyen TV, Battenberg K, Berry AM, Lundin D, Pawlowski K. Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales). FRONTIERS IN PLANT SCIENCE 2018; 9:1629. [PMID: 30487804 PMCID: PMC6246699 DOI: 10.3389/fpls.2018.01629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/19/2018] [Indexed: 05/09/2023]
Abstract
Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.
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Affiliation(s)
- Marco G. Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Alison M. Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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9
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Hocher V, Ngom M, Carré-Mlouka A, Tisseyre P, Gherbi H, Svistoonoff S. Signalling in actinorhizal root nodule symbioses. Antonie van Leeuwenhoek 2018; 112:23-29. [PMID: 30306463 DOI: 10.1007/s10482-018-1182-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/06/2018] [Indexed: 11/29/2022]
Abstract
Plants able to establish a nitrogen-fixing root nodule symbiosis with the actinobacterium Frankia are called actinorhizal. These interactions lead to the formation of new root organs, called actinorhizal nodules, where the bacteria are hosted intracellularly and fix atmospheric nitrogen thus providing the plant with an almost unlimited source of nitrogen for its nutrition. Like other symbiotic interactions, actinorhizal nodulation involves elaborate signalling between both partners of the symbiosis, leading to specific recognition between the plant and its compatible microbial partner, its accommodation inside plant cells and the development of functional root nodules. Actinorhizal nodulation shares many features with rhizobial nodulation but our knowledge on the molecular mechanisms involved in actinorhizal nodulation remains very scarce. However recent technical achievements for several actinorhizal species are allowing major discoveries in this field. In this review, we provide an outline on signalling molecules involved at different stages of actinorhizal nodule formation and the corresponding signalling pathways and gene networks.
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Affiliation(s)
- Valérie Hocher
- LSTM, UMR 040 IRD/INRA/CIRAD, Université Montpellier/Supagro, TA A-82/J, Campus International de Baillarguet, 34398, Montpellier CDX 5, France
| | - Mariama Ngom
- LCM, IRD/ISRA, UCAD, Centre de Recherche de Bel Air, BP 1386, Dakar, Senegal.,LMI LAPSE, Centre de Recherche de Bel Air, BP 1386, Dakar, Senegal
| | - Alyssa Carré-Mlouka
- LSTM, UMR 040 IRD/INRA/CIRAD, Université Montpellier/Supagro, TA A-82/J, Campus International de Baillarguet, 34398, Montpellier CDX 5, France.,MCAM, UMR 7245 CNRS/MNHN, Sorbonne Universités, CP 54, 57 rue Cuvier, 75005, Paris, France
| | - Pierre Tisseyre
- LSTM, UMR 040 IRD/INRA/CIRAD, Université Montpellier/Supagro, TA A-82/J, Campus International de Baillarguet, 34398, Montpellier CDX 5, France
| | - Hassen Gherbi
- LSTM, UMR 040 IRD/INRA/CIRAD, Université Montpellier/Supagro, TA A-82/J, Campus International de Baillarguet, 34398, Montpellier CDX 5, France
| | - Sergio Svistoonoff
- LSTM, UMR 040 IRD/INRA/CIRAD, Université Montpellier/Supagro, TA A-82/J, Campus International de Baillarguet, 34398, Montpellier CDX 5, France. .,LCM, IRD/ISRA, UCAD, Centre de Recherche de Bel Air, BP 1386, Dakar, Senegal. .,LMI LAPSE, Centre de Recherche de Bel Air, BP 1386, Dakar, Senegal.
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