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Manley BF, Lotharukpong JS, Barrera-Redondo J, Llewellyn T, Yildirir G, Sperschneider J, Corradi N, Paszkowski U, Miska EA, Dallaire A. A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis. G3 (BETHESDA, MD.) 2023; 13:jkad077. [PMID: 36999556 PMCID: PMC10234402 DOI: 10.1093/g3journal/jkad077] [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: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 06/02/2023]
Abstract
The root systems of most plant species are aided by the soil-foraging capacities of symbiotic arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of R. irregularis, alongside short- and long-read RNA-Sequencing data, was used to produce a comprehensive annotation catalog of gene models, repetitive elements, small RNA loci, and DNA cytosine methylome. A phylostratigraphic gene age inference framework revealed that the birth of genes associated with nutrient transporter activity and transmembrane ion transport systems predates the emergence of Glomeromycotina. While nutrient cycling in AM fungi relies on genes that existed in ancestor lineages, a burst of Glomeromycotina-restricted genetic innovation is also detected. Analysis of the chromosomal distribution of genetic and epigenetic features highlights evolutionarily young genomic regions that produce abundant small RNAs, suggesting active RNA-based monitoring of genetic sequences surrounding recently evolved genes. This chromosome-scale view of the genome of an AM fungus genome reveals previously unexplored sources of genomic novelty in an organism evolving under an obligate symbiotic life cycle.
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Affiliation(s)
- Bethan F Manley
- SPUN|Society for the Protection of Underground Networks, 3500 South DuPont Highway, Suite EI-101, Dover, DE 19901, USA
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Jaruwatana S Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Theo Llewellyn
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Jana Sperschneider
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5
| | - Uta Paszkowski
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge CB3 0LE, UK
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Alexandra Dallaire
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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Nguyen CT, Saito K. Role of Cell Wall Polyphosphates in Phosphorus Transfer at the Arbuscular Interface in Mycorrhizas. FRONTIERS IN PLANT SCIENCE 2021; 12:725939. [PMID: 34616416 PMCID: PMC8488203 DOI: 10.3389/fpls.2021.725939] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/20/2021] [Indexed: 06/01/2023]
Abstract
Arbuscular mycorrhizal fungi provide plants with soil mineral nutrients, particularly phosphorus. In this symbiotic association, the arbuscular interface is the main site for nutrient exchange. To understand phosphorus transfer at the interface, we analyzed the subcellular localization of polyphosphate (polyP) in mature arbuscules of Rhizophagus irregularis colonizing roots of Lotus japonicus wild-type (WT) and H+-ATPase ha1-1 mutant, which is defective in phosphorus acquisition through the mycorrhizal pathway. In both, the WT and the ha1-1 mutant, polyP accumulated in the cell walls of trunk hyphae and inside fine branch modules close to the trunk hyphae. However, many fine branches lacked polyP. In the mutant, most fine branch modules showed polyP signals compared to the WT. Notably, polyP was also observed in the cell walls of some fine branches formed in the ha1-1 mutant, indicating phosphorus release from fungal cells to the apoplastic regions. Intense acid phosphatase (ACP) activity was detected in the periarbuscular spaces around the fine branches. Furthermore, double staining of ACP activity and polyP revealed that these had contrasting distribution patterns in arbuscules. These observations suggest that polyP in fungal cell walls and apoplastic phosphatases may play an important role in phosphorus transfer at the symbiotic interface in arbuscules.
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Affiliation(s)
- Cuc Thi Nguyen
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Faculty of Agriculture and Forestry, Dalat University, Dalat, Vietnam
| | - Katsuharu Saito
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Nagano, Japan
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Balestrini R, Brunetti C, Chitarra W, Nerva L. Photosynthetic Traits and Nitrogen Uptake in Crops: Which Is the Role of Arbuscular Mycorrhizal Fungi? PLANTS (BASEL, SWITZERLAND) 2020; 9:E1105. [PMID: 32867243 PMCID: PMC7570035 DOI: 10.3390/plants9091105] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi are root symbionts that provide mineral nutrients to the host plant in exchange for carbon compounds. AM fungi positively affect several aspects of plant life, improving nutrition and leading to a better growth, stress tolerance, and disease resistance and they interact with most crop plants such as cereals, horticultural species, and fruit trees. For this reason, they receive expanding attention for the potential use in sustainable and climate-smart agriculture context. Although several positive effects have been reported on photosynthetic traits in host plants, showing improved performances under abiotic stresses such as drought, salinity and extreme temperature, the involved mechanisms are still to be fully discovered. In this review, some controversy aspects related to AM symbiosis and photosynthesis performances will be discussed, with a specific focus on nitrogen acquisition-mediated by AM fungi.
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Affiliation(s)
- Raffaella Balestrini
- National Research Council-Institute for Sustainable Plant Protection (CNR-IPSP), 10125 Turin, Italy; (C.B.); (W.C.); (L.N.)
| | - Cecilia Brunetti
- National Research Council-Institute for Sustainable Plant Protection (CNR-IPSP), 10125 Turin, Italy; (C.B.); (W.C.); (L.N.)
| | - Walter Chitarra
- National Research Council-Institute for Sustainable Plant Protection (CNR-IPSP), 10125 Turin, Italy; (C.B.); (W.C.); (L.N.)
- Council for Agricultural Research and Economics, Research Center for Viticulture and Enology, (CREA-VE), 31015 Conegliano (TV), Italy
| | - Luca Nerva
- National Research Council-Institute for Sustainable Plant Protection (CNR-IPSP), 10125 Turin, Italy; (C.B.); (W.C.); (L.N.)
- Council for Agricultural Research and Economics, Research Center for Viticulture and Enology, (CREA-VE), 31015 Conegliano (TV), Italy
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Min K, Naseem S, Konopka JB. N-Acetylglucosamine Regulates Morphogenesis and Virulence Pathways in Fungi. J Fungi (Basel) 2019; 6:jof6010008. [PMID: 31878148 PMCID: PMC7151181 DOI: 10.3390/jof6010008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
N-acetylglucosamine (GlcNAc) is being increasingly recognized for its ability to stimulate cell signaling. This amino sugar is best known as a component of cell wall peptidoglycan in bacteria, cell wall chitin in fungi and parasites, exoskeletons of arthropods, and the extracellular matrix of animal cells. In addition to these structural roles, GlcNAc is now known to stimulate morphological and stress responses in a wide range of organisms. In fungi, the model organisms Saccharomyces cerevisiae and Schizosaccharomyces pombe lack the ability to respond to GlcNAc or catabolize it, so studies with the human pathogen Candida albicans have been providing new insights into the ability of GlcNAc to stimulate cellular responses. GlcNAc potently induces C. albicans to transition from budding to filamentous hyphal growth. It also promotes an epigenetic switch from White to Opaque cells, which differ in morphology, metabolism, and virulence properties. These studies have led to new discoveries, such as the identification of the first eukaryotic GlcNAc transporter. Other results have shown that GlcNAc can induce signaling in C. albicans in two ways. One is to act as a signaling molecule independent of its catabolism, and the other is that its catabolism can cause the alkalinization of the extracellular environment, which provides an additional stimulus to form hyphae. GlcNAc also induces the expression of virulence genes in the C. albicans, indicating it can influence pathogenesis. Therefore, this review will describe the recent advances in understanding the role of GlcNAc signaling pathways in regulating C. albicans morphogenesis and virulence.
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Affiliation(s)
- Benoit Lefebvre
- Laboratory of Plant-Microbe Interactions (LIPM), Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
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Nadal M, Sawers R, Naseem S, Bassin B, Kulicke C, Sharman A, An G, An K, Ahern KR, Romag A, Brutnell TP, Gutjahr C, Geldner N, Roux C, Martinoia E, Konopka JB, Paszkowski U. An N-acetylglucosamine transporter required for arbuscular mycorrhizal symbioses in rice and maize. NATURE PLANTS 2017; 3:17073. [PMID: 28548655 PMCID: PMC5685555 DOI: 10.1038/nplants.2017.73] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 04/25/2017] [Indexed: 05/20/2023]
Abstract
Most terrestrial plants, including crops, engage in beneficial interactions with arbuscular mycorrhizal fungi. Vital to the association is mutual recognition involving the release of diffusible signals into the rhizosphere. Previously, we identified the maize no perception 1 (nope1) mutant to be defective in early signalling. Here, we report cloning of ZmNope1 on the basis of synteny with rice. NOPE1 encodes a functional homologue of the Candida albicans N-acetylglucosamine (GlcNAc) transporter NGT1, and represents the first plasma membrane GlcNAc transporter identified from plants. In C. albicans, exposure to GlcNAc activates cell signalling and virulence. Similarly, in Rhizophagus irregularis treatment with rice wild-type but not nope1 root exudates induced transcriptome changes associated with signalling function, suggesting a requirement of NOPE1 function for presymbiotic fungal reprogramming.
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Affiliation(s)
- Marina Nadal
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ruairidh Sawers
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Shamoon Naseem
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Barbara Bassin
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Corinna Kulicke
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Abigail Sharman
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Kyungsook An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Kevin R. Ahern
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Amanda Romag
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Thomas P. Brutnell
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
| | - Caroline Gutjahr
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Niko Geldner
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christophe Roux
- Université de Toulouse, UPS, UMR5546, Laboratoire de recherche en Sciences Végétales, BP 42617, F-31326 Castanet-Tolosan CEDEX, France
| | - Enrico Martinoia
- Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland
| | - James B. Konopka
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Uta Paszkowski
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland
- to whom correspondence should be addressed: Uta Paszkowski,
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Regulation of Hyphal Growth and N-Acetylglucosamine Catabolism by Two Transcription Factors in Candida albicans. Genetics 2017; 206:299-314. [PMID: 28348062 DOI: 10.1534/genetics.117.201491] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/24/2017] [Indexed: 02/07/2023] Open
Abstract
The amino sugar N-acetylglucosamine (GlcNAc) is increasingly recognized as an important signaling molecule in addition to its well-known structural roles at the cell surface. In the human fungal pathogen Candida albicans, GlcNAc stimulates several responses including the induction of the genes needed for its catabolism and a switch from budding to filamentous hyphal growth. We identified two genes needed for growth on GlcNAc (RON1 and NGS1) and found that mutants lacking these genes fail to induce the genes needed for GlcNAc catabolism. NGS1 was also important for growth on other sugars, such as maltose, but RON1 appeared to be specific for GlcNAc. Both mutants could grow on nonfermentable carbon sources indicating that they do not affect mitochondrial function, which we show is important for growth on GlcNAc but not for GlcNAc induction of hyphal morphogenesis. Interestingly, both the ron1Δ and ngs1Δ mutants were defective in forming hyphae in response to GlcNAc, even though GlcNAc catabolism is not required for induction of hyphal morphogenesis. The ron1Δ mutant showed a partial defect in forming hyphae, which was surprising since it displayed an elevated level of filamentous cells under noninducing conditions. The ron1Δ mutant also displayed an elevated basal level of expression of genes that are normally upregulated during hyphal growth. Consistent with this, Ron1 contains an Ndt80-like DNA-binding domain, indicating that it regulates gene expression. Thus, Ron1 is a key new component of the GlcNAc response pathway that acts as both an activator and a repressor of hyphal morphogenesis.
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Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls. PLoS One 2016; 11:e0160356. [PMID: 27479250 PMCID: PMC4968797 DOI: 10.1371/journal.pone.0160356] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/18/2016] [Indexed: 11/19/2022] Open
Abstract
Association between arbuscular mycorrhizal fungi (AMF) and bacteria has long been studied. However, the factors influencing their association in the natural environment is still unknown. This study aimed to isolate bacteria associated with spore walls of AMF and identify their potential characters for association. Spores collected from coastal reclamation land were differentiated based on their morphology and identified by 18S rDNA sequencing as Funneliformis caledonium, Racocetra alborosea and Funneliformis mosseae. Bacteria associated with AMF spore walls were isolated after treating them with disinfection solution at different time intervals. After 0, 10 and 20 min of spore disinfection, 86, 24 and 10 spore associated bacteria (SAB) were isolated, respectively. BOX-PCR fingerprinting analysis showed that diverse bacterial communities were associated to AMF spores. Bacteria belonging to the same genera could associate with different AMF spores. Gram positive bacteria were more closely associated with AMF spores. Isolated SAB were characterized and tested for spore association characters such as chitinase, protease, cellulase enzymes and exopolysaccharide production (EPS). Among the 120 SAB, 113 SAB were able to show one or more characters for association and seven SAB did not show any association characters. The 16S rDNA sequence of SAB revealed that bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria and Bactereiodes were associated with AMF spore walls.
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