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Pujic P, Carro L, Fournier P, Armengaud J, Miotello G, Dumont N, Bourgeois C, Saupin X, Jame P, Selak GV, Alloisio N, Normand P. Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles. Int J Mol Sci 2023; 24:ijms24119162. [PMID: 37298114 DOI: 10.3390/ijms24119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among these were known symbiosis-associated genes such as nif (nitrogenase), and genes which are not know as symbiosis-associated genes such as can (carbonic anhydrase, CAN). The role of CAN, which supplies carbonate ions necessary for carboxylases and acidifies the cytoplasm, was thus analyzed by staining cells with pH-responsive dyes; assaying for CO2 levels in N-fixing propionate-fed cells (that require a propionate-CoA carboxylase to yield succinate-CoA), fumarate-fed cells and N-replete propionate-fed cells; conducting proteomics on N-fixing fumarate and propionate-fed cells and direct measurement of organic acids in nodules and in roots. The interiors of both in vitro and nodular vesicles were found to be at a lower pH than that of hyphae. CO2 levels in N2-fixing propionate-fed cultures were lower than in N-replete ones. Proteomics of propionate-fed cells showed carbamoyl-phosphate synthase (CPS) as the most overabundant enzyme relative to fumarate-fed cells. CPS combines carbonate and ammonium in the first step of the citrulline pathway, something which would help manage acidity and NH4+. Nodules were found to have sizeable amounts of pyruvate and acetate in addition to TCA intermediates. This points to CAN reducing the vesicles' pH to prevent the escape of NH3 and to control ammonium assimilation by GS and GOGAT, two enzymes that work in different ways in vesicles and hyphae. Genes with related functions (carboxylases, biotin operon and citrulline-aspartate ligase) appear to have undergone decay in non-symbiotic lineages.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
| | - Lorena Carro
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
- Departamento de Microbiología y Genética, Facultad de CC Agrarias y Ambientales, Universidad de Salamanca, Plaza Doctores de la Reina, 37007 Salamanca, Spain
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
| | | | - Caroline Bourgeois
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Xavier Saupin
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Patrick Jame
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Gabriela Vuletin Selak
- Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, 21000 Split, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Nicole Alloisio
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRAE, UMRA1418, Cedex, 69622 Villeurbanne, France
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Xu Y, Xu Y, Huang Z, Luo Y, Gao R, Xue J, Lin C, Pawlowski K, Zhou Z, Wei X. 3-Pentanol glycosides from root nodules of the actinorhizal plant Alnus cremastogyne. PHYTOCHEMISTRY 2023; 207:113582. [PMID: 36596436 DOI: 10.1016/j.phytochem.2022.113582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Alnus cremastogyne Burkill (Betulaceae), an actinorhizal plant, can enter a mutualistic symbiosis with Frankia species that leads to the formation of nitrogen fixing root nodules. Some primary metabolites (carbohydrates, dicarboxylic acids, amino acids, citrulline and amides) involved in carbon and nitrogen metabolism in actinorhizal nodules have been identified, while specialized metabolites in A. cremastogyne root nodules are yet to be characterized. In this study, we isolated and identified three undescribed 3-pentanol glycosides, i.e., 3-pentyl α-l-arabinofuranosyl-(1''→6')-β-d-glucopyranoside, 3-pentyl α-l-rhamnopyranosyl-(1''→6')-β-d-glucopyranoside, and 3-pentyl 6'-(3-hydroxy3-methylglutaryl)-β-d-glucopyranoside, as well as seventeen known compounds from A. cremastogyne root nodules. 3-Pentanol glycosides are abundantly distributed in root nodules, while they are distributed in stems, roots, leaves and fruits at low/zero levels. A. cremastogyne plants treated by root nodule suspension emit 3-pentanol. This study enriches the knowledge about specialized metabolites in the actinorhizal host, and provides preliminarily information on the signal exchange in the actinorhizal symbiosis between A. cremastogyne and Frankia.
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Affiliation(s)
- Yingting Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhengwan Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucai Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruanling Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jinghua Xue
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China
| | - Changli Lin
- Yunhe Forestry Bureau, Lishui, 323000, China
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Zhongyu Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Xiaoyi Wei
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China
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Gasser M, Alloisio N, Fournier P, Balmand S, Kharrat O, Tulumello J, Carro L, Heddi A, Da Silva P, Normand P, Pujic P, Boubakri H. A Nonspecific Lipid Transfer Protein with Potential Functions in Infection and Nodulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1096-1108. [PMID: 36102948 DOI: 10.1094/mpmi-06-22-0131-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The response of Alnus glutinosa to Frankia alni ACN14a is driven by several sequential physiological events from calcium spiking and root-hair deformation to the development of the nodule. Early stages of actinorhizal symbiosis were monitored at the transcriptional level to observe plant host responses to Frankia alni. Forty-two genes were significantly upregulated in inoculated compared with noninoculated roots. Most of these genes encode proteins involved in biological processes induced during microbial infection, such as oxidative stress or response to stimuli, but a large number of them are not differentially modulated or downregulated later in the process of nodulation. In contrast, several of them remained upregulated in mature nodules, and this included the gene most upregulated, which encodes a nonspecific lipid transfer protein (nsLTP). Classified as an antimicrobial peptide, this nsLTP was immunolocalized on the deformed root-hair surfaces that are points of contact for Frankia spp. during infection. Later in nodules, it binds to the surface of F. alni ACN14a vesicles, which are the specialized cells for nitrogen fixation. This nsLTP, named AgLTP24, was biologically produced in a heterologous host and purified for assay on F. alni ACN14a to identify physiological effects. Thus, the activation of the plant immunity response occurs upon first contact, while the recognition of F. alni ACN14a genes switches off part of the defense system during nodulation. AgLTP24 constitutes a part of the defense system that is maintained all along the symbiosis, with potential functions such as the formation of infection threads or nodule primordia to the control of F. alni proliferation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mélanie Gasser
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Pascale Fournier
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Severine Balmand
- INSA-Lyon, INRAE, UMR203 BF2i, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Ons Kharrat
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Joris Tulumello
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Lorena Carro
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Abdelaziz Heddi
- INSA-Lyon, INRAE, UMR203 BF2i, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Pedro Da Silva
- INSA-Lyon, INRAE, UMR203 BF2i, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69361, Lyon, France; Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRAE UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
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Pujic P, Alloisio N, Miotello G, Armengaud J, Abrouk D, Fournier P, Normand P. The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules. Microorganisms 2022; 10:microorganisms10030651. [PMID: 35336227 PMCID: PMC8951365 DOI: 10.3390/microorganisms10030651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N2-fixing pure cultures with propionate as the carbon source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-fixing pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
- Correspondence: (P.P.); (P.N.)
| | - Nicole Alloisio
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France; (G.M.); (J.A.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France; (G.M.); (J.A.)
| | - Danis Abrouk
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Pascale Fournier
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Philippe Normand
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
- Correspondence: (P.P.); (P.N.)
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Hay AE, Herrera-Belaroussi A, Rey M, Fournier P, Normand P, Boubakri H. Feedback Regulation of N Fixation in Frankia-Alnus Symbiosis Through Amino Acids Profiling in Field and Greenhouse Nodules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:499-508. [PMID: 31916486 DOI: 10.1094/mpmi-10-19-0289-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Symbiosis established between actinorhizal plants and Frankia spp., which are nitrogen-fixing actinobacteria, promotes nodule organogenesis, the site of metabolic exchange. The present study aimed to identify amino acid markers involved in Frankia-Alnus interactions by comparing nodules and associated roots from field and greenhouse samples. Our results revealed a high level of citrulline in all samples, followed by arginine (Arg), aspartate (Asp), glutamate (Glu), γ-amino-n-butyric acid (GABA), and alanine (Ala). Interestingly, the field metabolome approach highlighted more contrasted amino acid patterns between nodules and roots compared with greenhouse samples. Indeed, 12 amino acids had a mean relative abundance significantly different between field nodule and root samples, against only four amino acids in greenhouse samples, underlining the importance of developing "ecometabolome" approaches. In order to monitor the effects on Frankia cells (respiration and nitrogen fixation activities) of amino acid with an abundance pattern evocative of a role in symbiosis, in-vitro assays were performed by supplementing them in nitrogen-free cultures. Amino acids had three types of effects: i) those used by Frankia as nitrogen source (Glu, Gln, Asp), ii) amino acids stimulating both nitrogen fixation and respiration (e.g., Cit, GABA, Ala, valine, Asn), and iii) amino acids triggering a toxic effect (Arg, histidine). In this paper, a N-metabolic model was proposed to discuss how the host plant and bacteria modulate amino acids contents in nodules, leading to a fine regulation sustaining high bacterial nitrogen fixation.
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Affiliation(s)
- Anne-Emmanuelle Hay
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
- Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, Centre d'Etude des Substances Naturelles
| | - Aude Herrera-Belaroussi
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Marjolaine Rey
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
- Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, Centre d'Etude des Substances Naturelles
| | - Pascale Fournier
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
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Pujic P, Alloisio N, Fournier P, Roche D, Sghaier H, Miotello G, Armengaud J, Berry AM, Normand P. Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton. Environ Microbiol 2019; 21:3328-3345. [PMID: 30917411 DOI: 10.1111/1462-2920.14606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/13/2022]
Abstract
The early Frankia-Alnus symbiotic molecular exchanges were analyzed in detail by protein and RNA omics. For this, Frankia cells were placed in the presence of Alnus roots but separated by a dialysis membrane for 64 h. The bacterial cells were then harvested and analyzed by high-throughput proteomics and transcriptomics (RNA-seq). The most upregulated gene clusters were found to be the potassium transporter operon kdp and an ABC transporter operon of uncharacterized function. The most upregulated proteins were found to be acyl dehydrogenases and the potassium transporter Kdp. These suggest a preadaptation to the impending stresses linked to the penetration into isotonic host tissues and a possible rearrangement of the membrane. Another cluster among the 60 most upregulated ones that comprised two cellulases and a cellulose synthase was conserved among the Frankia and other actinobacteria such as Streptomyces. Cellulase activity was detected on CMC all along the length of the root but not away from it. Frankia alni ACN14a was found to be unable to respire or grow on glucose as sole carbon source. The cellulose synthase was found active at the tip of hyphae in response to Alnus root exudates, resulting in a calcofluor stained tip.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
| | - Nicole Alloisio
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
| | - David Roche
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Haitham Sghaier
- National Center for Nuclear Sciences and Technology, Sidi Thabet Technopark, Ariana, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMRA1418, Cedex 69622, Villeurbanne, France
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Ghedira K, Harigua-Souiai E, Ben Hamda C, Fournier P, Pujic P, Guesmi S, Guizani I, Miotello G, Armengaud J, Normand P, Sghaier H. The PEG-responding desiccome of the alder microsymbiont Frankia alni. Sci Rep 2018; 8:759. [PMID: 29335550 PMCID: PMC5768760 DOI: 10.1038/s41598-017-18839-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
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Affiliation(s)
- Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
- Université de Carthage, Faculté des Sciences de Bizerte, Tunis, 7021, Tunisia
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Sihem Guesmi
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- National Agronomy Institute (INAT), Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- Associated with Laboratory "Biotechnology and Nuclear Technology" (LR16CNSTN01) & Laboratory "Biotechnology and Bio-Geo Resources Valorization" (LR11ES31), Sidi Thabet Technopark, 2020, Tunisia
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Anne-Emmanuelle H, Hasna B, Antoine B, Marjolaine R, Guillaume M, Laetitia CG, Gilles C, Aude HB. Control of Endophytic Frankia Sporulation by Alnus Nodule Metabolites. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:205-214. [PMID: 28072559 DOI: 10.1094/mpmi-11-16-0235-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A unique case of microbial symbiont capable of dormancy within its living host cells has been reported in actinorhizal symbioses. Some Frankia strains, named Sp+, are able to sporulate inside plant cells, contrarily to Sp- strains. The presence of metabolically slowed-down bacterial structures in host cells alters our understanding of symbiosis based on reciprocal benefits between both partners, and its impact on the symbiotic processes remains unknown. The present work reports a metabolomic study of Sp+ and Sp- nodules (from Alnus glutinosa), in order to highlight variabilities associated with in-planta sporulation. A total of 21 amino acids, 44 sugars and organic acids, and 213 secondary metabolites were detected using UV and mass spectrometric-based profiling. Little change was observed in primary metabolites, suggesting that in-planta sporulation would not strongly affect the primary functionalities of the symbiosis. One secondary metabolite (M27) was detected only in Sp+ nodules. It was identified as gentisic acid 5-O-β-d-xylopyranoside, previously reported as involved in plant defenses against microbial pathogens. This metabolite significantly increased Frankia in-vitro sporulation, unlike another metabolite significantly more abundant in Sp- nodules [M168 = (5R)-1,7-bis-(3,4-dihydroxyphenyl)-heptane-5-O-β-d-glucopyranoside]. All these results suggest that the plant could play an important role in the Frankia ability to sporulate in planta and allow us to discuss a possible sanction emitted by the host against less cooperative Sp+ symbionts.
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Affiliation(s)
- Hay Anne-Emmanuelle
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Boubakri Hasna
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Buonomo Antoine
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Rey Marjolaine
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Meiffren Guillaume
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Cotin-Galvan Laetitia
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Comte Gilles
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
| | - Herrera-Belaroussi Aude
- 1 PRES Université de Lyon, F-69361, Lyon, France and Université Lyon 1, F-69622, Villeurbanne, France; and
- 2 Laboratoire Ecologie Microbienne, UMR 5557 CNRS-Lyon1, Villeurbanne
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Musilova L, Ridl J, Polivkova M, Macek T, Uhlik O. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments. Int J Mol Sci 2016; 17:E1205. [PMID: 27483244 PMCID: PMC5000603 DOI: 10.3390/ijms17081205] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/20/2016] [Accepted: 07/15/2016] [Indexed: 12/19/2022] Open
Abstract
Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.
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Affiliation(s)
- Lucie Musilova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
| | - Marketa Polivkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Tomas Macek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technicka 3, 166 28 Prague, Czech Republic.
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An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis. Symbiosis 2016. [DOI: 10.1007/s13199-016-0431-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Persson T, Van Nguyen T, Alloisio N, Pujic P, Berry AM, Normand P, Pawlowski K. The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata: can D. glomerata change N-transport forms when nodulated? Symbiosis 2016. [DOI: 10.1007/s13199-016-0407-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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