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Soyano T, Akamatsu A, Takeda N, Watahiki MK, Goh T, Okuma N, Suganuma N, Kojima M, Takebayashi Y, Sakakibara H, Nakajima K, Kawaguchi M. Periodic cytokinin responses in Lotus japonicus rhizobium infection and nodule development. Science 2024; 385:288-294. [PMID: 39024445 DOI: 10.1126/science.adk5589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 04/26/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Host plants benefit from legume root nodule symbiosis with nitrogen-fixing bacteria under nitrogen-limiting conditions. In this interaction, the hosts must regulate nodule numbers and distribution patterns to control the degree of symbiosis and maintain root growth functions. The host response to symbiotic bacteria occurs discontinuously but repeatedly at the region behind the tip of the growing roots. Here, live-imaging and transcriptome analyses revealed oscillating host gene expression with approximately 6-hour intervals upon bacterial inoculation. Cytokinin response also exhibited a similar oscillation pattern. Cytokinin signaling is crucial to maintaining the periodicity, as observed in cytokinin receptor mutants displaying altered infection foci distribution. This periodic regulation influences the size of the root region responsive to bacteria, as well as the nodulation process progression.
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Affiliation(s)
- Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Basic Biology Program, Graduate University for Advanced Studies, SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Akira Akamatsu
- Graduate School of Biological and Environmental Sciences, Kwansei Gakuin University, Gakuen Uegahara 1, Sanda, Hyogo 669-1330, Japan
| | - Naoya Takeda
- Graduate School of Biological and Environmental Sciences, Kwansei Gakuin University, Gakuen Uegahara 1, Sanda, Hyogo 669-1330, Japan
| | - Masaaki K Watahiki
- Faculty of Science, Division of Biological Sciences, Hokkaido University, Kitaku Kita 10, Nishi 8, Sapporo 060-0810, Japan
| | - Tatsuaki Goh
- Nara Institute of Science and Technology, Graduate School of Science and Technology, Division of Biological Science, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Nao Okuma
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Norio Suganuma
- Department of Life Science, Aichi University of Education, Kariya, Aichi 448-8542, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Yumiko Takebayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Keiji Nakajima
- Nara Institute of Science and Technology, Graduate School of Science and Technology, Division of Biological Science, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Basic Biology Program, Graduate University for Advanced Studies, SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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2
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Li H, Ou Y, Huang K, Zhang Z, Cao Y, Zhu H. A pathogenesis-related protein, PRP1, negatively regulates root nodule symbiosis in Lotus japonicus. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3542-3556. [PMID: 38457346 DOI: 10.1093/jxb/erae103] [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: 10/04/2023] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
The legume-rhizobium symbiosis represents a unique model within the realm of plant-microbe interactions. Unlike typical cases of pathogenic invasion, the infection of rhizobia and their residence within symbiotic cells do not elicit a noticeable immune response in plants. Nevertheless, there is still much to uncover regarding the mechanisms through which plant immunity influences rhizobial symbiosis. In this study, we identify an important player in this intricate interplay: Lotus japonicus PRP1, which serves as a positive regulator of plant immunity but also exhibits the capacity to decrease rhizobial colonization and nitrogen fixation within nodules. The PRP1 gene encodes an uncharacterized protein and is named Pathogenesis-Related Protein1, owing to its orthologue in Arabidopsis thaliana, a pathogenesis-related family protein (At1g78780). The PRP1 gene displays high expression levels in nodules compared to other tissues. We observed an increase in rhizobium infection in the L. japonicus prp1 mutants, whereas PRP1-overexpressing plants exhibited a reduction in rhizobium infection compared to control plants. Intriguingly, L. japonicus prp1 mutants produced nodules with a pinker colour compared to wild-type controls, accompanied by elevated levels of leghaemoglobin and an increased proportion of infected cells within the prp1 nodules. The transcription factor Nodule Inception (NIN) can directly bind to the PRP1 promoter, activating PRP1 gene expression. Furthermore, we found that PRP1 is a positive mediator of innate immunity in plants. In summary, our study provides clear evidence of the intricate relationship between plant immunity and symbiosis. PRP1, acting as a positive regulator of plant immunity, simultaneously exerts suppressive effects on rhizobial infection and colonization within nodules.
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Affiliation(s)
- Hao Li
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yajuan Ou
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Kui Huang
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongming Zhang
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangrong Cao
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Zhu
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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3
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Zhuang Y, Wang H, Tan F, Wu B, Liu L, Qin H, Yang Z, He M. Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108619. [PMID: 38604013 DOI: 10.1016/j.plaphy.2024.108619] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.
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Affiliation(s)
- Yong Zhuang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
| | - Hao Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Linpei Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - ZhiJuan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
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4
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Tao K, Jensen IT, Zhang S, Villa-Rodríguez E, Blahovska Z, Salomonsen CL, Martyn A, Björgvinsdóttir ÞN, Kelly S, Janss L, Glasius M, Waagepetersen R, Radutoiu S. Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly. Nat Commun 2024; 15:3436. [PMID: 38653767 DOI: 10.1038/s41467-024-47752-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how the interaction between the legume host and rhizobia impacts the remaining microbiota and whether it depends on nitrogen nutrition. Here, we use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We find that Nod factors are produced by symbionts to activate Nod factor signaling in the host and that this modulates the root exudate profile and the assembly of a symbiotic root microbiota. Lotus plants with different symbiotic abilities, grown in unfertilized or nitrate-supplemented soils, display three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We find that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrate that selected bacterial genera characterizing state-dependent microbiomes have a high level of accurate prediction.
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Affiliation(s)
- Ke Tao
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ib T Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Mathematical Sciences, Aalborg University, Aarhus, Denmark
| | - Sha Zhang
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eber Villa-Rodríguez
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Zuzana Blahovska
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anna Martyn
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | | | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Biotechnology, Lincoln Agritech, Canterbury, New Zealand
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | | | | | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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5
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Hata S, Tsuda R, Kojima S, Tanaka A, Kouchi H. Both incompatible and compatible rhizobia inhabit the intercellular spaces of leguminous root nodules. PLANT SIGNALING & BEHAVIOR 2023; 18:2245995. [PMID: 37573516 PMCID: PMC10424618 DOI: 10.1080/15592324.2023.2245995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
In addition to rhizobia, many types of co-existent bacteria are found in leguminous root nodules, but their habitats are unclear. To investigate this phenomenon, we labeled Bradyrhizobium diazoefficiens USDA122 and Bradyrhizobium sp. SSBR45 with Discosoma sp. red fluorescent protein (DsRed) or enhanced green fluorescent protein (eGFP). USDA122 enhances soybean growth by forming effective root nodules, but SSBR45 does not form any nodules. Using low-magnification laser scanning confocal microscopy, we found that infected cells in the central zone of soybean nodules appeared to be occupied by USDA122. Notably, high-magnification microscopy after co-inoculation of non-fluorescent USDA122 and fluorescence-labeled SSBR45 also revealed that SSBR45 inhabits the intercellular spaces of healthy nodules. More unexpectedly, co-inoculation of eGFP-labeled USDA122 and DsRed-labeled SSBR45 (and vice versa) revealed the presence of USDA122 bacteria in both the symbiosomes of infected cells and in the apoplasts of healthy nodules. We then next inspected nodules formed after a mixed inoculation of differently-labeled USDA122, without SSBR45, and confirmed the inhabitation of the both populations of USDA122 in the intercellular spaces. In contrast, infected cells were occupied by single-labeled USDA122. We also observed Mesorhizobium loti in the intercellular spaces of active wild-type nodules of Lotus japonicus using transmission electron microscopy. Compatible intercellular rhizobia have been described during nodule formation of several legume species and in some mutants, but our evidence suggests that this type of colonization may occur much more commonly in leguminous root nodules.
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Affiliation(s)
- Shingo Hata
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Risa Tsuda
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Serina Kojima
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hiroshi Kouchi
- Division of Arts and Sciences, International Christian University, Mitaka, Japan
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6
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Hata S, Kojima S, Tsuda R, Kawajiri N, Kouchi H, Suzuki T, Uesaka K, Tanaka A. Characterization of photosynthetic Bradyrhizobium sp. strain SSBR45 isolated from the root nodules of Aeschynomene indica. PLANT SIGNALING & BEHAVIOR 2023; 18:2184907. [PMID: 36879507 PMCID: PMC10012927 DOI: 10.1080/15592324.2023.2184907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
We isolated a novel strain of Bradyrhizobium sp., SSBR45, from the nodulated roots of Aeschynomene indica and labeled it with Discosoma sp. red fluorescent protein (dsRED) or enhanced green fluorescent protein (eGFP) and determined its draft genomic sequence. The labeled SSBR45 stimulated the growth of A. indica markedly on a nitrogen-free medium, as observed by visualizing the fluorescent root nodules. The nodulated roots also exhibited high acetylene reduction activities. The SSBR45 genome included genes involved in nitrogen fixation, photosynthesis, and type IV secretion system; however, it did not consist of canonical nodABC genes and type III secretion system genes. SSBR45, a novel species of the genus Bradyrhizobium, consisted of an average nucleotide identity and average amino acid identity of 87% and 90%, respectively, with the closest strain B. oligotrophicum S58.
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Affiliation(s)
- Shingo Hata
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Serina Kojima
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | - Risa Tsuda
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | | | - Hiroshi Kouchi
- Division of Arts and Sciences, International Christian University, Mitaka, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Aiko Tanaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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7
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Luo Z, Liu H, Xie F. Cellular and molecular basis of symbiotic nodule development. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102478. [PMID: 37857037 DOI: 10.1016/j.pbi.2023.102478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023]
Abstract
Root nodule development plays a vital role in establishing the mutualistic relationship between legumes and nitrogen-fixing rhizobia. Two primary processes are involved in nodule development: formative cell divisions in the root cortex and the subsequent differentiation of nodule cells. The first process involves the mitotic reactivation of differentiated root cortex cells to form nodule primordium after perceiving symbiotic signals. The second process enables the nascent nodule primordium cells to develop into various cell types, leading to the creation of a functional nodule capable of supporting nitrogen fixation. Thus, both division and differentiation of nodule cells are crucial for root nodule development. This review provides an overview of the most recent advancements in comprehending the cellular and molecular mechanisms underlying symbiotic nodule development in legumes.
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Affiliation(s)
- Zhenpeng Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Haiyue Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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8
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Frank M, Fechete LI, Tedeschi F, Nadzieja M, Nørgaard MMM, Montiel J, Andersen KR, Schierup MH, Reid D, Andersen SU. Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus. Nat Commun 2023; 14:7171. [PMID: 37935666 PMCID: PMC10630511 DOI: 10.1038/s41467-023-42911-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.
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Affiliation(s)
- Manuel Frank
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Lavinia Ioana Fechete
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Francesca Tedeschi
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | | | - Jesus Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | - Kasper Røjkjær Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Australia.
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.
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9
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Montiel J, García-Soto I, James EK, Reid D, Cárdenas L, Napsucialy-Mendivil S, Ferguson S, Dubrovsky JG, Stougaard J. Aromatic amino acid biosynthesis impacts root hair development and symbiotic associations in Lotus japonicus. PLANT PHYSIOLOGY 2023; 193:1508-1526. [PMID: 37427869 PMCID: PMC10517252 DOI: 10.1093/plphys/kiad398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall-related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.
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Affiliation(s)
- Jesús Montiel
- Departamento de Genómica Funcional de Eucariotas. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
| | - Ivette García-Soto
- Departamento de Genómica Funcional de Eucariotas. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Euan K James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
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10
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Liu Y, Lin Y, Wei F, Lv Y, Xie F, Chen D, Lin H, Li Y. G-type receptor-like kinase AsNIP43 interacts with rhizobia effector nodulation outer protein P and is required for symbiosis. PLANT PHYSIOLOGY 2023; 193:1527-1546. [PMID: 37432453 PMCID: PMC10517198 DOI: 10.1093/plphys/kiad318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/27/2023] [Indexed: 07/12/2023]
Abstract
In the Rhizobium-Legume symbiosis, the nodulation outer protein P (NopP) effector is one of the key regulators for rhizobial infection and nodule organogenesis. However, the molecular mechanism through which host legume plants sense NopP remains largely unknown. Here, we constructed an nopP deletion mutant of Mesorhizobium huakuii and found that nopP negatively regulates nodulation on Chinese milk vetch (Astragalus sinicus). Screening for NopP interacting proteins in host plants using the yeast 2-hybrid system identified NopP interacting protein 43 (AsNIP43), which encodes a G-type receptor-like kinase (LecRLK). The B-lectin domain at the N terminus of AsNIP43 was essential in mediating its interaction with NopP, which was confirmed in vitro and in vivo. Subcellular localization, co-localization, and gene expression analyses showed that AsNIP43 and NopP function tightly associated with earlier infection events. RNA interference (RNAi) knockdown of AsNIP43 expression by hairy root transformation led to decreased nodule formation. AsNIP43 plays a positive role in symbiosis, which was further verified in the model legume Medicago truncatula. Transcriptome analysis indicated that MtRLK (a homolog of AsNIP43 in M. truncatula) may function to affect defense gene expression and thus to regulate early nodulation. Taken together, we show that LecRLK AsNIP43 is a legume host target that interacts with rhizobia effector NopP is essential for rhizobial infection and nodulation.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Ye Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Feng Wei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Yanfei Lv
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Fuli Xie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Dasong Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Hui Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
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11
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Zhao Z, Wang Y, Peng Z, Luo Z, Zhao M, Wang J. Allelic expression of AhNSP2-B07 due to parent of origin affects peanut nodulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1193465. [PMID: 37426991 PMCID: PMC10325728 DOI: 10.3389/fpls.2023.1193465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/19/2023] [Indexed: 07/11/2023]
Abstract
Legumes are well-known for establishing a symbiotic relationship with rhizobia in root nodules to fix nitrogen from the atmosphere. The nodulation signaling pathway 2 (NSP2) gene plays a critical role in the symbiotic signaling pathway. In cultivated peanut, an allotetraploid (2n = 4x = 40, AABB) legume crop, natural polymorphisms in a pair of NSP2 homoeologs (Na and Nb) located on chromosomes A08 and B07, respectively, can cause loss of nodulation. Interestingly, some heterozygous (NBnb) progeny produced nodules, while some others do not, suggesting non-Mendelian inheritance in the segregating population at the Nb locus. In this study, we investigated the non-Mendelian inheritance at the NB locus. Selfing populations were developed to validate the genotypical and phenotypical segregating ratios. Allelic expression was detected in roots, ovaries, and pollens of heterozygous plants. Bisulfite PCR and sequencing of the Nb gene in gametic tissue were performed to detect the DNA methylation variations of this gene in different gametic tissues. The results showed that only one allele at the Nb locus expressed in peanut roots during symbiosis. In the heterozygous (Nbnb) plants, if dominant allele expressed, the plants produced nodules, if recessive allele expressed, then no nodules were produced. qRT-PCR experiments revealed that the expression of Nb gene in the ovary was extremely low, about seven times lower than that in pollen, regardless of genotypes or phenotypes of the plants at this locus. The results indicated that Nb gene expression in peanut depends on the parent of origin and is imprinted in female gametes. However, no significant differences of DNA methylation level were detected between these two gametic tissues by bisulfite PCR and sequencing. The results suggested that the remarkable low expression of Nb in female gametes may not be caused by DNA methylation. This study provided a unique genetic basis of a key gene involved in peanut symbiosis, which could facilitate understanding the regulation of gene expression in symbiosis in polyploid legumes.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Yichun Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
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12
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Nasrollahi V, Allam G, Kohalmi SE, Hannoufa A. MsSPL9 Modulates Nodulation under Nitrate Sufficiency Condition in Medicago sativa. Int J Mol Sci 2023; 24:ijms24119615. [PMID: 37298564 DOI: 10.3390/ijms24119615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Nodulation in Leguminous spp. is induced by common environmental cues, such as low nitrogen availability conditions, in the presence of the specific Rhizobium spp. in the rhizosphere. Medicago sativa (alfalfa) is an important nitrogen-fixing forage crop that is widely cultivated around the world and relied upon as a staple source of forage in livestock feed. Although alfalfa's relationship with these bacteria is one of the most efficient between rhizobia and legume plants, breeding for nitrogen-related traits in this crop has received little attention. In this report, we investigate the role of Squamosa-Promoter Binding Protein-Like 9 (SPL9), a target of miR156, in nodulation in alfalfa. Transgenic alfalfa plants with SPL9-silenced (SPL9-RNAi) and overexpressed (35S::SPL9) were compared to wild-type (WT) alfalfa for phenotypic changes in nodulation in the presence and absence of nitrogen. Phenotypic analyses showed that silencing of MsSPL9 in alfalfa caused an increase in the number of nodules. Moreover, the characterization of phenotypic and molecular parameters revealed that MsSPL9 regulates nodulation under a high concentration of nitrate (10 mM KNO3) by regulating the transcription levels of the nitrate-responsive genes Nitrate Reductase1 (NR1), NR2, Nitrate transporter 2.5 (NRT2.5), and a shoot-controlled autoregulation of nodulation (AON) gene, Super numeric nodules (SUNN). While MsSPL9-overexpressing transgenic plants have dramatically increased transcript levels of SUNN, NR1, NR2, and NRT2.5, reducing MsSPL9 caused downregulation of these genes and displayed a nitrogen-starved phenotype, as downregulation of the MsSPL9 transcript levels caused a nitrate-tolerant nodulation phenotype. Taken together, our results suggest that MsSPL9 regulates nodulation in alfalfa in response to nitrate.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Gamalat Allam
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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13
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Kelly S, Hansen SB, Rübsam H, Saake P, Pedersen EB, Gysel K, Madland E, Wu S, Wawra S, Reid D, Sullivan JT, Blahovska Z, Vinther M, Muszynski A, Azadi P, Thygesen MB, Aachmann FL, Ronson CW, Zuccaro A, Andersen KR, Radutoiu S, Stougaard J. A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus. PLoS Biol 2023; 21:e3002127. [PMID: 37200394 DOI: 10.1371/journal.pbio.3002127] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 05/31/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023] Open
Abstract
Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro, the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus. The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.
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Affiliation(s)
- Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simon B Hansen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Henriette Rübsam
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Pia Saake
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Sciences, Cologne, Germany
| | - Emil B Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eva Madland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Stephan Wawra
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Sciences, Cologne, Germany
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Zuzana Blahovska
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Maria Vinther
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Artur Muszynski
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Finn L Aachmann
- NOBIPOL (Norwegian Biopolymer Laboratory), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alga Zuccaro
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Sciences, Cologne, Germany
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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14
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Rübsam H, Krönauer C, Abel NB, Ji H, Lironi D, Hansen SB, Nadzieja M, Kolte MV, Abel D, de Jong N, Madsen LH, Liu H, Stougaard J, Radutoiu S, Andersen KR. Nanobody-driven signaling reveals the core receptor complex in root nodule symbiosis. Science 2023; 379:272-277. [PMID: 36656954 DOI: 10.1126/science.ade9204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding the composition and activation of multicomponent receptor complexes is a challenge in biology. To address this, we developed a synthetic approach based on nanobodies to drive assembly and activation of cell surface receptors and apply the concept by manipulating receptors that govern plant symbiosis with nitrogen-fixing bacteria. We show that the Lotus japonicus Nod factor receptors NFR1 and NFR5 constitute the core receptor complex initiating the cortical root nodule organogenesis program as well as the epidermal program controlling infection. We find that organogenesis signaling is mediated by the intracellular kinase domains whereas infection requires functional ectodomains. Finally, we identify evolutionarily distant barley receptors that activate root nodule organogenesis, which could enable engineering of biological nitrogen-fixation into cereals.
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Affiliation(s)
- Henriette Rübsam
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Christina Krönauer
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Nikolaj B Abel
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Hongtao Ji
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Damiano Lironi
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Simon B Hansen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Marie V Kolte
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Dörte Abel
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Noor de Jong
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Lene H Madsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Huijun Liu
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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15
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Chiba Y, Sasaki M, Masuda S, Shibata A, Shirasu K, Kawaharada Y. A Novel Rhizobium sp. Chiba-1 Strain Exhibits a Host Range for Nodule Symbiosis in Lotus Species. Microbes Environ 2023; 38:ME23056. [PMID: 38044128 PMCID: PMC10728632 DOI: 10.1264/jsme2.me23056] [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: 06/28/2023] [Accepted: 09/16/2023] [Indexed: 12/05/2023] Open
Abstract
Rhizobia are soil bacteria that induce the formation of nodules in the roots of leguminous plants for mutualistic establishment. Although the symbiotic mechanism between Lotus japonicus and its major symbiotic rhizobia, Mesorhizobium loti, has been extensively characterized, our understanding of symbiotic mechanisms, such as host specificity and host ranges, remains limited. In the present study, we isolated a novel Rhizobium strain capable of forming nodules on L. burttii from agricultural soil at Iwate prefecture in Japan. We conducted genomic and host range ana-lyses of various Lotus species. The results obtained revealed that the novel isolated Rhizobium sp. Chiba-1 was closely related to R. leguminosarum and had a wide host range that induced nodule development, including L. burttii and several L. japonicus wild-type accessions. However, L. japonicus Gifu exhibited an incompatible nodule phenotype. We also identified the formation of an epidermal infection threads that was dependent on the Lotus species and independent of nodule organ development. In conclusion, this newly isolated Rhizobium strain displays a distinct nodulation phenotype from Lotus species, and the results obtained herein provide novel insights into the functional mechanisms underlying host specificity and host ranges.
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Affiliation(s)
- Yuhei Chiba
- United Graduate School of Agricultural Sciences, Iwate University, 3–18–8, Ueda, Morioka, Iwate 020–8550, Japan
| | - Mao Sasaki
- Graduate School of Arts and Sciences, Iwate University, 3–18–8 Ueda, Morioka, Iwate 020–8550, Japan
| | - Sachiko Masuda
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Yasuyuki Kawaharada
- United Graduate School of Agricultural Sciences, Iwate University, 3–18–8, Ueda, Morioka, Iwate 020–8550, Japan
- Graduate School of Arts and Sciences, Iwate University, 3–18–8 Ueda, Morioka, Iwate 020–8550, Japan
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3–18–8, Ueda, Morioka, 020–8550, Iwate, Japan
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16
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Liu Y, Lin Y, Guan N, Song Y, Li Y, Xie X. A Lipopolysaccharide Synthesis Gene rfaD from Mesorhizobium huakuii Is Involved in Nodule Development and Symbiotic Nitrogen Fixation. Microorganisms 2022; 11:microorganisms11010059. [PMID: 36677351 PMCID: PMC9866225 DOI: 10.3390/microorganisms11010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Rhizobium lipopolysaccharide (LPS) is an important component of the cell wall of gram-negative bacteria and serves as a signal molecule on the surface of rhizobia, participating in the symbiosis during rhizobia-legume interaction. In this study, we constructed a deletion mutant of ADP-L-glycerol-D-mannoheptosyl-6-exoisomerase (rfaD) of Mesorhizobium huakuii 7653R and a functional complementary strain. The results showed that the deletion of rfaD did not affect the free-living growth rate of 7653R, but that it did affect the LPS synthesis and that it increased sensitivity to abiotic stresses. The rfaD promoter-GUS reporter assay showed that the gene was mainly expressed in the infection zone of the mature nodules. The root nodules formation of the rfaD mutant was delayed during symbiosis with the host plant of Astragalus sinicus. The symbiotic phenotype analyses showed that the nodules of A. sinicus lost symbiotic nitrogen fixation ability, when inoculated with the rfaD mutant strain. In conclusion, our results reveal that the 7653R rfaD gene plays a crucial role in the LPS synthesis involved in the symbiotic interaction between rhizobia and A. sinicus. This study also provides new insights into the molecular mechanisms by which the rhizobia regulate their own gene expression and cell wall components enabling nodulation in legumes.
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Affiliation(s)
- Yuan Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ye Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Guan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuting Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (Y.L.); (X.X.); Tel.: +86-127-8728-1685 (Y.L.); +86-159-1855-2425 (X.X.)
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (X.X.); Tel.: +86-127-8728-1685 (Y.L.); +86-159-1855-2425 (X.X.)
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17
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Nasrollahi V, Yuan ZC, Lu QSM, McDowell T, Kohalmi SE, Hannoufa A. Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa. PLANT MOLECULAR BIOLOGY 2022; 110:511-529. [PMID: 35976552 PMCID: PMC9684250 DOI: 10.1007/s11103-022-01303-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/17/2022] [Indexed: 05/11/2023]
Abstract
Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Qing Shi Mimmie Lu
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada.
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18
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Ghantasala S, Roy Choudhury S. Nod factor perception: an integrative view of molecular communication during legume symbiosis. PLANT MOLECULAR BIOLOGY 2022; 110:485-509. [PMID: 36040570 DOI: 10.1007/s11103-022-01307-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Compatible interaction between rhizobial Nod factors and host receptors enables initial recognition and signaling events during legume-rhizobia symbiosis. Molecular communication is a new paradigm of information relay, which uses chemical signals or molecules as dialogues for communication and has been witnessed in prokaryotes, plants as well as in animal kingdom. Understanding this fascinating relay of signals between plants and rhizobia during the establishment of a synergistic relationship for biological nitrogen fixation represents one of the hotspots in plant biology research. Predominantly, their interaction is initiated by flavonoids exuding from plant roots, which provokes changes in the expression profile of rhizobial genes. Compatible interactions promote the secretion of Nod factors (NFs) from rhizobia, which are recognised by cognate host receptors. Perception of NFs by host receptors initiates the symbiosis and ultimately leads to the accommodation of rhizobia within root nodules via a series of mutual exchange of signals. This review elucidates the bacterial and plant perspectives during the early stages of symbiosis, explicitly emphasizing the significance of NFs and their cognate NF receptors.
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Affiliation(s)
- Swathi Ghantasala
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Swarup Roy Choudhury
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India.
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19
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Nasrollahi V, Yuan ZC, Kohalmi SE, Hannoufa A. SPL12 Regulates AGL6 and AGL21 to Modulate Nodulation and Root Regeneration under Osmotic Stress and Nitrate Sufficiency Conditions in Medicago sativa. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223071. [PMID: 36432802 PMCID: PMC9697194 DOI: 10.3390/plants11223071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 06/12/2023]
Abstract
The highly conserved plant microRNA, miR156, affects root architecture, nodulation, symbiotic nitrogen fixation, and stress response. In Medicago sativa, transcripts of eleven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE, SPLs, including SPL12, are targeted for cleavage by miR156. Our previous research revealed the role of SPL12 and its target gene, AGL6, in nodulation in alfalfa. Here, we investigated the involvement of SPL12, AGL6 and AGL21 in nodulation under osmotic stress and different nitrate availability conditions. Characterization of phenotypic and molecular parameters revealed that the SPL12/AGL6 module plays a negative role in maintaining nodulation under osmotic stress. While there was a decrease in the nodule numbers in WT plants under osmotic stress, the SPL12-RNAi and AGL6-RNAi genotypes maintained nodulation under osmotic stress. Moreover, the results showed that SPL12 regulates nodulation under a high concentration of nitrate by silencing AGL21. AGL21 transcript levels were increased under nitrate treatment in WT plants, but SPL12 was not affected throughout the treatment period. Given that AGL21 was significantly upregulated in SPL12-RNAi plants, we conclude that SPL12 may be involved in regulating nitrate inhibition of nodulation in alfalfa by targeting AGL21. Taken together, our results suggest that SPL12, AGL6, and AGL21 form a genetic module that regulates nodulation in alfalfa under osmotic stress and in response to nitrate.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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20
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Zarrabian M, Montiel J, Sandal N, Ferguson S, Jin H, Lin YY, Klingl V, Marín M, James EK, Parniske M, Stougaard J, Andersen SU. A Promiscuity Locus Confers Lotus burttii Nodulation with Rhizobia from Five Different Genera. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1006-1017. [PMID: 35852471 DOI: 10.1094/mpmi-06-22-0124-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil-dwelling bacteria and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, in which the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity quantitative trait loci (QTL) to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for symbiont-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mohammad Zarrabian
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico. Cuernavaca, Mexico
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Yen-Yu Lin
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Verena Klingl
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Macarena Marín
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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21
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Li XR, Sun J, Albinsky D, Zarrabian D, Hull R, Lee T, Jarratt-Barnham E, Chiu CH, Jacobsen A, Soumpourou E, Albanese A, Kohlen W, Luginbuehl LH, Guillotin B, Lawrensen T, Lin H, Murray J, Wallington E, Harwood W, Choi J, Paszkowski U, Oldroyd GED. Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2. Nat Commun 2022; 13:6421. [PMID: 36307431 PMCID: PMC9616857 DOI: 10.1038/s41467-022-33908-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.
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Affiliation(s)
- Xin-Ran Li
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Jongho Sun
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK
| | - Doris Albinsky
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Darius Zarrabian
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Raphaella Hull
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Tak Lee
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Edwin Jarratt-Barnham
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Chai Hao Chiu
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Amy Jacobsen
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Eleni Soumpourou
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Alessio Albanese
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wouter Kohlen
- grid.4818.50000 0001 0791 5666Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Leonie H. Luginbuehl
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Bruno Guillotin
- grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France ,grid.137628.90000 0004 1936 8753Present Address: NYU-Center of Genomic and System Biology, 12 Waverly Place, New York, NY USA
| | - Tom Lawrensen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Hui Lin
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeremy Murray
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Emma Wallington
- grid.17595.3f0000 0004 0383 6532NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Wendy Harwood
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jeongmin Choi
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Uta Paszkowski
- grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Giles E. D. Oldroyd
- grid.5335.00000000121885934Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR UK ,grid.5335.00000000121885934Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
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22
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Ma W, Tang S, Dengzeng Z, Zhang D, Zhang T, Ma X. Root exudates contribute to belowground ecosystem hotspots: A review. Front Microbiol 2022; 13:937940. [PMID: 36274740 PMCID: PMC9581264 DOI: 10.3389/fmicb.2022.937940] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/30/2022] [Indexed: 09/19/2023] Open
Abstract
Root exudates are an essential carrier for material cycling, energy exchange, and information transfer between the belowground parts of plants and the soil. We synthesize current properties and regulators of root exudates and their role in the belowground ecosystem as substances cycle and signal regulation. We discussed the composition and amount of root exudates and their production mechanism, indicating that plant species, growth stage, environmental factors, and microorganisms are primary influence factors. The specific mechanisms by which root secretions mobilize the soil nutrients were summarized. First, plants improve the nutrient status of the soil by releasing organic acids for acidification and chelation. Then, root exudates accelerated the SOC turnover due to their dual impacts, forming and destabilizing aggregates and MASOC. Eventually, root exudates mediate the plant-plant interaction and plant-microbe interaction. Additionally, a summary of the current collection methods of root exudates is presented.
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Affiliation(s)
- Wenming Ma
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
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23
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Jiménez-Guerrero I, Medina C, Vinardell JM, Ollero FJ, López-Baena FJ. The Rhizobial Type 3 Secretion System: The Dr. Jekyll and Mr. Hyde in the Rhizobium–Legume Symbiosis. Int J Mol Sci 2022; 23:ijms231911089. [PMID: 36232385 PMCID: PMC9569860 DOI: 10.3390/ijms231911089] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 01/14/2023] Open
Abstract
Rhizobia are soil bacteria that can establish a symbiotic association with legumes. As a result, plant nodules are formed on the roots of the host plants where rhizobia differentiate to bacteroids capable of fixing atmospheric nitrogen into ammonia. This ammonia is transferred to the plant in exchange of a carbon source and an appropriate environment for bacterial survival. This process is subjected to a tight regulation with several checkpoints to allow the progression of the infection or its restriction. The type 3 secretion system (T3SS) is a secretory system that injects proteins, called effectors (T3E), directly into the cytoplasm of the host cell, altering host pathways or suppressing host defense responses. This secretion system is not present in all rhizobia but its role in symbiosis is crucial for some symbiotic associations, showing two possible faces as Dr. Jekyll and Mr. Hyde: it can be completely necessary for the formation of nodules, or it can block nodulation in different legume species/cultivars. In this review, we compile all the information currently available about the effects of different rhizobial effectors on plant symbiotic phenotypes. These phenotypes are diverse and highlight the importance of the T3SS in certain rhizobium–legume symbioses.
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24
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Velandia K, Reid JB, Foo E. Right time, right place: The dynamic role of hormones in rhizobial infection and nodulation of legumes. PLANT COMMUNICATIONS 2022; 3:100327. [PMID: 35605199 PMCID: PMC9482984 DOI: 10.1016/j.xplc.2022.100327] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/24/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Many legume plants form beneficial associations with rhizobial bacteria that are hosted in new plant root organs, nodules, in which atmospheric nitrogen is fixed. This association requires the precise coordination of two separate programs, infection in the epidermis and nodule organogenesis in the cortex. There is extensive literature indicating key roles for plant hormones during nodulation, but a detailed analysis of the spatial and temporal roles of plant hormones during the different stages of nodulation is required. This review analyses the current literature on hormone regulation of infection and organogenesis to reveal the differential roles and interactions of auxin, cytokinin, brassinosteroids, ethylene, and gibberellins during epidermal infection and cortical nodule initiation, development, and function. With the exception of auxin, all of these hormones suppress infection events. By contrast, there is evidence that all of these hormones promote nodule organogenesis, except ethylene, which suppresses nodule initiation. This differential role for many of the hormones between the epidermal and cortical programs is striking. Future work is required to fully examine hormone interactions and create a robust model that integrates this knowledge into our understanding of nodulation pathways.
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Affiliation(s)
- Karen Velandia
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - James B Reid
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | - Eloise Foo
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia.
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25
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Mathesius U. Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153765. [PMID: 35952452 DOI: 10.1016/j.jplph.2022.153765] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 05/14/2023]
Abstract
Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.
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Affiliation(s)
- Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia.
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26
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Akamatsu A, Nagae M, Takeda N. The CYCLOPS Response Element in the NIN Promoter Is Important but Not Essential for Infection Thread Formation During Lotus japonicus-Rhizobia Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:650-658. [PMID: 35343248 DOI: 10.1094/mpmi-10-21-0252-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The establishment of the legume-rhizobia symbiosis, termed the root-nodule symbiosis (RNS), requires elaborate interactions at the molecular level. The host plant-derived transcription factor NODULE INCEPTION (NIN) is known to be crucial for RNS, regulating associated processes such as alteration of root hair morphology, infection thread formation, and cell division during nodulation. This emphasizes the importance of the precise spatiotemporal regulation of NIN expression for the establishment of RNS; however, the detailed role of NIN promoter sequences in this process remains unclear. The daphne mutant, a nin mutant allele containing a chromosomal translocation approximately 7 kb upstream of the start codon, does not form nodules but does form infection threads, indicating that the region within 7 kb of the NIN start codon contributes to NIN expression during infection thread formation. CYCLOPS binds to a CYCLOPS response element (CYC-RE) in the NIN promoter, and cyclops mutants are defective in infection thread formation. Here, we performed complementation analysis in nin mutants, using various truncated forms of the NIN promoter, and found that the CYC-RE is important for infection thread formation. Additionally, the CYC-RE deletion mutant, generated through CRISPR/Cas9 technology, displayed a significant reduction in infection thread formation, indicating that the CYC-RE is important for the fine-tuning of NIN expression during this process. However, the fact that infection thread formation is not completely abolished in the CYC-RE deletion mutant suggests that cis and trans factors other than CYCLOPS and the CYC-RE may cooperatively regulate NIN expression for the induction of infection thread formation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Akira Akamatsu
- Graduate School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Miwa Nagae
- National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Naoya Takeda
- Graduate School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo 669-1330, Japan
- National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
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27
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Alías-Villegas C, Fuentes-Romero F, Cuéllar V, Navarro-Gómez P, Soto MJ, Vinardell JM, Acosta-Jurado S. Surface Motility Regulation of Sinorhizobium fredii HH103 by Plant Flavonoids and the NodD1, TtsI, NolR, and MucR1 Symbiotic Bacterial Regulators. Int J Mol Sci 2022; 23:7698. [PMID: 35887044 PMCID: PMC9316994 DOI: 10.3390/ijms23147698] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Bacteria can spread on surfaces to colonize new environments and access more resources. Rhizobia, a group of α- and β-Proteobacteria, establish nitrogen-fixing symbioses with legumes that rely on a complex signal interchange between the partners. Flavonoids exuded by plant roots and the bacterial transcriptional activator NodD control the transcription of different rhizobial genes (the so-called nod regulon) and, together with additional bacterial regulatory proteins (such as TtsI, MucR or NolR), influence the production of different rhizobial molecular signals. In Sinorhizobium fredii HH103, flavonoids and NodD have a negative effect on exopolysaccharide production and biofilm production. Since biofilm formation and motility are often inversely regulated, we have analysed whether flavonoids may influence the translocation of S. fredii HH103 on surfaces. We show that the presence of nod gene-inducing flavonoids does not affect swimming but promotes a mode of surface translocation, which involves both flagella-dependent and -independent mechanisms. This surface motility is regulated in a flavonoid-NodD1-TtsI-dependent manner, relies on the assembly of the symbiotic type 3 secretion system (T3SS), and involves the participation of additional modulators of the nod regulon (NolR and MucR1). To our knowledge, this is the first evidence indicating the participation of T3SS in surface motility in a plant-interacting bacterium. Interestingly, flavonoids acting as nod-gene inducers also participate in the inverse regulation of surface motility and biofilm formation, which could contribute to a more efficient plant colonisation.
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Affiliation(s)
- Cynthia Alías-Villegas
- Centro Andaluz de Biología del Desarrollo, CSIC/Junta de Andalucía, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, 41013 Seville, Spain;
| | - Francisco Fuentes-Romero
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain; (F.F.-R.); (P.N.-G.)
| | - Virginia Cuéllar
- Estación Experimental del Zaidín, CSIC, Departamento de Biotecnología y Protección Ambiental, 18008 Granada, Spain; (V.C.); (M.J.S.)
| | - Pilar Navarro-Gómez
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain; (F.F.-R.); (P.N.-G.)
| | - María J. Soto
- Estación Experimental del Zaidín, CSIC, Departamento de Biotecnología y Protección Ambiental, 18008 Granada, Spain; (V.C.); (M.J.S.)
| | - José-María Vinardell
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain; (F.F.-R.); (P.N.-G.)
| | - Sebastián Acosta-Jurado
- Centro Andaluz de Biología del Desarrollo, CSIC/Junta de Andalucía, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, 41013 Seville, Spain;
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28
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Quilbé J, Montiel J, Arrighi JF, Stougaard J. Molecular Mechanisms of Intercellular Rhizobial Infection: Novel Findings of an Ancient Process. FRONTIERS IN PLANT SCIENCE 2022; 13:922982. [PMID: 35812902 PMCID: PMC9260380 DOI: 10.3389/fpls.2022.922982] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Establishment of the root-nodule symbiosis in legumes involves rhizobial infection of nodule primordia in the root cortex that is dependent on rhizobia crossing the root epidermal barrier. Two mechanisms have been described: either through root hair infection threads or through the intercellular passage of bacteria. Among the legume genera investigated, around 75% use root hair entry and around 25% the intercellular entry mode. Root-hair infection thread-mediated infection has been extensively studied in the model legumes Medicago truncatula and Lotus japonicus. In contrast, the molecular circuit recruited during intercellular infection, which is presumably an ancient and simpler pathway, remains poorly known. In recent years, important discoveries have been made to better understand the transcriptome response and the genetic components involved in legumes with obligate (Aeschynomene and Arachis spp.) and conditional (Lotus and Sesbania spp.) intercellular rhizobial infections. This review addresses these novel findings and briefly considers possible future research to shed light on the molecular players that orchestrate intercellular infection in legumes.
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Affiliation(s)
- Johan Quilbé
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Centre for Genomic Sciences, National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico
| | - Jean-François Arrighi
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, Montpellier, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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29
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New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia. Int J Microbiol 2022; 2022:4623713. [PMID: 35637770 PMCID: PMC9148247 DOI: 10.1155/2022/4623713] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. As a result, the number of new taxa descriptions is exponentially increasing, while an increasing number of others has been subject of reclassification, demanding from the taxonomists more effort to maintain an organized hierarchical system. However, expectations are that the taxonomy of prokaryotes will acquire a more stable status with the genomic era. Other analyses may continue to be necessary to determine microbial features, but the use of genomic data might be sufficient to provide reliable taxa delineation, helping taxonomy to reach the goal of correct classification and identification. Here we describe the evolution of prokaryotes' taxonomy until the genomic era, emphasizing bacteria and taking as an example the history of rhizobia taxonomy. This example was chosen because of the importance of the symbiotic nitrogen fixation of legumes with rhizobia to the nitrogen input to both natural ecosystems and agricultural crops. This case study reports the technological advances and the methodologies used to classify and identify bacterial species and indicates the actual rules required for an accurate description of new taxa.
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30
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Visualization of the Crossroads between a Nascent Infection Thread and the First Cell Division Event in Phaseolus vulgaris Nodulation. Int J Mol Sci 2022; 23:ijms23095267. [PMID: 35563659 PMCID: PMC9105610 DOI: 10.3390/ijms23095267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
The development of a symbiotic nitrogen-fixing nodule in legumes involves infection and organogenesis. Infection begins when rhizobia enter a root hair through an inward structure, the infection thread (IT), which guides the bacteria towards the cortical tissue. Concurrently, organogenesis takes place by inducing cortical cell division (CCD) at the infection site. Genetic analysis showed that both events are well-coordinated; however, the dynamics connecting them remain to be elucidated. To visualize the crossroads between IT and CCD, we benefited from the fact that, in Phaseolus vulgaris nodulation, where the first division occurs in subepidermal cortical cells located underneath the infection site, we traced a Rhizobium etli strain expressing DsRed, the plant cytokinesis marker YFP-PvKNOLLE, a nuclear stain and cell wall auto-fluorescence. We found that the IT exits the root hair to penetrate an underlying subepidermal cortical (S-E) cell when it is concluding cytokinesis.
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31
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Wang D, Dong W, Murray J, Wang E. Innovation and appropriation in mycorrhizal and rhizobial Symbioses. THE PLANT CELL 2022; 34:1573-1599. [PMID: 35157080 PMCID: PMC9048890 DOI: 10.1093/plcell/koac039] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/20/2023]
Abstract
Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.
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Affiliation(s)
- Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wentao Dong
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Ertao Wang
- Authors for correspondence: (E.W) and (J.M.)
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Teulet A, Camuel A, Perret X, Giraud E. The Versatile Roles of Type III Secretion Systems in Rhizobia-Legume Symbioses. Annu Rev Microbiol 2022; 76:45-65. [PMID: 35395168 DOI: 10.1146/annurev-micro-041020-032624] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To suppress plant immunity and promote the intracellular infection required for fixing nitrogen for the benefit of their legume hosts, many rhizobia use type III secretion systems (T3SSs) that deliver effector proteins (T3Es) inside host cells. As reported for interactions between pathogens and host plants, the immune system of legume hosts and the cocktail of T3Es secreted by rhizobia determine the symbiotic outcome. If they remain undetected, T3Es may reduce plant immunity and thus promote infection of legumes by rhizobia. If one or more of the secreted T3Es are recognized by the cognate plant receptors, defense responses are triggered and rhizobial infection may abort. However, some rhizobial T3Es can also circumvent the need for nodulation (Nod) factors to trigger nodule formation. Here we review the multifaceted roles played by rhizobial T3Es during symbiotic interactions with legumes. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Albin Teulet
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France;
| | - Alicia Camuel
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France; .,PHIM Plant Health Institute, IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France
| | - Xavier Perret
- Laboratory of Microbial Genetics, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France; .,PHIM Plant Health Institute, IRD, Institut Agro, INRAE, Université de Montpellier, and CIRAD, Montpellier, France
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Cabrera J, Conesa CM, Del Pozo JC. May the dark be with roots: a perspective on how root illumination may bias in vitro research on plant-environment interactions. THE NEW PHYTOLOGIST 2022; 233:1988-1997. [PMID: 34942016 DOI: 10.1111/nph.17936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Roots anchor plants to the soil, providing them with nutrients and water while creating a defence network and facilitating beneficial interactions with a multitude of living organisms and climatological conditions. To facilitate morphological and molecular studies, root research has been conducted using in vitro systems. However, under natural conditions, roots grow in the dark, mainly in the absence of illumination, except for the relatively low illumination of the upper soil surface, and this has been largely ignored. Here, we discuss the results found over the last decade on how experimental exposure of roots to light may bias root development and responses through the alteration of hormonal signalling, cytoskeleton organization, reactive oxygen species or the accumulation of flavonoids, among other factors. Illumination alters the uptake of nutrients or water, and also affects the response of the roots to abiotic stresses and root interactions with the microbiota. Furthermore, we review in vitro systems created to maintain roots in darkness, and provide a comparative analysis of root transcriptomes obtained with these devices. Finally, we identify other experimental variables that should be considered to better mimic soil conditions, whose improvement would benefit studies using in vitro cultivation or enclosed ecosystems.
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Affiliation(s)
- Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), UPM, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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Triozzi PM, Irving TB, Schmidt HW, Keyser ZP, Chakraborty S, Balmant K, Pereira WJ, Dervinis C, Mysore KS, Wen J, Ané JM, Kirst M, Conde D. Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development. PLANT PHYSIOLOGY 2022; 188:560-575. [PMID: 34599592 PMCID: PMC8774767 DOI: 10.1093/plphys/kiab447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Most legumes can establish a symbiotic association with soil rhizobia that trigger the development of root nodules. These nodules host the rhizobia and allow them to fix nitrogen efficiently. The perception of bacterial lipo-chitooligosaccharides (LCOs) in the epidermis initiates a signaling cascade that allows rhizobial intracellular infection in the root and de-differentiation and activation of cell division that gives rise to the nodule. Thus, nodule organogenesis and rhizobial infection need to be coupled in space and time for successful nodulation. The plant hormone cytokinin (CK) contributes to the coordination of this process, acting as an essential positive regulator of nodule organogenesis. However, the temporal regulation of tissue-specific CK signaling and biosynthesis in response to LCOs or Sinorhizobium meliloti inoculation in Medicago truncatula remains poorly understood. In this study, using a fluorescence-based CK sensor (pTCSn::nls:tGFP), we performed a high-resolution tissue-specific temporal characterization of the sequential activation of CK response during root infection and nodule development in M. truncatula after inoculation with S. meliloti. Loss-of-function mutants of the CK-biosynthetic gene ISOPENTENYLTRANSFERASE 3 (IPT3) showed impairment of nodulation, suggesting that IPT3 is required for nodule development in M. truncatula. Simultaneous live imaging of pIPT3::nls:tdTOMATO and the CK sensor showed that IPT3 induction in the pericycle at the base of nodule primordium contributes to CK biosynthesis, which in turn promotes expression of positive regulators of nodule organogenesis in M. truncatula.
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Affiliation(s)
- Paolo M Triozzi
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Henry W Schmidt
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Zachary P Keyser
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kelly Balmant
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Wendell J Pereira
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | | | - Jiangqi Wen
- Noble Research Institute, Ardmore, Oklahoma 73401, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Daniel Conde
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
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Guha S, Molla F, Sarkar M, Ibańez F, Fabra A, DasGupta M. Nod factor-independent 'crack-entry' symbiosis in dalbergoid legume Arachis hypogaea. Environ Microbiol 2022; 24:2732-2746. [PMID: 34995397 DOI: 10.1111/1462-2920.15888] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/09/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022]
Abstract
Dalbergoids are typified by crack-entry symbiosis which is evidenced to be Nod Factor (NF)- independent in several Aeschynomene legumes. Natural symbionts of the dalbergoid legume Arachis hypogaea are always NF-producing, prompting us to check whether symbiosis in this legume could also be NF-independent. For this, we followed the symbiosis with two NF containing bradyrhizobial strains- SEMIA6144, a natural symbiont of Arachis and ORS285, a versatile nodulator of Aeschynomene legumes, along with their corresponding nodulation (nod) mutants. Additionally, we investigated NF-deficient bradyrhizobia like BTAi1, a natural symbiont of Aeschynomene indica and the WBOS strains that were natural endophytes of Oryza sativa, collected from an Arachis-Oryza intercropped field. While SEMIA6144ΔnodC was non-nodulating, both ORS285 and ORS285ΔnodB could induce functional nodulation, although with lower efficiency than SEMIA6144. On the other hand, all the NF-deficient strains- BTAi1, WBOS2 and WBOS4 showed comparable nodulation with ORS285 indicating Arachis to harbour a NF-independent mechanism of symbiosis. Intriguingly, symbiosis in Arachis, irrespective of whether it was NF-dependent or independent, was always associated with the curling or branching of the rosette root hairs at the lateral root bases. Thus, despite being predominantly described as NF-dependent legume, Arachis does retain a vestigial, less-efficient form of NF-independent symbiosis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sohini Guha
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Firoz Molla
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Monolina Sarkar
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Fernando Ibańez
- Instituto de Investigaciones Agrobiotecnologicas (CONCINET-UNRC), Ruta 36 Km 601, Río Cuarto, Argentina
| | - Adriana Fabra
- Instituto de Investigaciones Agrobiotecnologicas (CONCINET-UNRC), Ruta 36 Km 601, Río Cuarto, Argentina
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
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37
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Nitrate restricts nodule organogenesis through inhibition of cytokinin biosynthesis in Lotus japonicus. Nat Commun 2021; 12:6544. [PMID: 34764268 PMCID: PMC8585978 DOI: 10.1038/s41467-021-26820-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Legumes balance nitrogen acquisition from soil nitrate with symbiotic nitrogen fixation. Nitrogen fixation requires establishment of a new organ, which is a cytokinin dependent developmental process in the root. We found cytokinin biosynthesis is a central integrator, balancing nitrate signalling with symbiotic acquired nitrogen. Low nitrate conditions provide a permissive state for induction of cytokinin by symbiotic signalling and thus nodule development. In contrast, high nitrate is inhibitory to cytokinin accumulation and nodule establishment in the root zone susceptible to nodule formation. This reduction of symbiotic cytokinin accumulation was further exacerbated in cytokinin biosynthesis mutants, which display hypersensitivity to nitrate inhibition of nodule development, maturation and nitrogen fixation. Consistent with this, cytokinin application rescues nodulation and nitrogen fixation of biosynthesis mutants in a concentration dependent manner. These inhibitory impacts of nitrate on symbiosis occur in a Nlp1 and Nlp4 dependent manner and contrast with the positive influence of nitrate on cytokinin biosynthesis that occurs in species that do not form symbiotic root nodules. Altogether this shows that legumes, as exemplified by Lotus japonicus, have evolved a different cytokinin response to nitrate compared to non-legumes.
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Khokhani D, Carrera Carriel C, Vayla S, Irving TB, Stonoha-Arther C, Keller NP, Ané JM. Deciphering the Chitin Code in Plant Symbiosis, Defense, and Microbial Networks. Annu Rev Microbiol 2021; 75:583-607. [PMID: 34623896 DOI: 10.1146/annurev-micro-051921-114809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chitin is a structural polymer in many eukaryotes. Many organisms can degrade chitin to defend against chitinous pathogens or use chitin oligomers as food. Beneficial microorganisms like nitrogen-fixing symbiotic rhizobia and mycorrhizal fungi produce chitin-based signal molecules called lipo-chitooligosaccharides (LCOs) and short chitin oligomers to initiate a symbiotic relationship with their compatible hosts and exchange nutrients. A recent study revealed that a broad range of fungi produce LCOs and chitooligosaccharides (COs), suggesting that these signaling molecules are not limited to beneficial microbes. The fungal LCOs also affect fungal growth and development, indicating that the roles of LCOs beyond symbiosis and LCO production may predate mycorrhizal symbiosis. This review describes the diverse structures of chitin; their perception by eukaryotes and prokaryotes; and their roles in symbiotic interactions, defense, and microbe-microbe interactions. We also discuss potential strategies of fungi to synthesize LCOs and their roles in fungi with different lifestyles.
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Affiliation(s)
- Devanshi Khokhani
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , , .,Current affiliation: Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108, USA;
| | - Cristobal Carrera Carriel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Shivangi Vayla
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Christina Stonoha-Arther
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , ,
| | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , , .,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , , , , .,Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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He Q, Xiang S, Wang W, Shu Y, Li Z, Wang S, Chen L, Yang X, Zhao T. Transcriptomic and photosynthetic responses to grafting of the Nod1 gene in nodulated and non-nodulated soybeans. G3 (BETHESDA, MD.) 2021; 11:jkab209. [PMID: 34544123 PMCID: PMC8496209 DOI: 10.1093/g3journal/jkab209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/04/2021] [Indexed: 01/04/2023]
Abstract
Legume plants form symbiotic relationships with rhizobia to convert N2 into ammonia, and the nodulation status can affect plant development including photosynthesis. However, the relationship between nitrogen fixation and photosynthesis during carbon and nitrogen metabolism remains unclear. This study was undertaken to unravel regulation of nodulation and photosynthesis using a spontaneous nonnodulated soybean mutant by grafting. The results of inheritance and gene mapping showed that the nonnodulated mutant was controlled by a recessive gene overlapped with the reported rj1 locus, and might be a new rj1 allele with 1 bp deletion in the fourth exon in comparison to the sequence of normal nodulation plants. According to grafting results, soybean nodulation is obviously determined by the roots, not the seedlings. Moreover, nitrogen content along with related metabolic enzyme activity, and photosynthetic capacity were enhanced by nonnodulated scions grafted with nodulated roots. Contrary results were obtained for nodulated scions grafted with nonnodulated roots. A total of 853 differentially expressed genes (DEGs) in the leaves and 1874 in the roots were identified by transcriptome analyses of the grafting treatments. We identified 285 differential gene ontology (GO) terms and 57 differential pathway terms identified in the leaves, while 856 differential GO terms and 207 differential pathway terms in the roots. Twenty DEGs interacting at translation level were selected, and the results of transcriptome analyses were verified by q-PCR. These findings indicated that the nodulation-related Nod allelic gene increases the nitrogen content of nonnodulated plants, which affects the enzymes involved in nitrogen metabolism, leading to changes in hormone levels and further regulation of photosynthesis and carbon metabolism.
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Affiliation(s)
- Qingyuan He
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
- Soybean Research Institute/National Center for Soybean Improvement, Ministry of Agriculture/Key Laboratory of Biology and Genetic Improvement of Soybean/Ministry of Agriculture/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shihua Xiang
- Zigong Institute of Agricultural Sciences, Zigong 643000, China
| | - Wubin Wang
- Soybean Research Institute/National Center for Soybean Improvement, Ministry of Agriculture/Key Laboratory of Biology and Genetic Improvement of Soybean/Ministry of Agriculture/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yingjie Shu
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
| | - Zhengpeng Li
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
| | - Songhua Wang
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
| | - Lei Chen
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
| | - Xiaoyan Yang
- College of Life and Health Science, Anhui Science and Technology University, Fengyang 233100, China
| | - Tuanjie Zhao
- Soybean Research Institute/National Center for Soybean Improvement, Ministry of Agriculture/Key Laboratory of Biology and Genetic Improvement of Soybean/Ministry of Agriculture/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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Kawaharada Y, Sandal N, Gupta V, Jin H, Kawaharada M, Taniuchi M, Ruman H, Nadzieja M, Andersen KR, Schneeberger K, Stougaard J, Andersen SU. Natural variation identifies a Pxy gene controlling vascular organisation and formation of nodules and lateral roots in Lotus japonicus. THE NEW PHYTOLOGIST 2021; 230:2459-2473. [PMID: 33759450 DOI: 10.1111/nph.17356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Forward and reverse genetics using the model legumes Lotus japonicus and Medicago truncatula have been instrumental in identifying the essential genes governing legume-rhizobia symbiosis. However, little information is known about the effects of intraspecific variation on symbiotic signalling. Here, we use quantitative trait locus sequencing (QTL-seq) to investigate the genetic basis of the differentiated phenotypic responses shown by the Lotus accessions Gifu and MG20 to inoculation with the Mesorhizobium loti exoU mutant that produces truncated exopolysaccharides. We identified through genetic complementation the Pxy gene as a component of this differential exoU response. Lotus Pxy encodes a leucine-rich repeat receptor-like kinase similar to Arabidopsis thaliana PXY, which regulates stem vascular development. We show that Lotus pxy insertion mutants displayed defects in root and stem vascular organisation, as well as lateral root and nodule formation. Our work links Pxy to de novo organogenesis in the root, highlights the genetic overlap between regulation of lateral root and nodule formation, and demonstrates that natural variation in Pxy affects nodulation signalling.
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Affiliation(s)
- Yasuyuki Kawaharada
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Maya Kawaharada
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Makoto Taniuchi
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Hafijur Ruman
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Korbinian Schneeberger
- Department for Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
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Quides KW, Weisberg AJ, Trinh J, Salaheldine F, Cardenas P, Lee HH, Jariwala R, Chang JH, Sachs JL. Experimental evolution can enhance benefits of rhizobia to novel legume hosts. Proc Biol Sci 2021; 288:20210812. [PMID: 34034525 PMCID: PMC8150021 DOI: 10.1098/rspb.2021.0812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Legumes preferentially associate with and reward beneficial rhizobia in root nodules, but the processes by which rhizobia evolve to provide benefits to novel hosts remain poorly understood. Using cycles of in planta and in vitro evolution, we experimentally simulated lifestyles where rhizobia repeatedly interact with novel plant genotypes with which they initially provide negligible benefits. Using a full-factorial replicated design, we independently evolved two rhizobia strains in associations with each of two Lotus japonicus genotypes that vary in regulation of nodule formation. We evaluated phenotypic evolution of rhizobia by quantifying fitness, growth effects and histological features on hosts, and molecular evolution via genome resequencing. Rhizobia evolved enhanced host benefits and caused changes in nodule development in one of the four host–symbiont combinations, that appeared to be driven by reduced costs during symbiosis, rather than increased nitrogen fixation. Descendant populations included genetic changes that could alter rhizobial infection or proliferation in host tissues, but lack of evidence for fixation of these mutations weakens the results. Evolution of enhanced rhizobial benefits occurred only in a subset of experiments, suggesting a role for host–symbiont genotype interactions in mediating the evolution of enhanced benefits from symbionts.
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Affiliation(s)
- Kenjiro W Quides
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Jerry Trinh
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Fathi Salaheldine
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Paola Cardenas
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Hsu-Han Lee
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Ruchi Jariwala
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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Rahimlou S, Bahram M, Tedersoo L. Phylogenomics reveals the evolution of root nodulating alpha- and beta-Proteobacteria (rhizobia). Microbiol Res 2021; 250:126788. [PMID: 34051611 DOI: 10.1016/j.micres.2021.126788] [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: 02/04/2021] [Revised: 04/05/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
The symbiosis between legumes and nodulating Proteobacteria (so-called rhizobia) contributes greatly to nitrogen fixation in terrestrial ecosystems. Root nodulating Proteobacteria produce nodulation (Nod) factors during the initiation of rhizobial nodule organogenesis on the roots of legumes. Here, we screened the Nod factor production capacity of the previously reported nodule inducing Proteobacteria genera using their genome sequences and assessed the evolutionary history of symbiosis based on phylogenomics. Our analysis revealed 12 genera as potentially Nod factor producing taxa exclusively from alpha- and beta-Proteobacteria. Based on molecular clock analysis, we estimate that rhizobial nitrogen-fixing symbiosis appeared for the first time about 51 Mya (Eocene epoch) in Rhizobiaceae, and it was laterally transferred to multiple symbiotic taxa in alpha- and beta-Proteobacteria. Coevolutionary tests conducted for measuring the phylogenetic congruence between hosts and symbionts revealed only weak topological similarity between legumes and their bacterial symbionts. We conclude that frequent lateral transfer of symbiotic genes, facultative symbiotic nature of rhizobia, differential evolutionary processes of chromosome versus plasmids, and complex multispecies coevolutionary processes have shaped the rhizobia-host associations.
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Affiliation(s)
- Saleh Rahimlou
- Institute of Ecology and Earth Sciences, University of Tartu, 14A Ravila, 50411, Tartu, Estonia.
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, 14A Ravila, 50411, Tartu, Estonia; Natural History Museum, University of Tartu, 46 Vanemuise, 51003 Tartu, Estonia
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43
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Structure and Development of the Legume-Rhizobial Symbiotic Interface in Infection Threads. Cells 2021; 10:cells10051050. [PMID: 33946779 PMCID: PMC8146911 DOI: 10.3390/cells10051050] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The intracellular infection thread initiated in a root hair cell is a unique structure associated with Rhizobium-legume symbiosis. It is characterized by inverted tip growth of the plant cell wall, resulting in a tunnel that allows invasion of host cells by bacteria during the formation of the nitrogen-fixing root nodule. Regulation of the plant-microbial interface is essential for infection thread growth. This involves targeted deposition of the cell wall and extracellular matrix and tight control of cell wall remodeling. This review describes the potential role of different actors such as transcription factors, receptors, and enzymes in the rearrangement of the plant-microbial interface and control of polar infection thread growth. It also focuses on the composition of the main polymers of the infection thread wall and matrix and the participation of reactive oxygen species (ROS) in the development of the infection thread. Mutant analysis has helped to gain insight into the development of host defense reactions. The available data raise many new questions about the structure, function, and development of infection threads.
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Montiel J, Reid D, Grønbæk TH, Benfeldt CM, James EK, Ott T, Ditengou FA, Nadzieja M, Kelly S, Stougaard J. Distinct signaling routes mediate intercellular and intracellular rhizobial infection in Lotus japonicus. PLANT PHYSIOLOGY 2021; 185:1131-1147. [PMID: 33793909 PMCID: PMC8133683 DOI: 10.1093/plphys/kiaa049] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 05/07/2023]
Abstract
Rhizobial infection of legume roots during the development of nitrogen-fixing root nodules can occur intracellularly, through plant-derived infection threads traversing cells, or intercellularly, via bacterial entry between epidermal plant cells. Although it is estimated that around 25% of all legume genera are intercellularly infected, the pathways and mechanisms supporting this process have remained virtually unexplored due to a lack of genetically amenable legumes that exhibit this form of infection. In this study, we report that the model legume Lotus japonicus is infected intercellularly by the IRBG74 strain, recently proposed to belong to the Agrobacterium clade of the Rhizobiaceae. We demonstrate that the resources available for L. japonicus enable insight into the genetic requirements and fine-tuning of the pathway governing intercellular infection in this species. Inoculation of L. japonicus mutants shows that Ethylene-responsive factor required for nodulation 1 (Ern1) and Leu-rich Repeat Receptor-Like Kinase (RinRK1) are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including nod factor receptor 5 (NFR5), symbiosis receptor-like kinase (SymRK), Ca2+/calmodulin dependent kinase (CCaMK), exopolysaccharide receptor 3 (Epr3), Cyclops, nodule inception (Nin), nodulation signaling pathway 1 (Nsp1), nodulation signaling pathway 2 (Nsp2), cystathionine-β-synthase (Cbs), and Vapyrin are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared with intracellular colonization. In particular, several cytokinin-related genes were differentially regulated. Corroborating this observation, cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74, whereas lhk1 cytokinin receptor mutants formed no nodules. These results indicate a differential requirement for cytokinin signaling during intercellular rhizobial entry and highlight distinct modalities of inter- and intracellular infection mechanisms in L. japonicus.
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Affiliation(s)
- Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Thomas H Grønbæk
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Caroline M Benfeldt
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas Ott
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Franck A Ditengou
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
- Author for ommunication:
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45
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Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem. SUSTAINABILITY 2021. [DOI: 10.3390/su13042400] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) in the agricultural production system influences many aspects of agroecosystems and several critical ecosystem services widely depend on the N availability in the soil. Cumulative changes in regional ecosystem services may lead to global environmental changes. Thus, the soil N status in agriculture is of critical importance to strategize its most efficient use. Nitrogen is also one of the most susceptible macronutrients to environmental loss, such as ammonia volatilization (NH3), nitrous oxide (N2O) emissions, nitrate leaching (NO3), etc. Any form of N losses from agricultural systems can be major limitations for crop production, soil sustainability, and environmental safeguard. There is a need to focus on mitigation strategies to minimize global N pollution and implement agricultural management practices that encourage regenerative and sustainable agriculture. In this review, we identified the avenues of N loss into the environment caused by current agronomic practices and discussed the potential practices that can be adapted to prevent this N loss in production agriculture. This review also explored the N status in agriculture during the COVID-19 pandemic and the existing knowledge gaps and questions that need to be addressed.
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46
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Quilbé J, Lamy L, Brottier L, Leleux P, Fardoux J, Rivallan R, Benichou T, Guyonnet R, Becana M, Villar I, Garsmeur O, Hufnagel B, Delteil A, Gully D, Chaintreuil C, Pervent M, Cartieaux F, Bourge M, Valentin N, Martin G, Fontaine L, Droc G, Dereeper A, Farmer A, Libourel C, Nouwen N, Gressent F, Mournet P, D'Hont A, Giraud E, Klopp C, Arrighi JF. Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis. Nat Commun 2021; 12:829. [PMID: 33547303 PMCID: PMC7864950 DOI: 10.1038/s41467-021-21094-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium-legume symbiosis.
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Affiliation(s)
- Johan Quilbé
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Philippe Leleux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Thomas Benichou
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Bárbara Hufnagel
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Amandine Delteil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Mickaël Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Valentin
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Loïc Fontaine
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34398, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Cyril Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France.
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Shrestha A, Zhong S, Therrien J, Huebert T, Sato S, Mun T, Andersen SU, Stougaard J, Lepage A, Niebel A, Ross L, Szczyglowski K. Lotus japonicus Nuclear Factor YA1, a nodule emergence stage-specific regulator of auxin signalling. THE NEW PHYTOLOGIST 2021; 229:1535-1552. [PMID: 32978812 PMCID: PMC7984406 DOI: 10.1111/nph.16950] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/05/2020] [Indexed: 05/07/2023]
Abstract
Organogenesis of legume root nodules begins with the nodulation factor-dependent stimulation of compatible root cells to initiate divisions, signifying an early nodule primordium formation event. This is followed by cellular differentiation, including cell expansion and vascular bundle formation, and we previously showed that Lotus japonicus NF-YA1 is essential for this process, presumably by regulating three members of the SHORT INTERNODES/STYLISH (STY) transcription factor gene family. In this study, we used combined genetics, genomics and cell biology approaches to characterize the role of STY genes during root nodule formation and to test a hypothesis that they mediate nodule development by stimulating auxin signalling. We show here that L. japonicus STYs are required for nodule emergence. This is attributed to the NF-YA1-dependent regulatory cascade, comprising STY genes and their downstream targets, YUCCA1 and YUCCA11, involved in a local auxin biosynthesis at the post-initial cell division stage. An analogous NF-YA1/STY regulatory module seems to operate in Medicago truncatula in association with the indeterminate nodule patterning. Our data define L. japonicus and M. truncatula NF-YA1 genes as important nodule emergence stage-specific regulators of auxin signalling while indicating that the inductive stage and subsequent formation of early nodule primordia are mediated through an independent mechanism(s).
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Affiliation(s)
- Arina Shrestha
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Sihui Zhong
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Jasmine Therrien
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Terry Huebert
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Shusei Sato
- Graduate School of Life SciencesTohoku University2‐1‐1 KatahiraSendai980‐8577Japan
| | - Terry Mun
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Stig U. Andersen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Agnes Lepage
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Loretta Ross
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Krzysztof Szczyglowski
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
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48
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Zhang B, Wang M, Sun Y, Zhao P, Liu C, Qing K, Hu X, Zhong Z, Cheng J, Wang H, Peng Y, Shi J, Zhuang L, Du S, He M, Wu H, Liu M, Chen S, Wang H, Chen X, Fan W, Tian K, Wang Y, Chen Q, Wang S, Dong F, Yang C, Zhang M, Song Q, Li Y, Wang X. Glycine max NNL1 restricts symbiotic compatibility with widely distributed bradyrhizobia via root hair infection. NATURE PLANTS 2021; 7:73-86. [PMID: 33452487 DOI: 10.1038/s41477-020-00832-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Symbiosis between soybean (Glycine max) and rhizobia is essential for efficient nitrogen fixation. Rhizobial effectors secreted through the type-III secretion system are key for mediating the interactions between plants and rhizobia, but the molecular mechanism remains largely unknown. Here, our genome-wide association study for nodule number identified G. max Nodule Number Locus 1 (GmNNL1), which encodes a new R protein. GmNNL1 directly interacts with the nodulation outer protein P (NopP) effector from Bradyrhizobium USDA110 to trigger immunity and inhibit nodulation through root hair infection. The insertion of a 179 bp short interspersed nuclear element (SINE)-like transposon into GmNNL1 leads to the loss of function of GmNNL1, enabling bradyrhizobia to successfully nodulate soybeans through the root hair infection route and enhancing nitrogen fixation. Our findings provide important insights into the coevolution of soybean-bradyrhizobia compatibility and offer a way to design new legume-rhizobia interactions for efficient symbiotic nitrogen fixation.
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Affiliation(s)
- Bao Zhang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Mengdi Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Yifang Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Peng Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chang Liu
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Ke Qing
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Xiaotong Hu
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Zhedong Zhong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jialong Cheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Haijiao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Yaqi Peng
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Jiajia Shi
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Lili Zhuang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Si Du
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Miao He
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Hui Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Liu
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengcai Chen
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Hong Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xu Chen
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Wei Fan
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Kewei Tian
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China
| | - Yin Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiang Chen
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, China
| | - Shixiang Wang
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Faming Dong
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Soybean Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, USA
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, China
| | - Mengchen Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, USA
| | - Youguo Li
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China.
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Luo Y, Liu D, Jiao S, Liu S, Wang X, Shen X, Wei G. Identification of Robinia pseudoacacia target proteins responsive to Mesorhizobium amphore CCNWGS0123 effector protein NopT. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7347-7363. [PMID: 32865563 DOI: 10.1093/jxb/eraa405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Nodulation outer proteins secreted via type 3 secretion systems are involved in the process of symbiosis between legume plants and rhizobia. To study the function of NopT in symbiosis, we mutated nopT in Mesorhizobium amphore CCNWGS0123 (GS0123), which can nodulate black locust (Robinia pseudoacacia). The nopT mutant induced higher levels of jasmonic acid, salicylic acid, and hydrogen peroxide accumulation in the roots of R. pseudoacacia compared with wild-type GS0123. The ΔnopT mutant induced higher disease-resistant gene expression 72 hours post-inoculation (hpi), whereas GS0123 induced higher disease-resistant gene expression earlier, at 36 hpi. Compared with the nopT mutant, GS0123 induced the up-regulation of most genes at 36 hpi and the down-regulation of most genes at 72 hpi. Proteolytically active NopT_GS0123 induced hypersensitive responses when expressed transiently in tobacco leaves (Nicotiana benthamiana). Two NopT_GS0123 targets in R. pseudoacacia were identified, ATP-citrate synthase alpha chain protein 2 and hypersensitive-induced response protein. Their interactions with NopT_GS0123 triggered resistance by the plant immune system. In conclusion, NopT_GS0123 inhibited the host plant immune system and had minimal effect on nodulation in R. pseudoacacia. Our results reveal the underlying molecular mechanism of NopT function in plant-symbiont interactions.
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Affiliation(s)
- Yantao Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Dongying Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Shuang Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Xinye Wang
- Department of Liquor Making Engineering, Moutai College, Renhuai, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi, China
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50
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Zorin EA, Afonin AM, Kulaeva OA, Gribchenko ES, Shtark OY, Zhukov VA. Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi ( Rhizophagus irregularis) in Pea ( Pisum sativum L.) Roots. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1700. [PMID: 33287282 PMCID: PMC7761762 DOI: 10.3390/plants9121700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022]
Abstract
Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (Pisum sativum L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.
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Affiliation(s)
| | | | | | | | | | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (E.A.Z.); (A.M.A.); (O.A.K.); (E.S.G.); (O.Y.S.)
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