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Loo EPI, Durán P, Pang TY, Westhoff P, Deng C, Durán C, Lercher M, Garrido-Oter R, Frommer WB. Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis. Cell Host Microbe 2024; 32:543-556.e6. [PMID: 38479394 DOI: 10.1016/j.chom.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile, metabolic state, and microbial immunity. We hypothesized that axial differentiation may also impact spatial colonization by root microbiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotron, to grow and then dissect Arabidopsis thaliana roots into three segments. We demonstrate that distinct endospheric and rhizosphere bacterial communities colonize the segments, supporting the hypothesis of microbiota differentiation along the axis. Root metabolite profiling of each segment reveals differential metabolite enrichment and specificity. Bioinformatic analyses and GUS histochemistry indicate microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root segments from sweet mutants shows altered spatial metabolic profiles and reorganization of endospheric root microbiota. This work reveals the interdependency between root metabolites and microbial colonization and the contribution of SWEETs to spatial diversity and stability of microbial ecosystem.
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Affiliation(s)
- Eliza P-I Loo
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany.
| | - Paloma Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Tin Yau Pang
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Computer Science and Department of Biology, 40225 Düsseldorf, Germany; Heinrich Heine University Düsseldorf, Medical Faculty and University Hospital Düsseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, 40225 Düsseldorf, Germany
| | - Philipp Westhoff
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Plant Metabolism and Metabolomics Laboratory, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Chen Deng
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany
| | - Carlos Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Martin Lercher
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Computer Science and Department of Biology, 40225 Düsseldorf, Germany; Heinrich Heine University Düsseldorf, Medical Faculty and University Hospital Düsseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, 40225 Düsseldorf, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany; Earlham Institute, Norwich NR4 7UZ, UK
| | - Wolf B Frommer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, 464-8601 Nagoya, Japan.
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2
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Li Y, Liu Q, Zhang DX, Zhang ZY, Xu A, Jiang YL, Chen ZC. Metal nutrition and transport in the process of symbiotic nitrogen fixation. PLANT COMMUNICATIONS 2024; 5:100829. [PMID: 38303509 PMCID: PMC11009365 DOI: 10.1016/j.xplc.2024.100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Symbiotic nitrogen fixation (SNF) facilitated by the interaction between legumes and rhizobia is a well-documented and eco-friendly alternative to chemical nitrogen fertilizers. Host plants obtain fixed nitrogen from rhizobia by providing carbon and mineral nutrients. These mineral nutrients, which are mostly in the form of metal ions, are implicated in various stages of the SNF process. This review describes the functional roles played by metal ions in nodule formation and nitrogen fixation and specifically addresses their transport mechanisms and associated transporters within root nodules. Future research directions and potential strategies for enhancing SNF efficiency are also discussed.
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Affiliation(s)
- Yuan Li
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qian Liu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dan-Xun Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhuo-Yan Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ao Xu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Long Jiang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhi-Chang Chen
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Fan K, Wang Z, Sze CC, Niu Y, Wong FL, Li MW, Lam HM. MicroRNA 4407 modulates nodulation in soybean by repressing a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). THE NEW PHYTOLOGIST 2023; 240:1034-1051. [PMID: 37653681 DOI: 10.1111/nph.19222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function of miR4407 in soybean is still unknown. MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development. Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild-type GmIPT3 or a miR4407-resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root-derived CK. Overall, our data revealed a new miRNA-mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development.
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Affiliation(s)
- Kejing Fan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhili Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongchao Niu
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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4
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Singh J, Isidra-Arellano MC, Valdés-López O. Harnessing the Potential of Symbiotic Associations of Plants in Phosphate-Deficient Soil for Sustainable Agriculture. PLANT & CELL PHYSIOLOGY 2023; 64:850-857. [PMID: 37300552 DOI: 10.1093/pcp/pcad059] [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: 03/09/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Many plants associate with arbuscular mycorrhizal (AM) fungi for nutrient acquisition, and most legumes also associate with nitrogen-fixing rhizobial bacteria for nitrogen acquisition. The association of plants with AM fungi and rhizobia depends on the perception of lipo-chitooligosaccharides (LCOs) produced by these micro-symbionts. Recent studies reveal that cereals can perceive LCOs better in soil deprived of phosphate (Pi) and nitrogen to activate symbiosis signaling and form efficient AM symbiosis. Nevertheless, the Pi deficiency in the soil hinders the symbiotic association of legumes with rhizobia, ultimately reducing nitrogen fixation. Here, we discuss a mechanistic overview of the factors regulating root nodule symbiosis under Pi-deficient conditions and further emphasize the possible ways to overcome this hurdle. Ignoring the low Pi problem not only can compromise the functionality of the nitrogen cycle by nitrogen fixation through legumes but can also put food security at risk globally. This review aims to bring the scientific community's attention toward the detrimental response of legumes toward Pi-deficient soil for the formation of root nodule symbiosis and hence reduced nitrogen fixation. In this review, we have highlighted the recent studies that have advanced our understanding of these critical areas and discussed some future directions. Furthermore, this review highlights the importance of communicating science with farmers and the agriculture community to fully harness the potential of the symbiotic association of plants in nutrient-deficient soil for sustainable agriculture.
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Affiliation(s)
- Jawahar Singh
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Department of Biology, Universidad Nacional Autónoma de México, Tlalnepantla 54090, México
| | - Mariel C Isidra-Arellano
- Royal Botanic Gardens, Kew, Department of Trait Diversity and Function, Richmond, Surrey TW9 3AE, UK
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Department of Biology, Universidad Nacional Autónoma de México, Tlalnepantla 54090, México
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5
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Wang J, Pislariu CI, Liu CW, Tsyganov VE, DasGupta M. Editorial: Molecular and cellular mechanisms of the legume-rhizobia symbiosis, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1208904. [PMID: 37313254 PMCID: PMC10258313 DOI: 10.3389/fpls.2023.1208904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 06/15/2023]
Affiliation(s)
- Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Catalina Iulia Pislariu
- School of the Sciences, Division of Biology, Texas Woman’s University, Denton, TX, United States
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Viktor E. Tsyganov
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
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6
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Liu Y, Xiong Z, Wu W, Ling HQ, Kong D. Iron in the Symbiosis of Plants and Microorganisms. PLANTS (BASEL, SWITZERLAND) 2023; 12:1958. [PMID: 37653875 PMCID: PMC10223382 DOI: 10.3390/plants12101958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 09/02/2023]
Abstract
Iron is an essential element for most organisms. Both plants and microorganisms have developed different mechanisms for iron uptake, transport and storage. In the symbiosis systems, such as rhizobia-legume symbiosis and arbuscular mycorrhizal (AM) symbiosis, maintaining iron homeostasis to meet the requirements for the interaction between the host plants and the symbiotic microbes is a new challenge. This intriguing topic has drawn the attention of many botanists and microbiologists, and many discoveries have been achieved so far. In this review, we discuss the current progress on iron uptake and transport in the nodules and iron homeostasis in rhizobia-legume symbiosis. The discoveries with regard to iron uptake in AM fungi, iron uptake regulation in AM plants and interactions between iron and other nutrient elements during AM symbiosis are also summarized. At the end of this review, we propose prospects for future studies in this fascinating research area.
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Affiliation(s)
- Yi Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Y.L.)
| | - Zimo Xiong
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Y.L.)
| | - Weifeng Wu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Y.L.)
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China;
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Danyu Kong
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (Y.L.)
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7
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Li S, Wu C, Liu H, Lyu X, Xiao F, Zhao S, Ma C, Yan C, Liu Z, Li H, Wang X, Gong Z. Systemic regulation of nodule structure and assimilated carbon distribution by nitrate in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1101074. [PMID: 36814755 PMCID: PMC9939697 DOI: 10.3389/fpls.2023.1101074] [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: 11/17/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The nitrate regulates soybean nodulation and nitrogen fixation systemically, mainly in inhibiting nodule growth and reducing nodule nitrogenase activity, but the reason for its inhibition is still inconclusive. METHODS The systemic effect of nitrate on nodule structure, function, and carbon distribution in soybean (Glycine max (L.) Merr.) was studied in a dual-root growth system, with both sides inoculated with rhizobia and only one side subjected to nitrate treatment for four days. The non-nodulating side was genetically devoid of the ability to form nodules. Nutrient solutions with nitrogen concentrations of 0, 100, and 200 mg L-1 were applied as KNO3 to the non-nodulating side, while the nodulating side received a nitrogen-free nutrient solution. Carbon partitioning in roots and nodules was monitored using 13C-labelled CO2. Other nodule responses were measured via the estimation of the nitrogenase activity and the microscopic observation of nodule ultrastructure. RESULTS Elevated concentrations of nitrate applied on the non-nodulating side caused a decrease in the number of bacteroids, fusion of symbiosomes, enlargement of the peribacteroid spaces, and onset of degradation of poly-β-hydroxybutyrate granules, which is a form of carbon storage in bacteroids. These microscopic observations were associated with a strong decrease in the nitrogenase activity of nodules. Furthermore, our data demonstrate that the assimilated carbon is more likely to be allocated to the non-nodulating roots, as follows from the competition for carbon between the symbiotic and non-symbiotic sides of the dual-root system. CONCLUSION We propose that there is no carbon competition between roots and nodules when they are indirectly supplied with nitrate, and that the reduction of carbon fluxes to nodules and roots on the nodulating side is the mechanism by which the plant systemically suppresses nodulation under nitrogen-replete conditions.
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Affiliation(s)
- Sha Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Chengbin Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hao Liu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaochen Lyu
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Fengsheng Xiao
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Shuhong Zhao
- College of Engineering, Northeast Agricultural University, Harbin, China
| | - Chunmei Ma
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chao Yan
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhilei Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Hongyu Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xuelai Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhenping Gong
- College of Agriculture, Northeast Agricultural University, Harbin, China
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8
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Luo Y, Liu W, Sun J, Zhang ZR, Yang WC. Quantitative proteomics reveals key pathways in the symbiotic interface and the likely extracellular property of soybean symbiosome. J Genet Genomics 2023; 50:7-19. [PMID: 35470091 DOI: 10.1016/j.jgg.2022.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/06/2023]
Abstract
An effective symbiosis between legumes and rhizobia relies largely on diverse proteins at the plant-rhizobium interface for material transportation and signal transduction during symbiotic nitrogen fixation. Here, we report a comprehensive proteome atlas of the soybean symbiosome membrane (SM), peribacteroid space (PBS), and root microsomal fraction (RMF) using state-of-the-art label-free quantitative proteomic technology. In total, 1759 soybean proteins with diverse functions are detected in the SM, and 1476 soybean proteins and 369 rhizobial proteins are detected in the PBS. The diversity of SM proteins detected suggests multiple origins of the SM. Quantitative comparative analysis highlights amino acid metabolism and nutrient uptake in the SM, indicative of the key pathways in nitrogen assimilation. The detection of soybean secretory proteins in the PBS and receptor-like kinases in the SM provides evidence for the likely extracellular property of the symbiosome and the potential signaling communication between both symbionts at the symbiotic interface. Our proteomic data provide clues for how some of the sophisticated regulation between soybean and rhizobium at the symbiotic interface is achieved, and suggest approaches for symbiosis engineering.
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Affiliation(s)
- Yu Luo
- The State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Wei Liu
- The State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Sun
- The State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng-Rong Zhang
- The State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Cai Yang
- The State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Fan K, Sze CC, Li MW, Lam HM. Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2022; 13:997037. [PMID: 36330261 PMCID: PMC9623164 DOI: 10.3389/fpls.2022.997037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
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Wekesa C, Jalloh AA, Muoma JO, Korir H, Omenge KM, Maingi JM, Furch ACU, Oelmüller R. Distribution, Characterization and the Commercialization of Elite Rhizobia Strains in Africa. Int J Mol Sci 2022; 23:ijms23126599. [PMID: 35743041 PMCID: PMC9223902 DOI: 10.3390/ijms23126599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Grain legumes play a significant role in smallholder farming systems in Africa because of their contribution to nutrition and income security and their role in fixing nitrogen. Biological Nitrogen Fixation (BNF) serves a critical role in improving soil fertility for legumes. Although much research has been conducted on rhizobia in nitrogen fixation and their contribution to soil fertility, much less is known about the distribution and diversity of the bacteria strains in different areas of the world and which of the strains achieve optimal benefits for the host plants under specific soil and environmental conditions. This paper reviews the distribution, characterization, and commercialization of elite rhizobia strains in Africa.
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Affiliation(s)
- Clabe Wekesa
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany; (C.W.); (K.M.O.); (A.C.U.F.)
| | - Abdul A. Jalloh
- International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi 00100, Kenya;
| | - John O. Muoma
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, P.O. Box 190, Kakamega 50100, Kenya;
| | - Hezekiah Korir
- Crops, Horticulture and Soils Department, Egerton University, P.O. Box 536, Egerton 20115, Kenya;
| | - Keziah M. Omenge
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany; (C.W.); (K.M.O.); (A.C.U.F.)
| | - John M. Maingi
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844, Nairobi 00100, Kenya;
| | - Alexandra C. U. Furch
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany; (C.W.); (K.M.O.); (A.C.U.F.)
| | - Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany and Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany; (C.W.); (K.M.O.); (A.C.U.F.)
- Correspondence: ; Tel.: +49-3641949232
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11
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Yang Z, Du H, Sun J, Xing X, Kong Y, Li W, Li X, Zhang C. A Nodule-Localized Small Heat Shock Protein GmHSP17.1 Confers Nodule Development and Nitrogen Fixation in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:838718. [PMID: 35356122 PMCID: PMC8959767 DOI: 10.3389/fpls.2022.838718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Small heat shock proteins (sHSPs) are ubiquitous proteins present in all organisms. The sHSPs are not only upregulated under heat shock as well as other stresses but also are expressed in unstressed cells, indicating quite diverse functions of sHSPs. However, there is little known about the role of sHSPs in nodulation and nitrogen fixation in soybean. In this study, we cloned a candidate protein of sHSP, GmHSP17.1, from proteome of nodule and analyzed its function in soybean nodulation. We found that GmHSP17.1 was a cytosolic protein and preferentially expressed during nodule development. An overexpression of GmHSP17.1 in composite transgenic plants showed increases in nodule number, fresh weight, nodule size, area of infection cells, and nitrogenase activity, and subsequently promoted the content of nitrogen and growth of soybean plants. While GmHSP17.1 RNA interference (RNAi) lines showed significantly impaired nodule development and nitrogen fixation efficiency. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS), GmRIP1 was identified as the first potential target of GmHSP17.1, and was shown to be specifically expressed in soybean nodules. The interaction between GmHSP17.1 and GmRIP1 was further confirmed by yeast-two hybrid (Y2H), bimolecular fluorescence complementation (BiFC) in vivo and pull-down assay in vitro. Furthermore, peroxidase activity was markedly increased in GmHSP17.1 overexpressed nodules and decreased in RNAi lines. As a result, the reactive oxygen species (ROS) content greatly decreased in GmHSP17.1 overexpression lines and increased in suppression lines. Taken together, we conclude that GmHSP17.1 plays an important role in soybean nodulation through interacting with GmRIP1. Our results provide foundation for studying the mechanism of nitrogen fixation and for the genetics improvement of legume plants.
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Affiliation(s)
- Zhanwu Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hui Du
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jingyi Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinzhu Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Youbin Kong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Wenlong Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xihuan Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Caiying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
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12
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Frailey DC, Zhang Q, Wood DJ, Davis TM. Defining the mutation sites in chickpea nodulation mutants PM233 and PM405. BMC PLANT BIOLOGY 2022; 22:66. [PMID: 35139814 PMCID: PMC8827291 DOI: 10.1186/s12870-022-03446-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/20/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Like most legumes, chickpeas form specialized organs called root nodules. These nodules allow for a symbiotic relationship with rhizobium bacteria. The rhizobia provide fixed atmospheric nitrogen to the plant in a usable form. It is of both basic and practical interest to understand the host plant genetics of legume root nodulation. Chickpea lines PM233 and PM405, which harbor the mutationally identified nodulation genes rn1 and rn4, respectively, both display nodulation-deficient phenotypes. Previous investigators identified the rn1 mutation with the chickpea homolog of Medicago truncatula nodulation gene NSP2, but were unable to define the mutant rn1 allele. We used Illumina and Nanopore sequencing reads to attempt to identify and characterize candidate mutation sites responsible for the PM233 and PM405 phenotypes. RESULTS We aligned Illumina reads to the available desi chickpea reference genome, and did a de novo contig assembly of Nanopore reads. In mutant PM233, the Nanopore contigs allowed us to identify the breakpoints of a ~ 35 kb deleted region containing the CaNSP2 gene, the Medicago truncatula homolog of which is involved in nodulation. In mutant PM405, we performed variant calling in read alignments and identified 10 candidate mutations. Genotyping of a segregating progeny population narrowed that pool down to a single candidate gene which displayed homology to M. truncatula nodulation gene NIN. CONCLUSIONS We have characterized the nodulation mutation sites in chickpea mutants PM233 and PM405. In mutant PM233, the rn1 mutation was shown to be due to deletion of the entire CaNSP2 nodulation gene, while in mutant PM405 the rn4 mutation was due to a single base deletion resulting in a frameshift mutation between the predicted RWP-RK and PB1 domains of the NIN nodulation gene. Critical to characterization of the rn1 allele was the generation of Nanopore contigs for mutant PM233 and its wild type parent ICC 640, without which the deletional boundaries could not be defined. Our results suggest that efforts of prior investigators were hampered by genomic misassemblies in the CaNSP2 region of both the desi and kabuli reference genomes.
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Affiliation(s)
- Daniel C. Frailey
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | - Qian Zhang
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
- Department of Forest Resources and Environmental Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - David J. Wood
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | - Thomas M. Davis
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
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13
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Zhang M, Zhong X, Li M, Yang X, Abou Elwafa SF, Albaqami M, Tian H. Genome-wide analyses of the Nodulin-like gene family in bread wheat revealed its potential roles during arbuscular mycorrhizal symbiosis. Int J Biol Macromol 2022; 201:424-436. [PMID: 35041884 DOI: 10.1016/j.ijbiomac.2022.01.076] [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: 12/03/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/05/2022]
Abstract
Nodulin-like (NL) genes are involved in transporting of various substances and may play key roles during the establishment of symbiosis in legumes plants. However, basic biological information of NL genes in the wheat genome is still largely unknown. Here, we identified and characterized NL genes in wheat via integrating genomic information, collinearity analysis, co-expression network analysis (WGCNA) and transcriptome analysis. In addition, we analyzed the polymorphisms and the roles of NL genes during arbuscular mycorrhizal (AM) symbiosis using a large wheat panel consists of 259 wheat genotypes. We identified 181 NL genes in the wheat genome, which were classified into SWEET, Early Nodulin-Like (ENODL), Major Facilitator Superfamily-Nodulin (MFS), Vacuolar Iron Transporter (VIT) and Early nodulin 93 (ENOD93) subfamily. The expansion of NL genes was mainly driven by segmental duplication. The bHLH genes are potential unrecognized transcription factors regulating NL genes. Moreover, two NL genes were more sensitive than other NL genes to AM colonization. The polymorphisms of NL genes are mainly due to random drift, and the natural mutation of NL genes led to significant differences in the mycorrhizal dependence of wheat in phosphorus uptake. The results concluded that NL genes potentially play important roles during AM symbiosis with wheat.
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Affiliation(s)
- Mingming Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiong Zhong
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengjiao Li
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiuming Yang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Salah F Abou Elwafa
- Agronomy department, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hui Tian
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
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14
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Henderson SW, Nourmohammadi S, Ramesh SA, Yool AJ. Aquaporin ion conductance properties defined by membrane environment, protein structure, and cell physiology. Biophys Rev 2022; 14:181-198. [PMID: 35340612 PMCID: PMC8921385 DOI: 10.1007/s12551-021-00925-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023] Open
Abstract
Aquaporins (AQPs) are multifunctional transmembrane channel proteins permeable to water and an expanding array of solutes. AQP-mediated ion channel activity was first observed when purified AQP0 from bovine lens was incorporated into lipid bilayers. Electrophysiological properties of ion-conducting AQPs since discovered in plants, invertebrates, and mammals have been assessed using native, reconstituted, and heterologously expressed channels. Accumulating evidence is defining amino acid residues that govern differential solute permeability through intrasubunit and central pores of AQP tetramers. Rings of charged and hydrophobic residues around pores influence AQP selectivity, and are candidates for further work to define motifs that distinguish ion conduction capability, versus strict water and glycerol permeability. Similarities between AQP ion channels thus far include large single channel conductances and long open times, but differences in ionic selectivity, permeability to divalent cations, and mechanisms of gating (e.g., by voltage, pH, and cyclic nucleotides) are unique to subtypes. Effects of lipid environments in modulating parameters such as single channel amplitude could explain in part the variations in AQP ion channel properties observed across preparations. Physiological roles of the ion-conducting AQP classes span diverse processes including regulation of cell motility, organellar pH, neural development, signaling, and nutrient acquisition. Advances in computational methods can generate testable predictions of AQP structure-function relationships, which combined with innovative high-throughput assays could revolutionize the field in defining essential properties of ion-conducting AQPs, discovering new AQP ion channels, and understanding the effects of AQP interactions with proteins, signaling cascades, and membrane lipids.
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Affiliation(s)
- Sam W. Henderson
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005 Australia
| | | | - Sunita A. Ramesh
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042 Australia
| | - Andrea J. Yool
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005 Australia
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15
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Booth NJ, Smith PMC, Ramesh SA, Day DA. Malate Transport and Metabolism in Nitrogen-Fixing Legume Nodules. Molecules 2021; 26:6876. [PMID: 34833968 PMCID: PMC8618214 DOI: 10.3390/molecules26226876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/22/2022] Open
Abstract
Legumes form a symbiosis with rhizobia, a soil bacterium that allows them to access atmospheric nitrogen and deliver it to the plant for growth. Biological nitrogen fixation occurs in specialized organs, termed nodules, that develop on the legume root system and house nitrogen-fixing rhizobial bacteroids in organelle-like structures termed symbiosomes. The process is highly energetic and there is a large demand for carbon by the bacteroids. This carbon is supplied to the nodule as sucrose, which is broken down in nodule cells to organic acids, principally malate, that can then be assimilated by bacteroids. Sucrose may move through apoplastic and/or symplastic routes to the uninfected cells of the nodule or be directly metabolised at the site of import within the vascular parenchyma cells. Malate must be transported to the infected cells and then across the symbiosome membrane, where it is taken up by bacteroids through a well-characterized dct system. The dicarboxylate transporters on the infected cell and symbiosome membranes have been functionally characterized but remain unidentified. Proteomic and transcriptomic studies have revealed numerous candidates, but more work is required to characterize their function and localise the proteins in planta. GABA, which is present at high concentrations in nodules, may play a regulatory role, but this remains to be explored.
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Affiliation(s)
- Nicholas J. Booth
- College of Science & Engineering, Flinders University, GPO Box 5100, Adelaide, SA 5001, Australia; (N.J.B.); (S.A.R.)
| | | | - Sunita A. Ramesh
- College of Science & Engineering, Flinders University, GPO Box 5100, Adelaide, SA 5001, Australia; (N.J.B.); (S.A.R.)
| | - David A. Day
- College of Science & Engineering, Flinders University, GPO Box 5100, Adelaide, SA 5001, Australia; (N.J.B.); (S.A.R.)
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16
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Fan K, Wong-Bajracharya J, Lin X, Ni M, Ku YS, Li MW, Tian CF, Chan TF, Lam HM. Differentially expressed microRNAs that target functional genes in mature soybean nodules. THE PLANT GENOME 2021; 14:e20103. [PMID: 33973410 DOI: 10.1002/tpg2.20103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr.], we identified high-confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium-inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA-seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high-affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole-plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole-plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi-nitrogen balance to promote SNF in nodules.
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Affiliation(s)
- Kejing Fan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Johanna Wong-Bajracharya
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Xiao Lin
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Meng Ni
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Yee-Shan Ku
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting-Fung Chan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
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17
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Xiu L, Zhang W, Wu D, Sun Y, Zhang H, Gu W, Wang Y, Meng J, Chen W. Biochar can improve biological nitrogen fixation by altering the root growth strategy of soybean in Albic soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:144564. [PMID: 33940700 DOI: 10.1016/j.scitotenv.2020.144564] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 05/22/2023]
Abstract
Albic soil is a low-yielding soil that is widely distributed in Northeast China. The high viscosity and acidity and the lack of nutrients in the Albic layer limit the growth of crop. In our previous studies, we found that applying biochar as a soil amendment could improve the properties of Albic soil and promote soybean growth. Increases in the nitrogen contents of the soil and the soybeans were key aspects of these improvements. Soybean is a nitrogen-fixing crop, the increase in nitrogen in the Albic soil may have been due to an improvement in biological nitrogen fixation by the soybean with biochar amendment, but the function mechanism was still uncertain. We hypothesized that biochar could improve biological nitrogen fixation of soybean by affecting soybean root growth in the Albic soil. Therefore, we conducted pot experiments with five treatment levels (0, 10, 20, 30, and 40 g·kg-1 biochar) for two years to study how biochar affects the root growth strategy and biological nitrogen fixation of soybean based on its root structure and root nutrient acquisition ability at different stages. The soybean root structure and activity indexes, nodulation ability and nitrogen uptake were measured at different growth stages; in the second year, at the late seed-filling stage, the stable 15N isotope method was used to elucidate the biological nitrogen fixation process. Regarding root structure at the pod-setting stage, biochar resulted in increases in root length density, specific root length, root diameter and specific tip density but a decrease in root tissue mass density at the pod-setting stage. Biochar improved root nutrient acquisition by increasing root activity, root tip number and root-bleeding sap amount. The change in root growth strategy contributed to the promotion of biological nitrogen fixation by the rhizobia that live symbiotically with soybean, thereby increasing crop yield.
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Affiliation(s)
- Liqun Xiu
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Weiming Zhang
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
| | - Di Wu
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yuanyuan Sun
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Honggui Zhang
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Wenqi Gu
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yuning Wang
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Jun Meng
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Wenfu Chen
- Biochar Engineering & Technology Research Center of Liaoning Province, Rice Research Institute, Agronomy College, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.
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18
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Gavrin A, Loughlin PC, Brear E, Griffith OW, Bedon F, Suter Grotemeyer M, Escudero V, Reguera M, Qu Y, Mohd-Noor SN, Chen C, Osorio MB, Rentsch D, González-Guerrero M, Day DA, Smith PMC. Soybean Yellow Stripe-like 7 is a symbiosome membrane peptide transporter important for nitrogen fixation. PLANT PHYSIOLOGY 2021; 186:581-598. [PMID: 33619553 PMCID: PMC8154080 DOI: 10.1093/plphys/kiab044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 01/21/2021] [Indexed: 05/05/2023]
Abstract
Legumes form a symbiosis with rhizobia that convert atmospheric nitrogen (N2) to ammonia and provide it to the plant in return for a carbon and nutrient supply. Nodules, developed as part of the symbiosis, harbor rhizobia that are enclosed in a plant-derived symbiosome membrane (SM) to form an organelle-like structure called the symbiosome. In mature nodules exchanges between the symbionts occur across the SM. Here we characterize Yellow Stripe-like 7 (GmYSL7), a Yellow stripe-like family member localized on the SM in soybean (Glycine max) nodules. It is expressed specifically in infected cells with expression peaking soon after nitrogenase becomes active. Unlike most YSL family members, GmYSL7 does not transport metals complexed with phytosiderophores. Rather, it transports oligopeptides of between four and 12 amino acids. Silencing GmYSL7 reduces nitrogenase activity and blocks infected cell development so that symbiosomes contain only a single bacteroid. This indicates the substrate of YSL7 is required for proper nodule development, either by promoting symbiosome development directly or by preventing inhibition of development by the plant. RNAseq of nodules where GmYSL7 was silenced suggests that the plant initiates a defense response against rhizobia with genes encoding proteins involved in amino acid export downregulated and some transcripts associated with metal homeostasis altered. These changes may result from the decrease in nitrogen fixation upon GmYSL7 silencing and suggest that the peptide(s) transported by GmYSL7 monitor the functional state of the bacteroids and regulate nodule metabolism and transport processes accordingly. Further work to identify the physiological substrate for GmYSL7 will allow clarification of this role.
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Affiliation(s)
- Aleksandr Gavrin
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Patrick C Loughlin
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ella Brear
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Oliver W Griffith
- Department of Biological Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Frank Bedon
- School of Life Sciences, La Trobe University, Bundoora, Victoria 3083, Australia
| | | | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Crta, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Maria Reguera
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Crta, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Yihan Qu
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Siti N Mohd-Noor
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chi Chen
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Marina Borges Osorio
- School of Life Sciences, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Doris Rentsch
- IPS, Molecular Plant Physiology, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). Universidad Politécnica de Madrid, Campus de Montegancedo, Crta, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - David A Day
- College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, Australia
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19
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Ram H, Sardar S, Gandass N. Vacuolar Iron Transporter (Like) proteins: Regulators of cellular iron accumulation in plants. PHYSIOLOGIA PLANTARUM 2021; 171:823-832. [PMID: 33580885 DOI: 10.1111/ppl.13363] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/28/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Iron is not only important for plant physiology, but also a very important micronutrient in human diets. The vacuole is the main site for accumulation of excess amounts of various nutrients and toxic substances in plant cells. During the past decade, many Vacuolar Iron Transporter (VIT) and VIT-Like (VTL) genes have been identified and shown to play important roles in iron homeostasis in different plants. Furthermore, recent reports identified novel roles of these transporter genes in symbiotic nitrogen fixation (SNF) in legume crops as well as in the blue coloration of petals in flowers. The literature indicates their universal role in Fe transport across different tissues (grains, nodules, flowers) to different biological processes (cellular iron homeostasis, SNF, petal coloration) in different plants. Here, we have systematically reviewed different aspects, such as structure, molecular evolution, expression, and function of VIT/VTL proteins. This will help future studies aimed at functional analysis of VIT/VTL genes in other plant species, vacuolar transportation mechanisms, and iron biofortification at large.
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Affiliation(s)
- Hasthi Ram
- National Institute of Plant Genome Research, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, India
| | | | - Nishu Gandass
- National Agri-Food Biotechnology Institute, Mohali, India
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20
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Day DA, Smith PMC. Iron Transport across Symbiotic Membranes of Nitrogen-Fixing Legumes. Int J Mol Sci 2021; 22:E432. [PMID: 33406726 PMCID: PMC7794740 DOI: 10.3390/ijms22010432] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/30/2022] Open
Abstract
Iron is an essential nutrient for the legume-rhizobia symbiosis and nitrogen-fixing bacteroids within root nodules of legumes have a very high demand for the metal. Within the infected cells of nodules, the bacteroids are surrounded by a plant membrane to form an organelle-like structure called the symbiosome. In this review, we focus on how iron is transported across the symbiosome membrane and accessed by the bacteroids.
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Affiliation(s)
- David A. Day
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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21
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Waters JK, Mawhinney TP, Emerich DW. Nitrogen Assimilation and Transport by Ex Planta Nitrogen-Fixing Bradyrhizobium diazoefficiens Bacteroids Is Modulated by Oxygen, Bacteroid Density and l-Malate. Int J Mol Sci 2020; 21:E7542. [PMID: 33066093 PMCID: PMC7589128 DOI: 10.3390/ijms21207542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022] Open
Abstract
Symbiotic nitrogen fixation requires the transfer of fixed organic nitrogen compounds from the symbiotic bacteria to a host plant, yet the chemical nature of the compounds is in question. Bradyrhizobium diazoefficiens bacteroids were isolated anaerobically from soybean nodules and assayed at varying densities, varying partial pressures of oxygen, and varying levels of l-malate. Ammonium was released at low bacteroid densities and high partial pressures of oxygen, but was apparently taken up at high bacteroid densities and low partial pressures of oxygen in the presence of l-malate; these later conditions were optimal for amino acid excretion. The ratio of partial pressure of oxygen/bacteroid density of apparent ammonium uptake and of alanine excretion displayed an inverse relationship. Ammonium uptake, alanine and branch chain amino acid release were all dependent on the concentration of l-malate displaying similar K0.5 values of 0.5 mM demonstrating concerted regulation. The hyperbolic kinetics of ammonium uptake and amino acid excretion suggests transport via a membrane carrier and also suggested that transport was rate limiting. Glutamate uptake displayed exponential kinetics implying transport via a channel. The chemical nature of the compounds released were dependent upon bacteroid density, partial pressure of oxygen and concentration of l-malate demonstrating an integrated metabolism.
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Affiliation(s)
| | | | - David W. Emerich
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (J.K.W.); (T.P.M.)
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22
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Brear EM, Bedon F, Gavrin A, Kryvoruchko IS, Torres-Jerez I, Udvardi MK, Day DA, Smith PMC. GmVTL1a is an iron transporter on the symbiosome membrane of soybean with an important role in nitrogen fixation. THE NEW PHYTOLOGIST 2020; 228:667-681. [PMID: 32533710 DOI: 10.1111/nph.16734] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/27/2020] [Indexed: 05/07/2023]
Abstract
Legumes establish symbiotic relationships with soil bacteria (rhizobia), housed in nodules on roots. The plant supplies carbon substrates and other nutrients to the bacteria in exchange for fixed nitrogen. The exchange occurs across a plant-derived symbiosome membrane (SM), which encloses rhizobia to form a symbiosome. Iron supplied by the plant is crucial for rhizobial enzyme nitrogenase that catalyses nitrogen fixation, but the SM iron transporter has not been identified. We use yeast complementation, real-time PCR and proteomics to study putative soybean (Glycine max) iron transporters GmVTL1a and GmVTL1b and have characterized the role of GmVTL1a using complementation in plant mutants, hairy root transformation and microscopy. GmVTL1a and GmVTL1b are members of the vacuolar iron transporter family and homologous to Lotus japonicus SEN1 (LjSEN1), which is essential for nitrogen fixation. GmVTL1a expression is enhanced in nodule infected cells and both proteins are localized to the SM. GmVTL1a transports iron in yeast and restores nitrogen fixation when expressed in the Ljsen1 mutant. Three GmVTL1a amino acid substitutions that block nitrogen fixation in Ljsen1 plants reduce iron transport in yeast. We conclude GmVTL1a is responsible for transport of iron across the SM to bacteroids and plays a crucial role in the nitrogen-fixing symbiosis.
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Affiliation(s)
- Ella M Brear
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Frank Bedon
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aleksandr Gavrin
- School of Life and Environmental Science, The University of Sydney, Sydney, NSW, 2006, Australia
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Igor S Kryvoruchko
- Noble Research Institute, Ardmore, OK, 73401, USA
- Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | | | - David A Day
- College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Penelope M C Smith
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC, 3083, Australia
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23
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Lambert I, Pervent M, Le Queré A, Clément G, Tauzin M, Severac D, Benezech C, Tillard P, Martin-Magniette ML, Colella S, Lepetit M. Responses of mature symbiotic nodules to the whole-plant systemic nitrogen signaling. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5039-5052. [PMID: 32386062 PMCID: PMC7410188 DOI: 10.1093/jxb/eraa221] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/30/2020] [Indexed: 05/26/2023]
Abstract
In symbiotic root nodules of legumes, terminally differentiated rhizobia fix atmospheric N2 producing an NH4+ influx that is assimilated by the plant. The plant, in return, provides photosynthates that fuel the symbiotic nitrogen acquisition. Mechanisms responsible for the adjustment of the symbiotic capacity to the plant N demand remain poorly understood. We have investigated the role of systemic signaling of whole-plant N demand on the mature N2-fixing nodules of the model symbiotic association Medicago truncatula/Sinorhizobium using split-root systems. The whole-plant N-satiety signaling rapidly triggers reductions of both N2 fixation and allocation of sugars to the nodule. These responses are associated with the induction of nodule senescence and the activation of plant defenses against microbes, as well as variations in sugars transport and nodule metabolism. The whole-plant N-deficit responses mirror these changes: a rapid increase of sucrose allocation in response to N-deficit is associated with a stimulation of nodule functioning and development resulting in nodule expansion in the long term. Physiological, transcriptomic, and metabolomic data together provide evidence for strong integration of symbiotic nodules into whole-plant nitrogen demand by systemic signaling and suggest roles for sugar allocation and hormones in the signaling mechanisms.
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Affiliation(s)
- Ilana Lambert
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Marjorie Pervent
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Antoine Le Queré
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Marc Tauzin
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Dany Severac
- MGX, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Claire Benezech
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Pascal Tillard
- Biologie et Physiologie Moléculaire des Plantes, INRAE, CNRS, SupAgro, Univ. Montpellier, Montpellier, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, Univ. Evry, CNRS, INRAE, Orsay, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, Orsay, France
- UMR MIA-Paris, AgroParisTech, INRAE, Université Paris-Saclay, Paris, France
| | - Stefano Colella
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
| | - Marc Lepetit
- Laboratoire de Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, SupAgro, Univ. Montpellier, Montpellier, France
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24
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diCenzo GC, Tesi M, Pfau T, Mengoni A, Fondi M. Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium. Nat Commun 2020; 11:2574. [PMID: 32444627 PMCID: PMC7244743 DOI: 10.1038/s41467-020-16484-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/28/2020] [Indexed: 11/09/2022] Open
Abstract
The mutualistic association between leguminous plants and endosymbiotic rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, we report the reconstruction and modelling of a genome-scale metabolic network of Medicago truncatula (plant) nodulated by Sinorhizobium meliloti (bacterium). The reconstructed nodule tissue contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance analysis (FBA) suggests that the metabolic costs associated with symbiotic nitrogen fixation are primarily related to supporting nitrogenase activity, and increasing N2-fixation efficiency is associated with diminishing returns in terms of plant growth. Our analyses support that differentiating bacteroids have access to sugars as major carbon sources, ammonium is the main nitrogen export product of N2-fixing bacteria, and N2 fixation depends on proton transfer from the plant cytoplasm to the bacteria through acidification of the peribacteroid space. We expect that our model, called 'Virtual Nodule Environment' (ViNE), will contribute to a better understanding of the functioning of legume nodules, and may guide experimental studies and engineering of symbiotic nitrogen fixation.
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Affiliation(s)
- George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Michelangelo Tesi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Thomas Pfau
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
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25
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Arumugaperumal A, Paul S, Lathakumari S, Balasubramani R, Sivasubramaniam S. The draft genome of a new Verminephrobacter eiseniae strain: a nephridial symbiont of earthworms. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01549-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Purpose
Verminephrobacter is a genus of symbiotic bacteria that live in the nephridia of earthworms. The bacteria are recruited during the embryonic stage of the worm and transferred from generation to generation in the same manner. The worm provides shelter and food for the bacteria. The bacteria deliver micronutrients to the worm. The present study reports the genome sequence assembly and annotation of a new strain of Verminephrobacter called Verminephrobacter eiseniae msu.
Methods
We separated the sequences of a new Verminephrobacter strain from the whole genome of Eisenia fetida using the sequence of V. eiseniae EF01-2, and the bacterial genome was assembled using the CLC Workbench. The de novo-assembled genome was annotated and analyzed for the protein domains, functions, and metabolic pathways. Besides, the multigenome comparison was performed to interpret the phylogenomic relationship of the strain with other proteobacteria.
Result
The FastqSifter sifted a total of 593,130 Verminephrobacter genomic reads. The de novo assembly of the reads generated 1832 contigs with a total genome size of 4.4 Mb. The Average Nucleotide Identity denoted the bacterium belongs to the species V. eiseniae, and the 16S rRNA analysis confirmed it as a new strain of V. eiseniae. The AUGUSTUS genome annotation predicted a total of 3809 protein-coding genes; of them, 3805 genes were identified from the homology search.
Conclusion
The bioinformatics analysis confirmed the bacterium is an isolate of V. eiseniae, and it was named Verminephrobacter eiseniae msu. The whole genome of the bacteria can be utilized as a useful resource to explore the area of symbiosis further.
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26
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van Schadewijk R, Krug JR, Shen D, Sankar Gupta KBS, Vergeldt FJ, Bisseling T, Webb AG, Van As H, Velders AH, de Groot HJM, Alia A. Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla. Sci Rep 2020; 10:971. [PMID: 31969628 PMCID: PMC6976659 DOI: 10.1038/s41598-020-57861-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Interactions between plants and the soil’s microbial & fungal flora are crucial for the health of soil ecosystems and food production. Microbe-plant interactions are difficult to investigate in situ due to their intertwined relationship involving morphology and metabolism. Here, we describe an approach to overcome this challenge by elucidating morphology and the metabolic profile of Medicago truncatula root nodules using Magnetic Resonance (MR) Microscopy, at the highest magnetic field strength (22.3 T) currently available for imaging. A home-built solenoid RF coil with an inner diameter of 1.5 mm was used to study individual root nodules. A 3D imaging sequence with an isotropic resolution of (7 μm)3 was able to resolve individual cells, and distinguish between cells infected with rhizobia and uninfected cells. Furthermore, we studied the metabolic profile of cells in different sections of the root nodule using localised MR spectroscopy and showed that several metabolites, including betaine, asparagine/aspartate and choline, have different concentrations across nodule zones. The metabolite spatial distribution was visualised using chemical shift imaging. Finally, we describe the technical challenges and outlook towards future in vivo MR microscopy of nodules and the plant root system.
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Affiliation(s)
- Remco van Schadewijk
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Julia R Krug
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, Wageningen, 6708 WG, The Netherlands
| | - Defeng Shen
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Karthick B S Sankar Gupta
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Frank J Vergeldt
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Andrew G Webb
- C.J. Gorter Center for High Field MRI, Radiology department, Leiden University Medical Centre, Leiden University, Leiden, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Henk Van As
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Aldrik H Velders
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, Wageningen, 6708 WG, The Netherlands
| | - Huub J M de Groot
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - A Alia
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands. .,Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16/18, Leipzig, 04107, Germany.
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27
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The rhizobial autotransporter determines the symbiotic nitrogen fixation activity of Lotus japonicus in a host-specific manner. Proc Natl Acad Sci U S A 2020; 117:1806-1815. [PMID: 31900357 DOI: 10.1073/pnas.1913349117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Leguminous plants establish endosymbiotic associations with rhizobia and form root nodules in which the rhizobia fix atmospheric nitrogen. The host plant and intracellular rhizobia strictly control this symbiotic nitrogen fixation. We recently reported a Lotus japonicus Fix- mutant, apn1 (aspartic peptidase nodule-induced 1), that impairs symbiotic nitrogen fixation. APN1 encodes a nodule-specific aspartic peptidase involved in the Fix- phenotype in a rhizobial strain-specific manner. This host-strain specificity implies that some molecular interactions between host plant APN1 and rhizobial factors are required, although the biological function of APN1 in nodules and the mechanisms governing the interactions are unknown. To clarify how rhizobial factors are involved in strain-specific nitrogen fixation, we explored transposon mutants of Mesorhizobium loti strain TONO, which normally form Fix- nodules on apn1 roots, and identified TONO mutants that formed Fix+ nodules on apn1 The identified causal gene encodes an autotransporter, part of a protein secretion system of Gram-negative bacteria. Expression of the autotransporter gene in M. loti strain MAFF3030399, which normally forms Fix+ nodules on apn1 roots, resulted in Fix- nodules. The autotransporter of TONO functions to secrete a part of its own protein (a passenger domain) into extracellular spaces, and the recombinant APN1 protein cleaved the passenger protein in vitro. The M. loti autotransporter showed the activity to induce the genes involved in nodule senescence in a dose-dependent manner. Therefore, we conclude that the nodule-specific aspartic peptidase, APN1, suppresses negative effects of the rhizobial autotransporter in order to maintain effective symbiotic nitrogen fixation in root nodules.
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28
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Berger A, Boscari A, Horta Araújo N, Maucourt M, Hanchi M, Bernillon S, Rolin D, Puppo A, Brouquisse R. Plant Nitrate Reductases Regulate Nitric Oxide Production and Nitrogen-Fixing Metabolism During the Medicago truncatula-Sinorhizobium meliloti Symbiosis. FRONTIERS IN PLANT SCIENCE 2020; 11:1313. [PMID: 33013954 PMCID: PMC7500168 DOI: 10.3389/fpls.2020.01313] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 08/11/2020] [Indexed: 05/08/2023]
Abstract
Nitrate reductase (NR) is the first enzyme of the nitrogen reduction pathway in plants, leading to the production of ammonia. However, in the nitrogen-fixing symbiosis between legumes and rhizobia, atmospheric nitrogen (N2) is directly reduced to ammonia by the bacterial nitrogenase, which questions the role of NR in symbiosis. Next to that, NR is the best-characterized source of nitric oxide (NO) in plants, and NO is known to be produced during the symbiosis. In the present study, we first surveyed the three NR genes (MtNR1, MtNR2, and MtNR3) present in the Medicago truncatula genome and addressed their expression, activity, and potential involvement in NO production during the symbiosis between M. truncatula and Sinorhizobium meliloti. Our results show that MtNR1 and MtNR2 gene expression and activity are correlated with NO production throughout the symbiotic process and that MtNR1 is particularly involved in NO production in mature nodules. Moreover, NRs are involved together with the mitochondrial electron transfer chain in NO production throughout the symbiotic process and energy regeneration in N2-fixing nodules. Using an in vivo NMR spectrometric approach, we show that, in mature nodules, NRs participate also in the regulation of energy state, cytosolic pH, carbon and nitrogen metabolism under both normoxia and hypoxia. These data point to the importance of NR activity for the N2-fixing symbiosis and provide a first explanation of its role in this process.
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Affiliation(s)
- Antoine Berger
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
- Department of Horticultural Science, University of Florida, Gainesville, FL, United States
| | - Alexandre Boscari
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Natasha Horta Araújo
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Mickaël Maucourt
- Univ. Bordeaux INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon, France
| | - Mohamed Hanchi
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Stéphane Bernillon
- PMB-Metabolome, INRAE, Bordeaux Metabolome Facility, Villenave d’Ornon, France
| | - Dominique Rolin
- Univ. Bordeaux INRAE, UMR Biologie du Fruit et Pathologie, Villenave d’Ornon, France
- PMB-Metabolome, INRAE, Bordeaux Metabolome Facility, Villenave d’Ornon, France
| | - Alain Puppo
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
| | - Renaud Brouquisse
- Institut Sophia Agrobiotech, UMR INRAE 1355, Université Côte d’Azur, CNRS, Sophia Antipolis, France
- *Correspondence: Renaud Brouquisse,
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29
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Alaswad AA, Oehrle NW, Krishnan HB. Classical Soybean ( Glycine max (L.) Merr) Symbionts, Sinorhizobium fredii USDA191 and Bradyrhizobium diazoefficiens USDA110, Reveal Contrasting Symbiotic Phenotype on Pigeon Pea ( Cajanus cajan (L.) Millsp). Int J Mol Sci 2019; 20:E1091. [PMID: 30832430 PMCID: PMC6429105 DOI: 10.3390/ijms20051091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 02/06/2023] Open
Abstract
Pigeon pea (Cajanus cajan (L.) Millspaugh) is cultivated widely in semiarid agricultural regions in over 90 countries around the world. This important legume can enter into symbiotic associations with a wide range of rhizobia including Bradyrhizobium and fast-growing rhizobia. In comparison with other major legumes such as soybean and common bean, only limited information is available on the symbiotic interaction of pigeon pea with rhizobia. In this study, we investigated the ability of two classical soybean symbionts-S. fredii USDA191 and B. diazoefficiens USDA110-and their type 3 secretion system (T3SS) mutants, to nodulate pigeon pea. Both S. fredii USDA191 and a T3SS mutant S. fredii RCB26 formed nitrogen-fixing nodules on pigeon pea. Inoculation of pigeon pea roots with B. diazoefficiens USDA110 and B. diazoefficiens Δ136 (a T3SS mutant) resulted in the formation of Fix- and Fix+ nodules, respectively. Light and transmission electron microscopy of Fix- nodules initiated by B. diazoefficiens USDA110 revealed the complete absence of rhizobia within these nodules. In contrast, Fix+ nodules formed by B. diazoefficiens Δ136 revealed a central region that was completely filled with rhizobia. Ultrastructural investigation revealed the presence of numerous bacteroids surrounded by peribacteroid membranes in the infected cells. Analysis of nodule proteins by one- and two-dimensional gel electrophoresis revealed that leghemoglobin was absent in B. diazoefficiens USDA110 nodules, while it was abundantly present in B. diazoefficiens Δ136 nodules. Results of competitive nodulation assays indicated that B. diazoefficiens Δ136 had greater competitiveness for nodulation on pigeon pea than did the wild type strain. Our results suggest that this T3SS mutant of B. diazoefficiens, due to its greater competitiveness and ability to form Fix+ nodules, could be exploited as a potential inoculant to boost pigeon pea productivity.
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Affiliation(s)
- Alaa A Alaswad
- Plant Science Division, University of Missouri, Columbia, MO 65211, USA.
- King Abdul Aziz University, 21589 Jeddah, Saudi Arabia.
| | - Nathan W Oehrle
- Plant Genetics Research Unit, USDA-Agricultural Research Service, Columbia, MO 65211, USA.
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MO 65211, USA.
- Plant Genetics Research Unit, USDA-Agricultural Research Service, Columbia, MO 65211, USA.
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30
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Pfau T, Christian N, Masakapalli SK, Sweetlove LJ, Poolman MG, Ebenhöh O. The intertwined metabolism during symbiotic nitrogen fixation elucidated by metabolic modelling. Sci Rep 2018; 8:12504. [PMID: 30131500 PMCID: PMC6104047 DOI: 10.1038/s41598-018-30884-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/07/2018] [Indexed: 11/09/2022] Open
Abstract
Genome-scale metabolic network models can be used for various analyses including the prediction of metabolic responses to changes in the environment. Legumes are well known for their rhizobial symbiosis that introduces nitrogen into the global nutrient cycle. Here, we describe a fully compartmentalised, mass and charge-balanced, genome-scale model of the clover Medicago truncatula, which has been adopted as a model organism for legumes. We employed flux balance analysis to demonstrate that the network is capable of producing biomass components in experimentally observed proportions, during day and night. By connecting the plant model to a model of its rhizobial symbiont, Sinorhizobium meliloti, we were able to investigate the effects of the symbiosis on metabolic fluxes and plant growth and could demonstrate how oxygen availability influences metabolic exchanges between plant and symbiont, thus elucidating potential benefits of inter organism amino acid cycling. We thus provide a modelling framework, in which the interlinked metabolism of plants and nodules can be studied from a theoretical perspective.
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Affiliation(s)
- Thomas Pfau
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Nils Christian
- Institute of Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, UK
| | - Shyam K Masakapalli
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Mark G Poolman
- Department Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology, Cluster of Excellence on Plant Sciences CEPLAS, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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31
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Harke MJ, Frischkorn KR, Haley ST, Aylward FO, Zehr JP, Dyhrman ST. Periodic and coordinated gene expression between a diazotroph and its diatom host. ISME JOURNAL 2018; 13:118-131. [PMID: 30116042 DOI: 10.1038/s41396-018-0262-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/28/2018] [Indexed: 01/30/2023]
Abstract
In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom-diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day-night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N2 fixation, and resource acquisition, among other processes. N2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont-host physiological ecology is strongly interconnected in the NPSG.
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Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Kyle R Frischkorn
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Columbia University, Palisades, NY, USA. .,Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA.
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32
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Thal B, Braun HP, Eubel H. Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology. PLANT MOLECULAR BIOLOGY 2018; 97:233-251. [PMID: 29779088 DOI: 10.1007/s11103-018-0736-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/08/2018] [Indexed: 05/25/2023]
Abstract
Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins. Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.
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Affiliation(s)
- Beate Thal
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany
| | - Holger Eubel
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hanover, Germany.
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Guerrero-Castro J, Lozano L, Sohlenkamp C. Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899. Front Microbiol 2018; 9:846. [PMID: 29760688 PMCID: PMC5936775 DOI: 10.3389/fmicb.2018.00846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/12/2018] [Indexed: 11/27/2022] Open
Abstract
Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic and physiological basis of the tolerance to acidic conditions. To identify genes in R. tropici involved in pH stress response we combined two different approaches: (1) A Tn5 mutant library of R. tropici CIAT899 was screened and 26 acid-sensitive mutants were identified. For 17 of these mutants, the transposon insertion sites could be identified. (2) We also studied the transcriptomes of cells grown under different pH conditions using RNA-Seq. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 min at pH 4.5. Of the 6,289 protein-coding genes annotated in the genome of R. tropici CIAT 899, 383 were differentially expressed under acidic conditions (pH 4.5) vs. control condition (pH 6.8). Three hundred and fifty one genes were induced and 32 genes were repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, enzymes involved in amino acid and carbohydrate metabolism and proton extrusion, in addition to several hypothetical genes. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.
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Affiliation(s)
- Julio Guerrero-Castro
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Christian Sohlenkamp
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Coba de la Peña T, Fedorova E, Pueyo JJ, Lucas MM. The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle? FRONTIERS IN PLANT SCIENCE 2018; 8:2229. [PMID: 29403508 PMCID: PMC5786577 DOI: 10.3389/fpls.2017.02229] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/19/2017] [Indexed: 05/21/2023]
Abstract
In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.
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Affiliation(s)
- Teodoro Coba de la Peña
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Elena Fedorova
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
- K. A. Timiryazev Institute of Plant Physiology, Russian Academy of Science, Moscow, Russia
| | - José J Pueyo
- Instituto de Ciencias Agrarias ICA-CSIC, Madrid, Spain
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Reagan BC, Kim PJY, Perry PD, Dunlap JR, Burch-Smith TM. Spatial distribution of organelles in leaf cells and soybean root nodules revealed by focused ion beam-scanning electron microscopy. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:180-191. [PMID: 32291032 DOI: 10.1071/fp16347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 12/23/2016] [Indexed: 06/11/2023]
Abstract
Analysis of cellular ultrastructure has been dominated by transmission electron microscopy (TEM), so images collected by this technique have shaped our current understanding of cellular structure. More recently, three-dimensional (3D) analysis of organelle structures has typically been conducted using TEM tomography. However, TEM tomography application is limited by sample thickness. Focused ion beam-scanning electron microscopy (FIB-SEM) uses a dual beam system to perform serial sectioning and imaging of a sample. Thus FIB-SEM is an excellent alternative to TEM tomography and serial section TEM tomography. Animal tissue samples have been more intensively investigated by this technique than plant tissues. Here, we show that FIB-SEM can be used to study the 3D ultrastructure of plant tissues in samples previously prepared for TEM via commonly used fixation and embedding protocols. Reconstruction of FIB-SEM sections revealed ultra-structural details of the plant tissues examined. We observed that organelles packed tightly together in Nicotiana benthamiana Domin leaf cells may form membrane contacts. 3D models of soybean nodule cells suggest that the bacteroids in infected cells are contained within one large membrane-bound structure and not the many individual symbiosomes that TEM thin-sections suggest. We consider the implications of these organelle arrangements for intercellular signalling.
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Affiliation(s)
- Brandon C Reagan
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
| | - Paul J-Y Kim
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
| | - Preston D Perry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
| | - John R Dunlap
- Advanced Microscopy and Imaging Center, University of Tennessee, Knoxville, 1499 Circle Dr Knoxville, TN 37996, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 1414 Cumberland Avenue , Knoxville ,TN 37996, USA
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Yamaya-Ito H, Shimoda Y, Hakoyama T, Sato S, Kaneko T, Hossain MS, Shibata S, Kawaguchi M, Hayashi M, Kouchi H, Umehara Y. Loss-of-function of ASPARTIC PEPTIDASE NODULE-INDUCED 1 (APN1) in Lotus japonicus restricts efficient nitrogen-fixing symbiosis with specific Mesorhizobium loti strains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:5-16. [PMID: 29086445 DOI: 10.1111/tpj.13759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 05/06/2023]
Abstract
The nitrogen-fixing symbiosis of legumes and Rhizobium bacteria is established by complex interactions between the two symbiotic partners. Legume Fix- mutants form apparently normal nodules with endosymbiotic rhizobia but fail to induce rhizobial nitrogen fixation. These mutants are useful for identifying the legume genes involved in the interactions essential for symbiotic nitrogen fixation. We describe here a Fix- mutant of Lotus japonicus, apn1, which showed a very specific symbiotic phenotype. It formed ineffective nodules when inoculated with the Mesorhizobium loti strain TONO. In these nodules, infected cells disintegrated and successively became necrotic, indicating premature senescence typical of Fix- mutants. However, it formed effective nodules when inoculated with the M. loti strain MAFF303099. Among nine different M. loti strains tested, four formed ineffective nodules and five formed effective nodules on apn1 roots. The identified causal gene, ASPARTIC PEPTIDASE NODULE-INDUCED 1 (LjAPN1), encodes a nepenthesin-type aspartic peptidase. The well characterized Arabidopsis aspartic peptidase CDR1 could complement the strain-specific Fix- phenotype of apn1. LjAPN1 is a typical late nodulin; its gene expression was exclusively induced during nodule development. LjAPN1 was most abundantly expressed in the infected cells in the nodules. Our findings indicate that LjAPN1 is required for the development and persistence of functional (nitrogen-fixing) symbiosis in a rhizobial strain-dependent manner, and thus determines compatibility between M. loti and L. japonicus at the level of nitrogen fixation.
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Affiliation(s)
- Hiroko Yamaya-Ito
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0800, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tsuneo Hakoyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Takakazu Kaneko
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Md Shakhawat Hossain
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoshi Shibata
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | | | - Makoto Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroshi Kouchi
- International Christian University, Mitaka, Tokyo, 181-8585, Japan
| | - Yosuke Umehara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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Liu A, Contador CA, Fan K, Lam HM. Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes. FRONTIERS IN PLANT SCIENCE 2018; 9:1860. [PMID: 30619423 PMCID: PMC6305480 DOI: 10.3389/fpls.2018.01860] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.
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Affiliation(s)
- Ailin Liu
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Carolina A. Contador
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kejing Fan
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- *Correspondence: Hon-Ming Lam,
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Andreev IM. Emerging evidence for potential role of Ca 2+-ATPase-mediated calcium accumulation in symbiosomes of infected root nodule cells. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:955-960. [PMID: 32480623 DOI: 10.1071/fp17042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/28/2017] [Indexed: 06/11/2023]
Abstract
Symbiosomes are organelle-like compartments responsible for nitrogen fixation in infected nodule cells of legumes, which are formed as a result of symbiotic association of soil bacteria rhizobia with certain plant root cells. They are virtually the only source of reduced nitrogen in the Earth's biosphere, and consequently, are of great importance. It has been proven that the functioning of symbiosomes depends to a large extent on the transport of various metabolites and ions - most likely including Ca2+ - across the symbiosome membrane (SM). Although it has been well established that this cation is involved in the regulation of a broad spectrum of processes in cells of living organisms, its role in the functioning of symbiosomes remains obscure. This is despite available data indicating both its transport through the SM and accumulation within these compartments. This review summarises the results obtained in the course of studies on the given aspects of calcium behaviour in symbiosomes, and on this basis gives a possible explanation of the proper functional role in them of Ca2+.
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Affiliation(s)
- Igor M Andreev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya st. 35, Moscow 127276, Russia. Email
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Burghardt LT, Guhlin J, Chun CL, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P. Transcriptomic basis of genome by genome variation in a legume‐rhizobia mutualism. Mol Ecol 2017; 26:6122-6135. [DOI: 10.1111/mec.14285] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/10/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Liana T. Burghardt
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Joseph Guhlin
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Chan Lan Chun
- BioTechnology Institute University of Minnesota St. Paul MN USA
| | - Junqi Liu
- Department of Agronomy and Plant Genetics University of Minnesota St. Paul MN USA
| | | | - Robert M. Stupar
- Department of Agronomy and Plant Genetics University of Minnesota St. Paul MN USA
| | - Nevin D. Young
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
- Department of Plant Pathology University of Minnesota St. Paul MN USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
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Sugiyama A, Saida Y, Yoshimizu M, Takanashi K, Sosso D, Frommer WB, Yazaki K. Molecular Characterization of LjSWEET3, a Sugar Transporter in Nodules of Lotus japonicus. PLANT & CELL PHYSIOLOGY 2017; 58:298-306. [PMID: 28007966 DOI: 10.1093/pcp/pcw190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
Symbiotic nitrogen fixation in legumes contributes greatly to the global nitrogen cycle on the earth. In nodules, resident rhizobia supply nitrogen nutrient fixed from atmospheric N2 to the host plant; in turn, the plant provides photosynthetic metabolites to bacteroids as a carbon source. In this process, various transporters are involved at different membrane systems; however, little is known at the molecular level about the flow of carbon from the host cells to the symbiotic bacteria. We have been studying transporters functioning in nodules of Lotus japonicus, and found that out of 13 SWEET genes in the L. japonicus genome LjSWEET3, a member of the SWEET transporter family, is highly expressed in nodules. The SWEET family was first identified in Arabidopsis, where members of the family are involved in phloem loading, nectar secretion, pollen nutrition and seed filling. The expression of LjSWEET3 strongly increased during nodule development and reached the highest level in mature nodules. Histochemical analysis using L. japonicus plants transformed with LjSWEET3 promoter:GUS (β-glucuronidase) showed strong expression in the vascular systems of nodules. Analysis of an LjSWEET3-green fluorescent protein (GFP) fusion expressed in Nicotiana banthamiana and Coptis japonica indicates that LjSWEET3 localizes to the plasma membrane. Together these data are consistent with a role for LjSWEET3 in sugar translocation towards nodules and also suggest the possible existence of multiple routes of carbon supply into nodules.
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Affiliation(s)
- Akifumi Sugiyama
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Yuka Saida
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Mayuko Yoshimizu
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
| | - Kojiro Takanashi
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
- Institute of Mountain Science, Shinshu University, Matsumoto, Japan
| | - Davide Sosso
- Department of Plant Biology, Carnegie Institution of Science, Stanford, CA , USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution of Science, Stanford, CA , USA
| | - Kazufumi Yazaki
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
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Wang X, Komatsu S. Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 82:117-148. [PMID: 28427531 DOI: 10.1016/bs.afnr.2016.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.
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Affiliation(s)
- Xin Wang
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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Takanashi K, Sasaki T, Kan T, Saida Y, Sugiyama A, Yamamoto Y, Yazaki K. A Dicarboxylate Transporter, LjALMT4, Mainly Expressed in Nodules of Lotus japonicus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:584-92. [PMID: 27183039 DOI: 10.1094/mpmi-04-16-0071-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Legume plants can establish symbiosis with soil bacteria called rhizobia to obtain nitrogen as a nutrient directly from atmospheric N2 via symbiotic nitrogen fixation. Legumes and rhizobia form nodules, symbiotic organs in which fixed-nitrogen and photosynthetic products are exchanged between rhizobia and plant cells. The photosynthetic products supplied to rhizobia are thought to be dicarboxylates but little is known about the movement of dicarboxylates in the nodules. In terms of dicarboxylate transporters, an aluminum-activated malate transporter (ALMT) family is a strong candidate responsible for the membrane transport of carboxylates in nodules. Among the seven ALMT genes in the Lotus japonicus genome, only one, LjALMT4, shows a high expression in the nodules. LjALMT4 showed transport activity in a Xenopus oocyte system, with LjALMT4 mediating the efflux of dicarboxylates including malate, succinate, and fumarate, but not tricarboxylates such as citrate. LjALMT4 also mediated the influx of several inorganic anions. Organ-specific gene expression analysis showed LjALMT4 mRNA mainly in the parenchyma cells of nodule vascular bundles. These results suggest that LjALMT4 may not be involved in the direct supply of dicarboxylates to rhizobia in infected cells but is responsible for supplying malate as well as several anions necessary for symbiotic nitrogen fixation, via nodule vasculatures.
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Affiliation(s)
- Kojiro Takanashi
- 1 Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
- 2 Institute of Mountain Science, Shinshu University, Matsumoto 390-8621, Japan; and
| | - Takayuki Sasaki
- 3 Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Tomohiro Kan
- 1 Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Yuka Saida
- 1 Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Akifumi Sugiyama
- 1 Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Yoko Yamamoto
- 3 Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Kazufumi Yazaki
- 1 Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
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Kant C, Pradhan S, Bhatia S. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.). PLoS One 2016; 11:e0157908. [PMID: 27348121 PMCID: PMC4922567 DOI: 10.1371/journal.pone.0157908] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/07/2016] [Indexed: 12/17/2022] Open
Abstract
A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.
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Affiliation(s)
- Chandra Kant
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Seema Pradhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
- * E-mail:
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Lardi M, Murset V, Fischer HM, Mesa S, Ahrens CH, Zamboni N, Pessi G. Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures. Int J Mol Sci 2016; 17:E815. [PMID: 27240350 PMCID: PMC4926349 DOI: 10.3390/ijms17060815] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/13/2016] [Accepted: 05/19/2016] [Indexed: 01/17/2023] Open
Abstract
Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection-time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots from four different B. diazoefficiens host plants; (ii) soybean nodules harvested at different time points during nodule development; and (iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by independent transcriptomics data. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions.
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Affiliation(s)
- Martina Lardi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland.
| | - Valérie Murset
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
| | - Hans-Martin Fischer
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), E-18080 Granada, Spain.
| | - Christian H Ahrens
- Agroscope, Institute for Plant Production Sciences, Research Group Molecular Diagnostics, Genomics and Bioinformatics & Swiss Institute of Bioinformatics (SIB), CH-8820 Wädenswil, Switzerland.
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, CH-8093 Zürich, Switzerland.
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland.
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Baral B, Teixeira da Silva JA, Izaguirre-Mayoral ML. Early signaling, synthesis, transport and metabolism of ureides. JOURNAL OF PLANT PHYSIOLOGY 2016; 193:97-109. [PMID: 26967003 DOI: 10.1016/j.jplph.2016.01.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/04/2015] [Accepted: 01/11/2016] [Indexed: 05/26/2023]
Abstract
The symbiosis between α nitrogen (N2)-fixing Proteobacteria (family Rhizobiaceae) and legumes belonging to the Fabaceae (a single phylogenetic group comprising three subfamilies: Caesalpinioideae, Mimosoideae and Papilionoideae) results in the formation of a novel root structure called a nodule, where atmospheric N2 is fixed into NH3(+). In the determinate type of nodules harbored by Rhizobium-nodulated Fabaceae species, newly synthesized NH3(+) is finally converted into allantoin (C4H6N4O3) and allantoic acid (C4H8N4O4) (ureides) through complex pathways involving at least 20 different enzymes that act synchronously in two types of nodule cells with contrasting ultrastructure, including the tree nodule cell organelles. Newly synthesized ureides are loaded into the network of nodule-root xylem vessels and transported to aerial organs by the transpirational water current. Once inside the leaves, ureides undergo an enzymatically driven reverse process to yield NH4(+) that is used for growth. This supports the role of ureides as key nitrogen (N)-compounds for the growth and yield of legumes nodulated by Rhizobium that grow in soils with a low N content. Thus, a concrete understanding of the mechanisms underlying ureide biogenesis and catabolism in legumes may help agrobiologists to achieve greater agricultural discoveries. In this review we focus on the transmembranal and transorganellar symplastic and apoplastic movement of N-precursors within the nodules, as well as on the occurrence, localization and properties of enzymes and genes involved in the biogenesis and catabolism of ureides. The synthesis and transport of ureides are not unique events in Rhizobium-nodulated N2-fixing legumes. Thus, a brief description of the synthesis and catabolism of ureides in non-legumes was included for comparison. The establishment of the symbiosis, nodule organogenesis and the plant's control of nodule number, synthesis and translocation of ureides via feed-back inhibition mechanisms are also reviewed.
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Affiliation(s)
- Bikash Baral
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, Latokartanonkaari 7, FIN-00014 Helsinki, Finland.
| | | | - Maria Luisa Izaguirre-Mayoral
- Biological Nitrogen Fixation Laboratory, Chemistry Department, Faculty of Science, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa.
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Kang Y, Li M, Sinharoy S, Verdier J. A Snapshot of Functional Genetic Studies in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2016; 7:1175. [PMID: 27555857 PMCID: PMC4977297 DOI: 10.3389/fpls.2016.01175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
In the current context of food security, increase of plant protein production in a sustainable manner represents one of the major challenges of agronomic research, which could be partially resolved by increased cultivation of legume crops. Medicago truncatula is now a well-established model for legume genomic and genetic studies. With the establishment of genomics tools and mutant populations in M. truncatula, it has become an important resource to answer some of the basic biological questions related to plant development and stress tolerance. This review has an objective to overview a decade of genetic studies in this model plant from generation of mutant populations to nowadays. To date, the three biological fields, which have been extensively studied in M. truncatula, are the symbiotic nitrogen fixation, the seed development, and the abiotic stress tolerance, due to their significant agronomic impacts. In this review, we summarize functional genetic studies related to these three major biological fields. We integrated analyses of a nearly exhaustive list of genes into their biological contexts in order to provide an overview of the forefront research advances in this important legume model plant.
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Affiliation(s)
- Yun Kang
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Minguye Li
- University of Chinese Academy of SciencesBeijing, China
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Senjuti Sinharoy
- Department of Biotechnology, University of CalcuttaCalcutta, India
| | - Jerome Verdier
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Jerome Verdier
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Tittabutr P, Sripakdi S, Boonkerd N, Tanthanuch W, Minamisawa K, Teaumroong N. Possible Role of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Activity of Sinorhizobium sp. BL3 on Symbiosis with Mung Bean and Determinate Nodule Senescence. Microbes Environ 2015; 30:310-20. [PMID: 26657304 PMCID: PMC4676554 DOI: 10.1264/jsme2.me15120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/19/2015] [Indexed: 01/03/2023] Open
Abstract
Sinorhizobium sp. BL3 forms symbiotic interactions with mung bean (Vigna radiata) and contains lrpL-acdS genes, which encode the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme that cleaves ACC, a precursor of plant ethylene synthesis. Since ethylene interferes with nodule formation in some legumes and plays a role in senescence in plant cells, BL3-enhancing ACC deaminase activity (BL3(+)) and defective mutant (BL3(-)) strains were constructed in order to investigate the effects of this enzyme on symbiosis and nodule senescence. Nodulation competitiveness was weaker in BL3(-) than in the wild-type, but was stronger in BL3(+). The inoculation of BL3(-) into mung bean resulted in less plant growth, a lower nodule dry weight, and smaller nodule number than those in the wild-type, whereas the inoculation of BL3(+) had no marked effects. However, similar nitrogenase activity was observed with all treatments; it was strongly detected 3 weeks after the inoculation and gradually declined with time, indicating senescence. The rate of plant nodulation by BL3(+) increased in a time-dependent manner. Nodules occupied by BL3(-) formed smaller symbiosomes, and bacteroid degradation was more prominent than that in the wild-type 7 weeks after the inoculation. Changes in biochemical molecules during nodulation were tracked by Fourier Transform Infrared (FT-IR) microspectroscopy, and the results obtained confirmed that aging processes differed in nodules occupied by BL3 and BL3(-). This is the first study to show the possible role of ACC deaminase activity in senescence in determinate nodules. Our results suggest that an increase in ACC deaminase activity in this strain does not extend the lifespan of nodules, whereas the lack of this activity may accelerate nodule senescence.
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Affiliation(s)
- Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
| | - Sudarat Sripakdi
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
| | - Waraporn Tanthanuch
- Synchrotron Light Research Institute (public organization)Nakhon Ratchasima 30000Thailand
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577Japan
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
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Vigna subterranea ammonium transporter gene ( VsAMT1): Some bioinformatics insights. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2015; 8:88-93. [PMID: 28352577 PMCID: PMC4980749 DOI: 10.1016/j.btre.2015.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/22/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
Abstract
Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which nitrogen is preferentially absorbed by plants. Vigna subterranea (VsAMT1) and Solanum tuberosum (StAMT1) AMT1s were characterized using molecular biology and bioinformatics methods. AMT1-specific primers were designed and used to amplify the AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned VsAMT1 and StAMT1 to the AMT1 family. The deduced amino acid sequences showed that VsAMT1 is 92% and 89% similar to Phaseolus vulgaris PvAMT1.1 and Glycine max AMT1 respectively, while StAMT1 is 92% similar to Solanum lycopersicum LeAMT1.1, and correspond to the 5th–10th trans-membrane domains. Residues VsAMT1 D23 and StAMT1 D15 are predicted to be essential for ammonium transport, while mutations of VsAMT1 W1A-L and S87A and StAMT1 S76A may further enhance ammonium transport. In addition to nitrogen uptake from the roots, VsAMT1 may also contribute to interactions with rhizobia.
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Yan Z, Hossain MS, Arikit S, Valdés-López O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC, Stacey G. Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j-3p in soybean nodulation. THE NEW PHYTOLOGIST 2015; 207:748-59. [PMID: 25783944 DOI: 10.1111/nph.13365] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/09/2015] [Indexed: 05/25/2023]
Abstract
Plant microRNAs (miRNAs) play important regulatory roles in a number of developmental processes. The present work investigated the roles of miRNAs during nodule development in the crop legume soybean (Glycine max). Fifteen soybean small RNA libraries were sequenced from different stages of nodule development, including young nodules, mature nodules and senescent nodules. In order to identify the regulatory targets of the miRNAs, five parallel analysis of RNA ends (PARE) libraries were also sequenced from the same stages of nodule development. Sequencing identified 284 miRNAs, including 178 novel soybean miRNAs. Analysis of miRNA abundance identified 139 miRNAs whose expression was significantly regulated during nodule development, including 12 miRNAs whose expression changed > 10-fold. Analysis of the PARE libraries identified 533 miRNA targets, including three nodulation-related genes and eight nodule-specific genes. miR393j-3p was selected for detailed analysis as its expression was significantly regulated during nodule formation, and it targeted a nodulin gene, Early Nodulin 93 (ENOD93). Strong, ectopic expression of miR393j-3p, as well as RNAi silencing of ENOD93 expression, significantly reduced nodule formation. The data indicate that miR393j-3p regulation of ENOD93 mRNA abundance is a key control point for soybean nodule formation.
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Affiliation(s)
- Zhe Yan
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Md Shakhawat Hossain
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Siwaret Arikit
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Oswaldo Valdés-López
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Jixian Zhai
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Jun Wang
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Marc Libault
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tieming Ji
- Department of Statistics, University of Missouri, 209D Middlebush Hall, Columbia, MO, 65211, USA
| | - Lijuan Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, USA
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, National Center for Soybean Biotechnology, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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Clarke VC, Loughlin PC, Gavrin A, Chen C, Brear EM, Day DA, Smith PMC. Proteomic analysis of the soybean symbiosome identifies new symbiotic proteins. Mol Cell Proteomics 2015; 14:1301-22. [PMID: 25724908 PMCID: PMC4424401 DOI: 10.1074/mcp.m114.043166] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 02/25/2015] [Indexed: 12/21/2022] Open
Abstract
Legumes form a symbiosis with rhizobia in which the plant provides an energy source to the rhizobia bacteria that it uses to fix atmospheric nitrogen. This nitrogen is provided to the legume plant, allowing it to grow without the addition of nitrogen fertilizer. As part of the symbiosis, the bacteria in the infected cells of a new root organ, the nodule, are surrounded by a plant-derived membrane, the symbiosome membrane, which becomes the interface between the symbionts. Fractions containing the symbiosome membrane (SM) and material from the lumen of the symbiosome (peribacteroid space or PBS) were isolated from soybean root nodules and analyzed using nongel proteomic techniques. Bicarbonate stripping and chloroform-methanol extraction of isolated SM were used to reduce complexity of the samples and enrich for hydrophobic integral membrane proteins. One hundred and ninety-seven proteins were identified as components of the SM, with an additional fifteen proteins identified from peripheral membrane and PBS protein fractions. Proteins involved in a range of cellular processes such as metabolism, protein folding and degradation, membrane trafficking, and solute transport were identified. These included a number of proteins previously localized to the SM, such as aquaglyceroporin nodulin 26, sulfate transporters, remorin, and Rab7 homologs. Among the proteome were a number of putative transporters for compounds such as sulfate, calcium, hydrogen ions, peptide/dicarboxylate, and nitrate, as well as transporters for which the substrate is not easy to predict. Analysis of the promoter activity for six genes encoding putative SM proteins showed nodule specific expression, with five showing expression only in infected cells. Localization of two proteins was confirmed using GFP-fusion experiments. The data have been deposited to the ProteomeXchange with identifier PXD001132. This proteome will provide a rich resource for the study of the legume-rhizobium symbiosis.
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Affiliation(s)
- Victoria C Clarke
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia
| | - Patrick C Loughlin
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia
| | - Aleksandr Gavrin
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia
| | - Chi Chen
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia
| | - Ella M Brear
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia
| | - David A Day
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia; §Flinders University, School of Biological Sciences, Adelaide Australia
| | - Penelope M C Smith
- From the ‡University of Sydney, School of Biological Sciences, Sydney Australia;
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