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Tisseyre P, Cartieaux F, Chabrillange N, Gully D, Hocher V, Svistoonoff S, Gherbi H. Setting up Agrobacterium tumefaciens-mediated transformation of the tropical legume Aeschynomene evenia, a powerful tool for studying gene function in Nod Factor-independent symbiosis. PLoS One 2024; 19:e0297547. [PMID: 38625963 PMCID: PMC11020691 DOI: 10.1371/journal.pone.0297547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/09/2024] [Indexed: 04/18/2024] Open
Abstract
Most legumes are able to develop a root nodule symbiosis in association with proteobacteria collectively called rhizobia. Among them, the tropical species Aeschynomene evenia has the remarkable property of being nodulated by photosynthetic Rhizobia without the intervention of Nod Factors (NodF). Thereby, A. evenia has emerged as a working model for investigating the NodF-independent symbiosis. Despite the availability of numerous resources and tools to study the molecular basis of this atypical symbiosis, the lack of a transformation system based on Agrobacterium tumefaciens significantly limits the range of functional approaches. In this report, we present the development of a stable genetic transformation procedure for A. evenia. We first assessed its regeneration capability and found that a combination of two growth regulators, NAA (= Naphthalene Acetic Acid) and BAP (= 6-BenzylAminoPurine) allows the induction of budding calli from epicotyls, hypocotyls and cotyledons with a high efficiency in media containing 0,5 μM NAA (up to 100% of calli with continuous stem proliferation). To optimize the generation of transgenic lines, we employed A. tumefaciens strain EHA105 harboring a binary vector carrying the hygromycin resistance gene and the mCherry fluorescent marker. Epicotyls and hypocotyls were used as the starting material for this process. We have found that one growth medium containing a combination of NAA (0,5 μM) and BAP (2,2 μM) was sufficient to induce callogenesis and A. tumefaciens strain EHA105 was sufficiently virulent to yield a high number of transformed calli. This simple and efficient method constitutes a valuable tool that will greatly facilitate the functional studies in NodF-independent symbiosis.
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Affiliation(s)
- Pierre Tisseyre
- IRD (French National Research Institute for Sustainable Development), UMR QualiSud, IRD-MONTPELLIER, Montpellier, France
| | - Fabienne Cartieaux
- IRD (French National Research Institute for Sustainable Development), UMR PHIM (Plant Health Institute of Montpellier), Montpellier, France
| | - Nathalie Chabrillange
- IRD (French National Research Institute for Sustainable Development), UMR PHIM (Plant Health Institute of Montpellier), Montpellier, France
| | - Djamel Gully
- IRD (French National Research Institute for Sustainable Development), UMR PHIM (Plant Health Institute of Montpellier), Montpellier, France
| | - Valérie Hocher
- IRD (French National Research Institute for Sustainable Development), UMR PHIM (Plant Health Institute of Montpellier), Montpellier, France
- Laboratoire commun de Microbiologie IRD/ISRA/UCAD, Centre de recherche de Bel Air, Dakar, Sénégal
| | - Sergio Svistoonoff
- IRD (French National Research Institute for Sustainable Development), UMR PHIM (Plant Health Institute of Montpellier), Montpellier, France
| | - Hassen Gherbi
- IRD (French National Research Institute for Sustainable Development), UMR PHIM (Plant Health Institute of Montpellier), Montpellier, France
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Manantsoa FF, Rakotoarisoa MF, Chaintreuil C, Razakatiana ATE, Gressent F, Pervent M, Bourge M, Andrianandrasana MD, Nouwen N, Randriambanona H, Ramanankierana H, Arrighi JF. Occurrence and diversity of stem nodulation in Aeschynomene and Sesbania legumes from wetlands of Madagascar. Sci Rep 2024; 14:5024. [PMID: 38424094 PMCID: PMC10904833 DOI: 10.1038/s41598-024-55247-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Legumes have the ability to establish a nitrogen-fixing symbiosis with soil rhizobia that they house in specific organs, the nodules. In most rhizobium-legume interactions, nodulation occurs on the root. However, certain tropical legumes growing in wetlands possess a unique trait: the capacity to form rhizobia-harbouring nodules on the stem. Despite the originality of the stem nodulation process, its occurrence and diversity in waterlogging-tolerant legumes remains underexplored, impeding a comprehensive analysis of its genetics and biology. Here, we aimed at filling this gap by surveying stem nodulation in legume species-rich wetlands of Madagascar. Stem nodulation was readily observed in eight hydrophytic species of the legume genera, Aeschynomene and Sesbania, for which significant variations in stem nodule density and morphology was documented. Among these species, A. evenia, which is used as genetic model to study the rhizobial symbiosis, was found to be frequently stem-nodulated. Two other Aeschynomene species, A. cristata and A. uniflora, were evidenced to display a profuse stem-nodulation as occurs in S. rostrata. These findings extend our knowledge on legumes species that are endowed with stem nodulation and further indicate that A. evenia, A. cristata, A. uniflora and S. rostrata are of special interest for the study of stem nodulation. As such, these legume species represent opportunities to investigate different modalities of the nitrogen-fixing symbiosis and this knowledge could provide cues for the engineering of nitrogen-fixation in non-legume crops.
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Affiliation(s)
- Faustin F Manantsoa
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Marrino F Rakotoarisoa
- Department of Ethnobotany and Botany, National Center for Applied Pharmaceutical Research, Antananarivo 101, Madagascar
| | - Clémence Chaintreuil
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Adamson T E Razakatiana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Frédéric Gressent
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Marjorie Pervent
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Mickaël Bourge
- Cytometry Facility, Institute for Integrative Biology of the Cell (I2BC), Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, 91198, Gif-Sur-Yvette, France
| | - Martial D Andrianandrasana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Nico Nouwen
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Jean-François Arrighi
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France.
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Nouwen N, Pervent M, El M’Chirgui F, Tellier F, Rios M, Horta Araújo N, Klopp C, Gressent F, Arrighi JF. OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia. PLANT PHYSIOLOGY 2024; 194:1611-1630. [PMID: 38039119 PMCID: PMC10904325 DOI: 10.1093/plphys/kiad642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 12/03/2023]
Abstract
Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accommodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signaling pathway that activates 2 coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing intercellular infection and lateral root base nodulation remains elusive. Here, we show that Aeschynomene evenia OROSOMUCOID PROTEIN 1 (AeORM1), a key regulator of sphingolipid biosynthesis, is required for nodule formation. Using A. evenia orm1 mutants, we demonstrate that alterations in AeORM1 function trigger numerous early aborted nodules, defense-like reactions, and shorter lateral roots. Accordingly, AeORM1 is expressed during lateral root initiation and elongation, including at lateral root bases where nodule primordium form in the presence of symbiotic bradyrhizobia. Sphingolipidomics revealed that mutations in AeORM1 lead to sphingolipid overaccumulation in roots relative to the wild type, particularly for very long-chain fatty acid-containing ceramides. Taken together, our findings reveal that AeORM1-regulated sphingolipid homeostasis is essential for rhizobial infection and nodule organogenesis, as well as for lateral root development in A. evenia.
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Affiliation(s)
- Nico Nouwen
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Marjorie Pervent
- Plant Health Institute of Montpellier (PHIM), INRAE, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Franck El M’Chirgui
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin (IJPB), INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Maëlle Rios
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Natasha Horta Araújo
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, 31326 Castanet-Tolosan, France
| | - Frédéric Gressent
- Plant Health Institute of Montpellier (PHIM), INRAE, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
| | - Jean-François Arrighi
- Plant Health Institute of Montpellier (PHIM), IRD, UMR Univ Montpellier/IRD/SupAgro/INRAE/CIRAD, TA-A82/J Campus de Baillarguet, 34398 Montpellier, France
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Zhao Z, Wang L, Kelley K, Jones JB, Tillman B, Wang J. GFP labeling of a Bradyrhizobium strain and an attempt to track the crack entry process during symbiosis with peanuts. World J Microbiol Biotechnol 2023; 39:219. [PMID: 37269424 DOI: 10.1007/s11274-023-03665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Compared to the well-studied model legumes, where symbiosis is established via root hair entry, the peanut is infected by Bradyrhizobium through the crack entry, which is less common and not fully understood. Crack entry is, however, considered a primitive symbiotic infection pathway, which could be potentially utilized for engineering non-legume species with nitrogen fixation ability. We utilized a fluorescence-labeled Bradyrhizobium strain to help in understanding the crack entry process at the cellular level. A modified plasmid pRJPaph-bjGFP, harboring the codon-optimized GFP gene and tetracycline resistance gene, was created and conjugated into Bradyrhizobium strain Lb8, an isolate from peanut nodules, through tri-parental mating. Microscopic observation and peanut inoculation assays confirmed the successful GFP tagging of Lb8, which is capable of generating root nodules. A marking system for peanut root potential infection sites and an optimized sample preparation protocol for cryostat sectioning was developed. The feasibility of using the GFP-tagged Lb8 for observing crack entry was examined. GFP signal was detected at the nodule primordial stage and the following nodule developmental stages with robust GFP signals observed in infected cells in the mature nodules. Spherical bacteroids in the root tissue were visualized at the nodules' inner cortex under higher magnification, reflecting the trace along the rhizobial infection path. The GFP labeled Lb8 can serve as an essential tool for plant-microbe studies between the cultivated peanut and Bradyrhizobium, which could facilitate further study of the crack entry process during the legume-rhizobia symbiosis.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Karen Kelley
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Jeffrey B Jones
- Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Plant Pathology Department, University of Florida, Gainesville, FL, 32610, USA
| | - Barry Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Biology Program, University of Florida, Gainesville, FL, 32610, USA.
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Quilbé J, Nouwen N, Pervent M, Guyonnet R, Cullimore J, Gressent F, Araújo NH, Gully D, Klopp C, Giraud E, Arrighi JF. A mutant-based analysis of the establishment of Nod-independent symbiosis in the legume Aeschynomene evenia. PLANT PHYSIOLOGY 2022; 190:1400-1417. [PMID: 35876558 PMCID: PMC9516736 DOI: 10.1093/plphys/kiac325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Intensive research on nitrogen-fixing symbiosis in two model legumes has uncovered the molecular mechanisms, whereby rhizobial Nod factors activate a plant symbiotic signaling pathway that controls infection and nodule organogenesis. In contrast, the so-called Nod-independent symbiosis found between Aeschynomene evenia and photosynthetic bradyrhizobia, which does not involve Nod factor recognition nor infection thread formation, is less well known. To gain knowledge on how Nod-independent symbiosis is established, we conducted a phenotypic and molecular characterization of A. evenia lines carrying mutations in different nodulation genes. Besides investigating the effect of the mutations on rhizobial symbiosis, we examined their consequences on mycorrhizal symbiosis and in nonsymbiotic conditions. Analyzing allelic mutant series for AePOLLUX, Ca2+/calmodulin dependent kinase, AeCYCLOPS, nodulation signaling pathway 2 (AeNSP2), and nodule inception demonstrated that these genes intervene at several stages of intercellular infection and during bacterial accommodation. We provide evidence that AeNSP2 has an additional nitrogen-dependent regulatory function in the formation of axillary root hairs at lateral root bases, which are rhizobia-colonized infection sites. Our investigation of the recently discovered symbiotic actor cysteine-rich receptor-like kinase specified that it is not involved in mycorrhization; however, it is essential for both symbiotic signaling and early infection during nodulation. These findings provide important insights on the modus operandi of Nod-independent symbiosis and contribute to the general understanding of how rhizobial-legume symbioses are established by complementing the information acquired in model legumes.
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Affiliation(s)
| | | | | | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
| | - Julie Cullimore
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, Castanet-Tolosan, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
| | - Natasha Horta Araújo
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
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Guha S, Molla F, Sarkar M, Ibańez F, Fabra A, DasGupta M. Nod factor-independent 'crack-entry' symbiosis in dalbergoid legume Arachis hypogaea. Environ Microbiol 2022; 24:2732-2746. [PMID: 34995397 DOI: 10.1111/1462-2920.15888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022]
Abstract
Dalbergoids are typified by crack-entry symbiosis which is evidenced to be Nod Factor (NF)- independent in several Aeschynomene legumes. Natural symbionts of the dalbergoid legume Arachis hypogaea are always NF-producing, prompting us to check whether symbiosis in this legume could also be NF-independent. For this, we followed the symbiosis with two NF containing bradyrhizobial strains- SEMIA6144, a natural symbiont of Arachis and ORS285, a versatile nodulator of Aeschynomene legumes, along with their corresponding nodulation (nod) mutants. Additionally, we investigated NF-deficient bradyrhizobia like BTAi1, a natural symbiont of Aeschynomene indica and the WBOS strains that were natural endophytes of Oryza sativa, collected from an Arachis-Oryza intercropped field. While SEMIA6144ΔnodC was non-nodulating, both ORS285 and ORS285ΔnodB could induce functional nodulation, although with lower efficiency than SEMIA6144. On the other hand, all the NF-deficient strains- BTAi1, WBOS2 and WBOS4 showed comparable nodulation with ORS285 indicating Arachis to harbour a NF-independent mechanism of symbiosis. Intriguingly, symbiosis in Arachis, irrespective of whether it was NF-dependent or independent, was always associated with the curling or branching of the rosette root hairs at the lateral root bases. Thus, despite being predominantly described as NF-dependent legume, Arachis does retain a vestigial, less-efficient form of NF-independent symbiosis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sohini Guha
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Firoz Molla
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Monolina Sarkar
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Fernando Ibańez
- Instituto de Investigaciones Agrobiotecnologicas (CONCINET-UNRC), Ruta 36 Km 601, Río Cuarto, Argentina
| | - Adriana Fabra
- Instituto de Investigaciones Agrobiotecnologicas (CONCINET-UNRC), Ruta 36 Km 601, Río Cuarto, Argentina
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
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Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium ( Ensifer) meliloti WSM1022. Microorganisms 2021; 9:microorganisms9122428. [PMID: 34946030 PMCID: PMC8706082 DOI: 10.3390/microorganisms9122428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we report an improved and complete genome sequence of Sinorhizobium (Ensifer) meliloti strain WSM1022, a microsymbiont of Medicago species, revealing its tripartite structure. This improved genome sequence was generated combining Illumina and Oxford nanopore sequencing technologies to better understand the symbiotic properties of the bacterium. The 6.75 Mb WSM1022 genome consists of three scaffolds, corresponding to a chromosome (3.70 Mb) and the pSymA (1.38 Mb) and pSymB (1.66 Mb) megaplasmids. The assembly has an average GC content of 62.2% and a mean coverage of 77X. Genome annotation of WSM1022 predicted 6058 protein coding sequences (CDSs), 202 pseudogenes, 9 rRNAs (3 each of 5S, 16S, and 23S), 55 tRNAs, and 4 ncRNAs. We compared the genome of WSM1022 to two other rhizobial strains, closely related Sinorhizobium (Ensifer) meliloti Sm1021 and Sinorhizobium (Ensifer) medicae WSM419. Both WSM1022 and WSM419 species are high-efficiency rhizobial strains when in symbiosis with Medicago truncatula, whereas Sm1021 is ineffective. Our findings report significant genomic differences across the three strains with some similarities between the meliloti strains and some others between the high efficiency strains WSM1022 and WSM419. The addition of this high-quality rhizobial genome sequence in conjunction with comparative analyses will help to unravel the features that make a rhizobial symbiont highly efficient for nitrogen fixation.
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Montiel J, Reid D, Grønbæk TH, Benfeldt CM, James EK, Ott T, Ditengou FA, Nadzieja M, Kelly S, Stougaard J. Distinct signaling routes mediate intercellular and intracellular rhizobial infection in Lotus japonicus. PLANT PHYSIOLOGY 2021; 185:1131-1147. [PMID: 33793909 PMCID: PMC8133683 DOI: 10.1093/plphys/kiaa049] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 05/07/2023]
Abstract
Rhizobial infection of legume roots during the development of nitrogen-fixing root nodules can occur intracellularly, through plant-derived infection threads traversing cells, or intercellularly, via bacterial entry between epidermal plant cells. Although it is estimated that around 25% of all legume genera are intercellularly infected, the pathways and mechanisms supporting this process have remained virtually unexplored due to a lack of genetically amenable legumes that exhibit this form of infection. In this study, we report that the model legume Lotus japonicus is infected intercellularly by the IRBG74 strain, recently proposed to belong to the Agrobacterium clade of the Rhizobiaceae. We demonstrate that the resources available for L. japonicus enable insight into the genetic requirements and fine-tuning of the pathway governing intercellular infection in this species. Inoculation of L. japonicus mutants shows that Ethylene-responsive factor required for nodulation 1 (Ern1) and Leu-rich Repeat Receptor-Like Kinase (RinRK1) are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including nod factor receptor 5 (NFR5), symbiosis receptor-like kinase (SymRK), Ca2+/calmodulin dependent kinase (CCaMK), exopolysaccharide receptor 3 (Epr3), Cyclops, nodule inception (Nin), nodulation signaling pathway 1 (Nsp1), nodulation signaling pathway 2 (Nsp2), cystathionine-β-synthase (Cbs), and Vapyrin are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared with intracellular colonization. In particular, several cytokinin-related genes were differentially regulated. Corroborating this observation, cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74, whereas lhk1 cytokinin receptor mutants formed no nodules. These results indicate a differential requirement for cytokinin signaling during intercellular rhizobial entry and highlight distinct modalities of inter- and intracellular infection mechanisms in L. japonicus.
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Affiliation(s)
- Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Thomas H Grønbæk
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Caroline M Benfeldt
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas Ott
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Franck A Ditengou
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
- Author for ommunication:
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Quilbé J, Arrighi JF. NSP2, a key symbiotic regulator in the spotlight. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:959-963. [PMID: 33626152 DOI: 10.1093/jxb/eraa540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article comments on:Peng Z, Chen H, Tan L, Shu H, Varshney R.K., Zhou Z, Zhao Z, Luo Z, Chitikineni A, Wang L, Maku J, López Y, Gallo M, Zhou H, Wang J. 2021. Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut. Journal of Experimental Botany 72, 1104–1118.
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Affiliation(s)
- Johan Quilbé
- LSTM, Université de Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France
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11
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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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12
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Tapia-Pastrana F, Delgado-Salinas A, Caballero J. Patterns of chromosomal variation in Mexican species of Aeschynomene (Fabaceae, Papilionoideae) and their evolutionary and taxonomic implications. COMPARATIVE CYTOGENETICS 2020; 14:157-182. [PMID: 32206208 PMCID: PMC7080853 DOI: 10.3897/compcytogen.v14i1.47264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
A cytogenetic analysis of sixteen taxa of the genus Aeschynomene Linnaeus, 1753, which includes species belonging to both subgenera Aeschynomene (Léonard, 1954) and Ochopodium (Vogel, 1838) J. Léonard, 1954, was performed. All studied species had the same chromosome number (2n = 20) but exhibited karyotype diversity originating in different combinations of metacentric, submetacentric and subtelocentric chromosomes, chromosome size and number of SAT chromosomes. The plasticity of the genomes included the observation in a taxon belonging to the subgenus Aeschynomene of an isolated spherical structure similar in appearance to the extra chromosomal circular DNA observed in other plant genera. By superimposing the karyotypes in a recent phylogenetic tree, a correspondence between morphology, phylogeny and cytogenetic characteristics of the taxa included in the subgenus Aeschynomene is observed. Unlike subgenus Aeschynomene, the species of Ochopodium exhibit notable karyotype heterogeneity. However the limited cytogenetic information recorded prevents us from supporting the proposal of their taxonomic separation and raise it to the genus category. It is shown that karyotype information is useful in the taxonomic delimitation of Aeschynomene and that the diversity in the diploid level preceded the hybridization/polyploidization demonstrated in the genus. The systematic implications of our results and their value can be extended to other Dalbergieae genera as knowledge about the chromosomal structure and its evolution increases.
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Affiliation(s)
- Fernando Tapia-Pastrana
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Laboratorio de Genecología, Batalla 5 de Mayo s/n esquina Fuerte de Loreto, Col. Ejército de Oriente, Iztapalapa, C.P. 09230, Ciudad de México, MexicoUniversidad Nacional Autónoma de MéxicoMéxicoMexico
| | - Alfonso Delgado-Salinas
- Instituto de Biología, Departamento de Botánica, Universidad Nacional Autónoma de México, Apartado Postal 70-233, 04510, Cd. de México, MexicoUniversidad Nacional Autónoma de MéxicoMéxicoMexico
| | - Javier Caballero
- Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Campos Deportivos, Ciudad Universitaria, Coyoacán 04510, Cd. de México, MexicoUniversidad Nacional Autónoma de MéxicoMéxicoMexico
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13
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Huisman R, Geurts R. A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis. PLANT COMMUNICATIONS 2020; 1:100019. [PMID: 33404552 PMCID: PMC7748023 DOI: 10.1016/j.xplc.2019.100019] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 05/26/2023]
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
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Affiliation(s)
- Rik Huisman
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Rene Geurts
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
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14
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Nouwen N, Gargani D, Giraud E. The Modification of the Flavonoid Naringenin by Bradyrhizobium sp. Strain ORS285 Changes the nod Genes Inducer Function to a Growth Stimulator. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1517-1525. [PMID: 31265361 DOI: 10.1094/mpmi-05-19-0133-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As inducers of nodulation (nod) genes, flavonoids play an important role in the symbiotic interaction between rhizobia and legumes. However, in addition to the control of expression of nod genes, many other effects of flavonoids on rhizobial cells have been described. Here, we show that the flavonoid naringenin stimulates the growth of the photosynthetic Bradyrhizobium sp. strain ORS285. This growth-stimulating effect was still observed for strain ORS285 with nodD1, nodD2, or the naringenin-degrading fde operon deleted. Phenotypic microarray analysis indicates that in cells grown in the presence of naringenin, the glycerol and fatty acid metabolism is activated. Moreover, electron microscopic and enzymatic analyses show that polyhydroxy alkanoate metabolism is altered in cells grown in the presence of naringenin. Although strain ORS285 was able to degrade naringenin, a fraction was converted into an intensely yellow-colored molecule with an m/z (+) of 363.0716. Further analysis indicates that this molecule is a hydroxylated and O-methylated form of naringenin. In contrast to naringenin, this derivative did not induce nod gene expression, but it did stimulate the growth of strain ORS285. We hypothesize that the growth stimulation and metabolic changes induced by naringenin are part of a mechanism to facilitate the colonization and infection of naringenin-exuding host plants.
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Affiliation(s)
- Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
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15
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Brottier L, Chaintreuil C, Simion P, Scornavacca C, Rivallan R, Mournet P, Moulin L, Lewis GP, Fardoux J, Brown SC, Gomez-Pacheco M, Bourges M, Hervouet C, Gueye M, Duponnois R, Ramanankierana H, Randriambanona H, Vandrot H, Zabaleta M, DasGupta M, D’Hont A, Giraud E, Arrighi JF. A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses. BMC PLANT BIOLOGY 2018; 18:333. [PMID: 30518342 PMCID: PMC6282307 DOI: 10.1186/s12870-018-1567-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene. RESULTS This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity. CONCLUSIONS The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.
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Affiliation(s)
- Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Paul Simion
- Institut des Sciences de l’Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Cedex 5 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Cedex 5 Montpellier, France
| | - Ronan Rivallan
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Pierre Mournet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Lionel Moulin
- IRD, Interactions Plantes Microorganismes Environnement, UMR IPME, 34394 Montpellier, France
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB UK
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Spencer C. Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mario Gomez-Pacheco
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourges
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Catherine Hervouet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Mathieu Gueye
- Laboratoire de Botanique, Institut Fondamental d’Afrique Noire, Ch. A. Diop, BP 206 Dakar, Sénégal
| | - Robin Duponnois
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Hervé Vandrot
- IAC, Laboratoire de Botanique et d’Ecologie Végétale Appliquée, UMR AMAP, 98825 Pouembout, Nouvelle-Calédonie France
| | - Maria Zabaleta
- Department of Biochemistry and Microbial Genomics, IIBCE, 11600 Montevideo, Uruguay
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019 India
| | - Angélique D’Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
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16
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Gully D, Czernic P, Cruveiller S, Mahé F, Longin C, Vallenet D, François P, Nidelet S, Rialle S, Giraud E, Arrighi JF, DasGupta M, Cartieaux F. Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia. Sci Rep 2018; 8:10934. [PMID: 30026595 PMCID: PMC6053390 DOI: 10.1038/s41598-018-29301-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/10/2018] [Indexed: 11/09/2022] Open
Abstract
Nod factors (NF) were assumed to be indispensable for the establishment of a rhizobium-legume symbiosis until the discovery that certain Bradyrhizobium strains interacting with certain Aeschynomene species lack the canonical nodABC genes required for their synthesis. So far, the molecular dialogue between Aeschynomene and its symbionts remains an open question. Here we report a time course transcriptional analysis of Aeschynomene evenia in response to inoculation with Bradyrhizobium ORS278. The NF-independent symbiotic process was monitored at five time points between bacterial infection and nodule maturity. The five time points correspond to three specific events, root infection by crack entry, nodule organogenesis, and the establishment of the nitrogen fixing process. During the third stage, about 80 NCR-like genes and eight symbiotic genes known to be involved in signaling, bacterial infection or nodulation regulation were highly expressed. Comparative gene expression analyses at the five time points also enabled the selection of genes with an expression profile that makes them promising markers to monitor early plant responses to bacteria. Such markers could be used in bioassays to identify the nature of the bacterial signal(s). Our data represent valuable resources for investigation of this Nod factor-independent symbiosis.
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Affiliation(s)
- Djamel Gully
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France
| | - Pierre Czernic
- Université de Montpellier, Place Eugène Bataillon, F-34095, Montpellier Cedex 5, France
| | - Stéphane Cruveiller
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
| | - Frédéric Mahé
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France
| | - Cyrille Longin
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, F-91057, Evry, France
| | - Philippe François
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France
| | - Sabine Nidelet
- MGX, Univ. Montpellier, CNRS, INSERM, BioCampus, Montpellier, France
| | - Stéphanie Rialle
- MGX, Univ. Montpellier, CNRS, INSERM, BioCampus, Montpellier, France
| | - Eric Giraud
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France
| | | | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Fabienne Cartieaux
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France.
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17
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Chaintreuil C, Perrier X, Martin G, Fardoux J, Lewis GP, Brottier L, Rivallan R, Gomez-Pacheco M, Bourges M, Lamy L, Thibaud B, Ramanankierana H, Randriambanona H, Vandrot H, Mournet P, Giraud E, Arrighi JF. Naturally occurring variations in the nod-independent model legume Aeschynomene evenia and relatives: a resource for nodulation genetics. BMC PLANT BIOLOGY 2018; 18:54. [PMID: 29614957 PMCID: PMC5883870 DOI: 10.1186/s12870-018-1260-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/06/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Among semi-aquatic species of the legume genus Aeschynomene, some have the unique property of being root and stem-nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the production of Nod factors. These species provide an excellent biological system with which to explore the evolution of nodulation in legumes. Among them, Aeschynomene evenia has emerged as a model legume to undertake the genetic dissection of the so-called Nod-independent symbiosis. In addition to the genetic analysis of nodulation on a reference line, natural variation in a germplasm collection could also be surveyed to uncover genetic determinants of nodulation. To this aim, we investigated the patterns of genetic diversity in a collection of 226 Nod-independent Aeschynomene accessions. RESULTS A combination of phylogenetic analyses, comprising ITS and low-copy nuclear genes, along with cytogenetic experiments and artificial hybridizations revealed the richness of the Nod-independent Aeschynomene group with the identification of 13 diploid and 6 polyploid well-differentiated taxa. A set of 54 SSRs was used to further delineate taxon boundaries and to identify different genotypes. Patterns of microsatellite diversity also illuminated the genetic basis of the Aeschynomene taxa that were all found to be predominantly autogamous and with a predicted simple disomic inheritance, two attributes favorable for genetics. In addition, taxa displaying a pronounced genetic diversity, notably A. evenia, A. indica and A. sensitiva, were characterized by a clear geographically-based genetic structure and variations in root and stem nodulation. CONCLUSION A well-characterized germplasm collection now exists as a major genetic resource to thoroughly explore the natural variation of nodulation in response to different bradyrhizobial strains. Symbiotic polymorphisms are expected to be found notably in the induction of nodulation, in nitrogen fixation and also in stem nodulation. Subsequent genetic analysis and locus mapping will pave the way for the identification of the underlying genes through forward or reverse genetics. Such discoveries will significantly contribute to our understanding of the molecular mechanisms underpinning how some Aeschynomene species can be efficiently nodulated in a Nod-independent fashion.
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Affiliation(s)
- Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Xavier Perrier
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Ronan Rivallan
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Mario Gomez-Pacheco
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud. Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourges
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud. Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Béatrice Thibaud
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Hervé Vandrot
- IAC, Laboratoire de Botanique et d’Ecologie Végétale Appliquée, UMR AMAP, 98825 Pouembout, Nouvelle-Calédonie, France
| | - Pierre Mournet
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
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18
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Abstract
Medicago truncatula is able to perform a symbiotic association with Sinorhizobium spp. This interaction leads to the formation of a new root organ, the nodule, in which bacteria infect the host cells and fix atmospheric nitrogen for the plant benefit. Multiple and complex processes are essential for the success of this interaction from the recognition phase to nodule formation and functioning, and a wide range of plant host genes is required to orchestrate this phenomenon. Thanks to direct and reverse genetic as well as transcriptomic approaches, numerous genes involved in this symbiosis have been described and improve our understanding of this fantastic association. Herein we propose to update the recent molecular knowledge of how M. truncatula associates to its symbiotic partner Sinorhizobium spp.
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19
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Chaintreuil C, Gully D, Hervouet C, Tittabutr P, Randriambanona H, Brown SC, Lewis GP, Bourge M, Cartieaux F, Boursot M, Ramanankierana H, D'Hont A, Teaumroong N, Giraud E, Arrighi JF. The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene. THE NEW PHYTOLOGIST 2016; 211:1077-1091. [PMID: 27061605 DOI: 10.1111/nph.13956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation.
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Affiliation(s)
- Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Spencer C Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Mickaël Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Fabienne Cartieaux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Marc Boursot
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Jean-François Arrighi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
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20
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Chaintreuil C, Rivallan R, Bertioli DJ, Klopp C, Gouzy J, Courtois B, Leleux P, Martin G, Rami JF, Gully D, Parrinello H, Séverac D, Patrel D, Fardoux J, Ribière W, Boursot M, Cartieaux F, Czernic P, Ratet P, Mournet P, Giraud E, Arrighi JF. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes. DNA Res 2016; 23:365-76. [PMID: 27298380 PMCID: PMC4991833 DOI: 10.1093/dnares/dsw020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/02/2016] [Indexed: 11/13/2022] Open
Abstract
Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far focused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species. Firstly, an RNAseq analysis was performed on the two parental lines selected to generate a F2 mapping population. The transcriptomic data were used to develop molecular markers and they allowed the identification of most symbiotic genes. The resulting map comprised 364 markers arranged in 10 linkage groups (2n = 20). A comparative analysis with the sequenced genomes of Arachis duranensis and A. ipaensis, the diploid ancestors of peanut, indicated blocks of conserved macrosynteny. Altogether, these results provided important clues regarding the evolution of symbiotic genes in a Nod factor-independent context. They provide a basis for a genome sequencing project and pave the way for forward genetic analysis of symbiosis in A. evenia.
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Affiliation(s)
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
| | - David J Bertioli
- University of Brasília, Institute of Biological Sciences, Campus Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Christophe Klopp
- INRA, Plateforme GenoToul Bioinfo, UR 875, INRA Auzeville, F-31326 Castanet-Tolosan, France
| | - Jérôme Gouzy
- INRA, UMR441 LIPM, INRA Auzeville, F-31326 Castanet-Tolosan, France
| | | | - Philippe Leleux
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France INRA, Plateforme GenoToul Bioinfo, UR 875, INRA Auzeville, F-31326 Castanet-Tolosan, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
| | | | - Djamel Gully
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, F-34094 Montpellier, France
| | - Dany Séverac
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, F-34094 Montpellier, France
| | - Delphine Patrel
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France IRD, Centre IRD de Montpellier France Sud, F-34394 Montpellier, France
| | - Joël Fardoux
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
| | - William Ribière
- IRD, Centre IRD de Montpellier France Sud, F-34394 Montpellier, France
| | - Marc Boursot
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
| | - Fabienne Cartieaux
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
| | - Pierre Czernic
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
| | - Pascal Ratet
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, 91405 Orsay, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
| | - Eric Giraud
- IRD, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
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21
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Busset N, De Felice A, Chaintreuil C, Gully D, Fardoux J, Romdhane S, Molinaro A, Silipo A, Giraud E. The LPS O-Antigen in Photosynthetic Bradyrhizobium Strains Is Dispensable for the Establishment of a Successful Symbiosis with Aeschynomene Legumes. PLoS One 2016; 11:e0148884. [PMID: 26849805 PMCID: PMC4743980 DOI: 10.1371/journal.pone.0148884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/25/2016] [Indexed: 11/18/2022] Open
Abstract
The photosynthetic bradyrhizobia are able to use a Nod-factor independent process to induce nitrogen-fixing nodules on some semi-aquatic Aeschynomene species. These bacteria display a unique LPS O-antigen composed of a new sugar, the bradyrhizose that is regarded as a key symbiotic factor due to its non-immunogenic character. In this study, to check this hypothesis, we isolated mutants affected in the O-antigen synthesis by screening a transposon mutant library of the ORS285 strain for clones altered in colony morphology. Over the 10,000 mutants screened, five were selected and found to be mutated in two genes, rfaL, encoding for a putative O-antigen ligase and gdh encoding for a putative dTDP-glucose 4,6-dehydratase. Biochemical analysis confirmed that the LPS of these mutants completely lack the O-antigen region. However, no effect of the mutations could be detected on the symbiotic properties of the mutants indicating that the O-antigen region of photosynthetic Bradyrhizobium strains is not required for the establishment of symbiosis with Aeschynomene.
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Affiliation(s)
- Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Antonia De Felice
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sana Romdhane
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant’Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126, Napoli, Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
- * E-mail:
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22
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Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes. Nat Commun 2014; 5:5106. [PMID: 25355435 DOI: 10.1038/ncomms6106] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/29/2014] [Indexed: 01/21/2023] Open
Abstract
Lipopolysaccharides (LPSs) are major components of the outer membrane of Gram-negative bacteria and are essential for their growth and survival. They act as a structural barrier and play an important role in the interaction with eukaryotic hosts. Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A. Biophysical analyses of reconstituted liposomes indicate that this hopanoid-lipid A structure reinforces the stability and rigidity of the outer membrane. In addition, the bacterium produces other hopanoid molecules not linked to LPS. A hopanoid-deficient strain, lacking a squalene hopene cyclase, displays increased sensitivity to stressful conditions and reduced ability to survive intracellularly in the host plant. This unusual combination of hopanoid and LPS molecules may represent an adaptation to optimize bacterial survival in both free-living and symbiotic states.
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23
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Arrighi JF, Chaintreuil C, Cartieaux F, Cardi C, Rodier-Goud M, Brown SC, Boursot M, D'Hont A, Dreyfus B, Giraud E. Radiation of the Nod-independent Aeschynomene relies on multiple allopolyploid speciation events. THE NEW PHYTOLOGIST 2014; 201:1457-1468. [PMID: 24237245 DOI: 10.1111/nph.12594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
• The semi-aquatic legumes belonging to the genus Aeschynomene constitute a premium system for investigating the origin and evolution of unusual symbiotic features such as stem nodulation and the presence of a Nod-independent infection process. This latter apparently arose in a single Aeschynomene lineage. But how this unique Nod-independent group then radiated is not yet known. • We have investigated the role of polyploidy in Aeschynomene speciation via a case study of the pantropical A. indica and then extended the analysis to the other Nod-independent species. For this, we combined SSR genotyping, genome characterization through flow cytometry, chromosome counting, FISH and GISH experiments, molecular phylogenies using ITS and single nuclear gene sequences, and artificial hybridizations. • These analyses demonstrate the existence of an A. indica polyploid species complex comprising A. evenia (C. Wright) (2n = 2x = 20), A. indica L. s.s. (2n = 4x = 40) and a new hexaploid form (2n = 6x = 60). This latter contains the two genomes present in the tetraploid (A. evenia and A. scabra) and another unidentified genome. Two other species, A. pratensis and A. virginica, are also shown to be of allopolyploid origin. • This work reveals multiple hybridization/polyploidization events, thus highlighting a prominent role of allopolyploidy in the radiation of the Nod-independent Aeschynomene.
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Affiliation(s)
- Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - C Cardi
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - M Rodier-Goud
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - Spencer C Brown
- CNRS, IBiSA Imagerie Gif et Imagif BioCell, Institut des Sciences du Végétal, UPR 2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Marc Boursot
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - Bernard Dreyfus
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
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24
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Chaintreuil C, Arrighi JF, Giraud E, Miché L, Moulin L, Dreyfus B, Munive-Hernández JA, Villegas-Hernandez MDC, Béna G. Evolution of symbiosis in the legume genus Aeschynomene. THE NEW PHYTOLOGIST 2013; 200:1247-59. [PMID: 23879229 DOI: 10.1111/nph.12424] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 06/24/2013] [Indexed: 05/22/2023]
Abstract
Legumes in the genus Aeschynomene form nitrogen-fixing root nodules in association with Bradyrhizobium strains. Several aquatic and subaquatic species have the additional capacity to form stem nodules, and some of them can symbiotically interact with specific strains that do not produce the common Nod factors synthesized by all other rhizobia. The question of the emergence and evolution of these nodulation characters has been the subject of recent debate. We conducted a molecular phylogenetic analysis of 38 different Aeschynomene species. The phylogeny was reconstructed with both the chloroplast DNA trnL intron and the nuclear ribosomal DNA ITS/5.8S region. We also tested 28 Aeschynomene species for their capacity to form root and stem nodules by inoculating different rhizobial strains, including nodABC-containing strains (ORS285, USDA110) and a nodABC-lacking strain (ORS278). Maximum likelihood analyses resolved four distinct phylogenetic groups of Aeschynomene. We found that stem nodulation may have evolved several times in the genus, and that all Aeschynomene species using a Nod-independent symbiotic process clustered in the same clade. The phylogenetic approach suggested that Nod-independent nodulation has evolved once in this genus, and should be considered as a derived character, and this result is discussed with regard to previous experimental studies.
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Affiliation(s)
- Clémence Chaintreuil
- IRD/CIRAD/UM2/Supagro, Laboratoire des Symbioses Tropicales et Méditerranéennes, F-34398, Montpellier, France
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25
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Podlešáková K, Fardoux J, Patrel D, Bonaldi K, Novák O, Strnad M, Giraud E, Spíchal L, Nouwen N. Rhizobial synthesized cytokinins contribute to but are not essential for the symbiotic interaction between photosynthetic Bradyrhizobia and Aeschynomene legumes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1232-8. [PMID: 23777431 DOI: 10.1094/mpmi-03-13-0076-r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cytokinins (CK) play an important role in the formation of nitrogen-fixing root nodules. It has been known for years that rhizobia secrete CK in the extracellular medium but whether they play a role in nodule formation is not known. We have examined this question using the photosynthetic Bradyrhizobium sp. strain ORS285 which is able to nodulate Aeschynomene afraspera and A. indica using a Nod-dependent or Nod-independent symbiotic process, respectively. CK profiling showed that the most abundant CK secreted by Bradyrhizobium sp. strain ORS285 are the 2MeS (2-methylthiol) derivatives of trans-zeatin and isopentenyladenine. In their pure form, these CK can activate legume CK receptors in vitro, and their exogenous addition induced nodule-like structures on host plants. Deletion of the miaA gene showed that transfer RNA degradation is the source of CK production in Bradyrhizobium sp. strain ORS285. In nodulation studies performed with A. indica and A. afraspera, the miaA mutant had a 1-day delay in nodulation and nitrogen fixation. Moreover, A. indica plants formed considerably smaller but more abundant nodules when inoculated with the miaA mutant. These data show that CK produced by Bradyrhizobium sp. strain ORS285 are not the key signal triggering nodule formation during the Nod-independent symbiosis but they contribute positively to nodule development in Aeschynomene plants.
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MESH Headings
- Acetylene/metabolism
- Bradyrhizobium/genetics
- Bradyrhizobium/metabolism
- Bradyrhizobium/physiology
- Cytokinins/metabolism
- Cytokinins/pharmacology
- Dose-Response Relationship, Drug
- Ethylenes/metabolism
- Fabaceae/drug effects
- Fabaceae/growth & development
- Fabaceae/metabolism
- Fabaceae/microbiology
- Genes, Reporter
- Nitrogen Fixation
- Nitrogenase
- Phylogeny
- Plant Growth Regulators/metabolism
- Plant Growth Regulators/pharmacology
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Root Nodulation
- Plant Roots/drug effects
- Plant Roots/growth & development
- Plant Roots/metabolism
- Plant Roots/microbiology
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Root Nodules, Plant/drug effects
- Root Nodules, Plant/growth & development
- Root Nodules, Plant/metabolism
- Root Nodules, Plant/microbiology
- Sequence Deletion
- Signal Transduction
- Symbiosis
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Arrighi JF, Cartieaux F, Chaintreuil C, Brown S, Boursot M, Giraud E. Genotype delimitation in the Nod-independent model legume Aeschynomene evenia. PLoS One 2013; 8:e63836. [PMID: 23717496 PMCID: PMC3662760 DOI: 10.1371/journal.pone.0063836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/18/2013] [Indexed: 11/28/2022] Open
Abstract
Research on the nitrogen-fixing symbiosis has been so far focused on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some semi-aquatic Aeschynomene species present the distinctive feature to form nitrogen-fixing nodules on both roots and stems following elicitation by photosynthetic bradyrhizobia that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium-legume symbiosis. To decipher the molecular mechanisms of this unique Nod-independent nitrogen-fixing symbiosis, we previously identified A. evenia C. Wright as an appropriate model legume, because it displays all the requisites for molecular and genetic approaches. To advance the use of this new model legume species, here we characterized the intraspecific diversity found in A. evenia. For this, the accessions available in germplasm banks were collected and subjected to morphological investigations, genotyping with RAPD and SSR markers, molecular phylogenies using ITS and single nuclear gene sequences, and cross-compatibility tests. These combined analyses revealed an important intraspecific differentiation that led us to propose a new taxonomic classification for A. evenia comprising two subspecies and four varieties. The A. evenia ssp. evenia contains var. evenia and var. pauciciliata whereas A. evenia ssp. serrulata comprises var. serrulata and var. major. This study provides information to exploit efficiently the diversity encountered in A. evenia and proposes subsp. evenia as the most appropriate subspecies for future projects aimed at identifying plant determinants of the Nod-independent symbiotic process.
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Affiliation(s)
- Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
- * E-mail:
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Spencer Brown
- Centre national de la recherche scientifique, IBiSA Imagerie Gif et Imagif BioCell, Institut des Sciences du Végétal, UPR 2355, Gif-sur-Yvette, France
| | - Marc Boursot
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
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Okubo T, Fukushima S, Minamisawa K. Evolution of Bradyrhizobium-Aeschynomene mutualism: living testimony of the ancient world or highly evolved state? PLANT & CELL PHYSIOLOGY 2012; 53:2000-2007. [PMID: 23161855 DOI: 10.1093/pcp/pcs150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Until recently it had been well established that the initial step in legume-rhizobia symbioses was flavonoid and Nod factor (NF) signaling. However, NF-independent symbiosis is now known to occur between Bradyrhizobium and some species of Aeschynomene. Since its discovery, this unusual symbiotic system has attracted attention, and efforts have been devoted to revealing the NF-independent symbiotic mechanism, although the molecular mechanisms of nodule initiation still remain to be elucidated. NF-independent symbiosis is also interesting from the perspective of the evolution of legume-rhizobia symbiosis. In this mini-review, we discuss the current literature on the NF-independent symbiotic system in terms of phylogeny of the partners, infection, bacteroid differentiation, nodule structure, photosynthesis, endophytic features and model host plant. We also discuss NF-independent symbiosis, which is generally regarded to be more primitive than NF-dependent symbiosis, because the bacteria invade host plants via 'crack entry'. We propose three possible scenarios concerning the evolution of NF-independent symbiosis, which do not exclude the possibility that the NF-independent system evolved from NF-dependent interactions. Finally, we examine an interesting question on Bradyrhizobium-Aeschynomene mutualism, which is how do they initiate symbiosis without NF. Phylogenetic and genomic analyses of symbiotic and non-symbiotic bradyrhizobia with A. indica may be crucial to address the question, because of the very narrow phylogeny of natural endosymbionts without nod genes compared with other legume-rhizobia symbioses.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, 980-8577 Japan
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