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Kirolinko C, Hobecker K, Cueva M, Botto F, Christ A, Niebel A, Ariel F, Blanco FA, Crespi M, Zanetti ME. A lateral organ boundaries domain transcription factor acts downstream of the auxin response factor 2 to control nodulation and root architecture in Medicago truncatula. THE NEW PHYTOLOGIST 2024; 242:2746-2762. [PMID: 38666352 DOI: 10.1111/nph.19766] [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: 12/20/2023] [Accepted: 03/21/2024] [Indexed: 05/24/2024]
Abstract
Legume plants develop two types of root postembryonic organs, lateral roots and symbiotic nodules, using shared regulatory components. The module composed by the microRNA390, the Trans-Acting SIRNA3 (TAS3) RNA and the Auxin Response Factors (ARF)2, ARF3, and ARF4 (miR390/TAS3/ARFs) mediates the control of both lateral roots and symbiotic nodules in legumes. Here, a transcriptomic approach identified a member of the Lateral Organ Boundaries Domain (LBD) family of transcription factors in Medicago truncatula, designated MtLBD17/29a, which is regulated by the miR390/TAS3/ARFs module. ChIP-PCR experiments evidenced that MtARF2 binds to an Auxin Response Element present in the MtLBD17/29a promoter. MtLBD17/29a is expressed in root meristems, lateral root primordia, and noninfected cells of symbiotic nodules. Knockdown of MtLBD17/29a reduced the length of primary and lateral roots and enhanced lateral root formation, whereas overexpression of MtLBD17/29a produced the opposite phenotype. Interestingly, both knockdown and overexpression of MtLBD17/29a reduced nodule number and infection events and impaired the induction of the symbiotic genes Nodulation Signaling Pathway (NSP) 1 and 2. Our results demonstrate that MtLBD17/29a is regulated by the miR390/TAS3/ARFs module and a direct target of MtARF2, revealing a new lateral root regulatory hub recruited by legumes to act in the root nodule symbiotic program.
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Affiliation(s)
- Cristina Kirolinko
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Marianela Cueva
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Florencia Botto
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, INRAE, CNRS, 31326, Castanet-Tolosan, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
| | - Martín Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
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Qiao M, Sun R, Wang Z, Dumack K, Xie X, Dai C, Wang E, Zhou J, Sun B, Peng X, Bonkowski M, Chen Y. Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification. Nat Commun 2024; 15:2924. [PMID: 38575565 PMCID: PMC10995168 DOI: 10.1038/s41467-024-47159-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.
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Affiliation(s)
- Mengjie Qiao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruibo Sun
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Zixuan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- College of Land Resource and Environment, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str 47b, Cologne, 50674, Germany
| | - Xingguang Xie
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chuanchao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, 73019, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xinhua Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str 47b, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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Zorin EA, Sulima AS, Zhernakov AI, Kuzmina DO, Rakova VA, Kliukova MS, Romanyuk DA, Kulaeva OA, Akhtemova GA, Shtark OY, Tikhonovich IA, Zhukov VA. Genomic and Transcriptomic Analysis of Pea ( Pisum sativum L.) Breeding Line 'Triumph' with High Symbiotic Responsivity. PLANTS (BASEL, SWITZERLAND) 2023; 13:78. [PMID: 38202386 PMCID: PMC10781049 DOI: 10.3390/plants13010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Pea (Pisum sativum L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype; thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown. Here, we compare the symbiotically responsive breeding line 'Triumph' of grain pea with its parental cultivars 'Vendevil' (a donor of high symbiotic responsivity) and 'Classic' (a donor of agriculturally valuable traits) using genome and transcriptome sequencing. We show that 'Triumph' inherited one-fourth of its genome from 'Vendevil', including the genes related to AM and nodule formation, and reveal that under combined inoculation with nodule bacteria and AM fungi, 'Triumph' and 'Vendevil', in contrast to 'Classic', demonstrate similar up-regulation of the genes related to solute transport, hormonal regulation and flavonoid biosynthesis in their roots. We also identify the gene PsGLP2, whose expression pattern distinguishing 'Triumph' and 'Vendevil' from 'Classic' correlates with difference within the promoter region sequence, making it a promising marker for the symbiotic responsivity trait. The results of this study may be helpful for future molecular breeding programs aimed at creation of symbiotically responsive cultivars of pea.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Aleksandr I. Zhernakov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Daria O. Kuzmina
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Valeria A. Rakova
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Gulnar A. Akhtemova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
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Abstract
Plants associate with nitrogen-fixing bacteria to secure nitrogen, which is generally the most limiting nutrient for plant growth. Endosymbiotic nitrogen-fixing associations are widespread among diverse plant lineages, ranging from microalgae to angiosperms, and are primarily one of three types: cyanobacterial, actinorhizal or rhizobial. The large overlap in the signaling pathways and infection components of arbuscular mycorrhizal, actinorhizal and rhizobial symbioses reflects their evolutionary relatedness. These beneficial associations are influenced by environmental factors and other microorganisms in the rhizosphere. In this review, we summarize the diversity of nitrogen-fixing symbioses, key signal transduction pathways and colonization mechanisms relevant to such interactions, and compare and contrast these interactions with arbuscular mycorrhizal associations from an evolutionary standpoint. Additionally, we highlight recent studies on environmental factors regulating nitrogen-fixing symbioses to provide insights into the adaptation of symbiotic plants to complex environments.
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Affiliation(s)
- Peng Xu
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen 518054, China.
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5
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Nasrollahi V, Allam G, Kohalmi SE, Hannoufa A. MsSPL9 Modulates Nodulation under Nitrate Sufficiency Condition in Medicago sativa. Int J Mol Sci 2023; 24:ijms24119615. [PMID: 37298564 DOI: 10.3390/ijms24119615] [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: 05/16/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Nodulation in Leguminous spp. is induced by common environmental cues, such as low nitrogen availability conditions, in the presence of the specific Rhizobium spp. in the rhizosphere. Medicago sativa (alfalfa) is an important nitrogen-fixing forage crop that is widely cultivated around the world and relied upon as a staple source of forage in livestock feed. Although alfalfa's relationship with these bacteria is one of the most efficient between rhizobia and legume plants, breeding for nitrogen-related traits in this crop has received little attention. In this report, we investigate the role of Squamosa-Promoter Binding Protein-Like 9 (SPL9), a target of miR156, in nodulation in alfalfa. Transgenic alfalfa plants with SPL9-silenced (SPL9-RNAi) and overexpressed (35S::SPL9) were compared to wild-type (WT) alfalfa for phenotypic changes in nodulation in the presence and absence of nitrogen. Phenotypic analyses showed that silencing of MsSPL9 in alfalfa caused an increase in the number of nodules. Moreover, the characterization of phenotypic and molecular parameters revealed that MsSPL9 regulates nodulation under a high concentration of nitrate (10 mM KNO3) by regulating the transcription levels of the nitrate-responsive genes Nitrate Reductase1 (NR1), NR2, Nitrate transporter 2.5 (NRT2.5), and a shoot-controlled autoregulation of nodulation (AON) gene, Super numeric nodules (SUNN). While MsSPL9-overexpressing transgenic plants have dramatically increased transcript levels of SUNN, NR1, NR2, and NRT2.5, reducing MsSPL9 caused downregulation of these genes and displayed a nitrogen-starved phenotype, as downregulation of the MsSPL9 transcript levels caused a nitrate-tolerant nodulation phenotype. Taken together, our results suggest that MsSPL9 regulates nodulation in alfalfa in response to nitrate.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Gamalat Allam
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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Liu M, Kameoka H, Oda A, Maeda T, Goto T, Yano K, Soyano T, Kawaguchi M. The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2023; 13:995589. [PMID: 36733592 PMCID: PMC9888413 DOI: 10.3389/fpls.2022.995589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.
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Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Akiko Oda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Goto
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
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7
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Wu X, Wang Y, Ni Q, Li H, Wu X, Yuan Z, Xiao R, Ren Z, Lu J, Yun J, Wang Z, Li X. GmYSL7 controls iron uptake, allocation, and cellular response of nodules in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:167-187. [PMID: 36107150 DOI: 10.1111/jipb.13364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Iron (Fe) is essential for DNA synthesis, photosynthesis and respiration of plants. The demand for Fe substantially increases during legumes-rhizobia symbiotic nitrogen fixation because of the synthesis of leghemoglobin in the host and Fe-containing proteins in bacteroids. However, the mechanism by which plant controls iron transport to nodules remains largely unknown. Here we demonstrate that GmYSL7 serves as a key regulator controlling Fe uptake from root to nodule and distribution in soybean nodules. GmYSL7 is Fe responsive and GmYSL7 transports iron across the membrane and into the infected cells of nodules. Alterations of GmYSL7 substantially affect iron distribution between root and nodule, resulting in defective growth of nodules and reduced nitrogenase activity. GmYSL7 knockout increases the expression of GmbHLH300, a transcription factor required for Fe response of nodules. Overexpression of GmbHLH300 decreases nodule number, nitrogenase activity and Fe content in nodules. Remarkably, GmbHLH300 directly binds to the promoters of ENOD93 and GmLbs, which regulate nodule number and nitrogenase activity, and represses their transcription. Our data reveal a new role of GmYSL7 in controlling Fe transport from host root to nodule and Fe distribution in nodule cells, and uncover a molecular mechanism by which Fe affects nodule number and nitrogenase activity.
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Affiliation(s)
- Xinying Wu
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongliang Wang
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiaohan Ni
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haizhen Li
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuesong Wu
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhanxin Yuan
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Renhao Xiao
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziyin Ren
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingjing Lu
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxia Yun
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhijuan Wang
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xia Li
- National Key Laboratory of Crop Genetic and Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, 510642, China
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8
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Cervantes-Pérez SA, Thibivilliers S, Laffont C, Farmer AD, Frugier F, Libault M. Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume. MOLECULAR PLANT 2022; 15:1868-1888. [PMID: 36321199 DOI: 10.1016/j.molp.2022.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell types, showing the strongest differential regulation in response to a short-term (48 h) rhizobium inoculation, revealed not only known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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9
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Nasrollahi V, Yuan ZC, Lu QSM, McDowell T, Kohalmi SE, Hannoufa A. Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa. PLANT MOLECULAR BIOLOGY 2022; 110:511-529. [PMID: 35976552 PMCID: PMC9684250 DOI: 10.1007/s11103-022-01303-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/17/2022] [Indexed: 05/11/2023]
Abstract
Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Qing Shi Mimmie Lu
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada.
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10
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Intracellular infection by symbiotic bacteria requires the mitotic kinase AURORA1. Proc Natl Acad Sci U S A 2022; 119:e2202606119. [PMID: 36252014 PMCID: PMC9618073 DOI: 10.1073/pnas.2202606119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The subcellular events occurring in cells of legume plants as they form transcellular symbiotic-infection structures have been compared with those occurring in premitotic cells. Here, we demonstrate that Aurora kinase 1 (AUR1), a highly conserved mitotic regulator, is required for intracellular infection by rhizobia in Medicago truncatula. AUR1 interacts with microtubule-associated proteins of the TPXL and MAP65 families, which, respectively, activate and are phosphorylated by AUR1, and localizes with them within preinfection structures. MYB3R1, a rhizobia-induced mitotic transcription factor, directly regulates AUR1 through two closely spaced, mitosis-specific activator cis elements. Our data are consistent with a model in which the MYB3R1-AUR1 regulatory module serves to properly orient preinfection structures to direct the transcellular deposition of cell wall material for the growing infection thread, analogous to its role in cell plate formation. Our findings indicate that the eukaryotically conserved MYB3R1-TPXL-AUR1-MAP65 mitotic module was conscripted to support endosymbiotic infection in legumes.
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11
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Clúa J, Rípodas C, Roda C, Battaglia ME, Zanetti ME, Blanco FA. NIPK, a protein pseudokinase that interacts with the C subunit of the transcription factor NF-Y, is involved in rhizobial infection and nodule organogenesis. FRONTIERS IN PLANT SCIENCE 2022; 13:992543. [PMID: 36212340 PMCID: PMC9532615 DOI: 10.3389/fpls.2022.992543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Heterotrimeric Nuclear Factor Y (NF-Y) transcription factors are key regulators of the symbiotic program that controls rhizobial infection and nodule organogenesis. Using a yeast two-hybrid screening, we identified a putative protein kinase of Phaseolus vulgaris that interacts with the C subunit of the NF-Y complex. Physical interaction between NF-YC1 Interacting Protein Kinase (NIPK) and NF-YC1 occurs in the cytoplasm and the plasma membrane. Only one of the three canonical amino acids predicted to be required for catalytic activity is conserved in NIPK and its putative homologs from lycophytes to angiosperms, indicating that NIPK is an evolutionary conserved pseudokinase. Post-transcriptional silencing on NIPK affected infection and nodule organogenesis, suggesting NIPK is a positive regulator of the NF-Y transcriptional complex. In addition, NIPK is required for activation of cell cycle genes and early symbiotic genes in response to rhizobia, including NF-YA1 and NF-YC1. However, strain preference in co-inoculation experiments was not affected by NIPK silencing, suggesting that some functions of the NF-Y complex are independent of NIPK. Our work adds a new component associated with the NF-Y transcriptional regulators in the context of nitrogen-fixing symbiosis.
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12
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Shoot-to-root translocated GmNN1/FT2a triggers nodulation and regulates soybean nitrogen nutrition. PLoS Biol 2022; 20:e3001739. [PMID: 35969610 PMCID: PMC9410562 DOI: 10.1371/journal.pbio.3001739] [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: 11/14/2021] [Revised: 08/25/2022] [Accepted: 06/30/2022] [Indexed: 11/19/2022] Open
Abstract
Symbiotic nitrogen fixation (SNF) provides sufficient nitrogen (N) to meet most legume nutrition demands. In return, host plants feed symbionts carbohydrates produced in shoots. However, the molecular dialogue between shoots and symbionts remains largely mysterious. Here, we report the map-based cloning and characterization of a natural variation in GmNN1, the ortholog of Arabidopsis thaliana FLOWERING LOCUS T (FT2a) that simultaneously triggers nodulation in soybean and modulates leaf N nutrition. A 43-bp insertion in the promoter region of GmNN1/FT2a significantly decreased its transcription level and yielded N deficiency phenotypes. Manipulating GmNN1/GmFT2a significantly enhanced soybean nodulation, plant growth, and N nutrition. The near-isogenic lines (NILs) carrying low mRNA abundance alleles of GmNN1/FT2a, along with stable transgenic soybeans with CRISPR/Cas9 knockouts of GmNN1/FT2a, had yellower leaves, lower N concentrations, and fewer nodules than wild-type control plants. Grafting together with split-root experiments demonstrated that only shoot GmNN1/FT2a was responsible for regulating nodulation and thereby N nutrition through shoot-to-root translocation, and this process depends on rhizobial infection. After translocating into roots, shoot-derived GmNN1/FT2a was found to interact with GmNFYA-C (nuclear factor-Y subunit A-C) to activate symbiotic signaling through the previously reported GmNFYA-C-ENOD40 module. In short, the description of the critical soybean nodulation regulatory pathway outlined herein sheds novel insights into the shoot-to-root signaling required for communications between host plants and root nodulating symbionts. Symbiotic nitrogen fixation provides a vital nitrogen source in agroecosystems but nodulation is tightly controlled by a long-distance signaling system. This study uses map-based cloning to reveal GmNN1/FT2a as a new shoot-to-root mobile protein that significantly regulates nodule formation and thus nitrogen nutrition in soybean.
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13
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Chakraborty S, Harris JM. At the Crossroads of Salinity and Rhizobium-Legume Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:540-553. [PMID: 35297650 DOI: 10.1094/mpmi-09-21-0231-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Jeanne M Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
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14
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Jardinaud MF, Fromentin J, Auriac MC, Moreau S, Pecrix Y, Taconnat L, Cottret L, Aubert G, Balzergue S, Burstin J, Carrere S, Gamas P. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development. PLANT PHYSIOLOGY 2022; 189:1587-1607. [PMID: 35471237 PMCID: PMC9237690 DOI: 10.1093/plphys/kiac177] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2022] [Indexed: 05/31/2023]
Abstract
Rhizobium-legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
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Affiliation(s)
| | | | | | - Sandra Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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15
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Kovács S, Kiss E, Jenei S, Fehér-Juhász E, Kereszt A, Endre G. The Medicago truncatula IEF Gene Is Crucial for the Progression of Bacterial Infection During Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:401-415. [PMID: 35171648 DOI: 10.1094/mpmi-11-21-0279-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Legumes are able to meet their nitrogen need by establishing nitrogen-fixing symbiosis with rhizobia. Nitrogen fixation is performed by rhizobia, which has been converted to bacteroids, in newly formed organs, the root nodules. In the model legume Medicago truncatula, nodule cells are invaded by rhizobia through transcellular tubular structures called infection threads (ITs) that are initiated at the root hairs. Here, we describe a novel M. truncatula early symbiotic mutant identified as infection-related epidermal factor (ief), in which the formation of ITs is blocked in the root hair cells and only nodule primordia are formed. We show that the function of MtIEF is crucial for the bacterial infection in the root epidermis but not required for the nodule organogenesis. The IEF gene that appears to have been recruited for a symbiotic function after the duplication of a flower-specific gene is activated by the ERN1-branch of the Nod factor signal transduction pathway and independent of the NIN activity. The expression of MtIEF is induced transiently in the root epidermal cells by the rhizobium partner or Nod factors. Although its expression was not detectable at later stages of symbiosis, complementation experiments indicate that MtIEF is also required for the proper invasion of the nodule cells by rhizobia. The gene encodes an intracellular protein of unknown function possessing a coiled-coil motif and a plant-specific DUF761 domain. The IEF protein interacts with RPG, another symbiotic protein essential for normal IT development, suggesting that combined action of these proteins plays a role in nodule infection.[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)
- Szilárd Kovács
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ernő Kiss
- Biological Research Centre, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Sándor Jenei
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erzsébet Fehér-Juhász
- Biological Research Centre, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Attila Kereszt
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gabriella Endre
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
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16
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Wang D, Dong W, Murray J, Wang E. Innovation and appropriation in mycorrhizal and rhizobial Symbioses. THE PLANT CELL 2022; 34:1573-1599. [PMID: 35157080 PMCID: PMC9048890 DOI: 10.1093/plcell/koac039] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/20/2023]
Abstract
Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.
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Affiliation(s)
- Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wentao Dong
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Ertao Wang
- Authors for correspondence: (E.W) and (J.M.)
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17
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Auxin methylation by IAMT1, duplicated in the legume lineage, promotes root nodule development in Lotus japonicus. Proc Natl Acad Sci U S A 2022; 119:e2116549119. [PMID: 35235457 PMCID: PMC8915983 DOI: 10.1073/pnas.2116549119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance IAA carboxyl methyltransferase 1 (IAMT1) converts auxin (IAA) into its methyl ester (MeIAA). IAMT1 is reportedly critical for shoot development of the nonsymbiotic plant Arabidopsis. On the other hand, the function of IAMT1 in roots is unknown. Here, we found that IAMT1 is duplicated in the legume lineage, which evolved root nodule symbiosis. In the model legume Lotus japonicus, one of two paralogs (named IAMT1a) was mainly expressed in root epidermis, but its function is required in the adjacent cell layer, root cortex, where it promotes nodule development. Application of MeIAA, but not IAA, significantly induced NIN, a master regulator of nodule development, without rhizobia. These findings illuminate our understanding of intertissue communication acquired during evolution of root nodule symbiosis.
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18
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Rudaya ES, Kozyulina PY, Pavlova OA, Dolgikh AV, Ivanova AN, Dolgikh EA. Regulation of the Later Stages of Nodulation Stimulated by IPD3/CYCLOPS Transcription Factor and Cytokinin in Pea Pisum sativum L. PLANTS (BASEL, SWITZERLAND) 2021; 11:56. [PMID: 35009060 PMCID: PMC8747635 DOI: 10.3390/plants11010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022]
Abstract
The IPD3/CYCLOPS transcription factor was shown to be involved in the regulation of nodule primordia development and subsequent stages of nodule differentiation. In contrast to early stages, the stages related to nodule differentiation remain less studied. Recently, we have shown that the accumulation of cytokinin at later stages may significantly impact nodule development. This conclusion was based on a comparative analysis of cytokinin localization between pea wild type and ipd3/cyclops mutants. However, the role of cytokinin at these later stages of nodulation is still far from understood. To determine a set of genes involved in the regulation of later stages of nodule development connected with infection progress, intracellular accommodation, as well as plant tissue and bacteroid differentiation, the RNA-seq analysis of pea mutant SGEFix--2 (sym33) nodules impaired in these processes compared to wild type SGE nodules was performed. To verify cytokinin's influence on late nodule development stages, the comparative RNA-seq analysis of SGEFix--2 (sym33) mutant plants treated with cytokinin was also conducted. Findings suggest a significant role of cytokinin in the regulation of later stages of nodule development.
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Affiliation(s)
- Elizaveta S. Rudaya
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Polina Yu. Kozyulina
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Olga A. Pavlova
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Alexandra V. Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Alexandra N. Ivanova
- Komarov Botanical Institute RAS, Prof. Popov St., 2, 197376 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, Universitetskaya Emb. 7-9, 199034 St. Petersburg, Russia
| | - Elena A. Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
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19
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Kovacs S, Fodor L, Domonkos A, Ayaydin F, Laczi K, Rákhely G, Kalo P. Amino Acid Polymorphisms in the VHIID Conserved Motif of Nodulation Signaling Pathways 2 Distinctly Modulate Symbiotic Signaling and Nodule Morphogenesis in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:709857. [PMID: 34966395 PMCID: PMC8711286 DOI: 10.3389/fpls.2021.709857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
Legumes establish an endosymbiotic association with nitrogen-fixing soil bacteria. Following the mutual recognition of the symbiotic partner, the infection process is controlled by the induction of the signaling pathway and subsequent activation of symbiosis-related host genes. One of the protein complexes regulating nitrogen-fixing root nodule symbiosis is formed by GRAS domain regulatory proteins Nodulation Signaling Pathways 1 and 2 (NSP1 and NSP2) that control the expression of several early nodulation genes. Here, we report on a novel point mutant allele (nsp2-6) affecting the function of the NSP2 gene and compared the mutant with the formerly identified nsp2-3 mutant. Both mutants carry a single amino acid substitution in the VHIID motif of the NSP2 protein. We found that the two mutant alleles show dissimilar root hair response to bacterial infection. Although the nsp2-3 mutant developed aberrant infection threads, rhizobia were able to colonize nodule cells in this mutant. The encoded NSP2 proteins of the nsp2-3 and the novel nsp2 mutants interact with NSP1 diversely and, as a consequence, the activation of early nodulin genes and nodule organogenesis are arrested in the new nsp2 allele. The novel mutant with amino acid substitution D244H in NSP2 shows similar defects in symbiotic responses as a formerly identified nsp2-2 mutant carrying a deletion in the NSP2 gene. Additionally, we found that rhizobial strains induce delayed nodule formation on the roots of the ns2-3 weak allele. Our study highlights the importance of a conserved Asp residue in the VHIID motif of NSP2 that is required for the formation of a functional NSP1-NSP2 signaling module. Furthermore, our results imply the involvement of NSP2 during differentiation of symbiotic nodule cells.
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Affiliation(s)
- Szilárd Kovacs
- Institute of Plant Biology, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
| | - Lili Fodor
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllö, Hungary
| | - Agota Domonkos
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllö, Hungary
| | - Ferhan Ayaydin
- Hungarian Centre of Excellence for Molecular Medicine (HCEMM) Nonprofit Ltd., Szeged, Hungary
- Cellular Imaging Laboratory, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
| | - Krisztián Laczi
- Institute of Plant Biology, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
| | - Péter Kalo
- Institute of Plant Biology, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllö, Hungary
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20
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Pervent M, Lambert I, Tauzin M, Karouani A, Nigg M, Jardinaud MF, Severac D, Colella S, Martin-Magniette ML, Lepetit M. Systemic control of nodule formation by plant nitrogen demand requires autoregulation-dependent and independent mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7942-7956. [PMID: 34427647 DOI: 10.1093/jxb/erab374] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
In legumes interacting with rhizobia, the formation of symbiotic organs involved in the acquisition of atmospheric nitrogen gas (N2) is dependent on the plant nitrogen (N) demand. We used Medicago truncatula plants cultivated in split-root systems to discriminate between responses to local and systemic N signaling. We evidenced a strong control of nodule formation by systemic N signaling but obtained no clear evidence of a local control by mineral nitrogen. Systemic signaling of the plant N demand controls numerous transcripts involved in root transcriptome reprogramming associated with early rhizobia interaction and nodule formation. SUPER NUMERIC NODULES (SUNN) has an important role in this control, but we found that major systemic N signaling responses remained active in the sunn mutant. Genes involved in the activation of nitrogen fixation are regulated by systemic N signaling in the mutant, explaining why its hypernodulation phenotype is not associated with higher nitrogen fixation of the whole plant. We show that the control of transcriptome reprogramming of nodule formation by systemic N signaling requires other pathway(s) that parallel the SUNN/CLE (CLAVATA3/EMBRYO SURROUNDING REGION-LIKE PEPTIDES) pathway.
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Affiliation(s)
- Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Ilana Lambert
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Marc Tauzin
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Alicia Karouani
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Martha Nigg
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Marie-Françoise Jardinaud
- Laboratoire des Interactions Plantes Microorganismes INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Dany Severac
- MGX, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Stefano Colella
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Marie-Laure Martin-Magniette
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
- UMR MIA-Paris, AgroParisTech, INRAE, Université Paris-Saclay, Paris, France
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditérranéennes INRAE, IRD, CIRAD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, Sophia-Antipolis, France
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21
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Wang T, Guo J, Peng Y, Lyu X, Liu B, Sun S, Wang X. Light-induced mobile factors from shoots regulate rhizobium-triggered soybean root nodulation. Science 2021; 374:65-71. [PMID: 34591638 DOI: 10.1126/science.abh2890] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Symbiotic nitrogen fixation is an energy-expensive process, and the light available to plants has been proposed to be a primary influencer. We demonstrate that the light-induced soybean TGACG-motif binding factor 3/4 (GmSTF3/4) and FLOWERING LOCUS T (GmFTs), which move from shoots to roots, interdependently induce nodule organogenesis. Rhizobium-activated calcium- and calmodulin-dependent protein kinase (CCaMK) phosphorylates GmSTF3, triggering GmSTF3–GmFT2a complex formation, which directly activates expression of nodule inception (NIN) and nuclear factor Y (NF-YA1 and NF-YB1). Accordingly, the CCaMK–STF–FT module integrates aboveground light signals with underground symbiotic signaling, ensuring that the host plant informs its roots that the aboveground environment is prepared to sustainably supply the carbohydrate necessary for symbiosis. These results suggest approaches that could enhance the balance of carbon and nitrogen in the biosphere.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaqi Peng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiangguang Lyu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shiyong Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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22
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Gao JP, Xu P, Wang M, Zhang X, Yang J, Zhou Y, Murray JD, Song CP, Wang E. Nod factor receptor complex phosphorylates GmGEF2 to stimulate ROP signaling during nodulation. Curr Biol 2021; 31:3538-3550.e5. [PMID: 34216556 DOI: 10.1016/j.cub.2021.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 02/09/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022]
Abstract
The establishment of the symbiotic interaction between rhizobia and legumes involves the Nod factor signaling pathway. Nod factor recognition occurs through two plant receptors, NFR1 and NFR5. However, the signal transduction mechanisms downstream of NFR1-NFR5-mediated Nod factor perception remain largely unknown. Here, we report that a small guanosine triphosphatase (GTPase), GmROP9, and a guanine nucleotide exchange factor, GmGEF2, are involved in the soybean-rhizobium symbiosis. We show that GmNFR1α phosphorylates GmGEF2a at its N-terminal S86, which stimulates guanosine diphosphate (GDP)-to-GTP exchange to activate GmROP9 and that the active form of GmROP9 can associate with both GmNFR1α and GmNFR5α. We further show that a scaffold protein, GmRACK1, interacts with active GmROP9 and contributes to root nodule symbiosis. Collectively, our results highlight the symbiotic role of GmROP9-GmRACK1 and support the hypothesis that rhizobial signals promote the formation of a protein complex comprising GmNFR1, GmNFR5, GmROP9, and GmRACK1 for symbiotic signal transduction in soybean.
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Affiliation(s)
- Jin-Peng Gao
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Peng Xu
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yun Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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23
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Chakraborty S, Driscoll HE, Abrahante JE, Zhang F, Fisher RF, Harris JM. Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:904-921. [PMID: 33819071 PMCID: PMC8578154 DOI: 10.1094/mpmi-01-21-0019-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heather E. Driscoll
- Vermont Biomedical Research Network (VBRN), Department of Biology, Norwich University, Northfield, Vermont 05663, USA
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute (UMII) (CCRB 1-210C), 2231 6th Street SE, Minneapolis, MN 55455, USA
| | - Fan Zhang
- Vermont Biomedical Research Network (VBRN), Department of Biology, University of Vermont, Burlington, Vermont 05405, USA
- Institute for Translational Research and Department of family medicine, University of North Texas Health Science Center, Fort Worth, TX, 76107
| | - Robert F. Fisher
- Stanford University, Department of Biology, 371 Serra Mall, Stanford, California 94305-5020, USA
| | - Jeanne M. Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Corresponding author: Jeanne M. Harris ()
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24
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Translational regulation in pathogenic and beneficial plant-microbe interactions. Biochem J 2021; 478:2775-2788. [PMID: 34297042 DOI: 10.1042/bcj20210066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022]
Abstract
Plants are surrounded by a vast diversity of microorganisms. Limiting pathogenic microorganisms is crucial for plant survival. On the other hand, the interaction of plants with beneficial microorganisms promotes their growth or allows them to overcome nutrient deficiencies. Balancing the number and nature of these interactions is crucial for plant growth and development, and thus, for crop productivity in agriculture. Plants use sophisticated mechanisms to recognize pathogenic and beneficial microorganisms and genetic programs related to immunity or symbiosis. Although most research has focused on characterizing changes in the transcriptome during plant-microbe interactions, the application of techniques such as Translating Ribosome Affinity Purification (TRAP) and Ribosome profiling allowed examining the dynamic association of RNAs to the translational machinery, highlighting the importance of the translational level of control of gene expression in both pathogenic and beneficial interactions. These studies revealed that the transcriptional and the translational responses are not always correlated, and that translational control operates at cell-specific level. In addition, translational control is governed by cis-elements present in the 5'mRNA leader of regulated mRNAs, e.g. upstream open reading frames (uORFs) and sequence-specific motifs. In this review, we summarize and discuss the recent advances made in the field of translational control during pathogenic and beneficial plant-microbe interactions.
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25
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Kawaharada Y, Sandal N, Gupta V, Jin H, Kawaharada M, Taniuchi M, Ruman H, Nadzieja M, Andersen KR, Schneeberger K, Stougaard J, Andersen SU. Natural variation identifies a Pxy gene controlling vascular organisation and formation of nodules and lateral roots in Lotus japonicus. THE NEW PHYTOLOGIST 2021; 230:2459-2473. [PMID: 33759450 DOI: 10.1111/nph.17356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Forward and reverse genetics using the model legumes Lotus japonicus and Medicago truncatula have been instrumental in identifying the essential genes governing legume-rhizobia symbiosis. However, little information is known about the effects of intraspecific variation on symbiotic signalling. Here, we use quantitative trait locus sequencing (QTL-seq) to investigate the genetic basis of the differentiated phenotypic responses shown by the Lotus accessions Gifu and MG20 to inoculation with the Mesorhizobium loti exoU mutant that produces truncated exopolysaccharides. We identified through genetic complementation the Pxy gene as a component of this differential exoU response. Lotus Pxy encodes a leucine-rich repeat receptor-like kinase similar to Arabidopsis thaliana PXY, which regulates stem vascular development. We show that Lotus pxy insertion mutants displayed defects in root and stem vascular organisation, as well as lateral root and nodule formation. Our work links Pxy to de novo organogenesis in the root, highlights the genetic overlap between regulation of lateral root and nodule formation, and demonstrates that natural variation in Pxy affects nodulation signalling.
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Affiliation(s)
- Yasuyuki Kawaharada
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Maya Kawaharada
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Makoto Taniuchi
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Hafijur Ruman
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Korbinian Schneeberger
- Department for Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
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26
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Structure and Development of the Legume-Rhizobial Symbiotic Interface in Infection Threads. Cells 2021; 10:cells10051050. [PMID: 33946779 PMCID: PMC8146911 DOI: 10.3390/cells10051050] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The intracellular infection thread initiated in a root hair cell is a unique structure associated with Rhizobium-legume symbiosis. It is characterized by inverted tip growth of the plant cell wall, resulting in a tunnel that allows invasion of host cells by bacteria during the formation of the nitrogen-fixing root nodule. Regulation of the plant-microbial interface is essential for infection thread growth. This involves targeted deposition of the cell wall and extracellular matrix and tight control of cell wall remodeling. This review describes the potential role of different actors such as transcription factors, receptors, and enzymes in the rearrangement of the plant-microbial interface and control of polar infection thread growth. It also focuses on the composition of the main polymers of the infection thread wall and matrix and the participation of reactive oxygen species (ROS) in the development of the infection thread. Mutant analysis has helped to gain insight into the development of host defense reactions. The available data raise many new questions about the structure, function, and development of infection threads.
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27
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Kirolinko C, Hobecker K, Wen J, Mysore KS, Niebel A, Blanco FA, Zanetti ME. Auxin Response Factor 2 (ARF2), ARF3, and ARF4 Mediate Both Lateral Root and Nitrogen Fixing Nodule Development in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:659061. [PMID: 33897748 PMCID: PMC8060633 DOI: 10.3389/fpls.2021.659061] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Auxin Response Factors (ARFs) constitute a large family of transcription factors that mediate auxin-regulated developmental programs in plants. ARF2, ARF3, and ARF4 are post-transcriptionally regulated by the microRNA390 (miR390)/trans-acting small interference RNA 3 (TAS3) module through the action of TAS3-derived trans - acting small interfering RNAs (ta-siRNA). We have previously reported that constitutive activation of the miR390/TAS3 pathway promotes elongation of lateral roots but impairs nodule organogenesis and infection by rhizobia during the nitrogen-fixing symbiosis established between Medicago truncatula and its partner Sinorhizobium meliloti. However, the involvement of the targets of the miR390/TAS3 pathway, i.e., MtARF2, MtARF3, MtARF4a, and MtARF4b, in root development and establishment of the nitrogen-fixing symbiosis remained unexplored. Here, promoter:reporter fusions showed that expression of both MtARF3 and MtARF4a was associated with lateral root development; however, only the MtARF4a promoter was active in developing nodules. In addition, up-regulation of MtARF2, MtARF3, and MtARF4a/b in response to rhizobia depends on Nod Factor perception. We provide evidence that simultaneous knockdown of MtARF2, MtARF3, MtARF4a, and MtARF4b or mutation in MtARF4a impaired nodule formation, and reduced initiation and progression of infection events. Silencing of MtARF2, MtARF3, MtARF4a, and MtARF4b altered mRNA levels of the early nodulation gene nodulation signaling pathway 2 (MtNSP2). In addition, roots with reduced levels of MtARF2, MtARF3, MtARF4a, and MtARF4b, as well as arf4a mutant plants exhibited altered root architecture, causing a reduction in primary and lateral root length, but increasing lateral root density. Taken together, our results suggest that these ARF members are common key players of the morphogenetic programs that control root development and the formation of nitrogen-fixing nodules.
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Affiliation(s)
- Cristina Kirolinko
- Instituto de Biotecnología y Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - Jiangqi Wen
- Noble Research Institute LLC, Ardmore, OK, United States
| | | | - Andreas Niebel
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
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28
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Xu H, Li Y, Zhang K, Li M, Fu S, Tian Y, Qin T, Li X, Zhong Y, Liao H. miR169c-NFYA-C-ENOD40 modulates nitrogen inhibitory effects in soybean nodulation. THE NEW PHYTOLOGIST 2021; 229:3377-3392. [PMID: 33245793 DOI: 10.1111/nph.17115] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 11/12/2020] [Indexed: 05/29/2023]
Abstract
Legume crops contribute a great portion of clean nitrogen (N) to agro-ecosystems through symbiotic N2 fixation in the nodule; however, the nodulation is always inhibited by high N availability which is known as the N inhibitory effect through largely unknown mechanisms. We functionally investigated miR169c-GmNFYA-C-GmENOD40 under multiple N conditions in soybean (Glycine max) (ENOD, Early Nodulin; NFYA, Nuclear Factor-Y Subunit A). We elucidated their regulatory roles in soybean nodulation through analyzing expression patterns, micro-messenger RNA (miRNA-mRNA) interactions, phenotypes of transgenic soybean plants and genetic interactions. We found that miR169c expression was induced by high N, whereas its target GmNFYA-C was preferentially expressed in nodules and induced by rhizobium inoculation. Overexpression of miR169c inhibited nodulation through targeting 3'-UTR of GmNFYA-C, whereas knockout miR169c through CRISPR-cas9 promoted nodulation. However, overexpression of GmNFYA-C promoted soybean nodulation through facilitating rhizobium infection and increasing the expression of symbiotic signaling gene GmENOD40. Besides, GmNFYA-C directly induced the expression of GmENOD40. In addition, overexpression of GmNFYA-C without the target site of miR169c partially attenuated the inhibitory effect of high N on soybean nodulation. We discovered a new regulatory pathway involving the miR169c-NFYA-C-ENOD40 module that regulates soybean nodulation in response to N availability. This pathway provides substantial new insights into the mechanisms underlying the N inhibitory effect on nodulation.
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Affiliation(s)
- Hanyu Xu
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanjun Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kefei Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingjia Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siyuan Fu
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingzhe Tian
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tongfei Qin
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinxin Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongjia Zhong
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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29
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Peng Z, Chen H, Tan L, Shu H, Varshney RK, Zhou Z, Zhao Z, Luo Z, Chitikineni A, Wang L, Maku J, López Y, Gallo M, Zhou H, Wang J. Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1104-1118. [PMID: 33130897 DOI: 10.1093/jxb/eraa505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Lubin Tan
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Hongmei Shu
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Zhekai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - James Maku
- Sciences and Mathematics Department, Glenville State College, Glenville, WV, USA
| | - Yolanda López
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Maria Gallo
- Delaware Valley University, Doylestown, PA, USA
| | - Hai Zhou
- Agronomy Department, University of Florida, Gainesville, FL, USA
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA
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Chaulagain D, Frugoli J. The Regulation of Nodule Number in Legumes Is a Balance of Three Signal Transduction Pathways. Int J Mol Sci 2021; 22:1117. [PMID: 33498783 PMCID: PMC7866212 DOI: 10.3390/ijms22031117] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen is a major determinant of plant growth and productivity and the ability of legumes to form a symbiotic relationship with nitrogen-fixing rhizobia bacteria allows legumes to exploit nitrogen-poor niches in the biosphere. But hosting nitrogen-fixing bacteria comes with a metabolic cost, and the process requires regulation. The symbiosis is regulated through three signal transduction pathways: in response to available nitrogen, at the initiation of contact between the organisms, and during the development of the nodules that will host the rhizobia. Here we provide an overview of our knowledge of how the three signaling pathways operate in space and time, and what we know about the cross-talk between symbiotic signaling for nodule initiation and organogenesis, nitrate dependent signaling, and autoregulation of nodulation. Identification of common components and points of intersection suggest directions for research on the fine-tuning of the plant's response to rhizobia.
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Affiliation(s)
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA;
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31
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Capstaff NM, Morrison F, Cheema J, Brett P, Hill L, Muñoz-García JC, Khimyak YZ, Domoney C, Miller AJ. Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5689-5704. [PMID: 32599619 PMCID: PMC7501823 DOI: 10.1093/jxb/eraa283] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/15/2020] [Indexed: 05/27/2023]
Abstract
The use of potential biostimulants is of broad interest in plant science for improving yields. The application of a humic derivative called fulvic acid (FA) may improve forage crop production. FA is an uncharacterized mixture of chemicals and, although it has been reported to increase growth parameters in many species including legumes, its mode of action remains unclear. Previous studies of the action of FA have lacked appropriate controls, and few have included field trials. Here we report yield increases due to FA application in three European Medicago sativa cultivars, in studies which include the appropriate nutritional controls which hitherto have not been used. No significant growth stimulation was seen after FA treatment in grass species in this study at the treatment rate tested. Direct application to bacteria increased Rhizobium growth and, in M. sativa trials, root nodulation was stimulated. RNA transcriptional analysis of FA-treated plants revealed up-regulation of many important early nodulation signalling genes after only 3 d. Experiments in plate, glasshouse, and field environments showed yield increases, providing substantial evidence for the use of FA to benefit M. sativa forage production.
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Affiliation(s)
- Nicola M Capstaff
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Freddie Morrison
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Jitender Cheema
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Lionel Hill
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Juan C Muñoz-García
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Claire Domoney
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Anthony J Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, UK
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Laffont C, Ivanovici A, Gautrat P, Brault M, Djordjevic MA, Frugier F. The NIN transcription factor coordinates CEP and CLE signaling peptides that regulate nodulation antagonistically. Nat Commun 2020; 11:3167. [PMID: 32576831 PMCID: PMC7311451 DOI: 10.1038/s41467-020-16968-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/31/2020] [Indexed: 12/14/2022] Open
Abstract
Legumes tightly regulate nodule number to balance the cost of supporting symbiotic rhizobia with the benefits of nitrogen fixation. C-terminally Encoded Peptides (CEPs) and CLAVATA3-like (CLE) peptides positively and negatively regulate nodulation, respectively, through independent systemic pathways, but how these regulations are coordinated remains unknown. Here, we show that rhizobia, Nod Factors, and cytokinins induce a symbiosis-specific CEP gene, MtCEP7, which positively regulates rhizobial infection. Via grafting and split root studies, we reveal that MtCEP7 increases nodule number systemically through the MtCRA2 receptor. MtCEP7 and MtCLE13 expression in rhizobia-inoculated roots rely on the MtCRE1 cytokinin receptor and on the MtNIN transcription factor. MtNIN binds and transactivates MtCEP7 and MtCLE13, and a NIN Binding Site (NBS) identified within the proximal MtCEP7 promoter is required for its symbiotic activation. Overall, these results demonstrate that a cytokinin-MtCRE1-MtNIN regulatory module coordinates the expression of two antagonistic, symbiosis-related, peptide hormones from different families to fine-tune nodule number. CLE and CEP peptides regulate rhizobial symbiosis in legumes to balance the benefits of nitrogen fixation with the metabolic costs of nodule production. Here Laffont et al. show that cytokinin and bacterial Nod factors induce Medicago CEP7 which acts antagonistically to CLE13 to fine-tune nodulation.
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Affiliation(s)
- Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Pierre Gautrat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mathias Brault
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michael Anthony Djordjevic
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France.
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33
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Feng K, Hou XL, Xing GM, Liu JX, Duan AQ, Xu ZS, Li MY, Zhuang J, Xiong AS. Advances in AP2/ERF super-family transcription factors in plant. Crit Rev Biotechnol 2020; 40:750-776. [PMID: 32522044 DOI: 10.1080/07388551.2020.1768509] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.
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Affiliation(s)
- Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guo-Ming Xing
- Collaborative Innovation Center for Improving Quality and Increased Profits of Protected Vegetables in Shanxi, Taigu, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Traubenik S, Reynoso MA, Hobecker K, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco F, Zanetti ME. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs. THE PLANT CELL 2020; 32:352-373. [PMID: 31748328 PMCID: PMC7008484 DOI: 10.1105/tpc.19.00647] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied translating ribosome affinity purification combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen-fixing symbiosis established between Medicago truncatula and Sinorhizobium meliloti Our analysis revealed a poor correlation between transcriptional and translational changes and identified hundreds of regulated protein-coding and long noncoding RNAs (lncRNAs), some of which are regulated in specific cell types. We demonstrated that a short variant of the lncRNA Trans-acting small interference RNA3 (TAS3) increased its association to the translational machinery in response to rhizobia. Functional analysis revealed that this short variant of TAS3 might act as a target mimic that captures microRNA390, contributing to reduce trans acting small interference Auxin Response Factor production and modulating nodule formation and rhizobial infection. The analysis of alternative transcript variants identified a translationally upregulated mRNA encoding subunit 3 of the SUPERKILLER complex (SKI3), which participates in mRNA decay. Knockdown of SKI3 decreased nodule initiation and development, as well as the survival of bacteria within nodules. Our results highlight the importance of translational control and mRNA decay pathways for the successful establishment of the nitrogen-fixing symbiosis.
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Affiliation(s)
- Soledad Traubenik
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Mauricio Alberto Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Marcos Lancia
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Maureen Hummel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | | | | | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
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35
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Kumar A, Cousins DR, Liu CW, Xu P, Murray JD. Nodule Inception Is Not Required for Arbuscular Mycorrhizal Colonization of Medicago truncatula. PLANTS 2020; 9:plants9010071. [PMID: 31935845 PMCID: PMC7020461 DOI: 10.3390/plants9010071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 11/29/2022]
Abstract
Most legumes can engage in symbiosis with N-fixing bacteria called rhizobia. This symbiosis, called nodulation, evolved from the more widespread symbiosis that most land plants form with arbuscular mycorrhiza, which is reflected in a common requirement of certain genes for both these symbioses. One key nodulation gene, Nodule Inception (NIN), has been intensively studied. Mutants in NIN are unable to form nodules, which has made it difficult to identify downstream genes under the control of NIN. The analysis of data from our recent transcriptomics study revealed that some genes with an altered expression of nin during nodulation are upregulated in mycorrhizal roots. In addition, another study reported the decreased colonization of nin roots by arbuscular mycorrhiza. We therefore investigated a role for NIN in mycorrhiza formation. Our time course study, using two nin alleles with differing genetic backgrounds, suggests that that loss of NIN does not affect colonization of Medicago truncatula roots, either in the presence or absence of rhizobia. This, and recent phylogenetic analyses showing that the loss of NIN is correlated with loss of nodulation in the FaFaCuRo clade, but not with the ability to form mycorrhiza, argue against NIN being required for arbuscular mycorrhization in legumes.
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Affiliation(s)
- Anil Kumar
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Donna R. Cousins
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.R.C.); (C.-W.L.)
| | - Cheng-Wu Liu
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.R.C.); (C.-W.L.)
| | - Ping Xu
- Shanghai Engineering Research Center of Plant Germplasm Resource, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Correspondence: (P.X.); (J.D.M.)
| | - Jeremy D. Murray
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (D.R.C.); (C.-W.L.)
- Correspondence: (P.X.); (J.D.M.)
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36
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Mergaert P, Kereszt A, Kondorosi E. Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants. THE PLANT CELL 2020; 32:42-68. [PMID: 31712407 PMCID: PMC6961632 DOI: 10.1105/tpc.19.00494] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/08/2019] [Indexed: 05/06/2023]
Abstract
Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs that function in the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells carrying thousands of intracellular bacteria without signs of immune responses, and the integration of symbiont and host metabolism. The early stages of nodulation are governed by a few well-defined functions, which together constitute the common symbiosis-signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in symbiotic cells. Many of these genes are only active in symbiotic cells, reflecting the unique nature of nodules as plant structures. Although how the nodule-specific transcriptome is activated and connected to early CSSP-signaling is poorly understood, candidate TFs have been identified using transcriptomic approaches, and the importance of epigenetic and chromatin-based regulation has been demonstrated. We discuss how gene regulation analyses have advanced our understanding of nodule organogenesis, the functioning of symbiotic cells, and the evolution of symbiosis in the NFC.
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Affiliation(s)
- Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Attila Kereszt
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| | - Eva Kondorosi
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
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37
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Kirienko AN, Dolgikh EA. Studying the effect of tissue-specific expression of the K1 gene encoding LysM-receptor-like kinase on the development of symbiosis in peas. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202303005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
To study the role of pea LysM receptor-like kinase K1 in the coordination of the infection process, starting in epidermis and nodule organogenesis in the root cortex of plants, during the development of rhizobium-legume symbiosis, the genetic constructs in which K1 gene was cloned under the control of tissue-specific promoter pLeEXT1 of tomato Lycopersicon esculentum extensin gene and the constitutive promoter of cauliflower mosaic virus (CaMV35S, cauliflower mosaic virus 35S) were obtained. During the transformation of the Nod- mutant line, the k1-1, with two types of constructs, the restoration of nodule formation was observed, which indicated the possible participation of K1 in the control not only early, but also later stages of symbiosis development in pea.
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38
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Shen D, Bisseling T. The Evolutionary Aspects of Legume Nitrogen-Fixing Nodule Symbiosis. Results Probl Cell Differ 2020; 69:387-408. [PMID: 33263880 DOI: 10.1007/978-3-030-51849-3_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nitrogen-fixing root nodule symbiosis can sustain the development of the host plants under nitrogen-limiting conditions. Such symbiosis occurs only in a clade of angiosperms known as the nitrogen-fixing clade (NFC). It has long been proposed that root nodule symbiosis evolved several times (in parallel) in the NFC. Two recent phylogenomic studies compared the genomes of nodulating and related non-nodulating species across the four orders of the NFC and found that genes essential for nodule formation are lost or pseudogenized in the non-nodulating species. As these symbiosis genes are specifically involved in the symbiotic interaction, it means that the presence of pseudogenes and the loss of symbiosis genes strongly suggest that their ancestor, which still had functional genes, most likely had a symbiosis with nitrogen-fixing bacteria. These findings agree with the hypothesis that nodulation evolved once at the common ancestor of the NFC, and challenge the hypothesis of parallel evolution. In this chapter, we will cover the current understandings on actinorhizal-type and legume nodule development, and discuss the evolution of the legume nodule type.
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Affiliation(s)
- Defeng Shen
- Laboratory of Molecular Biology, Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands.
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Roy S, Liu W, Nandety RS, Crook A, Mysore KS, Pislariu CI, Frugoli J, Dickstein R, Udvardi MK. Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation. THE PLANT CELL 2020; 32:15-41. [PMID: 31649123 PMCID: PMC6961631 DOI: 10.1105/tpc.19.00279] [Citation(s) in RCA: 337] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/17/2019] [Accepted: 10/24/2019] [Indexed: 05/13/2023]
Abstract
Since 1999, various forward- and reverse-genetic approaches have uncovered nearly 200 genes required for symbiotic nitrogen fixation (SNF) in legumes. These discoveries advanced our understanding of the evolution of SNF in plants and its relationship to other beneficial endosymbioses, signaling between plants and microbes, the control of microbial infection of plant cells, the control of plant cell division leading to nodule development, autoregulation of nodulation, intracellular accommodation of bacteria, nodule oxygen homeostasis, the control of bacteroid differentiation, metabolism and transport supporting symbiosis, and the control of nodule senescence. This review catalogs and contextualizes all of the plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean). We also briefly consider the future of SNF genetics in the era of pan-genomics and genome editing.
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Affiliation(s)
- Sonali Roy
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Wei Liu
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Ashley Crook
- College of Science, Clemson University, Clemson, South Carolina 29634
| | | | | | - Julia Frugoli
- College of Science, Clemson University, Clemson, South Carolina 29634
| | - Rebecca Dickstein
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton Texas 76203
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40
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Liu M, Soyano T, Yano K, Hayashi M, Kawaguchi M. ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus. JOURNAL OF PLANT RESEARCH 2019; 132:641-653. [PMID: 31313020 DOI: 10.1007/s10265-019-01122-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Legumes engage in symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia, under nitrogen-limited conditions. In many legumes, the root invasion of rhizobia is mediated by infection threads (ITs), tubular invaginations of the host cell wall and plasma membrane, developed from infection foci of deformed root hairs. IT formation is regulated by a series of signal transduction in host root. Nodulation signals activate the host transcription factor (TF), CYCLOPS, which directly induces expression of two TF genes, ERF REQUIRED FOR NODULATION1 (ERN1) and NODULE INCEPTION (NIN), essential for IT development. Here, we explored the relationship among these three symbiotic TF genes in the model legume Lotus japonicus and examined how their interplay contributes to IT formation. qRT-PCR analysis showed that NIN expression induced by rhizobial infection was attenuated in ern1-1, and further declined in cyclops-3 ern1-1. ERN1 overexpression led to induction of NIN expression in cyclops-3 ern1-1 in the presence of rhizobia. Thus, in addition to CYCLOPS, ERN1 is able to increase the NIN expression level depending on infection. Furthermore, consistent with this transcriptional hierarchy, ectopic expression of ERN1 as well as NIN suppressed the IT-deficient cyclops-3 phenotype, but ERN1 failed to confer ITs in the nin-2 root. However, the ern1-1 symbiotic epidermal phenotype was not suppressed by the NIN ectopic expression. The cyclops-3 ern1-1 double mutant was less sensitive to rhizobial infection than the single mutants and defective in the symbiotic root hair response at earlier stages. This more severe phenotype of the double mutant suggests a role for ERN1 that independent of the CYCLOPS-mediated transcriptional regulation. We conclude that ERN1 is involved in regulating NIN expression in addition to CYCLOPS, and these TFs coordinately promote the symbiotic root hair response and IT development. Our data help to reveal the extensive role of ERN1 in root nodule symbiosis signaling.
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Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan.
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41
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Zhang L, Yuan L, Staehelin C, Li Y, Ruan J, Liang Z, Xie Z, Wang W, Xie J, Huang S. The LYSIN MOTIF-CONTAINING RECEPTOR-LIKE KINASE 1 protein of banana is required for perception of pathogenic and symbiotic signals. THE NEW PHYTOLOGIST 2019; 223:1530-1546. [PMID: 31059122 DOI: 10.1111/nph.15888] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/27/2019] [Indexed: 05/28/2023]
Abstract
How plants can distinguish pathogenic and symbiotic fungi remains largely unknown. Here, we characterized the role of MaLYK1, a lysin motif receptor kinase of banana. Live cell imaging techniques were used in localization studies. RNA interference (RNAi)-silenced transgenic banana plants were generated to analyze the biological role of MaLYK1. The MaLYK1 ectodomain, chitin beads, chitooligosaccharides (COs) and mycorrhizal lipochitooligosaccharides (Myc-LCOs) were used in pulldown assays. Ligand-induced MaLYK1 complex formation was tested in immunoprecipitation experiments. Chimeric receptors were expressed in Lotus japonicus to characterize the function of the MaLYK1 kinase domain. MaLYK1 was localized to the plasma membrane. MaLYK1 expression was induced by Foc4 (Fusarium oxysporum f. sp. cubense race 4) and diverse microbe-associated molecular patterns. MaLYK1-silenced banana lines showed reduced chitin-triggered defense responses, increased Foc4-induced disease symptoms and reduced mycorrhization. The MaLYK1 ectodomain was pulled down by chitin beads and LCOs or COs impaired this process. Ligand treatments induced MaLYK1 complex formation in planta. The kinase domain of MaLYK1 could functionally replace that of the chitin elicitor receptor kinase 1 (AtCERK1) in Arabidopsis thaliana and of a rhizobial LCO (Nod factor) receptor (LjNFR1) in L. japonicus. MaLYK1 represents a central molecular switch that controls defense- and symbiosis-related signaling.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Liangbin Yuan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhiping Xie
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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42
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Liu CW, Breakspear A, Stacey N, Findlay K, Nakashima J, Ramakrishnan K, Liu M, Xie F, Endre G, de Carvalho-Niebel F, Oldroyd GED, Udvardi MK, Fournier J, Murray JD. A protein complex required for polar growth of rhizobial infection threads. Nat Commun 2019; 10:2848. [PMID: 31253759 PMCID: PMC6599036 DOI: 10.1038/s41467-019-10029-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
During root nodule symbiosis, intracellular accommodation of rhizobia by legumes is a prerequisite for nitrogen fixation. For many legumes, rhizobial colonization initiates in root hairs through transcellular infection threads. In Medicago truncatula, VAPYRIN (VPY) and a putative E3 ligase LUMPY INFECTIONS (LIN) are required for infection thread development but their cellular and molecular roles are obscure. Here we show that LIN and its homolog LIN-LIKE interact with VPY and VPY-LIKE in a subcellular complex localized to puncta both at the tip of the growing infection thread and at the nuclear periphery in root hairs and that the punctate accumulation of VPY is positively regulated by LIN. We also show that an otherwise nuclear and cytoplasmic exocyst subunit, EXO70H4, systematically co-localizes with VPY and LIN during rhizobial infection. Genetic analysis shows that defective rhizobial infection in exo70h4 is similar to that in vpy and lin. Our results indicate that VPY, LIN and EXO70H4 are part of the symbiosis-specific machinery required for polar growth of infection threads.
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Affiliation(s)
- Cheng-Wu Liu
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Andrew Breakspear
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicola Stacey
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kim Findlay
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jin Nakashima
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | | | - Miaoxia Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gabriella Endre
- Institute of Plant Biology, Biological Research Centre, Szeged, 6726, Hungary
| | | | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Michael K Udvardi
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Joëlle Fournier
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France.
| | - Jeremy D Murray
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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43
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Zhang Z, Ke D, Hu M, Zhang C, Deng L, Li Y, Li J, Zhao H, Cheng L, Wang L, Yuan H. Quantitative phosphoproteomic analyses provide evidence for extensive phosphorylation of regulatory proteins in the rhizobia-legume symbiosis. PLANT MOLECULAR BIOLOGY 2019; 100:265-283. [PMID: 30989446 DOI: 10.1007/s11103-019-00857-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of grain legumes is essential for high yielding. Protein phosphorylation/dephosphorylation plays important role in root nodule development. Differences in the phosphoproteomes may either be developmental specific and related to nitrogen fixation activity. An iTRAQ-based quantitative phosphoproteomic analyses during nodule development enables identification of specific phosphorylation signaling in the Lotus-rhizobia symbiosis. During evolution, legumes (Fabaceae) have evolved a symbiotic relationship with rhizobia, which fix atmospheric nitrogen and produce ammonia that host plants can then absorb. Root nodule development depends on the activation of protein phosphorylation-mediated signal transduction cascades. To investigate possible molecular mechanisms of protein modulation during nodule development, we used iTRAQ-based quantitative proteomic analyses to identify root phosphoproteins during rhizobial colonization and infection of Lotus japonicus. 1154 phosphoproteins with 2957 high-confidence phosphorylation sites were identified. Gene ontology enrichment analysis of functional groups of these genes revealed that the biological processes mediated by these proteins included cellular processes, signal transduction, and transporter activity. Quantitative data highlighted the dynamics of protein phosphorylation during nodule development and, based on regulatory trends, seven groups were identified. RNA splicing and brassinosteroid (BR) signaling pathways were extensively affected by phosphorylation, and most Ser/Arg-rich (SR) proteins were multiply phosphorylated. In addition, many proposed kinase-substrate pairs were predicted, and in these MAPK6 substrates were found to be highly enriched. This study offers insights into the regulatory processes underlying nodule development, provides an accessible resource cataloging the phosphorylation status of thousands of Lotus proteins during nodule development, and develops our understanding of post-translational regulatory mechanisms in the Lotus-rhizobia symbiosis.
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Affiliation(s)
- Zaibao Zhang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Danxia Ke
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Menghui Hu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Chi Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lijun Deng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Yuting Li
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Jiuli Li
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Hai Zhao
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Cheng
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Lei Wang
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Hongyu Yuan
- Henan Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, Henan, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
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44
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Liu CW, Breakspear A, Guan D, Cerri MR, Jackson K, Jiang S, Robson F, Radhakrishnan GV, Roy S, Bone C, Stacey N, Rogers C, Trick M, Niebel A, Oldroyd GED, de Carvalho-Niebel F, Murray JD. NIN Acts as a Network Hub Controlling a Growth Module Required for Rhizobial Infection. PLANT PHYSIOLOGY 2019; 179:1704-1722. [PMID: 30710053 PMCID: PMC6446755 DOI: 10.1104/pp.18.01572] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/20/2019] [Indexed: 05/22/2023]
Abstract
The symbiotic infection of root cells by nitrogen-fixing rhizobia during nodulation requires the transcription factor Nodule Inception (NIN). Our root hair transcriptomic study extends NIN's regulon to include Rhizobium Polar Growth and genes involved in cell wall modification, gibberellin biosynthesis, and a comprehensive group of nutrient (N, P, and S) uptake and assimilation genes, suggesting that NIN's recruitment to nodulation was based on its role as a growth module, a role shared with other NIN-Like Proteins. The expression of jasmonic acid genes in nin suggests the involvement of NIN in the resolution of growth versus defense outcomes. We find that the regulation of the growth module component Nodulation Pectate Lyase by NIN, and its function in rhizobial infection, are conserved in hologalegina legumes, highlighting its recruitment as a major event in the evolution of nodulation. We find that Nodulation Pectate Lyase is secreted to the infection chamber and the lumen of the infection thread. Gene network analysis using the transcription factor mutants for ERF Required for Nodulation1 and Nuclear Factor-Y Subunit A1 confirms hierarchical control of NIN over Nuclear Factor-Y Subunit A1 and shows that ERF Required for Nodulation1 acts independently to control infection. We conclude that while NIN shares functions with other NIN-Like Proteins, the conscription of key infection genes to NIN's control has made it a central regulatory hub for rhizobial infection.
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Affiliation(s)
- Cheng-Wu Liu
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andrew Breakspear
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Dian Guan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marion R Cerri
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Kirsty Jackson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Suyu Jiang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Centre of Excellence for Plant and Microbial Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fran Robson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Guru V Radhakrishnan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sonali Roy
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Caitlin Bone
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Nicola Stacey
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Christian Rogers
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andreas Niebel
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giles E D Oldroyd
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Fernanda de Carvalho-Niebel
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Jeremy D Murray
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Centre of Excellence for Plant and Microbial Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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45
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Karmakar K, Kundu A, Rizvi AZ, Dubois E, Severac D, Czernic P, Cartieaux F, DasGupta M. Transcriptomic Analysis With the Progress of Symbiosis in 'Crack-Entry' Legume Arachis hypogaea Highlights Its Contrast With 'Infection Thread' Adapted Legumes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:271-285. [PMID: 30109978 DOI: 10.1094/mpmi-06-18-0174-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In root-nodule symbiosis, rhizobial invasion and nodule organogenesis is host controlled. In most legumes, rhizobia enter through infection threads and nodule primordium in the cortex is induced from a distance. But in dalbergoid legumes like Arachis hypogaea, rhizobia directly invade cortical cells through epidermal cracks to generate the primordia. Herein, we report the transcriptional dynamics with the progress of symbiosis in A. hypogaea at 1 day postinfection (dpi) (invasion), 4 dpi (nodule primordia), 8 dpi (spread of infection in nodule-like structure), 12 dpi (immature nodules containing rod-shaped rhizobia), and 21 dpi (mature nodules with spherical symbiosomes). Expression of putative ortholog of symbiotic genes in 'crack entry' legume A. hypogaea was compared with infection thread-adapted model legumes. The contrasting features were i) higher expression of receptors like LYR3 and EPR3 as compared with canonical Nod factor receptors, ii) late induction of transcription factors like NIN and NSP2 and constitutive high expression of ERF1, EIN2, bHLH476, and iii) induction of divergent pathogenesis-responsive PR-1 genes. Additionally, symbiotic orthologs of SymCRK, ROP6, RR9, SEN1, and DNF2 were not detectable and microsynteny analysis indicated the absence of a RPG homolog in diploid parental genomes of A. hypogaea. The implications are discussed and a molecular framework that guides crack-entry symbiosis in A. hypogaea is proposed.
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Affiliation(s)
- Kanchan Karmakar
- 1 Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | - Anindya Kundu
- 1 Department of Biochemistry, University of Calcutta, Kolkata 700019, India
| | - Ahsan Z Rizvi
- 2 LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France; and
| | - Emeric Dubois
- 3 Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 05, France
| | - Dany Severac
- 3 Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 05, France
| | - Pierre Czernic
- 2 LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France; and
| | - Fabienne Cartieaux
- 2 LSTM, Univ. Montpellier, CIRAD, INRA, IRD, SupAgro, Montpellier, France; and
| | - Maitrayee DasGupta
- 1 Department of Biochemistry, University of Calcutta, Kolkata 700019, India
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Rípodas C, Castaingts M, Clúa J, Villafañe J, Blanco FA, Zanetti ME. The PvNF-YA1 and PvNF-YB7 Subunits of the Heterotrimeric NF-Y Transcription Factor Influence Strain Preference in the Phaseolus vulgaris-Rhizobium etli Symbiosis. FRONTIERS IN PLANT SCIENCE 2019; 10:221. [PMID: 30873199 PMCID: PMC6403126 DOI: 10.3389/fpls.2019.00221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/08/2019] [Indexed: 05/23/2023]
Abstract
Transcription factors of the Nuclear Factor Y (NF-Y) family play essential functions in plant development and plasticity, including the formation of lateral root organs such as lateral root and symbiotic nodules. NF-Ys mediate transcriptional responses by acting as heterotrimers composed of three subunits, NF-YA, NF-YB, and NF-YC, which in plants are encoded by relatively large gene families. We have previously shown that, in the Phaseolus vulgaris × Rhizobium etli interaction, the PvNF-YC1 subunit is involved not only in the formation of symbiotic nodules, but also in the preference exhibited by the plant for rhizobial strains that are more efficient and competitive in nodule formation. PvNF-YC1 forms a heterotrimer with the PvNF-YA1 and PvNF-YB7 subunits. Here, we used promoter:reporter fusions to show that both PvNF-YA1 and PvNF-YB7 are expressed in symbiotic nodules. In addition, we report that knock-down of PvNF-YA1 and its close paralog PvNF-YA9 abolished nodule formation by either high or low efficient strains and arrested rhizobial infection. On the other hand, knock-down of PvNF-YB7 only affected the symbiotic outcome of the high efficient interaction, suggesting that other symbiotic NF-YB subunits might be involved in the more general mechanisms of nodule formation. More important, we present functional evidence supporting that both PvNF-YA1 and PvNF-YB7 are part of the mechanisms that allow P. vulgaris plants to discriminate and select those bacterial strains that perform better in nodule formation, most likely by acting in the same heterotrimeric complex that PvNF-YC1.
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47
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Revalska M, Radkova M, Zagorchev L, Iantcheva A. Functional GUSassay of GRAStranscription factor from Medicago truncatula. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1649096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Miglena Revalska
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Mariana Radkova
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Lyuben Zagorchev
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Anelia Iantcheva
- Functional Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
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48
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Liu J, Rutten L, Limpens E, van der Molen T, van Velzen R, Chen R, Chen Y, Geurts R, Kohlen W, Kulikova O, Bisseling T. A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula. THE PLANT CELL 2019; 31:68-83. [PMID: 30610167 PMCID: PMC6391699 DOI: 10.1105/tpc.18.00478] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/13/2018] [Accepted: 01/04/2019] [Indexed: 05/22/2023]
Abstract
The legume-rhizobium symbiosis results in nitrogen-fixing root nodules, and their formation involves both intracellular infection initiated in the epidermis and nodule organogenesis initiated in inner root cell layers. NODULE INCEPTION (NIN) is a nodule-specific transcription factor essential for both processes. These NIN-regulated processes occur at different times and locations in the root, demonstrating a complex pattern of spatiotemporal regulation. We show that regulatory sequences sufficient for the epidermal infection process are located within a 5 kb region directly upstream of the NIN start codon in Medicago truncatula Furthermore, we identify a remote upstream cis-regulatory region required for the expression of NIN in the pericycle, and we show that this region is essential for nodule organogenesis. This region contains putative cytokinin response elements and is conserved in eight more legume species. Both the cytokinin receptor 1, which is essential for nodule primordium formation, and the B-type response regulator RR1 are expressed in the pericycle in the susceptible zone of the uninoculated root. This, together with the identification of the cytokinin-responsive elements in the NIN promoter, strongly suggests that NIN expression is initially triggered by cytokinin signaling in the pericycle to initiate nodule primordium formation.
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Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Tjitse van der Molen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rujin Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Yuhui Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
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49
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Mohammadi-Dehcheshmeh M, Niazi A, Ebrahimi M, Tahsili M, Nurollah Z, Ebrahimi Khaksefid R, Ebrahimi M, Ebrahimie E. Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:1550. [PMID: 30483277 PMCID: PMC6240842 DOI: 10.3389/fpls.2018.01550] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/03/2018] [Indexed: 05/25/2023]
Abstract
Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings.
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Affiliation(s)
- Manijeh Mohammadi-Dehcheshmeh
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | | | | | - Zahra Nurollah
- Department of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Reyhaneh Ebrahimi Khaksefid
- Department of Biotechnology, Shahrekord University, Shahrekord, Iran
- School of Agriculture Food and Wine, Department of Plant Science, The University of Adelaide, Adelaide, SA, Australia
| | - Mahdi Ebrahimi
- Max-Planck-Institute for Informatics, Saarbrucken, Germany
| | - Esmaeil Ebrahimie
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, Australia
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Division of Information Technology, Engineering and the Environment, School of Information Technology and Mathematical Sciences, University of South Australia, Adelaide, SA, Australia
- Faculty of Science and Engineering, School of Biological Sciences, Flinders University, Adelaide, SA, Australia
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50
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Gaudioso-Pedraza R, Beck M, Frances L, Kirk P, Ripodas C, Niebel A, Oldroyd GED, Benitez-Alfonso Y, de Carvalho-Niebel F. Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development. Curr Biol 2018; 28:3562-3577.e6. [PMID: 30416059 DOI: 10.1016/j.cub.2018.09.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/27/2018] [Accepted: 09/13/2018] [Indexed: 01/08/2023]
Abstract
The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula β-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing β-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.
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Affiliation(s)
| | - Martina Beck
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Lisa Frances
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Philip Kirk
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carolina Ripodas
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Giles E D Oldroyd
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
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