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Porter SS, Dupin SE, Denison RF, Kiers ET, Sachs JL. Host-imposed control mechanisms in legume-rhizobia symbiosis. Nat Microbiol 2024:10.1038/s41564-024-01762-2. [PMID: 39095495 DOI: 10.1038/s41564-024-01762-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/17/2024] [Indexed: 08/04/2024]
Abstract
Legumes are ecologically and economically important plants that contribute to nutrient cycling and agricultural sustainability, features tied to their intimate symbiosis with nitrogen-fixing rhizobia. Rhizobia vary dramatically in quality, ranging from highly growth-promoting to non-beneficial; therefore, legumes must optimize their symbiosis with rhizobia through host mechanisms that select for beneficial rhizobia and limit losses to non-beneficial strains. In this Perspective, we examine the considerable scientific progress made in decoding host control over rhizobia, empirically examining both molecular and cellular mechanisms and their effects on rhizobia symbiosis and its benefits. We consider pre-infection controls, which require the production and detection of precise molecular signals by the legume to attract and select for compatible rhizobia strains. We also discuss post-infection mechanisms that leverage the nodule-level and cell-level compartmentalization of symbionts to enable host control over rhizobia development and proliferation in planta. These layers of host control each contribute to legume fitness by directing host resources towards a narrowing subset of more-beneficial rhizobia.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Simon E Dupin
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - R Ford Denison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joel L Sachs
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, USA.
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2
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Ding Y, Wang T, Gasciolli V, Reyt G, Remblière C, Marcel F, François T, Bendahmane A, He G, Bono JJ, Lefebvre B. The LysM Receptor-Like Kinase SlLYK10 Controls Lipochitooligosaccharide Signaling in Inner Cell Layers of Tomato Roots. PLANT & CELL PHYSIOLOGY 2024; 65:1149-1159. [PMID: 38581668 DOI: 10.1093/pcp/pcae035] [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: 11/22/2023] [Revised: 03/04/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024]
Abstract
Establishment of arbuscular mycorrhiza relies on a plant signaling pathway that can be activated by fungal chitinic signals such as short-chain chitooligosaccharides and lipo-chitooligosaccharides (LCOs). The tomato LysM receptor-like kinase SlLYK10 has high affinity for LCOs and is involved in root colonization by arbuscular mycorrhizal fungi (AMF); however, its role in LCO responses has not yet been studied. Here, we show that SlLYK10 proteins produced by the Sllyk10-1 and Sllyk10-2 mutant alleles, which both cause decreases in AMF colonization and carry mutations in LysM1 and 2, respectively, have similar LCO-binding affinities compared to the WT SlLYK10. However, the mutant forms were no longer able to induce cell death in Nicotiana benthamiana when co-expressed with MtLYK3, a Medicago truncatula LCO co-receptor, while they physically interacted with MtLYK3 in co-purification experiments. This suggests that the LysM mutations affect the ability of SlLYK10 to trigger signaling through a potential co-receptor rather than its ability to bind LCOs. Interestingly, tomato lines that contain a calcium (Ca2+) concentration reporter [genetically encoded Ca2+ indicators (GECO)], showed Ca2+ spiking in response to LCO applications, but this occurred only in inner cell layers of the roots, while short-chain chitooligosaccharides also induced Ca2+ spiking in the epidermis. Moreover, LCO-induced Ca2+ spiking was decreased in Sllyk10-1*GECO plants, suggesting that the decrease in AMF colonization in Sllyk10-1 is due to abnormal LCO signaling.
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Affiliation(s)
- Yi Ding
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Tongming Wang
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Virginie Gasciolli
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Guilhem Reyt
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Céline Remblière
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Fabien Marcel
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Gif sur Yvette 91190, France
| | - Tracy François
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Gif sur Yvette 91190, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Gif sur Yvette 91190, France
| | - Guanghua He
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jean Jacques Bono
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
| | - Benoit Lefebvre
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan 31326, France
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3
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Dallachiesa D, Aguilar OM, Lozano MJ. Improved detection and phylogenetic analysis of plant proteins containing LysM domains. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:NULL. [PMID: 38007819 DOI: 10.1071/fp23131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/31/2023] [Indexed: 11/28/2023]
Abstract
Plants perceive N-acetyl-d-glucosamine-containing oligosaccharides that play a role in the interaction with bacteria and fungi, through cell-surface receptors containing a tight bundle of three LysM domains in their extracellular region. However, the identification of LysM domains of receptor-like kinases (RLK)/receptor-like proteins (RLP) using sequence based methods has led to some ambiguity, as some proteins have been annotated with only one or two LysM domains. This missing annotation was likely produced by the failure of the LysM hidden Markov model (HMM) from the Pfam database to correctly identify some LysM domains in proteins of plant origin. In this work, we provide improved HMMs for LysM domain detection in plants, that were built from the structural alignment of manually curated LysM domain structures from the Protein Data Bank and AlphaFold Protein Structure Database. Furthermore, we evaluated different sets of ligand-specific HMMs that were able to correctly classify a limited set of fully characterised RLK/Ps by their ligand specificity. In contrast, the phylogenetic analysis of the extracellular region of RLK/Ps, or of their individual LysM domains, was unable to discriminate these proteins by their ligand specificity. The HMMs reported here will allow a more sensitive detection of plant proteins containing LysM domains and help improve their characterisation.
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Affiliation(s)
- Dardo Dallachiesa
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET-CCT La Plata - Universidad Nacional de La Plata, La Plata, Argentina
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET-CCT La Plata - Universidad Nacional de La Plata, La Plata, Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET-CCT La Plata - Universidad Nacional de La Plata, La Plata, Argentina
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Zartdinova R, Nikitin A. Calcium in the Life Cycle of Legume Root Nodules. Indian J Microbiol 2023; 63:410-420. [PMID: 38031601 PMCID: PMC10682328 DOI: 10.1007/s12088-023-01107-3] [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: 10/26/2022] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
The present review highlights both the fundamental questions of calcium localization, compartmentation, and its participation in symbiosome signaling cascades during nodule formation and functioning. Apparently, the main link of such signaling is the calmodulin…calcium- and calmodulin-dependent protein kinases…CYCLOPS…NIN…target genes cascade. The minimum threshold level of calcium as a signaling agent in the presence of intracellular reserves determines the possibility of oligotrophy and ultraoligotrophy in relation to this element. During the functioning of root nodules, the Ca2+-ATPases activity maintains homeostasis of low calcium concentrations in the cytosol of nodule parenchyma cells. Disturbation of this homeostasis can trigger the root nodule senescence. The same reasons determine the increase in the effectiveness of symbiosis with the help of seed priming with sources of calcium. Examples of calcium response polymorphism in components of nitrogen fixing simbiosis important in practical terms are shown.
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Affiliation(s)
- Rozaliya Zartdinova
- Nitrogen Exchange Laboratory, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Nikitin
- Nitrogen Exchange Laboratory, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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Faysal Ahmed F, Dola FS, Zohra FT, Rahman SM, Konak JN, Sarkar MAR. Genome-wide identification, classification, and characterization of lectin gene superfamily in sweet orange (Citrus sinensis L.). PLoS One 2023; 18:e0294233. [PMID: 37956187 PMCID: PMC10642848 DOI: 10.1371/journal.pone.0294233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Lectins are sugar-binding proteins found abundantly in plants. Lectin superfamily members have diverse roles, including plant growth, development, cellular processes, stress responses, and defense against microbes. However, the genome-wide identification and functional analysis of lectin genes in sweet orange (Citrus sinensis L.) remain unexplored. Therefore, we used integrated bioinformatics approaches (IBA) for in-depth genome-wide identification, characterization, and regulatory factor analysis of sweet orange lectin genes. Through genome-wide comparative analysis, we identified a total of 141 lectin genes distributed across 10 distinct gene families such as 68 CsB-Lectin, 13 CsLysin Motif (LysM), 4 CsChitin-Bind1, 1 CsLec-C, 3 CsGal-B, 1 CsCalreticulin, 3 CsJacalin, 13 CsPhloem, 11 CsGal-Lec, and 24 CsLectinlegB.This classification relied on characteristic domain and phylogenetic analysis, showing significant homology with Arabidopsis thaliana's lectin gene families. A thorough analysis unveiled common similarities within specific groups and notable variations across different protein groups. Gene Ontology (GO) enrichment analysis highlighted the predicted genes' roles in diverse cellular components, metabolic processes, and stress-related regulation. Additionally, network analysis of lectin genes with transcription factors (TFs) identified pivotal regulators like ERF, MYB, NAC, WRKY, bHLH, bZIP, and TCP. The cis-acting regulatory elements (CAREs) found in sweet orange lectin genes showed their roles in crucial pathways, including light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and more. These findings will aid in the in-depth molecular examination of these potential genes and their regulatory elements, contributing to targeted enhancements of sweet orange species in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Department of Biochemistry and Molecular Biology, Faculty of LifeScience, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Cullimore J, Fliegmann J, Gasciolli V, Gibelin-Viala C, Carles N, Luu TB, Girardin A, Cumener M, Maillet F, Pradeau S, Fort S, Bono JJ, Gough C, Lefebvre B. Evolution of lipochitooligosaccharide binding to a LysM-RLK for nodulation in Medicago truncatula. PLANT & CELL PHYSIOLOGY 2023:pcad033. [PMID: 37098213 DOI: 10.1093/pcp/pcad033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 06/19/2023]
Abstract
Lysin motif receptor like kinases (LysM-RLKs) are involved in the perception of chitooligosaccharides (COs) and related lipochitooligosaccharides (LCOs) in plants. Expansion and divergence of the gene family during evolution have led to various roles in symbiosis and defence. By studying proteins of the LYR-IA subclass of LysM-RLKs of the Poaceae, we show here that they are high affinity LCO binding proteins with a lower affinity for COs, consistent with a role in LCO perception to establish arbuscular mycorrhiza (AM). In Papilionoid legumes whole genome duplication has resulted in two LYR-IA paralogs, MtLYR1 and MtNFP in Medicago truncatula, with MtNFP playing an essential role in the root nodule symbiosis with nitrogen-fixing rhizobia. We show that MtLYR1 has retained the ancestral LCO binding characteristic and is dispensable for AM. Domain swapping between the three Lysin motifs (LysMs) of MtNFP and MtLYR1 and mutagenesis in MtLYR1 suggest that the MtLYR1 LCO binding site is on the second LysM, and that divergence in MtNFP led to better nodulation, but surprisingly with decreased LCO binding. These results suggest that divergence of the LCO binding site has been important for the evolution of a role of MtNFP in nodulation with rhizobia.
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Affiliation(s)
- Julie Cullimore
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Judith Fliegmann
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Virginie Gasciolli
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Chrystel Gibelin-Viala
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Noémie Carles
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Thi-Bich Luu
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Ariane Girardin
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Marie Cumener
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Fabienne Maillet
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | | | - Sébastien Fort
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Jean-Jacques Bono
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Clare Gough
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
| | - Benoit Lefebvre
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, 31326 Castanet-Tolosan Cedex, France
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7
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Cope KR, Prates ET, Miller JI, Demerdash ON, Shah M, Kainer D, Cliff A, Sullivan KA, Cashman M, Lane M, Matthiadis A, Labbé J, Tschaplinski TJ, Jacobson DA, Kalluri UC. Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus. Comput Struct Biotechnol J 2022; 21:1122-1139. [PMID: 36789259 PMCID: PMC9900275 DOI: 10.1016/j.csbj.2022.12.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/18/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023] Open
Abstract
For plants, distinguishing between mutualistic and pathogenic microbes is a matter of survival. All microbes contain microbe-associated molecular patterns (MAMPs) that are perceived by plant pattern recognition receptors (PRRs). Lysin motif receptor-like kinases (LysM-RLKs) are PRRs attuned for binding and triggering a response to specific MAMPs, including chitin oligomers (COs) in fungi, lipo-chitooligosaccharides (LCOs), which are produced by mycorrhizal fungi and nitrogen-fixing rhizobial bacteria, and peptidoglycan in bacteria. The identification and characterization of LysM-RLKs in candidate bioenergy crops including Populus are limited compared to other model plant species, thus inhibiting our ability to both understand and engineer microbe-mediated gains in plant productivity. As such, we performed a sequence analysis of LysM-RLKs in the Populus genome and predicted their function based on phylogenetic analysis with known LysM-RLKs. Then, using predictive models, molecular dynamics simulations, and comparative structural analysis with previously characterized CO and LCO plant receptors, we identified probable ligand-binding sites in Populus LysM-RLKs. Using several machine learning models, we predicted remarkably consistent binding affinity rankings of Populus proteins to CO. In addition, we used a modified Random Walk with Restart network-topology based approach to identify a subset of Populus LysM-RLKs that are functionally related and propose a corresponding signal transduction cascade. Our findings provide the first look into the role of LysM-RLKs in Populus-microbe interactions and establish a crucial jumping-off point for future research efforts to understand specificity and redundancy in microbial perception mechanisms.
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Affiliation(s)
- Kevin R. Cope
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Erica T. Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John I. Miller
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Omar N.A. Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manesh Shah
- Genome Science and Technology, The University of Tennessee–Knoxville, Knoxville, TN 37996, USA
| | - David Kainer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ashley Cliff
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Kyle A. Sullivan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mikaela Cashman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew Lane
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Anna Matthiadis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Daniel A. Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,Corresponding author.
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Cervantes-Pérez SA, Thibivilliers S, Laffont C, Farmer AD, Frugier F, Libault M. Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume. MOLECULAR PLANT 2022; 15:1868-1888. [PMID: 36321199 DOI: 10.1016/j.molp.2022.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell types, showing the strongest differential regulation in response to a short-term (48 h) rhizobium inoculation, revealed not only known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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9
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do Nascimento SV, Herrera H, Costa PHDO, Trindade FC, da Costa IRC, Caldeira CF, Gastauer M, Ramos SJ, Oliveira G, Valadares RBDS. Molecular Mechanisms Underlying Mimosa acutistipula Success in Amazonian Rehabilitating Minelands. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14441. [PMID: 36361325 PMCID: PMC9654444 DOI: 10.3390/ijerph192114441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Mimosa acutistipula is endemic to Brazil and grows in ferruginous outcrops (canga) in Serra dos Carajás, eastern Amazon, where one of the largest iron ore deposits in the world is located. Plants that develop in these ecosystems are subject to severe environmental conditions and must have adaptive mechanisms to grow and thrive in cangas. Mimosa acutistipula is a native species used to restore biodiversity in post-mining areas in canga. Understanding the molecular mechanisms involved in the adaptation of M. acutistipula in canga is essential to deduce the ability of native species to adapt to possible stressors in rehabilitating minelands over time. In this study, the root proteomic profiles of M. acutistipula grown in a native canga ecosystem and rehabilitating minelands were compared to identify essential proteins involved in the adaptation of this species in its native environment and that should enable its establishment in rehabilitating minelands. The results showed differentially abundant proteins, where 436 proteins with significant values (p < 0.05) and fold change ≥ 2 were more abundant in canga and 145 in roots from the rehabilitating minelands. Among them, a representative amount and diversity of proteins were related to responses to water deficit, heat, and responses to metal ions. Other identified proteins are involved in biocontrol activity against phytopathogens and symbiosis. This research provides insights into proteins involved in M. acutistipula responses to environmental stimuli, suggesting critical mechanisms to support the establishment of native canga plants in rehabilitating minelands over time.
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Affiliation(s)
- Sidney Vasconcelos do Nascimento
- Instituto Tecnologico Vale, Rua Boaventura da Silva 955, Belém 66050-090, PA, Brazil
- Programa de Pos-Graduacão em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Héctor Herrera
- Laboratorio de Silvicultura, Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | | | - Felipe Costa Trindade
- Programa de Pos-Graduacão em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Isa Rebecca Chagas da Costa
- Programa de Pos-Graduacão em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | | | - Markus Gastauer
- Instituto Tecnologico Vale, Rua Boaventura da Silva 955, Belém 66050-090, PA, Brazil
| | - Silvio Junio Ramos
- Instituto Tecnologico Vale, Rua Boaventura da Silva 955, Belém 66050-090, PA, Brazil
| | - Guilherme Oliveira
- Instituto Tecnologico Vale, Rua Boaventura da Silva 955, Belém 66050-090, PA, Brazil
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Li XR, Sun J, Albinsky D, Zarrabian D, Hull R, Lee T, Jarratt-Barnham E, Chiu CH, Jacobsen A, Soumpourou E, Albanese A, Kohlen W, Luginbuehl LH, Guillotin B, Lawrensen T, Lin H, Murray J, Wallington E, Harwood W, Choi J, Paszkowski U, Oldroyd GED. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2. Nat Commun 2022; 13:6421. [PMID: 36307431 PMCID: PMC9616857 DOI: 10.1038/s41467-022-33908-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.
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Affiliation(s)
- Xin-Ran Li
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Jongho Sun
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Doris Albinsky
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Darius Zarrabian
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Raphaella Hull
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Tak Lee
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Edwin Jarratt-Barnham
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Chai Hao Chiu
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Amy Jacobsen
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Eleni Soumpourou
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Alessio Albanese
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wouter Kohlen
- grid.4818.50000 0001 0791 5666Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Leonie H. Luginbuehl
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bruno Guillotin
- grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France ,grid.137628.90000 0004 1936 8753Present Address: NYU-Center of Genomic and System Biology, 12 Waverly Place, New York, NY USA
| | - Tom Lawrensen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Hui Lin
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeremy Murray
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Emma Wallington
- grid.17595.3f0000 0004 0383 6532NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wendy Harwood
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeongmin Choi
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Uta Paszkowski
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Giles E. D. Oldroyd
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
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11
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Ren CG, Kong CC, Liu ZY, Zhong ZH, Yang JC, Wang XL, Qin S. A Perspective on Developing a Plant ‘Holobiont’ for Future Saline Agriculture. Front Microbiol 2022; 13:763014. [PMID: 35602056 PMCID: PMC9120776 DOI: 10.3389/fmicb.2022.763014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/28/2022] [Indexed: 11/24/2022] Open
Abstract
Soil salinity adversely affects plant growth and has become a major limiting factor for agricultural development worldwide. There is a continuing demand for sustainable technology innovation in saline agriculture. Among various bio-techniques being used to reduce the salinity hazard, symbiotic microorganisms such as rhizobia and arbuscular mycorrhizal (AM) fungi have proved to be efficient. These symbiotic associations each deploy an array of well-tuned mechanisms to provide salinity tolerance for the plant. In this review, we first comprehensively cover major research advances in symbiont-induced salinity tolerance in plants. Second, we describe the common signaling process used by legumes to control symbiosis establishment with rhizobia and AM fungi. Multi-omics technologies have enabled us to identify and characterize more genes involved in symbiosis, and eventually, map out the key signaling pathways. These developments have laid the foundation for technological innovations that use symbiotic microorganisms to improve crop salt tolerance on a larger scale. Thus, with the aim of better utilizing symbiotic microorganisms in saline agriculture, we propose the possibility of developing non-legume ‘holobionts’ by taking advantage of newly developed genome editing technology. This will open a new avenue for capitalizing on symbiotic microorganisms to enhance plant saline tolerance for increased sustainability and yields in saline agriculture.
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Affiliation(s)
- Cheng-Gang Ren
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China
| | - Cun-Cui Kong
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zheng-Yi Liu
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhi-Hai Zhong
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China
| | | | - Xiao-Li Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Song Qin
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Song Qin,
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12
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The microscopic mechanism between endophytic fungi and host plants: From recognition to building stable mutually beneficial relationships. Microbiol Res 2022; 261:127056. [DOI: 10.1016/j.micres.2022.127056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/21/2022]
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13
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Mukherjee A. What do we know from the transcriptomic studies investigating the interactions between plants and plant growth-promoting bacteria? FRONTIERS IN PLANT SCIENCE 2022; 13:997308. [PMID: 36186072 PMCID: PMC9521398 DOI: 10.3389/fpls.2022.997308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023]
Abstract
Major crops such as corn, wheat, and rice can benefit from interactions with various plant growth-promoting bacteria (PGPB). Naturally, several studies have investigated the primary mechanisms by which these PGPB promote plant growth. These mechanisms involve biological nitrogen fixation, phytohormone synthesis, protection against biotic and abiotic stresses, etc. Decades of genetic and biochemical studies in the legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis have identified a few key plant and microbial signals regulating these symbioses. Furthermore, genetic studies in legumes have identified the host genetic pathways controlling these symbioses. But, the same depth of information does not exist for the interactions between host plants and PGPB. For instance, our knowledge of the host genes and the pathways involved in these interactions is very poor. However, some transcriptomic studies have investigated the regulation of gene expression in host plants during these interactions in recent years. In this review, we discuss some of the major findings from these studies and discuss what lies ahead. Identifying the genetic pathway(s) regulating these plant-PGPB interactions will be important as we explore ways to improve crop production sustainably.
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14
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Kinetic proofreading of lipochitooligosaccharides determines signal activation of symbiotic plant receptors. Proc Natl Acad Sci U S A 2021; 118:2111031118. [PMID: 34716271 PMCID: PMC8612216 DOI: 10.1073/pnas.2111031118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/21/2021] [Indexed: 01/31/2023] Open
Abstract
Plants and animals use cell surface receptors to sense and interpret environmental signals. In legume symbiosis with nitrogen-fixing bacteria, the specific recognition of bacterial lipochitooligosaccharide (LCO) signals by single-pass transmembrane receptor kinases determines compatibility. Here, we determine the structural basis for LCO perception from the crystal structures of two lysin motif receptor ectodomains and identify a hydrophobic patch in the binding site essential for LCO recognition and symbiotic function. We show that the receptor monitors the composition of the amphiphilic LCO molecules and uses kinetic proofreading to control receptor activation and signaling specificity. We demonstrate engineering of the LCO binding site to fine-tune ligand selectivity and correct binding kinetics required for activation of symbiotic signaling in plants. Finally, the hydrophobic patch is found to be a conserved structural signature in this class of LCO receptors across legumes that can be used for in silico predictions. Our results provide insights into the mechanism of cell-surface receptor activation by kinetic proofreading of ligands and highlight the potential in receptor engineering to capture benefits in plant-microbe interactions.
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15
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Rousseau A, Armand S, Cottaz S, Fort S. Size-Controlled Synthesis of β(1→4)-GlcNAc Oligosaccharides Using an Endo-Glycosynthase. Chemistry 2021; 27:17637-17646. [PMID: 34633724 DOI: 10.1002/chem.202103212] [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: 09/03/2021] [Indexed: 11/11/2022]
Abstract
Chitin and peptidoglycan fragments are well recognized as pathogen associated molecular patterns (PAMPs). Long-chain oligosaccharides of β(1→4)-linked N-acetyl-D-glucosamine (GlcNAc) units indeed activate plants and mammals innate immune system. However, the mechanisms underlying PAMPs perception by lysine motif (LysM) domain receptors remain largely unknown because of insufficient availability of high-affinity molecular probes. Here, we report a two-enzyme cascade to synthesize long-chain β(1→4)-linked GlcNAc oligomers. Expression of the D52S mutant of hen egg-white lysozyme (HEWL) in Pichia pastoris at 52 mg L-1 provided a new glycosynthase catalyzing efficient polymerization of α-chitintriosyl fluoride. Selective N-deacetylation at the non-reducing unit of the glycosyl fluoride donor by Sinorhizobium meliloti NodB chitin-N-deacetylase abolished its ability to be polymerized by the glycosynthase but not to be transferred onto an acceptor. Using NodB and D52S HEWL in a one-pot cascade reaction allowed the synthesis on a milligram scale of chitin hexa-, hepta- and octasaccharides with yields up to 65 % and a perfect control over their size.
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Affiliation(s)
| | - Sylvie Armand
- CERMAV, Univ. Grenoble Alpes, CNRS, 38000, Grenoble, France
| | - Sylvain Cottaz
- CERMAV, Univ. Grenoble Alpes, CNRS, 38000, Grenoble, France
| | - Sébastien Fort
- CERMAV, Univ. Grenoble Alpes, CNRS, 38000, Grenoble, France
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16
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Quilbé J, Lamy L, Brottier L, Leleux P, Fardoux J, Rivallan R, Benichou T, Guyonnet R, Becana M, Villar I, Garsmeur O, Hufnagel B, Delteil A, Gully D, Chaintreuil C, Pervent M, Cartieaux F, Bourge M, Valentin N, Martin G, Fontaine L, Droc G, Dereeper A, Farmer A, Libourel C, Nouwen N, Gressent F, Mournet P, D'Hont A, Giraud E, Klopp C, Arrighi JF. Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis. Nat Commun 2021; 12:829. [PMID: 33547303 PMCID: PMC7864950 DOI: 10.1038/s41467-021-21094-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium-legume symbiosis.
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Affiliation(s)
- Johan Quilbé
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Philippe Leleux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Thomas Benichou
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Bárbara Hufnagel
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Amandine Delteil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Mickaël Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Valentin
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Loïc Fontaine
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34398, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Cyril Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France.
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Soyano T, Liu M, Kawaguchi M, Hayashi M. Leguminous nodule symbiosis involves recruitment of factors contributing to lateral root development. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:102000. [PMID: 33454544 DOI: 10.1016/j.pbi.2020.102000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 05/27/2023]
Abstract
Legumes and several plant species in the monophyletic nitrogen-fixing clade produce root nodules that function as symbiotic organs and establish mutualistic relationships with nitrogen-fixing bacteria. The modes of nodule organogenesis are distinct from those of lateral root development and also differ among different types of nodules formed in legumes and actinorhizal plants. It is considered that the evolution of new organs occurs through rearrangement of molecular networks interposed by certain neo-functionalized factors. Accumulating evidence has suggested that root nodule organogenesis involves root or lateral root developmental pathways. This review describes the current knowledge about the factors/pathways acquired by the common ancestor of the nitrogen-fixing clade in order to control nodule organogenesis.
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Affiliation(s)
- Takashi Soyano
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (the Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan.
| | - Meng Liu
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (the Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
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18
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Rutten L, Miyata K, Roswanjaya YP, Huisman R, Bu F, Hartog M, Linders S, van Velzen R, van Zeijl A, Bisseling T, Kohlen W, Geurts R. Duplication of Symbiotic Lysin Motif Receptors Predates the Evolution of Nitrogen-Fixing Nodule Symbiosis. PLANT PHYSIOLOGY 2020; 184:1004-1023. [PMID: 32669419 PMCID: PMC7536700 DOI: 10.1104/pp.19.01420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/07/2020] [Indexed: 05/02/2023]
Abstract
Rhizobium nitrogen-fixing nodule symbiosis occurs in two taxonomic lineages: legumes (Fabaceae) and the genus Parasponia (Cannabaceae). Both symbioses are initiated upon the perception of rhizobium-secreted lipochitooligosaccharides (LCOs), called Nod factors. Studies in the model legumes Lotus japonicus and Medicago truncatula showed that rhizobium LCOs are perceived by a heteromeric receptor complex of distinct Lys motif (LysM)-type transmembrane receptors named NOD FACTOR RECEPTOR1 (LjNFR1) and LjNFR5 (L. japonicus) and LYSM DOMAIN CONTAINING RECEPTOR KINASE3 (MtLYK3)-NOD FACTOR PERCEPTION (MtNFP; M. truncatula). Recent phylogenomic comparative analyses indicated that the nodulation traits of legumes, Parasponia spp., as well as so-called actinorhizal plants that establish a symbiosis with diazotrophic Frankia spp. bacteria share an evolutionary origin about 110 million years ago. However, the evolutionary trajectory of LysM-type LCO receptors remains elusive. By conducting phylogenetic analysis, transcomplementation studies, and CRISPR-Cas9 mutagenesis in Parasponia andersonii, we obtained insight into the origin of LCO receptors essential for nodulation. We identified four LysM-type receptors controlling nodulation in P. andersonii: PanLYK1, PanLYK3, PanNFP1, and PanNFP2 These genes evolved from ancient duplication events predating and coinciding with the origin of nodulation. Phylogenetic and functional analyses associated the occurrence of a functional NFP2-orthologous receptor to LCO-driven nodulation. Legumes and Parasponia spp. use orthologous LysM-type receptors to perceive rhizobium LCOs, suggesting a shared evolutionary origin of LCO-driven nodulation. Furthermore, we found that both PanLYK1 and PanLYK3 are essential for intracellular arbuscule formation of mutualistic endomycorrhizal fungi. PanLYK3 also acts as a chitin oligomer receptor essential for innate immune signaling, demonstrating functional analogy to CHITIN ELECITOR RECEPTOR KINASE-type receptors.
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Affiliation(s)
- Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Kana Miyata
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Yuda Purwana Roswanjaya
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
- Centre of Technology for Agricultural Production, Agency for the Assessment and Application of Technology, 10340 Jakarta, Indonesia
| | - Rik Huisman
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Fengjiao Bu
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Marijke Hartog
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Sidney Linders
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Arjan van Zeijl
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
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19
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Engelhardt S, Trutzenberg A, Hückelhoven R. Regulation and Functions of ROP GTPases in Plant-Microbe Interactions. Cells 2020; 9:E2016. [PMID: 32887298 PMCID: PMC7565977 DOI: 10.3390/cells9092016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023] Open
Abstract
Rho proteins of plants (ROPs) form a specific clade of Rho GTPases, which are involved in either plant immunity or susceptibility to diseases. They are intensively studied in grass host plants, in which ROPs are signaling hubs downstream of both cell surface immune receptor kinases and intracellular nucleotide-binding leucine-rich repeat receptors, which activate major branches of plant immune signaling. Additionally, invasive fungal pathogens may co-opt the function of ROPs for manipulation of the cytoskeleton, cell invasion and host cell developmental reprogramming, which promote pathogenic colonization. Strikingly, mammalian bacterial pathogens also initiate both effector-triggered susceptibility for cell invasion and effector-triggered immunity via Rho GTPases. In this review, we summarize central concepts of Rho signaling in disease and immunity of plants and briefly compare them to important findings in the mammalian research field. We focus on Rho activation, downstream signaling and cellular reorganization under control of Rho proteins involved in disease progression and pathogen resistance.
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Affiliation(s)
| | | | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany; (S.E.); (A.T.)
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20
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Maillet F, Fournier J, Mendis HC, Tadege M, Wen J, Ratet P, Mysore KS, Gough C, Jones KM. Sinorhizobium meliloti succinylated high-molecular-weight succinoglycan and the Medicago truncatula LysM receptor-like kinase MtLYK10 participate independently in symbiotic infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:311-326. [PMID: 31782853 PMCID: PMC9327734 DOI: 10.1111/tpj.14625] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/08/2019] [Accepted: 11/19/2019] [Indexed: 05/12/2023]
Abstract
The formation of nitrogen-fixing nodules on legume hosts is a finely tuned process involving many components of both symbiotic partners. Production of the exopolysaccharide succinoglycan by the nitrogen-fixing bacterium Sinorhizobium meliloti 1021 is needed for an effective symbiosis with Medicago spp., and the succinyl modification to this polysaccharide is critical. However, it is not known when succinoglycan intervenes in the symbiotic process, and it is not known whether the plant lysin-motif receptor-like kinase MtLYK10 intervenes in recognition of succinoglycan, as might be inferred from work on the Lotus japonicus MtLYK10 ortholog, LjEPR3. We studied the symbiotic infection phenotypes of S. meliloti mutants deficient in succinoglycan production or producing modified succinoglycan, in wild-type Medicago truncatula plants and in Mtlyk10 mutant plants. On wild-type plants, S. meliloti strains producing no succinoglycan or only unsuccinylated succinoglycan still induced nodule primordia and epidermal infections, but further progression of the symbiotic process was blocked. These S. meliloti mutants induced a more severe infection phenotype on Mtlyk10 mutant plants. Nodulation by succinoglycan-defective strains was achieved by in trans rescue with a Nod factor-deficient S. meliloti mutant. While the Nod factor-deficient strain was always more abundant inside nodules, the succinoglycan-deficient strain was more efficient than the strain producing only unsuccinylated succinoglycan. Together, these data show that succinylated succinoglycan is essential for infection thread formation in M. truncatula, and that MtLYK10 plays an important, but different role in this symbiotic process. These data also suggest that succinoglycan is more important than Nod factors for bacterial survival inside nodules.
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Affiliation(s)
- Fabienne Maillet
- LIPMUniversité de Toulouse, INRA, CNRSCastanet‐TolosanCS 52627France
| | - Joëlle Fournier
- LIPMUniversité de Toulouse, INRA, CNRSCastanet‐TolosanCS 52627France
| | - Hajeewaka C. Mendis
- Department of Biological ScienceFlorida State UniversityTallahasseeFL32306USA
| | - Million Tadege
- Department of Plant and Soil SciencesInstitute for Agricultural BiosciencesOklahoma State UniversityArdmoreOK73401USA
| | - Jiangqi Wen
- Noble Research InstituteLLC.2510 Sam Noble ParkwayArdmoreOK73401USA
| | - Pascal Ratet
- IPS2Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-SaclayBâtiment 63091405OrsayFrance
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-CitéBâtiment 63091405OrsayFrance
| | | | - Clare Gough
- LIPMUniversité de Toulouse, INRA, CNRSCastanet‐TolosanCS 52627France
| | - Kathryn M. Jones
- Department of Biological ScienceFlorida State UniversityTallahasseeFL32306USA
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21
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Favre-Godal Q, Gourguillon L, Lordel-Madeleine S, Gindro K, Choisy P. Orchids and their mycorrhizal fungi: an insufficiently explored relationship. MYCORRHIZA 2020; 30:5-22. [PMID: 31982950 DOI: 10.1007/s00572-020-00934-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/17/2020] [Indexed: 05/03/2023]
Abstract
Orchids are associated with diverse fungal taxa, including nonmycorrhizal endophytic fungi as well as mycorrhizal fungi. The orchid mycorrhizal (OM) symbiosis is an excellent model for investigating the biological interactions between plants and fungi due to their high dependency on these symbionts for growth and survival. To capture the complexity of OM interactions, significant genomic, numerous transcriptomic, and proteomic studies have been performed, unraveling partly the role of each partner. On the other hand, several papers studied the bioactive metabolites from each partner but rarely interpreted their significance in this symbiotic relationship. In this review, we focus from a biochemical viewpoint on the OM dynamics and its molecular interactions. The ecological functions of OM in plant development and stress resistance are described first, summarizing recent literature. Secondly, because only few studies have specifically looked on OM molecular interactions, the signaling pathways and compounds allowing the establishment/maintenance of mycorrhizal association involved in arbuscular mycorrhiza (AM) are discussed in parallel with OM. Based on mechanistic similarities between OM and AM, and recent findings on orchids' endophytes, a putative model representing the different molecular strategies that OM fungi might employ to establish this association is proposed. It is hypothesized here that (i) orchids would excrete plant molecule signals such as strigolactones and flavonoids but also other secondary metabolites; (ii) in response, OM fungi would secrete mycorrhizal factors (Myc factors) or similar compounds to activate the common symbiosis genes (CSGs); (iii) overcome the defense mechanism by evasion of the pathogen-associated molecular patterns (PAMPs)-triggered immunity and by secretion of effectors such as small inhibitor proteins; and (iv) finally, secrete phytohormones to help the colonization or disrupt the crosstalk of plant defense phytohormones. To challenge this putative model, targeted and untargeted metabolomics studies with special attention to each partner's contribution are finally encouraged and some technical approaches are proposed.
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Affiliation(s)
- Quentin Favre-Godal
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France.
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France.
| | - Lorène Gourguillon
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
| | - Sonia Lordel-Madeleine
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France
| | - Katia Gindro
- Agroscope, Swiss Federal Research Station, Plant Protection, 60 Route de Duiller, PO Box, 1260, Nyon, Switzerland
| | - Patrick Choisy
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
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22
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Sulima AS, Zhukov VA, Kulaeva OA, Vasileva EN, Borisov AY, Tikhonovich IA. New sources of Sym2A allele in the pea ( Pisum sativum L.) carry the unique variant of candidate LysM-RLK gene LykX. PeerJ 2019; 7:e8070. [PMID: 31768303 PMCID: PMC6874852 DOI: 10.7717/peerj.8070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/20/2019] [Indexed: 01/09/2023] Open
Abstract
At the onset of legume-rhizobial symbiosis, the mutual recognition of partners occurs based on a complicated interaction between signal molecules and receptors. Bacterial signal molecules named Nod factors ("nodulation factors") are perceived by the plant LysM-containing receptor-like kinases (LysM-RLKs) that recognize details of its structure (i.e., unique substitutions), thus providing the conditions particular to symbiosis. In the garden pea (Pisum sativum L.), the allelic state of Sym2 gene has long been reported to regulate the symbiotic specificity: for infection to be successful, plants with the Sym2 A allele (for "Sym2 Afghan", as these genotypes originate mostly from Afghanistan) require an additional acetylation of the Nod factor which is irrelevant for genotypes with the Sym2 E allele (for "Sym2 European"). Despite being described about 90 years ago, Sym2 has not yet been cloned, though phenotypic analysis suggests it probably encodes a receptor for the Nod factor. Recently, we described a novel pea gene LykX (PsLykX) from the LysM-RLK gene family that demonstrates a perfect correlation between its allelic state and the symbiotic specificity of the Sym2 A-type. Here we report on a series of Middle-Eastern pea genotypes exhibiting the phenotype of narrow symbiotic specificity discovered in the VIR plant genetic resources gene bank (Saint-Petersburg, Russia). These genotypes are new sources of Sym2 A, as has been confirmed by an allelism test with Sym2 A pea cv. Afghanistan. Within these genotypes, LykX is present either in the allelic state characteristic for cv. Afghanistan, or in another, minor allelic state found in two genotypes from Tajikistan and Turkmenistan. Plants carrying the second allele demonstrate the same block of rhizobial infection as cv. Afghanistan when inoculated with an incompatible strain. Intriguingly, this "Tajik" allele of LykX differs from the "European" one by a single nucleotide polymorphism leading to an R75P change in the receptor part of the putative protein. Thus, our new data are in agreement with the hypothesis concerning the identity of LykX and the elusive Sym2 gene.
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Affiliation(s)
- Anton S Sulima
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Vladimir A Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Olga A Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Ekaterina N Vasileva
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Alexey Y Borisov
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Igor A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia.,Faculty of Biology, St. Petersburg State University, Saint-Petersburg, Russia
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23
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Gibelin-Viala C, Amblard E, Puech-Pages V, Bonhomme M, Garcia M, Bascaules-Bedin A, Fliegmann J, Wen J, Mysore KS, le Signor C, Jacquet C, Gough C. The Medicago truncatula LysM receptor-like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis. THE NEW PHYTOLOGIST 2019; 223:1516-1529. [PMID: 31058335 DOI: 10.1111/nph.15891] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/24/2019] [Indexed: 05/26/2023]
Abstract
Plant -specific lysin-motif receptor-like kinases (LysM-RLKs) are implicated in the perception of N-acetyl glucosamine-containing compounds, some of which are important signal molecules in plant-microbe interactions. Among these, both lipo-chitooligosaccharides (LCOs) and chitooligosaccharides (COs) are proposed as arbuscular mycorrhizal (AM) fungal symbiotic signals. COs can also activate plant defence, although there are scarce data about CO production by pathogens, especially nonfungal pathogens. We tested Medicago truncatula mutants in the LysM-RLK MtLYK9 for their abilities to interact with the AM fungus Rhizophagus irregularis and the oomycete pathogen Aphanomyces euteiches. This prompted us to analyse whether A. euteiches can produce COs. Compared with wild-type plants, Mtlyk9 mutants had fewer infection events and were less colonised by the AM fungus. By contrast, Mtlyk9 mutants were more heavily infected by A. euteiches and showed more disease symptoms. Aphanomyces euteiches was also shown to produce short COs, mainly CO II, but also CO III and CO IV, and traces of CO V, both ex planta and in planta. MtLYK9 thus has a dual role in plant immunity and the AM symbiosis, which raises questions about the functioning and the ancestral origins of such a receptor protein.
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Affiliation(s)
| | - Emilie Amblard
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Virginie Puech-Pages
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Magali Garcia
- LIPM, INRA, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Adeline Bascaules-Bedin
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Judith Fliegmann
- LIPM, INRA, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Jiangqi Wen
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kirankumar S Mysore
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | | | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales, CNRS, UPS, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Clare Gough
- LIPM, INRA, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France
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24
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Zhao C, Jiang G, Zhou S, Wang G, Sha Z, Sun Y, Xiu Y. Molecular identification and expression analysis of four Lysin motif (LysM) domain-containing proteins from turbot (Scophthalmus maximus). FISH & SHELLFISH IMMUNOLOGY 2019; 89:271-280. [PMID: 30940580 DOI: 10.1016/j.fsi.2019.03.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
Lysin motif (LysM) is involved in chitin, peptidoglycan and other structurally-related oligosaccharides recognition and binding, and it is important for the biological processes of responsing to bacterial and viral infections and pathogen defense. LysM is also a widely spread protein, ranging from prokaryotes to eukaryotes, including bacteria, plants and mammals. However, research of LysM in teleosts especially in marine fish was rarely scarce. In the present study, four novel LysM domain-containing proteins in turbot (Scophthalmus maximus), named as SmLysMd1, SmLysMd2, SmLysMd3, and SmLysMd4, were cloned and identified firstly. The full-length cDNA of SmLysMd1 was 1235 bp with a 678 bp ORF, capable of encoding a peptide of 225 amino acids. The complete cDNA sequence of SmLysMd2 was 1273 bp, and contained a 675 bp ORF, encoding a predicted protein of 224 amino acids. The full-length of SmLysMd3 cDNA was 2132 bp, containing a ORF of 987 bp, with a ORF of encoding 328 amino acids. The full-length SmLysMd4 cDNA was 1115 bp contained a 888 bp ORF, encoding 295 amino acids. And all the four predicated proteins contained a specific LYSM domain. Moreover, SmLysMd1 and SmLysMd2 belong to the intracellular non-secretory types, and SmLysMd3 and SmLysMd4 belong to the anchored transmembrane types. In addition, the four SmLysMd were ubiquitously expressed in all the examined tissues. Moreover, the SmLysMds levels were up-regulated in muscle and liver, and had a reduce tendency immediately in different degree following Vibrio vulnificus challenge, indicating that the turbot LysM could be participant in the immune responses to bacterial infections. The present result of LysM in turbot for the first time in a marine fish will provide foundation knowledge for the functions studies of LysM in immune responses. Further studies should be carried out to better understand their immune mechanism in turbot and other teleosts.
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Affiliation(s)
- Chunyan Zhao
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Guangpeng Jiang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Shun Zhou
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Guodong Wang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China; Homey Group Co. Ltd, Rongcheng, 264306, PR China
| | - Zhenxia Sha
- College of Life Sciences, Qingdao University, Qingdao, 266071, PR China
| | - Yongjun Sun
- Homey Group Co. Ltd, Rongcheng, 264306, PR China
| | - Yunji Xiu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, 266109, PR China.
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25
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Thomas J, Kim HR, Rahmatallah Y, Wiggins G, Yang Q, Singh R, Glazko G, Mukherjee A. RNA-seq reveals differentially expressed genes in rice (Oryza sativa) roots during interactions with plant-growth promoting bacteria, Azospirillum brasilense. PLoS One 2019; 14:e0217309. [PMID: 31120967 PMCID: PMC6532919 DOI: 10.1371/journal.pone.0217309] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/08/2019] [Indexed: 11/24/2022] Open
Abstract
Major non-legume crops can form beneficial associations with nitrogen-fixing bacteria like Azospirillum brasilense. Our current understanding of the molecular aspects and signaling that occur between important crops like rice and these nitrogen-fixing bacteria is limited. In this study, we used an experimental system where the bacteria could colonize the plant roots and promote plant growth in wild type rice and symbiotic mutants (dmi3 and pollux) in rice. Our data suggest that plant growth promotion and root penetration is not dependent on these genes. We then used this colonization model to identify regulation of gene expression at two different time points during this interaction: at 1day post inoculation (dpi), we identified 1622 differentially expressed genes (DEGs) in rice roots, and at 14dpi, we identified 1995 DEGs. We performed a comprehensive data mining to classify the DEGs into the categories of transcription factors (TFs), protein kinases (PKs), and transporters (TRs). Several of these DEGs encode proteins that are involved in the flavonoid biosynthetic pathway, defense, and hormone signaling pathways. We identified genes that are involved in nitrate and sugar transport and are also implicated to play a role in other plant-microbe interactions. Overall, findings from this study will serve as an excellent resource to characterize the host genetic pathway controlling the interactions between non-legumes and beneficial bacteria which can have long-term implications towards sustainably improving agriculture.
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Affiliation(s)
- Jacklyn Thomas
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Ha Ram Kim
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Grant Wiggins
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Qinqing Yang
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Raj Singh
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Arijit Mukherjee
- Department of Biology, University of Central Arkansas, Conway, Arkansas, United States of America
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26
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Montero H, Choi J, Paszkowski U. Arbuscular mycorrhizal phenotyping: the dos and don'ts. THE NEW PHYTOLOGIST 2019; 221:1182-1186. [PMID: 30222191 PMCID: PMC7463165 DOI: 10.1111/nph.15489] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 09/07/2018] [Indexed: 05/20/2023]
Affiliation(s)
- Hector Montero
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Jeongmin Choi
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
| | - Uta Paszkowski
- Department of Plant SciencesUniversity of CambridgeCambridgeCB2 3EAUK
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