1
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Wongdee J, Piromyou P, Songwattana P, Greetatorn T, Boonkerd N, Teaumroong N, Giraud E, Gully D, Nouwen N, Kiatponglarp W, Tanthanuch W, Tittabutr P. Exploring the cellular surface polysaccharide and root nodule symbiosis characteristics of the rpoN mutants of Bradyrhizobium sp. DOA9 using synchrotron-based Fourier transform infrared microspectroscopy in conjunction with X-ray absorption spectroscopy. Microbiol Spectr 2023; 11:e0194723. [PMID: 37681944 PMCID: PMC10581086 DOI: 10.1128/spectrum.01947-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/09/2023] [Indexed: 09/09/2023] Open
Abstract
The functional significance of rpoN genes that encode two sigma factors in the Bradyrhizobium sp. strain DOA9 has been reported to affect colony formation, root nodulation characteristics, and symbiotic interactions with Aeschynomene americana. rpoN mutant strains are defective in cellular surface polysaccharide (CSP) production compared with the wild-type (WT) strain, and they accordingly exhibit smaller colonies and diminished symbiotic effectiveness. To gain deeper insights into the changes in CSP composition and the nodules of rpoN mutants, we employed synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy and X-ray absorption spectroscopy. FTIR analysis of the CSP revealed the absence of specific components in the rpoN mutants, including lipids, carboxylic groups, polysaccharide-pyranose rings, and β-galactopyranosyl residues. Nodules formed by DOA9WT exhibited a uniform distribution of lipids, proteins, and carbohydrates; mutant strains, particularly DOA9∆rpoNp:ΩrpoNc, exhibited decreased distribution uniformity and a lower concentration of C=O groups. Furthermore, Fe K-edge X-ray absorption near-edge structure and extended X-ray absorption fine structure analyses revealed deficiencies in the nitrogenase enzyme in the nodules of DOA9∆rpoNc and DOA9∆rpoNp:ΩrpoNc mutants; nodules from DOA9WT and DOA9∆rpoNp exhibited both leghemoglobin and the nitrogenase enzyme. IMPORTANCE This work provides valuable insights into how two rpoN genes affect the composition of cellular surface polysaccharides (CSPs) in Bradyrhizobium sp., which subsequently dictates root nodule chemical characteristics and nitrogenase production. We used advanced synchrotron methods, including synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy and X-ray absorption spectroscopy (XAS), for the first time in this field to analyze CSP components and reveal the biochemical changes occurring within nodules. These cutting-edge techniques confer significant advantages by providing detailed molecular information, enabling the identification of specific functional groups, chemical bonds, and biomolecule changes. This research not only contributes to our understanding of plant-microbe interactions but also establishes a foundation for future investigations and potential applications in this field. The combined use of the synchrotron-based FTIR and XAS techniques represents a significant advancement in facilitating a comprehensive exploration of bacterial CSPs and their implications in plant-microbe interactions.
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Affiliation(s)
- Jenjira Wongdee
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Pongdet Piromyou
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Pongpan Songwattana
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Teerana Greetatorn
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- IRD, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Plant Health Institute of Montpellier, UMR-PHIM, Montpellier, France
| | - Djamel Gully
- IRD, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Plant Health Institute of Montpellier, UMR-PHIM, Montpellier, France
| | - Nico Nouwen
- IRD, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Plant Health Institute of Montpellier, UMR-PHIM, Montpellier, France
| | - Worawikunya Kiatponglarp
- Thai wah public company limited @CU innovation hub, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Waraporn Tanthanuch
- Synchrotron Light Research Institute (Public Organization), Muang, Nakhon Ratchasima, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
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2
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Camuel A, Teulet A, Carcagno M, Haq F, Pacquit V, Gully D, Pervent M, Chaintreuil C, Fardoux J, Horta-Araujo N, Okazaki S, Ratu STN, Gueye F, Zilli J, Nouwen N, Arrighi JF, Luo H, Mergaert P, Deslandes L, Giraud E. Widespread Bradyrhizobium distribution of diverse Type III effectors that trigger legume nodulation in the absence of Nod factor. ISME J 2023; 17:1416-1429. [PMID: 37355742 PMCID: PMC10432411 DOI: 10.1038/s41396-023-01458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
The establishment of the rhizobium-legume symbiosis is generally based on plant perception of Nod factors (NFs) synthesized by the bacteria. However, some Bradyrhizobium strains can nodulate certain legume species, such as Aeschynomene spp. or Glycine max, independently of NFs, and via two different processes that are distinguished by the necessity or not of a type III secretion system (T3SS). ErnA is the first known type III effector (T3E) triggering nodulation in Aeschynomene indica. In this study, a collection of 196 sequenced Bradyrhizobium strains was tested on A. indica. Only strains belonging to the photosynthetic supergroup can develop a NF-T3SS-independent symbiosis, while the ability to use a T3SS-dependent process is found in multiple supergroups. Of these, 14 strains lacking ernA were tested by mutagenesis to identify new T3Es triggering nodulation. We discovered a novel T3E, Sup3, a putative SUMO-protease without similarity to ErnA. Its mutation in Bradyrhizobium strains NAS96.2 and WSM1744 abolishes nodulation and its introduction in an ernA mutant of strain ORS3257 restores nodulation. Moreover, ectopic expression of sup3 in A. indica roots led to the formation of spontaneous nodules. We also report three other new T3Es, Ubi1, Ubi2 and Ubi3, which each contribute to the nodulation capacity of strain LMTR13. These T3Es have no homology to known proteins but share with ErnA three motifs necessary for ErnA activity. Together, our results highlight an unsuspected distribution and diversity of T3Es within the Bradyrhizobium genus that may contribute to their symbiotic efficiency by participating in triggering legume nodulation.
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Affiliation(s)
- Alicia Camuel
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, CB2 1LR, UK
| | - Mélanie Carcagno
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fazal Haq
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Valérie Pacquit
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Natasha Horta-Araujo
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shin Okazaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Safirah Tasa Nerves Ratu
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Fatou Gueye
- Carrefour International, Bureau Régional Afrique de l'Ouest, Dakar, Sénégal
| | - Jerri Zilli
- Embrapa Agrobiologia, Bairro Ecologia, Seropedica, Rio de Janeiro, Brazil
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Haiwei Luo
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Laurent Deslandes
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France.
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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3
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Di Lorenzo F, Nicolardi S, Marchetti R, Vanacore A, Gallucci N, Duda K, Nieto Fabregat F, Nguyen HNA, Gully D, Saenz J, Giraud E, Paduano L, Molinaro A, D’Errico G, Silipo A. Expanding Knowledge of Methylotrophic Capacity: Structure and Properties of the Rough-Type Lipopolysaccharide from Methylobacterium extorquens and Its Role on Membrane Resistance to Methanol. JACS Au 2023; 3:929-942. [PMID: 37006758 PMCID: PMC10052234 DOI: 10.1021/jacsau.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
The ability of Methylobacterium extorquens to grow on methanol as the sole carbon and energy source has been the object of intense research activity. Unquestionably, the bacterial cell envelope serves as a defensive barrier against such an environmental stressor, with a decisive role played by the membrane lipidome, which is crucial for stress resistance. However, the chemistry and the function of the main constituent of the M. extorquens outer membrane, the lipopolysaccharide (LPS), is still undefined. Here, we show that M. extorquens produces a rough-type LPS with an uncommon, non-phosphorylated, and extensively O-methylated core oligosaccharide, densely substituted with negatively charged residues in the inner region, including novel monosaccharide derivatives such as O-methylated Kdo/Ko units. Lipid A is composed of a non-phosphorylated trisaccharide backbone with a distinctive, low acylation pattern; indeed, the sugar skeleton was decorated with three acyl moieties and a secondary very long chain fatty acid, in turn substituted by a 3-O-acetyl-butyrate residue. Spectroscopic, conformational, and biophysical analyses on M. extorquens LPS highlighted how structural and tridimensional features impact the molecular organization of the outer membrane. Furthermore, these chemical features also impacted and improved membrane resistance in the presence of methanol, thus regulating membrane ordering and dynamics.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Roberta Marchetti
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Adele Vanacore
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Noemi Gallucci
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Katarzyna Duda
- Research
Center Borstel Leibniz Lung Center, Parkallee 4a, 23845 Borstel, Germany
| | - Ferran Nieto Fabregat
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Ha Ngoc Anh Nguyen
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Djamel Gully
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - James Saenz
- B-CUBE
Center for Molecular Bioengineering, Technische
Universität Dresden, Tatzberg 41, 01307 Dresden, Germany
| | - Eric Giraud
- IRD,
Laboratoire des Symbioses Tropicales et Méditerranéennes
(LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Luigi Paduano
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Antonio Molinaro
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Gerardino D’Errico
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
- CSGI, Consorzio
Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Alba Silipo
- Department
of Chemical Sciences and Task Force for Microbiome Studies, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
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4
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Vergne A, Giraud E, Camuel A, Bardot C, Billard H, Bouquet C, Corbara B, Gully D, Mathonat F, Jeanthon C, Mary I, Caissard JC, Lehours AC. The Pharaoh's snakes of the Teasel: New insights into Francis Darwin's observations. Ecology 2023; 104:e4030. [PMID: 36912733 DOI: 10.1002/ecy.4030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/10/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023]
Affiliation(s)
- Antoine Vergne
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, 34398 Montpellier cedex 5, France.,Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Alicia Camuel
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, 34398 Montpellier cedex 5, France.,Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Corinne Bardot
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Hermine Billard
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Clémentin Bouquet
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Bruno Corbara
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, 34398 Montpellier cedex 5, France.,Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Frédéric Mathonat
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Christian Jeanthon
- CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France
| | - Isabelle Mary
- Université Clermont Auvergne, CNRS, LMGE, F-63000, Clermont-Ferrand, France
| | - Jean-Claude Caissard
- Université de Lyon, UJM-Saint-Etienne, CNRS, LBVpam UMR 5079, 23 rue du Dr Paul Michelon, F-42023, Saint-Etienne, France
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5
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Wongdee J, Piromyou P, Songwattana P, Greetatorn T, Teaumroong N, Boonkerd N, Giraud E, Nouwen N, Tittabutr P. Role of two RpoN in Bradyrhizobium sp. strain DOA9 in symbiosis and free-living growth. Front Microbiol 2023; 14:1131860. [PMID: 36876109 PMCID: PMC9977809 DOI: 10.3389/fmicb.2023.1131860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
RpoN is an alternative sigma factor (sigma 54) that recruits the core RNA polymerase to promoters of genes. In bacteria, RpoN has diverse physiological functions. In rhizobia, RpoN plays a key role in the transcription of nitrogen fixation (nif) genes. The Bradyrhizobium sp. DOA9 strain contains a chromosomal (c) and plasmid (p) encoded RpoN protein. We used single and double rpoN mutants and reporter strains to investigate the role of the two RpoN proteins under free-living and symbiotic conditions. We observed that the inactivation of rpoNc or rpoNp severely impacts the physiology of the bacteria under free-living conditions, such as the bacterial motility, carbon and nitrogen utilization profiles, exopolysaccharide (EPS) production, and biofilm formation. However, free-living nitrogen fixation appears to be under the primary control of RpoNc. Interestingly, drastic effects of rpoNc and rpoNp mutations were also observed during symbiosis with Aeschynomene americana. Indeed, inoculation with rpoNp, rpoNc, and double rpoN mutant strains resulted in decreases of 39, 64, and 82% in the number of nodules, respectively, as well as a reduction in nitrogen fixation efficiency and a loss of the bacterium's ability to survive intracellularly. Taken together, the results show that the chromosomal and plasmid encoded RpoN proteins in the DOA9 strain both play a pleiotropic role during free-living and symbiotic states.
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Affiliation(s)
- Jenjira Wongdee
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Pongdet Piromyou
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Pongpan Songwattana
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Teerana Greetatorn
- Institute of Research and Development, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- IRD, Plant Health Institute of Montpellier, UMR-PHIM, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Montpellier, France
| | - Nico Nouwen
- IRD, Plant Health Institute of Montpellier, UMR-PHIM, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Montpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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6
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Tighilt L, Boulila F, De Sousa BFS, Giraud E, Ruiz-Argüeso T, Palacios JM, Imperial J, Rey L. The Bradyrhizobium Sp. LmicA16 Type VI Secretion System Is Required for Efficient Nodulation of Lupinus Spp. Microb Ecol 2022; 84:844-855. [PMID: 34697646 DOI: 10.1007/s00248-021-01892-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/30/2021] [Indexed: 05/06/2023]
Abstract
Many bacteria of the genus Bradyrhizobium are capable of inducing nodules in legumes. In this work, the importance of a type VI secretion system (T6SS) in a symbiotic strain of the genus Bradyrhizobium is described. T6SS of Bradyrhizobium sp. LmicA16 (A16) is necessary for efficient nodulation with Lupinus micranthus and Lupinus angustifolius. A mutant in the gene vgrG, coding for a component of the T6SS nanostructure, induced less nodules and smaller plants than the wild-type (wt) strain and was less competitive when co-inoculated with the wt strain. A16 T6SS genes are organized in a 26-kb DNA region in two divergent gene clusters of nine genes each. One of these genes codes for a protein (Tsb1) of unknown function but containing a methyltransferase domain. A tsb1 mutant showed an intermediate symbiotic phenotype regarding vgrG mutant and higher mucoidity than the wt strain in free-living conditions. T6SS promoter fusions to the lacZ reporter indicate expression in nodules but not in free-living cells grown in different media and conditions. The analysis of nodule structure revealed that the level of nodule colonization was significantly reduced in the mutants with respect to the wt strain.
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Affiliation(s)
- L Tighilt
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
| | - F Boulila
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
| | - B F S De Sousa
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - E Giraud
- IRD, Laboratoire Des Symbioses Tropicales Et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J-Campus International de Baillarguet, 34398Cedex 5, Montpellier, France
| | - T Ruiz-Argüeso
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J M Palacios
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J Imperial
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Instituto de Ciencias Agrarias, CSIC, 28006, Madrid, Spain
| | - L Rey
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain.
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
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7
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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 Physiol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Giraud E, Chiong J, Martin J, Burger D, Erp N, Smolders E. 1595P QTc-prolonging drug-drug interactions related to CDK4/6 inhibitors. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Abstract
To suppress plant immunity and promote the intracellular infection required for fixing nitrogen for the benefit of their legume hosts, many rhizobia use type III secretion systems (T3SSs) that deliver effector proteins (T3Es) inside host cells. As reported for interactions between pathogens and host plants, the immune system of legume hosts and the cocktail of T3Es secreted by rhizobia determine the symbiotic outcome. If they remain undetected, T3Es may reduce plant immunity and thus promote infection of legumes by rhizobia. If one or more of the secreted T3Es are recognized by the cognate plant receptors, defense responses are triggered and rhizobial infection may abort. However, some rhizobial T3Es can also circumvent the need for nodulation (Nod) factors to trigger nodule formation. Here we review the multifaceted roles played by rhizobial T3Es during symbiotic interactions with legumes. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Albin Teulet
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France;
| | - Alicia Camuel
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France; .,PHIM Plant Health Institute, IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France
| | - Xavier Perret
- Laboratory of Microbial Genetics, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France; .,PHIM Plant Health Institute, IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France
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10
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Nouwen N, Chaintreuil C, Fardoux J, Giraud E. A glutamate synthase mutant of Bradyrhizobium sp. strain ORS285 is unable to induce nodules on Nod factor-independent Aeschynomene species. Sci Rep 2021; 11:20910. [PMID: 34686745 PMCID: PMC8536739 DOI: 10.1038/s41598-021-00480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
The Bradyrhizobium sp. strain ORS285 is able to establish a nitrogen-fixing symbiosis with both Nod factor (NF) dependent and NF-independent Aeschynomene species. Here, we have studied the growth characteristics and symbiotic interaction of a glutamate synthase (GOGAT; gltD::Tn5) mutant of Bradyrhizobium ORS285. We show that the ORS285 gltD::Tn5 mutant is unable to use ammonium, nitrate and many amino acids as nitrogen source for growth and is unable to fix nitrogen under free-living conditions. Moreover, on several nitrogen sources, the growth rate of the gltB::Tn5 mutant was faster and/or the production of the carotenoid spirilloxanthin was much higher as compared to the wild-type strain. The absence of GOGAT activity has a drastic impact on the symbiotic interaction with NF-independent Aeschynomene species. With these species, inoculation with the ORS285 gltD::Tn5 mutant does not result in the formation of nodules. In contrast, the ORS285 gltD::Tn5 mutant is capable to induce nodules on NF-dependent Aeschynomene species, but these nodules were ineffective for nitrogen fixation. Interestingly, in NF-dependent and NF-independent Aeschynomene species inoculation with the ORS285 gltD::Tn5 mutant results in browning of the plant tissue at the site of the infection suggesting that the mutant bacteria induce plant defence responses.
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Affiliation(s)
- Nico Nouwen
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France.
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France
| | - Joel Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France
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11
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Songwattana P, Chaintreuil C, Wongdee J, Teulet A, Mbaye M, Piromyou P, Gully D, Fardoux J, Zoumman AMA, Camuel A, Tittabutr P, Teaumroong N, Giraud E. Identification of type III effectors modulating the symbiotic properties of Bradyrhizobium vignae strain ORS3257 with various Vigna species. Sci Rep 2021; 11:4874. [PMID: 33649428 PMCID: PMC7921652 DOI: 10.1038/s41598-021-84205-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
The Bradyrhizobium vignae strain ORS3257 is an elite strain recommended for cowpea inoculation in Senegal. This strain was recently shown to establish symbioses on some Aeschynomene species using a cocktail of Type III effectors (T3Es) secreted by the T3SS machinery. In this study, using a collection of mutants in different T3Es genes, we sought to identify the effectors that modulate the symbiotic properties of ORS3257 in three Vigna species (V. unguiculata, V. radiata and V. mungo). While the T3SS had a positive impact on the symbiotic efficiency of the strain in V. unguiculata and V. mungo, it blocked symbiosis with V. radiata. The combination of effectors promoting nodulation in V. unguiculata and V. mungo differed, in both cases, NopT and NopAB were involved, suggesting they are key determinants for nodulation, and to a lesser extent, NopM1 and NopP1, which are additionally required for optimal symbiosis with V. mungo. In contrast, only one effector, NopP2, was identified as the cause of the incompatibility between ORS3257 and V. radiata. The identification of key effectors which promote symbiotic efficiency or render the interaction incompatible is important for the development of inoculation strategies to improve the growth of Vigna species cultivated in Africa and Asia.
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Affiliation(s)
- Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France.,IRD, Laboratoire Commun de Microbiologie, UR040, ISRA, UCAD, Centre de Recherche de Bel Air, Dakar, Senegal
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Mamadou Mbaye
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Joel Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Alexandre Mahougnon Aurel Zoumman
- IRD, Laboratoire Commun de Microbiologie, UR040, ISRA, UCAD, Centre de Recherche de Bel Air, Dakar, Senegal.,Département de Biologie Végétale, University Cheikh Anta Diop, Dakar, Senegal
| | - Alicia Camuel
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France.
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ratu STN, Teulet A, Miwa H, Masuda S, Nguyen HP, Yasuda M, Sato S, Kaneko T, Hayashi M, Giraud E, Okazaki S. Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling. Sci Rep 2021; 11:2034. [PMID: 33479414 PMCID: PMC7820406 DOI: 10.1038/s41598-021-81598-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023] Open
Abstract
Legume plants form a root-nodule symbiosis with rhizobia. This symbiosis establishment generally relies on rhizobium-produced Nod factors (NFs) and their perception by leguminous receptors (NFRs) that trigger nodulation. However, certain rhizobia hijack leguminous nodulation signalling via their type III secretion system, which functions in pathogenic bacteria to deliver effector proteins into host cells. Here, we report that rhizobia use pathogenic-like effectors to hijack legume nodulation signalling. The rhizobial effector Bel2-5 resembles the XopD effector of the plant pathogen Xanthomonas campestris and could induce nitrogen-fixing nodules on soybean nfr mutant. The soybean root transcriptome revealed that Bel2-5 induces expression of cytokinin-related genes, which are important for nodule organogenesis and represses ethylene- and defense-related genes that are deleterious to nodulation. Remarkably, Bel2-5 introduction into a strain unable to nodulate soybean mutant affected in NF perception conferred nodulation ability. Our findings show that rhizobia employ and have customized pathogenic effectors to promote leguminous nodulation signalling.
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Affiliation(s)
- Safirah Tasa Nerves Ratu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan
| | - Albin Teulet
- Laboratoire Des Symbioses Tropicales Et Méditerranéennes, Institut de Recherche Pour Le Développement, UMR Institut de Recherche Pour Le Développement/SupAgro/Institut National de Recherche Pour L'Agriculture, L'Alimentation Et L'Environnement, Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique Pour Le Développement, 34398, Montpellier Cedex 5, France
| | - Hiroki Miwa
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan
| | - Sachiko Masuda
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan
| | - Hien P Nguyen
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan
| | - Michiko Yasuda
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Takakazu Kaneko
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, 603-8555, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Eric Giraud
- Laboratoire Des Symbioses Tropicales Et Méditerranéennes, Institut de Recherche Pour Le Développement, UMR Institut de Recherche Pour Le Développement/SupAgro/Institut National de Recherche Pour L'Agriculture, L'Alimentation Et L'Environnement, Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique Pour Le Développement, 34398, Montpellier Cedex 5, France
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan.
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo, 183-8509, Japan.
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Nouwen N, Arrighi JF, Gully D, Giraud E. RibBX of Bradyrhizobium ORS285 Plays an Important Role in Intracellular Persistence in Various Aeschynomene Host Plants. Mol Plant Microbe Interact 2021; 34:88-99. [PMID: 33226302 DOI: 10.1094/mpmi-07-20-0209-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bradyrhizobium ORS285 forms a nitrogen-fixating symbiosis with both Nod factor (NF)-dependent and NF-independent Aeschynomene spp. The Bradyrhizobium ORS285 ribBA gene encodes for a putative bifunctional enzyme with 3,4-dihydroxybutanone phosphate (3,4-DHBP) synthase and guanosine triphosphate (GTP) cyclohydrolase II activities, catalyzing the initial steps in the riboflavin biosynthesis pathway. In this study, we show that inactivating the ribBA gene does not cause riboflavin auxotrophy under free-living conditions and that, as shown for RibBAs from other bacteria, the GTP cyclohydrolase II domain has no enzymatic activity. For this reason, we have renamed the annotated ribBA as ribBX. Because we were unable to identify other ribBA or ribA and ribB homologs in the genome of Bradyrhizobium ORS285, we hypothesize that the ORS285 strain can use unconventional enzymes or an alternative pathway for the initial steps of riboflavin biosynthesis. Inactivating ribBX has a drastic impact on the interaction of Bradyrhizobium ORS285 with many of the tested Aeschynomene spp. In these Aeschynomene spp., the ORS285 ribBX mutant is able to infect the plant host cells but the intracellular infection is not maintained and the nodules senesce early. This phenotype can be complemented by reintroduction of the 3,4-DHBP synthase domain alone. Our results indicate that, in Bradyrhizobium ORS285, the RibBX protein is not essential for riboflavin biosynthesis under free-living conditions and we hypothesize that its activity is needed to sustain riboflavin biosynthesis under certain symbiotic conditions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Nico Nouwen
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
| | - Jean-Francois Arrighi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
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Marchetti R, Nieto Fabregat F, Pallach M, Gully D, Giraud E, Molinaro A, Duda KA, Silipo A. The Peculiar Structure of Acetobacter pasteurianus CIP103108 LPS Core Oligosaccharide. Chembiochem 2020; 22:147-150. [PMID: 32965769 DOI: 10.1002/cbic.202000597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/21/2020] [Indexed: 11/07/2022]
Abstract
Acetobacter pasteurianus, a member of the Alphaproteobacteria, is an acetic acid-producing bacterium present on sugar-rich substrates such as such as fruits, flowers and vegetables and traditionally used in the production of fermented food. The preferred living habitat associated with acid conditions makes the structure of the bacterial cell wall interesting to study, due to expected uncommon features. We have used a combination of chemical, analytical and NMR spectroscopy approaches to define the complete structure of the core oligosaccharide from A. pasteurianus CIP103108 LPS. Interestingly, the core oligosaccharide displays a high concentration of negatively charged groups, structural features that might contribute to reinforcing the bacterial membrane.
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Affiliation(s)
- Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Ferran Nieto Fabregat
- Department of Chemical Sciences, University of Naples Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Mateusz Pallach
- Department of Chemical Sciences, University of Naples Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy.,Present address: Department of Organic Chemistry, Stockholm University, Svante Arrhenius väg 16C, 106 91, Stockholm, Sweden
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J, Campus de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Katarzyna A Duda
- Junior Group of Allergobiochemistry, Research Center Borstel Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research, 23845, Borstel, Germany.,Airway Research Center North (ARCN), German Center for Lung Research, 23845, Borstel, Germany
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
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Teulet A, Gully D, Rouy Z, Camuel A, Koebnik R, Giraud E, Lassalle F. Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium. Microb Genom 2020; 6:mgen000407. [PMID: 32783800 PMCID: PMC7643967 DOI: 10.1099/mgen.0.000407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/26/2020] [Indexed: 01/22/2023] Open
Abstract
Bradyrhizobium are abundant soil bacteria and the major symbiont of legumes. The recent availability of Bradyrhizobium genome sequences provides a large source of information for analysis of symbiotic traits. In this study, we investigated the evolutionary dynamics of the nodulation genes (nod) and their relationship with the genes encoding type III secretion systems (T3SS) and their effectors among bradyrhizobia. Based on the comparative analysis of 146 Bradyrhizobium genome sequences, we identified six different types of T3SS gene clusters. The two predominant cluster types are designated RhcIa and RhcIb and both belong to the RhcI-T3SS family previously described in other rhizobia. They are found in 92/146 strains, most of them also containing nod genes. RhcIa and RhcIb gene clusters differ in the genes they carry: while the translocon-encoding gene nopX is systematically found in strains containing RhcIb, the nopE and nopH genes are specifically conserved in strains containing RhcIa, suggesting that these last two genes might functionally substitute nopX and play a role related to effector translocation. Phylogenetic analysis suggests that bradyrhizobia simultaneously gained nod and RhcI-T3SS gene clusters via horizontal transfer or subsequent vertical inheritance of a symbiotic island containing both. Sequence similarity searches for known Nop effector proteins in bradyrhizobial proteomes revealed the absence of a so-called core effectome, i.e. that no effector is conserved among all Bradyrhizobium strains. However, NopM and SUMO proteases were found to be the main effector families, being represented in the majority of the genus. This study indicates that bradyrhizobial T3SSs might play a more significant symbiotic role than previously thought and provides new candidates among T3SS structural proteins and effectors for future functional investigations.
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Affiliation(s)
- Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/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/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Zoe Rouy
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Alicia Camuel
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Ralf Koebnik
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J – Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Florent Lassalle
- Department of Infectious Disease Epidemiology. Imperial College London, St Mary’s Hospital Campus, Praed Street, London W2 1NY, UK
- Pathogen and Microbes Program, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Present address: Pathogen and Microbes Program, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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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. Mol Plant Microbe Interact 2019; 32:1517-1525. [PMID: 31265361 DOI: 10.1094/mpmi-05-19-0133-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Songwattana P, Tittabutr P, Wongdee J, Teamtisong K, Wulandari D, Teulet A, Fardoux J, Boonkerd N, Giraud E, Teaumroong N. Symbiotic properties of a chimeric Nod-independent photosynthetic Bradyrhizobium strain obtained by conjugative transfer of a symbiotic plasmid. Environ Microbiol 2019; 21:3442-3454. [PMID: 31077522 DOI: 10.1111/1462-2920.14650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/23/2019] [Accepted: 05/07/2019] [Indexed: 11/30/2022]
Abstract
The lateral transfer of symbiotic genes converting a predisposed soil bacteria into a legume symbiont has occurred repeatedly and independently during the evolution of rhizobia. We experimented the transfer of a symbiotic plasmid between Bradyrhizobium strains. The originality of the DOA9 donor is that it harbours a symbiotic mega-plasmid (pDOA9) containing nod, nif and T3SS genes while the ORS278 recipient has the unique property of inducing nodules on some Aeschynomene species in the absence of Nod factors (NFs). We observed that the chimeric strain ORS278-pDOA9* lost its ability to develop a functional symbiosis with Aeschynomene. indica and Aeschynomene evenia. The mutation of rhcN and nodB led to partial restoration of nodule efficiency, indicating that T3SS effectors and NFs block the establishment of the NF-independent symbiosis. Conversely, ORS278-pDOA9* strain acquired the ability to form nodules on Crotalaria juncea and Macroptillium artropurpureum but not on NF-dependent Aeschynomene (A. afraspera and A. americana), suggesting that the ORS278 strain also harbours incompatible factors that block the interaction with these species. These data indicate that the symbiotic properties of a chimeric rhizobia cannot be anticipated due to new combination of symbiotic and non-symbiotic determinants that may interfere during the interaction with the host plant.
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Affiliation(s)
- Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 30000, Thailand
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 30000, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Dyah Wulandari
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 30000, Thailand
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro. Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Joel Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro. Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 30000, Thailand
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro. Campus de Baillarguet, TA-A82/J, 34398, Montpellier Cedex 5, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 30000, Thailand
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Piromyou P, Songwattana P, Teamtisong K, Tittabutr P, Boonkerd N, Tantasawat PA, Giraud E, Göttfert M, Teaumroong N. Mutualistic co-evolution of T3SSs during the establishment of symbiotic relationships between Vigna radiata and Bradyrhizobia. Microbiologyopen 2019; 8:e00781. [PMID: 30628192 PMCID: PMC6612562 DOI: 10.1002/mbo3.781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023] Open
Abstract
This study supports the idea that the evolution of type III secretion system (T3SS) is one of the factors that controls Vigna radiata-bradyrhizobia symbiosis. Based on phylogenetic tree data and gene arrangements, it seems that the T3SSs of the Thai bradyrhizobial strains SUTN9-2, DOA1, and DOA9 and the Senegalese strain ORS3257 may share the same origin. Therefore, strains SUTN9-2, DOA1, DOA9, and ORS3257 may have evolved their T3SSs independently from other bradyrhizobia, depending on biological and/or geological events. For functional analyses, the rhcJ genes of ORS3257, SUTN9-2, DOA9, and USDA110 were disrupted. These mutations had cultivar-specific effects on nodulation properties. The T3SSs of ORS3257 and DOA9 showed negative effects on V. radiata nodulation, while the T3SS of SUTN9-2 showed no effect on V. radiata symbiosis. In the roots of V. radiata CN72, the expression levels of the PR1 gene after inoculation with ORS3257 and DOA9 were significantly higher than those after inoculation with ORS3257 ΩT3SS, DOA9 ΩT3SS, and SUTN9-2. The T3Es from ORS3257 and DOA9 could trigger PR1 expression, which ultimately leads to abort nodulation. In contrast, the T3E from SUTN9-2 reduced PR1 expression. It seems that the mutualistic relationship between SUTN9-2 and V. radiata may have led to the selection of the most well-adapted combination of T3SS and symbiotic bradyrhizobial genotype.
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Affiliation(s)
- Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological EquipmentSuranaree University of TechnologyNakhon RatchasimaThailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Piyada Alisha Tantasawat
- School of Crop Production Technology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
| | - Eric Giraud
- IRD, Laboratory of Tropical and Mediterranean SymbiosesUMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de BaillarguetMontpellierFrance
| | | | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhon RatchasimaThailand
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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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Pallach M, Marchetti R, Di Lorenzo F, Fabozzi A, Giraud E, Gully D, Paduano L, Molinaro A, D'Errico G, Silipo A. Zymomonas mobilis exopolysaccharide structure and role in high ethanol tolerance. Carbohydr Polym 2018; 201:293-299. [PMID: 30241821 DOI: 10.1016/j.carbpol.2018.08.072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 10/28/2022]
Abstract
Bacterial cell surface exopolysaccharides (EPS) provide a protective barrier from the external milieu and participate in host-environment interactions. Zymomonas mobilis, an ethanologenic Gram negative bacterium, is used by the industry in bio-ethanol production process, due to its extraordinary resistance to a highly ethanolic environment. We found that Z. mobilis produces a mixture of two EPSs, an [α-(1→6)-D-Manp] mannose homopolymer and a galactose containing polysaccharide: [→2)-β-D-Galf-(1→3)-β-D-Galp-(1→]n. A physico-chemical study, conducted with diffusion-ordered spectroscopy (DOSY) and Dynamic Light Scattering (DLS), allowed to demonstrate that, differently from the majority of polysaccharides, ethanol is a good solvent for the galactose containing EPS, revealing that its chemical structure is specifically connected with the Zymomonas mobilis high ethanol tolerance.
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Affiliation(s)
- Mateusz Pallach
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Roberta Marchetti
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Flaviana Di Lorenzo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Antonio Fabozzi
- 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 (LSTM), UMR IRD/ SupAgro/INRA/ 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/INRA/ UM2 /CIRAD, TA-A82/J - Campus de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Luigi Paduano
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
| | - Gerardino D'Errico
- 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.
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22
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Lembo-Fazio L, Billod JM, Di Lorenzo F, Paciello I, Pallach M, Vaz-Francisco S, Holgado A, Beyaert R, Fresno M, Shimoyama A, Lanzetta R, Fukase K, Gully D, Giraud E, Martín-Santamaría S, Bernardini ML, Silipo A. Bradyrhizobium Lipid A: Immunological Properties and Molecular Basis of Its Binding to the Myeloid Differentiation Protein-2/Toll-Like Receptor 4 Complex. Front Immunol 2018; 9:1888. [PMID: 30154796 PMCID: PMC6102379 DOI: 10.3389/fimmu.2018.01888] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/31/2018] [Indexed: 11/24/2022] Open
Abstract
Lipopolysaccharides (LPS) are potent activator of the innate immune response through the binding to the myeloid differentiation protein-2 (MD-2)/toll-like receptor 4 (TLR4) receptor complexes. Although a variety of LPSs have been characterized so far, a detailed molecular description of the structure–activity relationship of the lipid A part has yet to be clarified. Photosynthetic Bradyrhizobium strains, symbiont of Aeschynomene legumes, express distinctive LPSs bearing very long-chain fatty acids with a hopanoid moiety covalently linked to the lipid A region. Here, we investigated the immunological properties of LPSs isolated from Bradyrhizobium strains on both murine and human immune systems. We found that they exhibit a weak agonistic activity and, more interestingly, a potent inhibitory effect on MD-2/TLR4 activation exerted by toxic enterobacterial LPSs. By applying computational modeling techniques, we also furnished a plausible explanation for the Bradyrhizobium LPS inhibitory activity at atomic level, revealing that its uncommon lipid A chemical features could impair the proper formation of the receptorial complex, and/or has a destabilizing effect on the pre-assembled complex itself.
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Affiliation(s)
- Luigi Lembo-Fazio
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Rome, Italy
| | - Jean-Marc Billod
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, Madrid, Spain
| | - Flaviana Di Lorenzo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Naples, Italy
| | - Ida Paciello
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Rome, Italy
| | - Mateusz Pallach
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Naples, Italy
| | | | - Aurora Holgado
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Manuel Fresno
- Diomune SL, Parque Científico de Madrid, Madrid, Spain
| | - Atsushi Shimoyama
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Rosa Lanzetta
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Naples, Italy
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet, Montpellier, France
| | - Sonsoles Martín-Santamaría
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC, Madrid, Spain
| | - Maria-Lina Bernardini
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Rome, Italy.,Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza-Università di Roma, Rome, Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Naples, Italy
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23
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Wongdee J, Boonkerd N, Teaumroong N, Tittabutr P, Giraud E. Regulation of Nitrogen Fixation in Bradyrhizobium sp. Strain DOA9 Involves Two Distinct NifA Regulatory Proteins That Are Functionally Redundant During Symbiosis but Not During Free-Living Growth. Front Microbiol 2018; 9:1644. [PMID: 30087663 PMCID: PMC6066989 DOI: 10.3389/fmicb.2018.01644] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/02/2018] [Indexed: 11/13/2022] Open
Abstract
The Bradyrhizobium sp. DOA9 strain displays the unusual properties to have a symbiotic plasmid and to fix nitrogen during both free-living and symbiotic growth. Sequence genome analysis shows that this strain contains the structural genes of dinitrogenase (nifDK) and the nifA regulatory gene on both the plasmid and chromosome. It was previously shown that both nifDK clusters are differentially expressed depending on growth conditions, suggesting different mechanisms of regulation. In this study, we examined the functional regulatory role of the two nifA genes found on the plasmid (nifAp) and chromosome (nifAc) that encode proteins with a moderate level of identity (55%) and different structural architectures. Using gusA (β-glucuronidase) reporter strains, we showed that both nifA genes were expressed during both the free-living and symbiotic growth stages. During symbiosis with Aeschynomene americana, mutants in only one nifA gene were not altered in their symbiotic properties, while a double nifA mutant was drastically impaired in nitrogen fixation, indicating that the two NifA proteins are functionally redundant during this culture condition. In contrast, under in vitro conditions, the nifAc mutant was unable to fix nitrogen, and no effect of the nifAp mutation was detected, indicating that NifAc is essential to activate nif genes during free-living growth. In accordance, the nitrogenase fixation deficiency of this mutant could be restored by the introduction of nifAc but not by nifAp or by two chimeric nifA genes encoding hybrid proteins with the N-terminus part of NifAc and the C-terminus of NifAp. Furthermore, transcriptional analysis by RT-qPCR of the WT and two nifA mutant backgrounds showed that NifAc and NifAp activated the expression of both chromosome and plasmid structural nifDK genes during symbiosis, while only NifAc activated the expression of nifDKc during free-living conditions. In summary, this study provides a better overview of the complex mechanisms of regulation of the nitrogenase genes in the DOA9 strain that involve two distinct NifA proteins, which are exchangeable during symbiosis for the activation of nif genes but not during free-living growth where NifAc is essential for the activation of nifDKc.
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Affiliation(s)
- Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut de Recherche Pour le Développement (IRD), UMR IRD, SupAgro, INRA, CIRAD, Université de Montpellier, Montpellier, France
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Lamouche F, Gully D, Chaumeret A, Nouwen N, Verly C, Pierre O, Sciallano C, Fardoux J, Jeudy C, Szücs A, Mondy S, Salon C, Nagy I, Kereszt A, Dessaux Y, Giraud E, Mergaert P, Alunni B. Transcriptomic dissection of Bradyrhizobium sp. strain ORS285 in symbiosis with Aeschynomene spp. inducing different bacteroid morphotypes with contrasted symbiotic efficiency. Environ Microbiol 2018; 21:3244-3258. [PMID: 29921018 DOI: 10.1111/1462-2920.14292] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 11/29/2022]
Abstract
To circumvent the paucity of nitrogen sources in the soil legume plants establish a symbiotic interaction with nitrogen-fixing soil bacteria called rhizobia. During symbiosis, the plants form root organs called nodules, where bacteria are housed intracellularly and become active nitrogen fixers known as bacteroids. Depending on their host plant, bacteroids can adopt different morphotypes, being either unmodified (U), elongated (E) or spherical (S). E- and S-type bacteroids undergo a terminal differentiation leading to irreversible morphological changes and DNA endoreduplication. Previous studies suggest that differentiated bacteroids display an increased symbiotic efficiency (E > U and S > U). In this study, we used a combination of Aeschynomene species inducing E- or S-type bacteroids in symbiosis with Bradyrhizobium sp. ORS285 to show that S-type bacteroids present a better symbiotic efficiency than E-type bacteroids. We performed a transcriptomic analysis on E- and S-type bacteroids formed by Aeschynomene afraspera and Aeschynomene indica nodules and identified the bacterial functions activated in bacteroids and specific to each bacteroid type. Extending the expression analysis in E- and S-type bacteroids in other Aeschynomene species by qRT-PCR on selected genes from the transcriptome analysis narrowed down the set of bacteroid morphotype-specific genes. Functional analysis of a selected subset of 31 bacteroid-induced or morphotype-specific genes revealed no symbiotic phenotypes in the mutants. This highlights the robustness of the symbiotic program but could also indicate that the bacterial response to the plant environment is partially anticipatory or even maladaptive. Our analysis confirms the correlation between differentiation and efficiency of the bacteroids and provides a framework for the identification of bacterial functions that affect the efficiency of bacteroids.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Affiliation(s)
- Florian Lamouche
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, 34398, France
| | - Anaïs Chaumeret
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Nico Nouwen
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, 34398, France
| | - Camille Verly
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Coline Sciallano
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, 34398, France
| | - Joël Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, 34398, France
| | - Christian Jeudy
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, 21065, France
| | - Attila Szücs
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Samuel Mondy
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, 21065, France
| | - István Nagy
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, 6726, Hungary
- Seqomics Biotechnology Ltd, Mórahalom, 6782, Hungary
| | - Attila Kereszt
- Biological Research Centre, Hungarian Academy of Sciences, Szeged, 6726, Hungary
- Seqomics Biotechnology Ltd, Mórahalom, 6782, Hungary
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, 34398, France
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
| | - Benoit Alunni
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, 91198, Gif-sur-Yvette, France
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26
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Marchetti R, Bedini E, Gully D, Lanzetta R, Giraud E, Molinaro A, Silipo A. Rhodopseudomonas palustris Strain CGA009 Produces an O-Antigen Built up by a C-4-Branched Monosaccharide: Structural and Conformational Studies. Org Lett 2018; 20:3656-3660. [PMID: 29874087 DOI: 10.1021/acs.orglett.8b01439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, the analysis of the peculiar homopolymeric O-chain, isolated from the lipopolysaccharide (LPS) of Rhodopseudomonas palustris strain CGA009, is reported. The O-chain is built up of a novel 4-C-branched sugar (12-deoxy-4- C-(d- altro-5,7,8,9-tetrahydroxyhexyl))-3- O-methyl-d-galactopyranose)) whose structure, absolute configuration, and conformational features were deduced by 2D NMR spectroscopy, optical rotation measurements, and molecular dynamics simulations.
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Affiliation(s)
- Roberta Marchetti
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Emiliano Bedini
- Dipartimento di Scienze Chimiche , Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II , Via Cintia 4 , I-80126 Napoli , Italy
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM) , UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet , Montpellier 34398 Cedex 5 , France
| | - Rosa Lanzetta
- 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 (LSTM) , UMR IRD/SupAgro/INRA/UM2/CIRAD, TA-A82/J - Campus de Baillarguet , Montpellier 34398 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
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27
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Abstract
Lipid research represents a frontier for microbiology, as showcased by hopanoid lipids. Hopanoids, which resemble sterols and are found in the membranes of diverse bacteria, have left an extensive molecular fossil record. They were first discovered by petroleum geologists. Today, hopanoid-producing bacteria remain abundant in various ecosystems, such as the rhizosphere. Recently, great progress has been made in our understanding of hopanoid biosynthesis, facilitated in part by technical advances in lipid identification and quantification. A variety of genetically tractable, hopanoid-producing bacteria have been cultured, and tools to manipulate hopanoid biosynthesis and detect hopanoids are improving. However, we still have much to learn regarding how hopanoid production is regulated, how hopanoids act biophysically and biochemically, and how their production affects bacterial interactions with other organisms, such as plants. The study of hopanoids thus offers rich opportunities for discovery.
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Affiliation(s)
- Brittany J. Belin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicolas Busset
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, University of Montpellier, CIRAD, France
| | - Eric Giraud
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, University of Montpellier, CIRAD, France
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Busset N, Di Lorenzo F, Palmigiano A, Sturiale L, Gressent F, Fardoux J, Gully D, Chaintreuil C, Molinaro A, Silipo A, Giraud E. The Very Long Chain Fatty Acid (C 26:25OH) Linked to the Lipid A Is Important for the Fitness of the Photosynthetic Bradyrhizobium Strain ORS278 and the Establishment of a Successful Symbiosis with Aeschynomene Legumes. Front Microbiol 2017; 8:1821. [PMID: 28983292 PMCID: PMC5613085 DOI: 10.3389/fmicb.2017.01821] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/06/2017] [Indexed: 11/13/2022] Open
Abstract
In rhizobium strains, the lipid A is modified by the addition of a very long-chain fatty acid (VLCFA) shown to play an important role in rigidification of the outer membrane, thereby facilitating their dual life cycle, outside and inside the plant. In Bradyrhizobium strains, the lipid A is more complex with the presence of at least two VLCFAs, one covalently linked to a hopanoid molecule, but the importance of these modifications is not well-understood. In this study, we identified a cluster of VLCFA genes in the photosynthetic Bradyrhizobium strain ORS278, which nodulates Aeschynomene plants in a Nod factor-independent process. We tried to mutate the different genes of the VLCFA gene cluster to prevent the synthesis of the VLCFAs, but only one mutant in the lpxXL gene encoding an acyltransferase was obtained. Structural analysis of the lipid A showed that LpxXL is involved in the transfer of the C26:25OH VLCFA to the lipid A but not in the one of the C30:29OH VLCFA which harbors the hopanoid molecule. Despite maintaining the second VLCFA, the ability of the mutant to cope with various stresses (low pH, high temperature, high osmolarity, and antimicrobial peptides) and to establish an efficient nitrogen-fixing symbiosis was drastically reduced. In parallel, we investigated whether the BRADO0045 gene, which encodes a putative acyltransferase displaying a weak identity with the apo-lipoprotein N-acyltransferase Lnt, could be involved in the transfer of the C30:29OH VLCFA to the lipid A. Although the mutant exhibited phenotypes similar to the lpxXL mutant, no difference in the lipid A structure was observed from that in the wild-type strain, indicating that this gene is not involved in the modification of lipid A. Our results advance our knowledge of the biosynthesis pathway and the role of VLCFAs-modified lipid A in free-living and symbiotic states of Bradyrhizobium strains.
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Affiliation(s)
- Nicolas Busset
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, Université de Montpellier, CIRADMontpellier, France
| | - Flaviana Di Lorenzo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico IINaples, Italy
| | - Angelo Palmigiano
- Istituto per i Polimeri, Compositi e Biomateriali IPCB, Consiglio Nazionale delle RicercheCatania, Italy
| | - Luisa Sturiale
- Istituto per i Polimeri, Compositi e Biomateriali IPCB, Consiglio Nazionale delle RicercheCatania, Italy
| | - Frederic Gressent
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, Université de Montpellier, CIRADMontpellier, France
| | - Joël Fardoux
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, Université de Montpellier, CIRADMontpellier, France
| | - Djamel Gully
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, Université de Montpellier, CIRADMontpellier, France
| | - Clémence Chaintreuil
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, Université de Montpellier, CIRADMontpellier, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico IINaples, Italy
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico IINaples, Italy
| | - Eric Giraud
- Institut de Recherche pour le Développement, LSTM, UMR IRD, SupAgro, INRA, Université de Montpellier, CIRADMontpellier, France
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Songwattana P, Noisangiam R, Teamtisong K, Prakamhang J, Teulet A, Tittabutr P, Piromyou P, Boonkerd N, Giraud E, Teaumroong N. Type 3 Secretion System (T3SS) of Bradyrhizobium sp. DOA9 and Its Roles in Legume Symbiosis and Rice Endophytic Association. Front Microbiol 2017; 8:1810. [PMID: 28979252 PMCID: PMC5611442 DOI: 10.3389/fmicb.2017.01810] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/05/2017] [Indexed: 11/15/2022] Open
Abstract
The Bradyrhizobium sp. DOA9 strain isolated from a paddy field has the ability to nodulate a wide spectrum of legumes. Unlike other bradyrhizobia, this strain has a symbiotic plasmid harboring nod, nif, and type 3 secretion system (T3SS) genes. This T3SS cluster contains all the genes necessary for the formation of the secretory apparatus and the transcriptional activator (TtsI), which is preceded by a nod-box motif. An in silico search predicted 14 effectors putatively translocated by this T3SS machinery. In this study, we explored the role of the T3SS in the symbiotic performance of DOA9 by evaluating the ability of a T3SS mutant (ΩrhcN) to nodulate legumes belonging to Dalbergioid, Millettioid, and Genistoid tribes. Among the nine species tested, four (Arachis hypogea, Vigna radiata, Crotalaria juncea, and Macroptilium atropurpureum) responded positively to the rhcN mutation (ranging from suppression of plant defense reactions, an increase in the number of nodules and a dramatic improvement in nodule development and infection), one (Stylosanthes hamata) responded negatively (fewer nodules and less nitrogen fixation) and four species (Aeschynomene americana, Aeschynomene afraspera, Indigofera tinctoria, and Desmodium tortuosum) displayed no phenotype. We also tested the role of the T3SS in the ability of the DOA9 strain to endophytically colonize rice roots, but detected no effect of the T3SS mutation, in contrast to what was previously reported in the Bradyrhizobium SUTN9-2 strain. Taken together, these data indicate that DOA9 contains a functional T3SS that interferes with the ability of the strain to interact symbiotically with legumes but not with rice.
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Affiliation(s)
- Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Rujirek Noisangiam
- National Bureau of Agricultural Commodity and Food Standards, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Janpen Prakamhang
- Department of Applied Biology, Faculty of Sciences and Liberal Arts, Rajamangala University of Technology IsanNakhon Ratchasima, Thailand
| | - Albin Teulet
- Institut de Recherche pour le Développement, LSTM, UMR IRD/SupAgro/INRA/Univ. Montpellier/CIRADMontpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
| | - Eric Giraud
- Institut de Recherche pour le Développement, LSTM, UMR IRD/SupAgro/INRA/Univ. Montpellier/CIRADMontpellier, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, Thailand
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Barrière Q, Guefrachi I, Gully D, Lamouche F, Pierre O, Fardoux J, Chaintreuil C, Alunni B, Timchenko T, Giraud E, Mergaert P. Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules. Sci Rep 2017; 7:9063. [PMID: 28831061 PMCID: PMC5567381 DOI: 10.1038/s41598-017-08830-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022] Open
Abstract
Legumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway.
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Affiliation(s)
- Quentin Barrière
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Ibtissem Guefrachi
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, 6072, Gabès, Tunisia.,Université de Pau et des Pays de l'Adour, Pau, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Florian Lamouche
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Institut Sophia AgroBiotech, Sophia-Antipolis, France
| | - Joël Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Benoît Alunni
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.
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Di Lorenzo F, Palmigiano A, Duda KA, Pallach M, Busset N, Sturiale L, Giraud E, Garozzo D, Molinaro A, Silipo A. Structure of the Lipopolysaccharide from the Bradyrhizobium sp. ORS285 rfaL Mutant Strain. ChemistryOpen 2017; 6:541-553. [PMID: 28794950 PMCID: PMC5542761 DOI: 10.1002/open.201700074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 12/13/2022] Open
Abstract
The importance of the outer membrane and of its main constituent, lipopolysaccharide, in the symbiosis between rhizobia and leguminous host plants has been well studied. Here, the first complete structural characterization of the entire lipopolysaccharide from an O‐chain‐deficient Bradyrhizobium ORS285 rfaL mutant is achieved by a combination of chemical analysis, NMR spectroscopy, MALDI MS and MS/MS. The lipid A structure is shown to be consistent with previously reported Bradyrhizobium lipid A, that is, a heterogeneous blend of penta‐ to hepta‐acylated species carrying a nonstoichiometric hopanoid unit and possessing very‐long‐chain fatty acids ranging from 26:0(25‐OH) to 32:0(31‐OH). The structure of the core oligosaccharide region, fully characterized for the first time here, is revealed to be a nonphosphorylated linear chain with methylated sugar residues, with a heptose residue exclusively present in the outer core region, and with the presence of two singly substituted 3‐deoxy‐d‐manno‐oct‐2‐ulosonic acid (Kdo) residues, one of which is located in the outer core region. The lipid A moiety is linked to the core moiety through an uncommon 4‐substituted Kdo unit.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Angelo Palmigiano
- CNR-Istituto per i Polimeri Compositi e Biomateriali IPCB-Unità di CataniaVia Gaifami 18 95126 Catania Italy
| | - Katarzyna A Duda
- Junior Group of Allergobiochemistry, Research Center Borstel, Leibniz Center for Medicine and Biosciences, Airway Research Center North (ARCN) German Center for Lung Research 23845 Borstel Germany
| | - Mateusz Pallach
- Department of Chemical Sciences University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J34398 Montpellier Cedex 5 France
| | - Luisa Sturiale
- CNR-Istituto per i Polimeri Compositi e Biomateriali IPCB-Unità di CataniaVia Gaifami 18 95126 Catania Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J34398 Montpellier Cedex 5 France
| | - Domenico Garozzo
- CNR-Istituto per i Polimeri Compositi e Biomateriali IPCB-Unità di CataniaVia Gaifami 18 95126 Catania Italy
| | - Antonio Molinaro
- Department of Chemical Sciences University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Alba Silipo
- Department of Chemical Sciences University of Naples Federico II Via Cinthia 4 80126 Naples Italy
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Grimaldi-Bensouda L, Rossignol M, Koné-Paut I, Krivitzky A, Lebrun-Frenay C, Clet J, Brassat D, Papeix C, Nicolino M, Benhamou PY, Fain O, Costedoat-Chalumeau N, Courcoux MF, Viallard JF, Godeau B, Papo T, Vermersch P, Bourgault-Villada I, Breart G, Abenhaim L, Abbas F, Abdelmoumni A, Hilliquin P, Requeda E, Adoue D, Brassat D, Agard C, Masseau A, Aladjidi N, Clet J, Fernandes H, Lemasson G, Perel Y, Raymond I, Richer O, Vital A, Allain-Launay E, Bru M, Nicolino M, Thomas C, Altman JJ, Amsallem D, Aras N, Boukari L, Dubrel M, Fain O, Letellier E, Lucidarme N, Mekinian A, Morin AS, Stirnemann J, Atlan C, Audry D, Augustin J, Bakir R, Bartolucci P, Chevalier X, Godeau B, Guillaud C, Khellaf M, Limal N, Lousteau V, Mahevas M, Méliksetyan G, Michel M, Roumier M, Bayart S, Bonnet F, Decaux O, Bekherraz A, Brihaye B, Dachez R, Daugas E, Hayem G, Meyer O, Papo T, Pasqualoni E, Sacre K, Travert F, Bellon H, Beltrand J, Lefrere F, Simon A, Benhamou PY, Benveniste O, Bolgert F, Costedoat-Chalumeau N, De Paz R, Demeret S, Fautrel B, Jacqueminet S, Louapre C, Maillart E, Morel N, Papeix C, Rigabert J, Bensaid P, Berger C, Berquin P, Le Moing AG, Berroir S, Besson G, Boutte C, Casez O, Bonnotte B, Audia S, Bossu-Estour C, Bourgarit A, Dupuy A, Keshmandt H, Bourre B, Brac A, Perrin A, Pondarré C, Villar-Fimbel S, Bruckert I, Cosson A, Magy-Bertrand N, Tisserand G, Camu W, Carlander B, Morales RJ, Cances C, Pasquet M, Castilla Lievre MA, Chabroux S, Charif M, Chatelus E, Sibilia J, Chevrant-Breton J, Clavel S, Bille-Turc F, Cohen J, Courcoux MF, Leverger G, Machet L, Cuisset JM, Cony-Makhoul P, Darsy P, Favre S, Giraud P, Leitenschenck L, Monteiro I, Morati C, DeSeze J, Dinulescu M, Dhaoui T, Dommange-Romero F, Drevard E, Dupuis C, Dumuis ML, Durand JM, Farad S, Lecomte P, Pierre P, Fouyssac F, Gaudin P, Gautier A, Gellen-Dautremer J, Jarrin I, Richette P, Georget E, Gras P, Moreau T, Giraud E, Hacini M, Mayer A, Guillaumat C, Guillaume S, Guitton C, Kone-Paut I, Marsaud C, Rossi L, Guyot MH, Hassler P, Heimfert C, Heinzlef O, Hillion B, Hocquelet C, Husson H, Ichai P, Jeziorski E, Deslandre CJ, Le Guern V, Kamenov K, Kerlan V, Lemoine P, Misery L, Pan-Petesch B, Krivitzky A, Labauge P, Rodier M, Lacade C, Razafimahefa B, Lachgar K, Larmarau MP, Leblanc T, Lebrun-Frenay C, Lefèbvre P, Lejoyeux P, Leske C, Ly K, Magy L, Mansuy S, Marechaud R, Martin Negrier ML, Sole G, Maupetit J, Mazingue F, Mochon S, Moktar B, Morcamp D, Morlet-Barla N, Nicolas G, Pautot V, Pellier I, Verret JL, Outteryck O, Vermersch P, Pallot-Prades B, Paquet JM, Puechal X, Sortais A, Pelletier J, Rico A, Pez D, Stankoff B, Quittet P, Rémy C, Roba E, Rosario H, Roudaut N, Sonnet E, Ruel M, Sebban S, Schaepelynck P, Simonin MJ, Vial C, Viallard JF, Ladedan I, Zenone T. Risk of autoimmune diseases and human papilloma virus (HPV) vaccines: Six years of case-referent surveillance. J Autoimmun 2017; 79:84-90. [DOI: 10.1016/j.jaut.2017.01.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/08/2016] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
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Di Lorenzo F, Palmigiano A, Al Bitar-Nehme S, Sturiale L, Duda KA, Gully D, Lanzetta R, Giraud E, Garozzo D, Bernardini ML, Molinaro A, Silipo A. The Lipid A from Rhodopseudomonas palustris Strain BisA53 LPS Possesses a Unique Structure and Low Immunostimulant Properties. Chemistry 2016; 23:3637-3647. [PMID: 28004420 DOI: 10.1002/chem.201604379] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Indexed: 12/15/2022]
Abstract
The search for novel lipid A analogues from any biological source that can act as antagonists, displaying inhibitory activity towards the production of pro-inflammatory cytokines, or as immunomodulators in mammals, is a very topical issue. To this aim, the structure and immunological properties of the lipopolysaccharide lipid A from the purple nonsulfur bacterium Rhodopseudomonas palustris strain BisA53 have been determined. This lipid A displays a unique structural feature, with a non-phosphorylated skeleton made up of the tetrasaccharide Manp-α-(1→4)-GlcpN3N-β-1→6-GlcpN3N-α-(1→1)-α-GalpA, and four primary amide-linked 14:0(3-OH) and, as secondary O-acyl substituents, a 16:0 and the very long-chain fatty acid 26:0(25-OAc), appended on the GlcpN3N units. This lipid A architecture is definitely rare, so far identified only in the genus Bradyrhizobium. Immunological tests on both murine bone-marrow-derived and human monocyte-derived macrophages revealed an extremely low immunostimulant capability of this LPS lipid A.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples, Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Angelo Palmigiano
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB-Unità di Catania, Via Gaifami 18, 95126, Catania, Italy
| | - Sami Al Bitar-Nehme
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Luisa Sturiale
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB-Unità di Catania, Via Gaifami 18, 95126, Catania, Italy
| | - Katarzyna A Duda
- Junior Group of Allergobiochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, 23845, Borstel, Airway Research Center North (ARCN), German Center for Lung Research, Germany
| | - 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
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples, Federico II, via Cinthia 4, 80126, Naples, 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
| | - Domenico Garozzo
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB-Unità di Catania, Via Gaifami 18, 95126, Catania, Italy
| | - Maria Lina Bernardini
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza-Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza-Università di Roma, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples, Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples, Federico II, via Cinthia 4, 80126, Naples, Italy
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Wongdee J, Songwattana P, Nouwen N, Noisangiam R, Fardoux J, Chaintreuil C, Teaumroong N, Tittabutr P, Giraud E. nifDK Clusters Located on the Chromosome and Megaplasmid of Bradyrhizobium sp. Strain DOA9 Contribute Differently to Nitrogenase Activity During Symbiosis and Free-Living Growth. Mol Plant Microbe Interact 2016; 29:767-773. [PMID: 27603559 DOI: 10.1094/mpmi-07-16-0140-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bradyrhizobium sp. strain DOA9 contains two copies of the nifDK genes, nifDKc, located on the chromosome, and nifDKp, located on a symbiotic megaplasmid. Unlike most rhizobia, this bacterium displays nitrogenase activity under both free-living and symbiotic conditions. Transcriptional analysis using gusA reporter strains showed that both nifDK operons were highly expressed under symbiosis, whereas nifDKc was the most abundantly expressed under free-living conditions. During free-living growth, the nifDKp mutation did not affect nitrogenase activity, whereas nitrogenase activity was drastically reduced with the nifDKc mutant. This led us to suppose that nifDKc is the main contributor of nitrogenase activity in the free-living state. In contrast, during symbiosis, no effect of the nifDKc mutation was observed and the nitrogen-fixation efficiency of plants inoculated with the nifDKp mutant was reduced. This suggests that nifDKp plays the main role in nitrogenase enzyme activity during symbiosis. Together, these data suggest that Bradyrhizobium sp. strain DOA9 contains two functional copies of nifDK genes that are regulated differently and that, depending on their lifestyle, contribute differently to nitrogenase activity.
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Affiliation(s)
- Jenjira Wongdee
- 1 School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand; and
| | - Pongpan Songwattana
- 1 School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand; and
| | - Nico Nouwen
- 2 IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro, Campus de Baillarguet, TA-A82/J, 34398 Montpellier Cedex 5, France
| | - Rujirek Noisangiam
- 1 School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand; and
| | - Joel Fardoux
- 2 IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro, Campus de Baillarguet, TA-A82/J, 34398 Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- 2 IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro, Campus de Baillarguet, TA-A82/J, 34398 Montpellier Cedex 5, France
| | - Neung Teaumroong
- 1 School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand; and
| | - Panlada Tittabutr
- 1 School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima 30000, Thailand; and
| | - Eric Giraud
- 2 IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, IRD/CIRAD/INRA/UM/SupAgro, Campus de Baillarguet, TA-A82/J, 34398 Montpellier Cedex 5, France
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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. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nouwen N, Fardoux J, Giraud E. NodD1 and NodD2 Are Not Required for the Symbiotic Interaction of Bradyrhizobium ORS285 with Nod-Factor-Independent Aeschynomene Legumes. PLoS One 2016; 11:e0157888. [PMID: 27315080 PMCID: PMC4912097 DOI: 10.1371/journal.pone.0157888] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/06/2016] [Indexed: 11/23/2022] Open
Abstract
Photosynthetic Bradyrhizobium strain ORS285 forms nitrogen-fixing nodules on the roots and stems of tropical aquatic legumes of the Aeschynomene genus. Depending on the Aeschynomene species, this symbiotic interaction does or does not rely on the synthesis of Nod-factors (NFs). However, whether during the interaction of Bradyrhizobium ORS285 with NF-independent Aeschynomene species the nod genes are expressed and if the general regulator NodD plays a symbiotic role is unknown. Expression studies showed that in contrast to the interaction with the NF-dependent Aeschynomene species, A. afraspera, the Bradyrhizobium ORS285 nod genes are not induced upon contact with the NF-independent host plant A. indica. Mutational analysis of the two nodD genes present in ORS285, showed that deletion of nodD1 and nodD2 did not affect the symbiotic interaction between Bradyrhizobium ORS285 and A. indica whereas the deletions had an effect on the symbiotic interaction with A. afraspera plants. In addition, when the expression of nod genes was artificially induced by adding naringenin to the plant growth medium, the nodulation of A. indica by Bradyrhizobium ORS285 is delayed and resulted in lower nodule numbers.
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Affiliation(s)
- Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/ SupAgro/INRA/ UM2 /CIRAD, Montpellier, France
- * E-mail:
| | - Joel Fardoux
- 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gully D, Gargani D, Bonaldi K, Grangeteau C, Chaintreuil C, Fardoux J, Nguyen P, Marchetti R, Nouwen N, Molinaro A, Mergaert P, Giraud E. A Peptidoglycan-Remodeling Enzyme Is Critical for Bacteroid Differentiation in Bradyrhizobium spp. During Legume Symbiosis. Mol Plant Microbe Interact 2016; 29:447-57. [PMID: 26959836 DOI: 10.1094/mpmi-03-16-0052-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In response to the presence of compatible rhizobium bacteria, legumes form symbiotic organs called nodules on their roots. These nodules house nitrogen-fixing bacteroids that are a differentiated form of the rhizobium bacteria. In some legumes, the bacteroid differentiation comprises a dramatic cell enlargement, polyploidization, and other morphological changes. Here, we demonstrate that a peptidoglycan-modifying enzyme in Bradyrhizobium strains, a DD-carboxypeptidase that contains a peptidoglycan-binding SPOR domain, is essential for normal bacteroid differentiation in Aeschynomene species. The corresponding mutants formed bacteroids that are malformed and hypertrophied. However, in soybean, a plant that does not induce morphological differentiation of its symbiont, the mutation does not affect the bacteroids. Remarkably, the mutation also leads to necrosis in a large fraction of the Aeschynomene nodules, indicating that a normally formed peptidoglycan layer is essential for avoiding the induction of plant immune responses by the invading bacteria. In addition to exopolysaccharides, capsular polysaccharides, and lipopolysaccharides, whose role during symbiosis is well defined, our work demonstrates an essential role in symbiosis for yet another rhizobial envelope component, the peptidoglycan layer.
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Affiliation(s)
- Djamel Gully
- 1 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
| | | | - Katia Bonaldi
- 3 Center for Chronobiology, Division of Biological Sciences, 9500 Gilman Drive, University of California San Diego, La Jolla, CA 92093, U.S.A
| | - Cédric Grangeteau
- 4 UMR Procédés Alimentaires et Microbiologiques, Equipe VAlMiS (Vin, Aliment, Microbiologie, Stress), AgroSup Dijon - Université de Bourgogne Franche-Comté, IUVV, Rue Claude Ladrey, BP 27877, 21000 Dijon, France
| | - Clémence Chaintreuil
- 1 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
- 1 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
| | - Phuong Nguyen
- 1 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
| | - Roberta Marchetti
- 5 Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy; and
| | - Nico Nouwen
- 1 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
- 5 Dipartimento di Scienze Chimiche, Complesso Universitario Monte Sant'Angelo, Università di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy; and
| | - Peter Mergaert
- 6 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Eric Giraud
- 1 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Okazaki S, Tittabutr P, Teulet A, Thouin J, Fardoux J, Chaintreuil C, Gully D, Arrighi JF, Furuta N, Miwa H, Yasuda M, Nouwen N, Teaumroong N, Giraud E. Rhizobium-legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS. ISME J 2016; 10:64-74. [PMID: 26161635 PMCID: PMC4681849 DOI: 10.1038/ismej.2015.103] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/28/2015] [Accepted: 05/08/2015] [Indexed: 02/07/2023]
Abstract
The occurrence of alternative Nod factor (NF)-independent symbiosis between legumes and rhizobia was first demonstrated in some Aeschynomene species that are nodulated by photosynthetic bradyrhizobia lacking the canonical nodABC genes. In this study, we revealed that a large diversity of non-photosynthetic bradyrhizobia, including B. elkanii, was also able to induce nodules on the NF-independent Aeschynomene species, A. indica. Using cytological analysis of the nodules and the nitrogenase enzyme activity as markers, a gradient in the symbiotic interaction between bradyrhizobial strains and A. indica could be distinguished. This ranged from strains that induced nodules that were only infected intercellularly to rhizobial strains that formed nodules in which the host cells were invaded intracellularly and that displayed a weak nitrogenase activity. In all non-photosynthetic bradyrhizobia, the type III secretion system (T3SS) appears required to trigger nodule organogenesis. In contrast, genome sequence analysis revealed that apart from a few exceptions, like the Bradyrhizobium ORS285 strain, photosynthetic bradyrhizobia strains lack a T3SS. Furthermore, analysis of the symbiotic properties of an ORS285 T3SS mutant revealed that the T3SS could have a positive or negative role for the interaction with NF-dependent Aeschynomene species, but that it is dispensable for the interaction with all NF-independent Aeschynomene species tested. Taken together, these data indicate that two NF-independent symbiotic processes are possible between legumes and rhizobia: one dependent on a T3SS and one using a so far unknown mechanism.
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Affiliation(s)
- Shin Okazaki
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Panlada Tittabutr
- Institute of Agricultural Technology, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Julien Thouin
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Jean- François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Noriyuki Furuta
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiroki Miwa
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Michiko Yasuda
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
| | - Neung Teaumroong
- Institute of Agricultural Technology, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France
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Fabre S, Gully D, Poitout A, Patrel D, Arrighi JF, Giraud E, Czernic P, Cartieaux F. Nod Factor-Independent Nodulation in Aeschynomene evenia Required the Common Plant-Microbe Symbiotic Toolkit. Plant Physiol 2015; 169:2654-64. [PMID: 26446590 PMCID: PMC4677901 DOI: 10.1104/pp.15.01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/04/2015] [Indexed: 05/06/2023]
Abstract
Nitrogen fixation in the legume-rhizobium symbiosis is a crucial area of research for more sustainable agriculture. Our knowledge of the plant cascade in response to the perception of bacterial Nod factors has increased in recent years. However, the discovery that Nod factors are not involved in the Aeschynomene-Bradyrhizobium spp. interaction suggests that alternative molecular dialogues may exist in the legume family. We evaluated the conservation of the signaling pathway common to other endosymbioses using three candidate genes: Ca(2+)/Calmodulin-Dependent Kinase (CCaMK), which plays a central role in cross signaling between nodule organogenesis and infection processes; and Symbiosis Receptor Kinase (SYMRK) and Histidine Kinase1 (HK1), which act upstream and downstream of CCaMK, respectively. We showed that CCaMK, SYMRK, and HK1 are required for efficient nodulation in Aeschynomene evenia. Our results demonstrate that CCaMK and SYMRK are recruited in Nod factor-independent symbiosis and, hence, may be conserved in all vascular plant endosymbioses described so far.
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Affiliation(s)
- Sandrine Fabre
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Djamel Gully
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Arthur Poitout
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Delphine Patrel
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Jean-François Arrighi
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Eric Giraud
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Pierre Czernic
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Fabienne Cartieaux
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
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Guefrachi I, Pierre O, Timchenko T, Alunni B, Barrière Q, Czernic P, Villaécija-Aguilar JA, Verly C, Bourge M, Fardoux J, Mars M, Kondorosi E, Giraud E, Mergaert P. Bradyrhizobium BclA Is a Peptide Transporter Required for Bacterial Differentiation in Symbiosis with Aeschynomene Legumes. Mol Plant Microbe Interact 2015; 28:1155-66. [PMID: 26106901 DOI: 10.1094/mpmi-04-15-0094-r] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen-fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called nodule-specific cysteine-rich (NCR) peptides in the symbiotic nodule cells which house the bacteroids. NCR peptides are related to antimicrobial peptides of innate immunity. They induce the endosymbionts into a differentiated, enlarged, and polyploid state. The bacterial symbionts, on their side, evolved functions for the response to the NCR peptides. Here, we identified the bclA gene of Bradyrhizobium sp. strains ORS278 and ORS285, which is required for the formation of differentiated and functional bacteroids in the nodules of the NCR peptide-producing Aeschynomene legumes. The BclA ABC transporter promotes the import of NCR peptides and provides protection against the antimicrobial activity of these peptides. Moreover, BclA can complement the role of the related BacA transporter of Sinorhizobium meliloti, which has a similar symbiotic function in the interaction with Medicago legumes.
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Affiliation(s)
- Ibtissem Guefrachi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Olivier Pierre
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Benoît Alunni
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Quentin Barrière
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Pierre Czernic
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Camille Verly
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Mickaël Bourge
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Joël Fardoux
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Mohamed Mars
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Eva Kondorosi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 4 Institute of Biochemistry, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary
| | - Eric Giraud
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Peter Mergaert
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
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Kulkarni G, Busset N, Molinaro A, Gargani D, Chaintreuil C, Silipo A, Giraud E, Newman DK. Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens. mBio 2015. [PMID: 26489859 DOI: 10.1128/mbio.01251-1215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
UNLABELLED A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage. IMPORTANCE Because bradyrhizobia provide fixed nitrogen to plants, this work has potential agronomical implications. An understanding of how hopanoids facilitate bacterial survival in soils and plant hosts may aid the engineering of more robust agronomic strains, especially relevant in regions that are becoming warmer and saline due to climate change. Moreover, this work has geobiological relevance: hopanes, molecular fossils of hopanoids, are enriched in ancient sedimentary rocks at discrete intervals in Earth history. This is the first study to uncover roles for 2Me- and C35 hopanoids in the context of an ecological niche that captures many of the stressful environmental conditions thought to be important during (2Me)-hopane deposition. Though much remains to be done to determine whether the conditions present within the plant host are shared with niches of relevance to the rock record, our findings represent an important step toward identifying conserved mechanisms whereby hopanoids contribute to fitness.
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Affiliation(s)
- Gargi Kulkarni
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | | | - Clemence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA Howard Hughes Medical Institute, Pasadena, California, USA Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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Kulkarni G, Busset N, Molinaro A, Gargani D, Chaintreuil C, Silipo A, Giraud E, Newman DK. Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens. mBio 2015; 6:e01251-15. [PMID: 26489859 PMCID: PMC4620461 DOI: 10.1128/mbio.01251-15] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage. IMPORTANCE Because bradyrhizobia provide fixed nitrogen to plants, this work has potential agronomical implications. An understanding of how hopanoids facilitate bacterial survival in soils and plant hosts may aid the engineering of more robust agronomic strains, especially relevant in regions that are becoming warmer and saline due to climate change. Moreover, this work has geobiological relevance: hopanes, molecular fossils of hopanoids, are enriched in ancient sedimentary rocks at discrete intervals in Earth history. This is the first study to uncover roles for 2Me- and C35 hopanoids in the context of an ecological niche that captures many of the stressful environmental conditions thought to be important during (2Me)-hopane deposition. Though much remains to be done to determine whether the conditions present within the plant host are shared with niches of relevance to the rock record, our findings represent an important step toward identifying conserved mechanisms whereby hopanoids contribute to fitness.
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Affiliation(s)
- Gargi Kulkarni
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Nicolas Busset
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Antonio Molinaro
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | | | - Clemence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Alba Silipo
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA Howard Hughes Medical Institute, Pasadena, California, USA Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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Czernic P, Gully D, Cartieaux F, Moulin L, Guefrachi I, Patrel D, Pierre O, Fardoux J, Chaintreuil C, Nguyen P, Gressent F, Da Silva C, Poulain J, Wincker P, Rofidal V, Hem S, Barrière Q, Arrighi JF, Mergaert P, Giraud E. Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides. Plant Physiol 2015; 169:1254-65. [PMID: 26286718 PMCID: PMC4587450 DOI: 10.1104/pp.15.00584] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/17/2015] [Indexed: 05/21/2023]
Abstract
Nutritional symbiotic interactions require the housing of large numbers of microbial symbionts, which produce essential compounds for the growth of the host. In the legume-rhizobium nitrogen-fixing symbiosis, thousands of rhizobium microsymbionts, called bacteroids, are confined intracellularly within highly specialized symbiotic host cells. In Inverted Repeat-Lacking Clade (IRLC) legumes such as Medicago spp., the bacteroids are kept under control by an arsenal of nodule-specific cysteine-rich (NCR) peptides, which induce the bacteria in an irreversible, strongly elongated, and polyploid state. Here, we show that in Aeschynomene spp. legumes belonging to the more ancient Dalbergioid lineage, bacteroids are elongated or spherical depending on the Aeschynomene spp. and that these bacteroids are terminally differentiated and polyploid, similar to bacteroids in IRLC legumes. Transcriptome, in situ hybridization, and proteome analyses demonstrated that the symbiotic cells in the Aeschynomene spp. nodules produce a large diversity of NCR-like peptides, which are transported to the bacteroids. Blocking NCR transport by RNA interference-mediated inactivation of the secretory pathway inhibits bacteroid differentiation. Together, our results support the view that bacteroid differentiation in the Dalbergioid clade, which likely evolved independently from the bacteroid differentiation in the IRLC clade, is based on very similar mechanisms used by IRLC legumes.
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Affiliation(s)
- Pierre Czernic
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Djamel Gully
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Fabienne Cartieaux
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Lionel Moulin
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Ibtissem Guefrachi
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Delphine Patrel
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Olivier Pierre
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Joël Fardoux
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Clémence Chaintreuil
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Phuong Nguyen
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Frédéric Gressent
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Corinne Da Silva
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Julie Poulain
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Patrick Wincker
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Valérie Rofidal
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Sonia Hem
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Quentin Barrière
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Jean-François Arrighi
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Peter Mergaert
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Eric Giraud
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
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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. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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48
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Delmotte N, Mondy S, Alunni B, Fardoux J, Chaintreuil C, Vorholt JA, Giraud E, Gourion B. A proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixA locus for symbiosis. Int J Mol Sci 2014; 15:3660-70. [PMID: 24590127 PMCID: PMC3975360 DOI: 10.3390/ijms15033660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 11/28/2022] Open
Abstract
Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. Here we used a proteomics approach to investigate the bacterial physiology of photosynthetic Bradyrhizobium sp. ORS278 during the symbiotic process with the semi aquatical plant Aeschynomene indica that forms root and stem nodules. We analyzed the proteomes of bacteria extracted from each type of nodule. First, we analyzed the bacteroid proteome at two different time points and found only minor variation between the bacterial proteomes of 2-week- and 3-week-old nodules. High conservation of the bacteroid proteome was also found when comparing stem nodules and root nodules. Among the stem nodule specific proteins were those related to the phototrophic ability of Bradyrhizobium sp. ORS278. Furthermore, we compared our data with those obtained during an extensive genetic screen previously published. The symbiotic role of four candidate genes which corresponding proteins were found massively produced in the nodules but not identified during this screening was examined. Mutant analysis suggested that in addition to the EtfAB system, the fixA locus is required for symbiotic efficiency.
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Affiliation(s)
- Nathanael Delmotte
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Samuel Mondy
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
| | - Benoit Alunni
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
| | - Joel Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Julia A Vorholt
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Benjamin Gourion
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
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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. New Phytol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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50
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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. Mol Plant Microbe Interact 2013; 26:1232-8. [PMID: 23777431 DOI: 10.1094/mpmi-03-13-0076-r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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