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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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Koltun A, Maniero RA, Vitti M, de Setta N, Giehl RFH, Lima JE, Figueira A. Functional characterization of the sugarcane ( Saccharum spp.) ammonium transporter AMT2;1 suggests a role in ammonium root-to-shoot translocation. FRONTIERS IN PLANT SCIENCE 2022; 13:1039041. [PMID: 36466275 PMCID: PMC9716016 DOI: 10.3389/fpls.2022.1039041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
AMMONIUM TRANSPORTER/METHYLAMMONIUM PERMEASE/RHESUS (AMT) family members transport ammonium across membranes in all life domains. Plant AMTs can be categorized into AMT1 and AMT2 subfamilies. Functional studies of AMTs, particularly AMT1-type, have been conducted using model plants but little is known about the function of AMTs from crops. Sugarcane (Saccharum spp.) is a major bioenergy crop that requires heavy nitrogen fertilization but depends on a low carbon-footprint for competitive sustainability. Here, we identified and functionally characterized sugarcane ScAMT2;1 by complementing ammonium uptake-defective mutants of Saccharomyces cerevisiae and Arabidopsis thaliana. Reporter gene driven by the ScAMT2;1 promoter in A. thaliana revealed preferential expression in the shoot vasculature and root endodermis/pericycle according to nitrogen availability and source. Arabidopsis quadruple mutant plants expressing ScAMT2;1 driven by the CaMV35S promoter or by a sugarcane endogenous promoter produced significantly more biomass than mutant plants when grown in NH4 + and showed more 15N-ammonium uptake by roots and nitrogen translocation to shoots. In A. thaliana, ScAMT2;1 displayed a Km of 90.17 µM and Vmax of 338.99 µmoles h-1 g-1 root DW. Altogether, our results suggest that ScAMT2;1 is a functional high-affinity ammonium transporter that might contribute to ammonium uptake and presumably to root-to-shoot translocation under high NH4 + conditions.
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Affiliation(s)
- Alessandra Koltun
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Rodolfo A. Maniero
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Marielle Vitti
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ricardo F. H. Giehl
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Joni E. Lima
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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The Exploring Functional Role of Ammonium Transporters of Aspergillus oryzae in Nitrogen Metabolism: Challenges towards Cell Biomass Production. Int J Mol Sci 2022; 23:ijms23147567. [PMID: 35886914 PMCID: PMC9319855 DOI: 10.3390/ijms23147567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
Ammonium is a source of fermentable inorganic nitrogen essential for the growth and development of filamentous fungi. It is involved in several cellular metabolic pathways underlying nitrogen transport and assimilation. Ammonium can be transferred into the cell by an ammonium transporter. This study explored the role of ammonium transporters in nitrogen metabolism and cell biomass production in Aspergillus oryzae strain BCC 7051. Specific sequences encoding ammonium transporters (Amts) in A. oryzae were identified using genomic analysis. Four of the identified ammonium transporter genes, aoamt1-aoamt4, showed similarity in deduced amino acid sequences to the proteins in the ammonium transporter/methylammonium permease (AMT/MEP) family. Transcriptional analysis showed that the expression of aoamt2 and aoamt3 was ammonium-dependent, and was highly upregulated under ammonium-limited conditions. Their functional roles are characterized by genetic perturbations. The gene disruption and overexpression of aoamt3 indicated that the protein encoded by it was a crucial ammonium transporter associated with nitrogen metabolism and was required for filamentous growth. Compared with the wild type, the aoamt3-overexpressing strain showed superior growth performance, high biomass yield, and low glucose consumption. These results shed light on further improvements in the production of potent bioproducts by A. oryzae by manipulating the ammonium uptake capacity and nitrogen metabolism.
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Kuo CC, Lin YC, Chen LH, Lin MY, Shih MC, Lee MH. CaNRT2.1 Is Required for Nitrate but Not Nitrite Uptake in Chili Pepper Pathogen Colletotrichum acutatum. Front Microbiol 2021; 11:613674. [PMID: 33469454 PMCID: PMC7813687 DOI: 10.3389/fmicb.2020.613674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
Chili peppers are an important food additive used in spicy cuisines worldwide. However, the yield and quality of chilis are threatened by anthracnose disease caused by Colletotrichum acutatum. Despite the impact of C. acutatum on chili production, the genes involved in fungal development and pathogenicity in this species have not been well characterized. In this study, through T-DNA insertional mutagenesis, we identified a mutant strain termed B7, which is defective for the growth of C. acutatum on a minimal nutrient medium. Our bioinformatics analysis revealed that a large fragment DNA (19.8 kb) is deleted from the B7 genome, thus resulting in the deletion of three genes, including CaGpiP1 encoding a glycosylphosphatidyl-inisotol (GPI)-anchored protein, CaNRT2.1 encoding a membrane-bound nitrate/nitrite transporter, and CaRQH1 encoding a RecQ helicase protein. In addition, T-DNA is inserted upstream of the CaHP1 gene encoding a hypothetical protein. Functional characterization of CaGpiP1, CaNRT2.1, and CaHP1 by targeted gene disruption and bioassays indicated that CaNRT2.1 is responsible for the growth-defective phenotype of B7. Both B7 and CaNRT2.1 mutant strains cannot utilize nitrate as nitrogen sources, thus restraining the fungal growth on a minimal nutrient medium. In addition to CaNRT2.1, our results showed that CaGpiP1 is a cell wall-associated GPI-anchored protein. However, after investigating the functions of CaGpiP1 and CaHP1 in fungal pathogenicity, growth, development and stress tolerance, we were unable to uncover the roles of these two genes in C. acutatum. Collectively, in this study, our results identify the growth-defective strain B7 via T-DNA insertion and reveal the critical role of CaNRT2.1 in nitrate transportation for the fungal growth of C. acutatum.
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Affiliation(s)
- Chia-Chi Kuo
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Yung-Chu Lin
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Li-Hung Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Meng-Yi Lin
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academic Sinica, Taipei, Taiwan
| | - Miin-Huey Lee
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan.,Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Rani M, Jogawat A, Loha A. Sugar Transporters in Plant–Fungal Symbiosis. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Calabrese S, Cusant L, Sarazin A, Niehl A, Erban A, Brulé D, Recorbet G, Wipf D, Roux C, Kopka J, Boller T, Courty PE. Imbalanced Regulation of Fungal Nutrient Transports According to Phosphate Availability in a Symbiocosm Formed by Poplar, Sorghum, and Rhizophagus irregularis. FRONTIERS IN PLANT SCIENCE 2019; 10:1617. [PMID: 31921260 PMCID: PMC6920215 DOI: 10.3389/fpls.2019.01617] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/18/2019] [Indexed: 05/05/2023]
Abstract
In arbuscular mycorrhizal (AM) symbiosis, key components of nutrient uptake and exchange are specialized transporters that facilitate nutrient transport across membranes. As phosphate is a nutrient and a regulator of nutrient exchanges, we investigated the effect of P availability to extraradical mycelium (ERM) on both plant and fungus transcriptomes and metabolomes in a symbiocosm system. By perturbing nutrient exchanges under the control of P, our objectives were to identify new fungal genes involved in nutrient transports, and to characterize in which extent the fungus differentially modulates its metabolism when interacting with two different plant species. We performed transportome analysis on the ERM and intraradical mycelium of the AM fungus Rhizophagus irregularis associated to Populus trichocarpa and Sorghum bicolor under high and low P availability in ERM, using quantitative RT-PCR and Illumina mRNA-sequencing. We observed that mycorrhizal symbiosis induces expression of specific phosphate and ammonium transporters in both plants. Furthermore, we identified new AM-inducible transporters and showed that a subset of phosphate transporters is regulated independently of symbiotic nutrient exchange. mRNA-Sequencing revealed that the fungal transportome was not similarly regulated in the two host plant species according to P availability. Mirroring this effect, many plant carbohydrate transporters were down-regulated in P. trichocarpa mycorrhizal root tissue. Metabolome analysis revealed further that AM root colonization led to a modification of root primary metabolism under low and high P availability and to a decrease of primary metabolite pools in general. Moreover, the down regulation of the sucrose transporters suggests that the plant limits carbohydrate long distance transport (i.e. from shoot to the mycorrhizal roots). By simultaneous uptake/reuptake of nutrients from the apoplast at the biotrophic interface, plant and fungus are both able to control reciprocal nutrient fluxes.
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Affiliation(s)
- Silvia Calabrese
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Loic Cusant
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, Castanet-Tolosan, France
| | - Alexis Sarazin
- Department of Biology at the Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
| | - Annette Niehl
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Daphnée Brulé
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Ghislaine Recorbet
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS, Castanet-Tolosan, France
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Pierre-Emmanuel Courty
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Basel, Switzerland
- Agroécologie, AgroSup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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Moonjely S, Zhang X, Fang W, Bidochka MJ. Metarhizium robertsii ammonium permeases (MepC and Mep2) contribute to rhizoplane colonization and modulates the transfer of insect derived nitrogen to plants. PLoS One 2019; 14:e0223718. [PMID: 31618269 PMCID: PMC6795453 DOI: 10.1371/journal.pone.0223718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022] Open
Abstract
The endophytic insect pathogenic fungi (EIPF) Metarhizium promotes plant growth through symbiotic association and the transfer of insect-derived nitrogen. However, little is known about the genes involved in this association and the transfer of nitrogen. In this study, we assessed the involvement of six Metarhizium robertsii genes in endophytic, rhizoplane and rhizospheric colonization with barley roots. Two ammonium permeases (MepC and Mep2) and a urease, were selected since homologous genes in arbuscular mycorrhizal fungi were reported to play a pivotal role in nitrogen mobilization during plant root colonization. Three other genes were selected on the basis on RNA-Seq data that showed high expression levels on bean roots, and these encoded a hydrophobin (Hyd3), a subtilisin-like serine protease (Pr1A) and a hypothetical protein. The root colonization assays revealed that the deletion of urease, hydrophobin, subtilisin-like serine protease and hypothetical protein genes had no impact on endophytic, rhizoplane and rhizospheric colonization at 10 or 20 days. However, the deletion of MepC resulted in significantly increased rhizoplane colonization at 10 days whereas ΔMep2 showed increased rhizoplane colonization at 20 days. In addition, the nitrogen transporter mutants also showed significantly higher 15N incorporation of insect derived nitrogen in barley leaves in the presence of nutrients. Insect pathogenesis assay revealed that disruption of MepC, Mep2, urease did not reduce virulence toward insects. The enhanced rhizoplane colonization of ΔMep2 and ΔMepC and insect derived nitrogen transfer to plant hosts suggests the role of MepC and Mep2 in Metarhizium-plant symbiosis.
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Affiliation(s)
- Soumya Moonjely
- Department of Biological Sciences, Brock University, St. Catharines, ON Canada
| | - Xing Zhang
- Institute of Microbiology, Zhejiang University, Hangzhou, China
| | - Weiguo Fang
- Institute of Microbiology, Zhejiang University, Hangzhou, China
| | - Michael J. Bidochka
- Department of Biological Sciences, Brock University, St. Catharines, ON Canada
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Tamayo E, Knight SAB, Valderas A, Dancis A, Ferrol N. The arbuscular mycorrhizal fungus Rhizophagus irregularis
uses a reductive iron assimilation pathway for high-affinity iron uptake. Environ Microbiol 2018; 20:1857-1872. [DOI: 10.1111/1462-2920.14121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Elisabeth Tamayo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos; Estación Experimental del Zaidín, CSIC; Granada Spain
| | - Simon A. B. Knight
- Department of Medicine, Division of Hematology-Oncology; Perelman School of Medicine, University of Pennsylvania; Philadelphia PA USA
| | - Ascensión Valderas
- Departamento de Microbiología del Suelo y Sistemas Simbióticos; Estación Experimental del Zaidín, CSIC; Granada Spain
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology; Perelman School of Medicine, University of Pennsylvania; Philadelphia PA USA
| | - Nuria Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos; Estación Experimental del Zaidín, CSIC; Granada Spain
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An Intracellular Ammonium Transporter Is Necessary for Replication, Differentiation, and Resistance to Starvation and Osmotic Stress in Trypanosoma cruzi. mSphere 2018; 3:mSphere00377-17. [PMID: 29359189 PMCID: PMC5770540 DOI: 10.1128/msphere.00377-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
Trypanosoma cruzi, the etiologic agent of Chagas disease, undergoes drastic metabolic changes when it transits between a vector and mammalian hosts. Amino acid catabolism leads to the production of ammonium (NH4+), which needs to be detoxified. However, T. cruzi does not possess a urea cycle, and it is unknown how intracellular levels of ammonium are controlled. In this work, we identified an intracellular ammonium transporter of T. cruzi (TcAMT) that localizes to acidic compartments (reservosomes, lysosomes). TcAMT has 11 transmembrane domains and possesses all conserved and functionally important amino acid residues that form the pore in other ammonium transporters. Functional expression in Xenopus oocytes followed by a two-electrode voltage clamp showed an inward current that is NH4+ dependent at a resting membrane potential (Vh ) lower than -120 mV and is not pH dependent, suggesting that TcAMT is not an NH4+/H+ cotransporter but an NH4+ or NH3/H+ transporter. Ablation of TcAMT by clustered regularly interspaced short palindromic repeat analysis with Cas9 (CRISPR-Cas9) resulted in significant defects in epimastigote and amastigote replication, differentiation, and resistance to starvation and osmotic stress. IMPORTANCETrypanosoma cruzi is an important human and animal pathogen and the etiologic agent of Chagas disease. The parasite undergoes drastic changes in its metabolism during its life cycle. Amino acid consumption becomes important in the infective stages and leads to the production of ammonia (NH3), which needs to be detoxified. We report here the identification of an ammonium (NH4+) transporter that localizes to acidic compartments and is important for replication, differentiation, and resistance to starvation and osmotic stress.
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Nakamura H, Shiozaki T, Gonda N, Furuya K, Matsunaga S, Okada S. Utilization of ammonium by the hydrocarbon-producing microalga, Botryococcus braunii Showa. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Calabrese S, Pérez-Tienda J, Ellerbeck M, Arnould C, Chatagnier O, Boller T, Schüßler A, Brachmann A, Wipf D, Ferrol N, Courty PE. GintAMT3 - a Low-Affinity Ammonium Transporter of the Arbuscular Mycorrhizal Rhizophagus irregularis. FRONTIERS IN PLANT SCIENCE 2016; 7:679. [PMID: 27252708 PMCID: PMC4879785 DOI: 10.3389/fpls.2016.00679] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/02/2016] [Indexed: 05/05/2023]
Abstract
Nutrient acquisition and transfer are essential steps in the arbuscular mycorrhizal (AM) symbiosis, which is formed by the majority of land plants. Mineral nutrients are taken up by AM fungi from the soil and transferred to the plant partner. Within the cortical plant root cells the fungal hyphae form tree-like structures (arbuscules) where the nutrients are released to the plant-fungal interface, i.e., to the periarbuscular space, before being taken up by the plant. In exchange, the AM fungi receive carbohydrates from the plant host. Besides the well-studied uptake of phosphorus (P), the uptake and transfer of nitrogen (N) plays a crucial role in this mutualistic interaction. In the AM fungus Rhizophagus irregularis (formerly called Glomus intraradices), two ammonium transporters (AMT) were previously described, namely GintAMT1 and GintAMT2. Here, we report the identification and characterization of a newly identified R. irregularis AMT, GintAMT3. Phylogenetic analyses revealed high sequence similarity to previously identified AM fungal AMTs and a clear separation from other fungal AMTs. Topological analysis indicated GintAMT3 to be a membrane bound pore forming protein, and GFP tagging showed it to be highly expressed in the intraradical mycelium of a fully established AM symbiosis. Expression of GintAMT3 in yeast successfully complemented the yeast AMT triple deletion mutant (MATa ura3 mep1Δ mep2Δ::LEU2 mep3Δ::KanMX2). GintAMT3 is characterized as a low affinity transport system with an apparent Km of 1.8 mM and a V max of 240 nmol(-1) min(-1) 10(8) cells(-1), which is regulated by substrate concentration and carbon supply.
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Affiliation(s)
- Silvia Calabrese
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of BaselBasel, Switzerland
| | - Jacob Pérez-Tienda
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Matthias Ellerbeck
- Faculty of Biology, Genetics, Ludwig-Maximilians-University MunichPlanegg-Martinsried, Germany
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Bourgogne Franche-ComtéDijon, France
| | - Odile Chatagnier
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Bourgogne Franche-ComtéDijon, France
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of BaselBasel, Switzerland
| | - Arthur Schüßler
- Faculty of Biology, Genetics, Ludwig-Maximilians-University MunichPlanegg-Martinsried, Germany
| | - Andreas Brachmann
- Faculty of Biology, Genetics, Ludwig-Maximilians-University MunichPlanegg-Martinsried, Germany
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Bourgogne Franche-ComtéDijon, France
| | - Nuria Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Pierre-Emmanuel Courty
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of BaselBasel, Switzerland
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13
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Tang N, San Clemente H, Roy S, Bécard G, Zhao B, Roux C. A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy. Front Microbiol 2016; 7:233. [PMID: 26973612 PMCID: PMC4771724 DOI: 10.3389/fmicb.2016.00233] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/15/2016] [Indexed: 01/22/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are a diverse group of soil fungi (Glomeromycota) that form the most ancient mutualistic association termed AM symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales). Among the 86332 non-redundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for Rhizophagus irregularis, several metabolic genes were not found, including the fatty acid synthase (FAS) gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and 100s of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales) and Gigaspora margarita (Diversisporales), reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation for forthcoming studies into the genomics of Diversisporales, and also illuminates the utility of comparing gene repertoires of species from Diversisporales and other clades of Glomeromycota to gain more insights into the genetics and evolution of this fungal group.
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Affiliation(s)
- Nianwu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Hélène San Clemente
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Sébastien Roy
- AGRONUTRITION Laboratoire de BiotechnologiesToulouse, France
| | - Guillaume Bécard
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Christophe Roux
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
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Tamayo E, Benabdellah K, Ferrol N. Characterization of Three New Glutaredoxin Genes in the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis: Putative Role of RiGRX4 and RiGRX5 in Iron Homeostasis. PLoS One 2016; 11:e0149606. [PMID: 26900849 PMCID: PMC4765768 DOI: 10.1371/journal.pone.0149606] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 02/02/2016] [Indexed: 01/07/2023] Open
Abstract
Glutaredoxins (GRXs) are small ubiquitous oxidoreductases involved in the regulation of the redox state in living cells. In an attempt to identify the full complement of GRXs in the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis, three additional GRX homologs, besides the formerly characterized GintGRX1 (renamed here as RiGRX1), were identified. The three new GRXs (RiGRX4, RiGRX5 and RiGRX6) contain the CXXS domain of monothiol GRXs, but whereas RiGRX4 and RiGRX5 belong to class II GRXs, RiGRX6 belongs to class I together with RiGRX1. By using a yeast expression system, we observed that the newly identified homologs partially reverted sensitivity of the GRX deletion yeast strains to external oxidants. Furthermore, our results indicated that RiGRX4 and RiGRX5 play a role in iron homeostasis in yeast. Gene expression analyses revealed that RiGRX1 and RiGRX6 were more highly expressed in the intraradical (IRM) than in the extraradical mycelium (ERM). Exposure of the ERM to hydrogen peroxide induced up-regulation of RiGRX1, RiGRX4 and RiGRX5 gene expression. RiGRX4 expression was also up-regulated in the ERM when the fungus was grown in media supplemented with a high iron concentration. These data indicate the two monothiol class II GRXs, RiGRX4 and RiGRX5, might be involved in oxidative stress protection and in the regulation of fungal iron homeostasis. Increased expression of RiGRX1 and RiGRX6 in the IRM suggests that these GRXs should play a key role in oxidative stress protection of R. irregularis during its in planta phase.
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Affiliation(s)
- Elisabeth Tamayo
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Nuria Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- * E-mail:
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