1
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Gao JP, Liang W, Liu CW, Xie F, Murray JD. Unraveling the rhizobial infection thread. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2235-2245. [PMID: 38262702 DOI: 10.1093/jxb/erae017] [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: 10/20/2023] [Accepted: 01/23/2024] [Indexed: 01/25/2024]
Abstract
Most legumes can form an endosymbiotic association with soil bacteria called rhizobia, which colonize specialized root structures called nodules where they fix nitrogen. To colonize nodule cells, rhizobia must first traverse the epidermis and outer cortical cell layers of the root. In most legumes, this involves formation of the infection thread, an intracellular structure that becomes colonized by rhizobia, guiding their passage through the outer cell layers of the root and into the newly formed nodule cells. In this brief review, we recount the early research milestones relating to the rhizobial infection thread and highlight two relatively recent advances in the symbiotic infection mechanism, the eukaryotically conserved 'MYB-AUR1-MAP' mitotic module, which links cytokinesis mechanisms to intracellular infection, and the discovery of the 'infectosome' complex, which guides infection thread growth. We also discuss the potential intertwining of the two modules and the hypothesis that cytokinesis served as a foundation for intracellular infection of symbiotic microbes.
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Affiliation(s)
- Jin-Peng Gao
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjie Liang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230026, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- John Innes Centre, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Norwich Research Park, Norwich NR4 7UH, UK
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2
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Pereira WJ, Boyd J, Conde D, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Boaventura-Novaes C, Chakraborty S, Knaack SA, Gao Y, Feltus FA, Roy S, Ané JM, Frugoli J, Kirst M. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula. Cell Rep 2024; 43:113747. [PMID: 38329875 DOI: 10.1016/j.celrep.2024.113747] [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: 06/21/2023] [Revised: 10/31/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.
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Affiliation(s)
- Wendell J Pereira
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jade Boyd
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Conde
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Madrid, Spain
| | - Paolo M Triozzi
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy
| | - Kelly M Balmant
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Christopher Dervinis
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Henry W Schmidt
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | | | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Sara A Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Frank Alexander Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, USA; Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53726, USA; Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Matias Kirst
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA.
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3
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Gupta G, Chauhan PS, Jha PN, Verma RK, Singh S, Yadav VK, Sahoo DK, Patel A. Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction. Front Microbiol 2024; 15:1355750. [PMID: 38468848 PMCID: PMC10925705 DOI: 10.3389/fmicb.2024.1355750] [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: 12/14/2023] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
Numerous bacterial species associate with plants through commensal, mutualistic, or parasitic association, affecting host physiology and health. The mechanism for such association is intricate and involves the secretion of multiple biochemical substances through dedicated protein systems called secretion systems SS. Eleven SS pathways deliver protein factors and enzymes in their immediate environment or host cells, as well as in competing microbial cells in a contact-dependent or independent fashion. These SS are instrumental in competition, initiation of infection, colonization, and establishment of association (positive or negative) with host organisms. The role of SS in infection and pathogenesis has been demonstrated for several phytopathogens, including Agrobacterium, Xanthomonas, Ralstonia, and Pseudomonas. Since there is overlap in mechanisms of establishing association with host plants, several studies have investigated the role of SSs in the interaction of plant and beneficial bacteria, including symbiotic rhizobia and plant growth bacteria (PGPB). Therefore, the present review updates the role of different SSs required for the colonization of beneficial bacteria such as rhizobia, Burkholderia, Pseudomonas, Herbaspirillum, etc., on or inside plants, which can lead to a long-term association. Most SS like T3SS, T4SS, T5SS, and T6SS are required for the antagonistic activity needed to prevent competing microbes, including phytopathogens, ameliorate biotic stress in plants, and produce substances for successful colonization. Others are required for chemotaxis, adherence, niche formation, and suppression of immune response to establish mutualistic association with host plants.
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Affiliation(s)
- Garima Gupta
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India
- Microbial Technologies Group, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Puneet Singh Chauhan
- Microbial Technologies Group, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Rakesh Kumar Verma
- Department of Biosciences, SLAS Mody University of Science and Technology, Sikar, Rajasthan, India
| | - Sachidanand Singh
- Department of Biotechnology, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, Gujarat, India
| | - Virendra Kumar Yadav
- Department of Lifesciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Ashish Patel
- Department of Lifesciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
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4
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Zhang X, Chen JX, Lian WT, Zhou HW, He Y, Li XX, Liao H. Molecular module GmPTF1a/b-GmNPLa regulates rhizobia infection and nodule formation in soybean. THE NEW PHYTOLOGIST 2024; 241:1813-1828. [PMID: 38062896 DOI: 10.1111/nph.19462] [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: 07/21/2023] [Accepted: 11/08/2023] [Indexed: 01/26/2024]
Abstract
Nodulation begins with the initiation of infection threads (ITs) in root hairs. Though mutual recognition and early symbiotic signaling cascades in legumes are well understood, molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis remain largely unexplored. We functionally investigated a novel pectate lyase enzyme, GmNPLa, and its transcriptional regulator GmPTF1a/b in soybean (Glycine max), where their regulatory roles in IT development and nodule formation were elucidated through investigation of gene expression patterns, bioinformatics analysis, biochemical verification of genetic interactions, and observation of phenotypic impacts in transgenic soybean plants. GmNPLa was specifically induced by rhizobium inoculation in root hairs. Manipulation of GmNPLa produced remarkable effects on IT and nodule formation. GmPTF1a/b displayed similar expression patterns as GmNPLa, and manipulation of GmPTF1a/b also severely influenced nodulation traits. LI soybeans with low nodulation phenotypes were nearly restored to HI nodulation level by complementation of GmNPLa and/or GmPTF1a. Further genetic and biochemical analysis demonstrated that GmPTF1a can bind to the E-box motif to activate transcription of GmNPLa, and thereby facilitate nodulation. Taken together, our findings potentially reveal novel mediation of cell wall gene expression involving the basic helix-loop-helix transcription factor GmPTF1a/b acts as a key early regulator of nodulation in soybean.
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Affiliation(s)
- Xiao Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jia-Xin Chen
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen-Ting Lian
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui-Wen Zhou
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying He
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin-Xin Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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5
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Shen L, Feng J. NIN-at the heart of NItrogen-fixing Nodule symbiosis. FRONTIERS IN PLANT SCIENCE 2024; 14:1284720. [PMID: 38283980 PMCID: PMC10810997 DOI: 10.3389/fpls.2023.1284720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
Legumes and actinorhizal plants establish symbiotic relationships with nitrogen-fixing bacteria, resulting in the formation of nodules. Nodules create an ideal environment for nitrogenase to convert atmospheric nitrogen into biological available ammonia. NODULE INCEPTION (NIN) is an indispensable transcription factor for all aspects of nodule symbiosis. Moreover, NIN is consistently lost in non-nodulating species over evolutions. Here we focus on recent advances in the signaling mechanisms of NIN during nodulation and discuss the role of NIN in the evolution of nitrogen-fixing nodule symbiosis.
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Affiliation(s)
- Lisha Shen
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jian Feng
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- CAS−JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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6
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Shumilina J, Soboleva A, Abakumov E, Shtark OY, Zhukov VA, Frolov A. Signaling in Legume-Rhizobia Symbiosis. Int J Mol Sci 2023; 24:17397. [PMID: 38139226 PMCID: PMC10743482 DOI: 10.3390/ijms242417397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/19/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.
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Affiliation(s)
- Julia Shumilina
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
| | - Alena Soboleva
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Evgeny Abakumov
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Vladimir A. Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
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7
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Schnabel E, Thomas J, El-Hawaz R, Gao Y, Poehlman WL, Chavan S, Pasha A, Esteban E, Provart N, Feltus FA, Frugoli J. Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:805-820. [PMID: 37717250 DOI: 10.1094/mpmi-03-23-0029-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 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)
- Elise Schnabel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Jacklyn Thomas
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Rabia El-Hawaz
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - William L Poehlman
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Sage Bionetworks, Seattle, WA 98121, U.S.A
| | - Suchitra Chavan
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Leidos, Inc., Atlanta, GA 30345, U.S.A
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - F Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, U.S.A
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, U.S.A
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
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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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Piya S, Pantalone V, Zadegan SB, Shipp S, Lakhssassi N, Knizia D, Krishnan HB, Meksem K, Hewezi T. Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development. MOLECULAR PLANT PATHOLOGY 2023; 24:628-636. [PMID: 36975024 DOI: 10.1111/mpp.13327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 05/18/2023]
Abstract
Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | | | - Sarah Shipp
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, Missouri, USA
- Plant Genetics Research, USDA Agricultural Research Service, Columbia, Missouri, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
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10
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Sun Z, Jiang S, Wang D, Li L, Liu B, Ran Q, Hu L, Xiong J, Tang Y, Gu X, Wu Y, Liang Z. Single-cell RNA-seq of Lotus japonicus provide insights into identification and function of root cell types of legume. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1147-1152. [PMID: 36537698 DOI: 10.1111/jipb.13435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/16/2022] [Indexed: 05/13/2023]
Abstract
The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single-cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume. We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single-cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes.
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Affiliation(s)
- Zhanmin Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | | | - Dan Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Nanchong, 637002, China
| | - Linxia Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Boxin Liu
- BGI Genomics, Shenzhen, 518083, China
| | - Qifan Ran
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
| | - Lizhen Hu
- Institute of Animal and Veterinary Science, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Junbo Xiong
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan, 430072, China
| | - Yixiong Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanmin Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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11
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Liu Z, Kong X, Long Y, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J, Yan Z. Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. NATURE PLANTS 2023; 9:515-524. [PMID: 37055554 DOI: 10.1038/s41477-023-01387-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule development, and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.
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Affiliation(s)
- Zhijian Liu
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiangying Kong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Long
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Sirui Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Hong Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jinbu Jia
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenhui Cui
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China
| | - Zunmian Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Zhe Yan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
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12
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Su C. Pectin modifications at the symbiotic interface. THE NEW PHYTOLOGIST 2023; 238:25-32. [PMID: 36565041 DOI: 10.1111/nph.18705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Plant cells are surrounded by a structured cell wall, which not only defines cell shape but also provides a structural barrier for protection against pathogen infection. However, the presence of this barrier does not impede the establishment of mutualistic symbioses between plants and several microbes (e.g. ectomycorrhizal fungi, arbuscular mycorrhizal fungi, and rhizobia). To establish such beneficial associations, symbiotic microbes need to colonize the plant tissues via intercellular and/or intracellular infection, a process that requires cell wall modifications. Although cell wall composition and changes during this process have interested researchers for years, the functional characterization of the molecular players involved is still limited. In this viewpoint, based on several new studies, I discuss how the PME-PL/PG pathway mediates cell wall pectin modifications at the symbiotic interface and highlight further research directions which can broaden our understanding of how beneficial root symbioses are established.
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Affiliation(s)
- Chao Su
- Plant Cell Biology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
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13
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Reyero-Saavedra R, Fuentes SI, Leija A, Jiménez-Nopala G, Peláez P, Ramírez M, Girard L, Porch TG, Hernández G. Identification and Characterization of Common Bean ( Phaseolus vulgaris) Non-Nodulating Mutants Altered in Rhizobial Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1310. [PMID: 36986997 PMCID: PMC10059843 DOI: 10.3390/plants12061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 06/19/2023]
Abstract
The symbiotic N2-fixation process in the legume-rhizobia interaction is relevant for sustainable agriculture. The characterization of symbiotic mutants, mainly in model legumes, has been instrumental for the discovery of symbiotic genes, but similar studies in crop legumes are scant. To isolate and characterize common bean (Phaseolus vulgaris) symbiotic mutants, an ethyl methanesulphonate-induced mutant population from the BAT 93 genotype was analyzed. Our initial screening of Rhizobium etli CE3-inoculated mutant plants revealed different alterations in nodulation. We proceeded with the characterization of three non-nodulating (nnod), apparently monogenic/recessive mutants: nnod(1895), nnod(2353) and nnod(2114). Their reduced growth in a symbiotic condition was restored when the nitrate was added. A similar nnod phenotype was observed upon inoculation with other efficient rhizobia species. A microscopic analysis revealed a different impairment for each mutant in an early symbiotic step. nnod(1895) formed decreased root hair curling but had increased non-effective root hair deformation and no rhizobia infection. nnod(2353) produced normal root hair curling and rhizobia entrapment to form infection chambers, but the development of the latter was blocked. nnod(2114) formed infection threads that did not elongate and thus did not reach the root cortex level; it occasionally formed non-infected pseudo-nodules. The current research is aimed at mapping the responsible mutated gene for a better understanding of SNF in this critical food crop.
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Affiliation(s)
- Rocío Reyero-Saavedra
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Sara Isabel Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Gladys Jiménez-Nopala
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Pablo Peláez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Lourdes Girard
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Timothy G. Porch
- USDA-ARS, Tropical Agriculture Research Station, 2200 P.A. Campos Avenue, Suite 201, Mayaguez 00680, Puerto Rico;
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
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14
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Kalmbach L, Bourdon M, Belevich I, Safran J, Lemaire A, Heo JO, Otero S, Blob B, Pelloux J, Jokitalo E, Helariutta Y. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis. Curr Biol 2023; 33:926-939.e9. [PMID: 36805125 DOI: 10.1016/j.cub.2023.01.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 11/12/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
In plants, the phloem distributes photosynthetic products for metabolism and storage over long distances. It relies on specialized cells, the sieve elements, which are enucleated and interconnected through large so-called sieve pores in their adjoining cell walls. Reverse genetics identified PECTATE LYASE-LIKE 12 (PLL12) as critical for plant growth and development. Using genetic complementations, we established that PLL12 is required exclusively late during sieve element differentiation. Structural homology modeling, enzyme inactivation, and overexpression suggest a vital role for PLL12 in sieve-element-specific pectin remodeling. While short distance symplastic diffusion is unaffected, the pll12 mutant is unable to accommodate sustained plant development due to an incapacity to accommodate increasing hydraulic demands on phloem long-distance transport as the plant grows-a defect that is aggravated when combined with another sieve-element-specific mutant callose synthase 7 (cals7). Establishing CALS7 as a specific sieve pore marker, we investigated the subcellular dynamics of callose deposition in the developing sieve plate. Using fluorescent CALS7 then allowed identifying structural defects in pll12 sieve pores that are moderate at the cellular level but become physiologically relevant due to the serial arrangement of sieve elements in the sieve tube. Overall, pectin degradation through PLL12 appears subtle in quantitative terms. We therefore speculate that PLL12 may act as a regulator to locally remove homogalacturonan, thus potentially enabling further extracellular enzymes to access and modify the cell wall during sieve pore maturation.
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Affiliation(s)
- Lothar Kalmbach
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ilya Belevich
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Josip Safran
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Adrien Lemaire
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Jung-Ok Heo
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Sofia Otero
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Bernhard Blob
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Jérôme Pelloux
- UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, Université de Picardie, 33 Rue St Leu, 80039 Amiens, France
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ykä Helariutta
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland.
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15
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Jhu MY, Oldroyd GED. Dancing to a different tune, can we switch from chemical to biological nitrogen fixation for sustainable food security? PLoS Biol 2023; 21:e3001982. [PMID: 36917569 PMCID: PMC10013914 DOI: 10.1371/journal.pbio.3001982] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Our current food production systems are unsustainable, driven in part through the application of chemically fixed nitrogen. We need alternatives to empower farmers to maximise their productivity sustainably. Therefore, we explore the potential for transferring the root nodule symbiosis from legumes to other crops. Studies over the last decades have shown that preexisting developmental and signal transduction processes were recruited during the evolution of legume nodulation. This allows us to utilise these preexisting processes to engineer nitrogen fixation in target crops. Here, we highlight our understanding of legume nodulation and future research directions that might help to overcome the barrier of achieving self-fertilising crops.
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Affiliation(s)
- Min-Yao Jhu
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Giles E. D. Oldroyd
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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16
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Suzaki T. Root nodule organogenesis: a unique lateral organogenesis in legumes. BREEDING SCIENCE 2023; 73:70-75. [PMID: 37168810 PMCID: PMC10165338 DOI: 10.1270/jsbbs.22067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/04/2022] [Indexed: 05/13/2023]
Abstract
During the course of plant evolution, leguminous and a few plants species have established root nodule symbiosis (RNS), one of the nitrogen nutrient acquisition strategies based on mutual interaction between plants and nitrogen-fixing bacteria. In addition to its useful agronomic trait, RNS comprises a unique form of plant lateral organogenesis; dedifferentiation and activation of cortical cells in the root are induced upon bacterial infection during nodule development. In the past few years, the elucidations of the significance of NODULE INCEPTION transcription factor as a potentially key innovative factor of RNS, the details of its function, and the successive discoveries of its target genes have advanced our understanding underlying molecular mechanisms of nodule organogenesis. In addition, a recent elucidation of the role of legume SHORTROOT-SCARECROW module has provided the insights into the unique properties of legume cortical cells. Here, I summarize such latest findings on the neofunctionalized key players of nodule organogenesis, which may provide clue to understand an evolutionary basis of RNS.
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Affiliation(s)
- Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Corresponding author (e-mail: )
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17
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Lace B, Su C, Invernot Perez D, Rodriguez-Franco M, Vernié T, Batzenschlager M, Egli S, Liu CW, Ott T. RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections. eLife 2023; 12:80741. [PMID: 36856086 PMCID: PMC9991063 DOI: 10.7554/elife.80741] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). In many host plants, this occurs via transcellular tubular structures (infection threads - ITs) that extend across cell layers via polar tip-growth. Comparative phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among the critical genetic determinants for bacterial infection. In Medicago truncatula, RPG is required for effective IT progression within root hairs but the cellular and molecular function of the encoded protein remains elusive. Here, we show that RPG resides in the protein complex formed by the core endosymbiotic components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, co-localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta of M. truncatula root hairs undergoing infection and is necessary for VPY recruitment into these structures. Fluorescence Lifetime Imaging Microscopy (FLIM) of phosphoinositide species during bacterial infection revealed that functional RPG is required to sustain strong membrane polarization at the advancing tip of the IT. In addition, loss of RPG functionality alters the cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects the polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). Our results integrate RPG into a core host machinery required to support symbiont accommodation, suggesting that its occurrence in plant host genomes is essential to co-opt a multimeric protein module committed to endosymbiosis to sustain IT-mediated bacterial infection.
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Affiliation(s)
- Beatrice Lace
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Chao Su
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | | | | | - Tatiana Vernié
- LRSV, Université de Toulouse, CNRS, UPS, INP ToulouseCastanet-TolosanFrance
| | | | - Sabrina Egli
- University of Freiburg, Faculty of BiologyFreiburgGermany
| | - Cheng-Wu Liu
- School of Life Sciences, Division of Life Sciences and Medicine, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of ChinaHefeiChina
| | - Thomas Ott
- University of Freiburg, Faculty of BiologyFreiburgGermany
- CIBSS – Centre of Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
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18
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Singh J, Verma PK. Role of Nod factor receptors and its allies involved in nitrogen fixation. PLANTA 2023; 257:54. [PMID: 36780015 DOI: 10.1007/s00425-023-04090-7] [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: 11/02/2022] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Lysin motif (LysM)-receptor-like kinase (RLK) and leucine-rich repeat (LRR)-RLK mediated signaling play important roles in the development and regulation of root nodule symbiosis in legumes. The availability of water and nutrients in the soil is a major limiting factor affecting crop productivity. Plants of the Leguminosae family form a symbiotic association with nitrogen-fixing Gram-negative soil bacteria, rhizobia for nitrogen fixation. This symbiotic relationship between legumes and rhizobia depends on the signal exchange between them. Plant receptor-like kinases (RLKs) containing lysin motif (LysM) and/or leucine-rich repeat (LRR) play an important role in the perception of chemical signals from rhizobia for initiation and establishment of root nodule symbiosis (RNS) that results in nitrogen fixation. This review highlights the diverse aspects of LysM-RLK and LRR receptors including their specificity, functions, interacting partners, regulation, and associated signaling in RNS. The activation of LysM-RLKs and LRR-RLKs is important for ensuring the successful interaction between legume roots and rhizobia. The intracellular regions of the receptors enable additional layers of signaling that help in the transduction of signals intracellularly. Additionally, symbiosis receptor-like kinase (SYMRK) containing the LRR motif acts as a co-receptor with Nod factors receptors (LysM-RLK). Cleavage of the malectin-like domain from the SYMRK ectodomain is a mechanism for controlling SYMRK stability. Overall, this review has discussed different aspects of legume receptors that are critical to the perception of signals from rhizobia and their subsequent role in creating the mutualistic relationship necessary for nitrogen fixation. Additionally, it has been discussed how crucial it is to extrapolate the knowledge gained from model legumes to crop legumes such as chickpea and common bean to better understand the mechanism underlying nodule formation in crop legumes. Future directions have also been proposed in this regard.
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Affiliation(s)
- Jawahar Singh
- Plant-Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México (UNAM), 54090, Tlalnepantla, State of Mexico, Mexico.
| | - Praveen Kumar Verma
- Plant-Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant-Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 10067, India.
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19
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Su C, Zhang G, Rodriguez-Franco M, Hinnenberg R, Wietschorke J, Liang P, Yang W, Uhler L, Li X, Ott T. Transcellular progression of infection threads in Medicago truncatula roots is associated with locally confined cell wall modifications. Curr Biol 2023; 33:533-542.e5. [PMID: 36657449 PMCID: PMC9937034 DOI: 10.1016/j.cub.2022.12.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/18/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023]
Abstract
The root nodule symbiosis with its global impact on nitrogen fertilization of soils is characterized by an intracellular colonization of legume roots by rhizobia. Although the symbionts are initially taken up by morphologically adapted root hairs, rhizobia persistently progress within a membrane-confined infection thread through several root cortical and later nodular cell layers. Throughout this transcellular passaging, rhizobia have to repeatedly pass host plasma membranes and cell walls. Here, we investigated this essential process and describe the concerted action of one of the symbiosis-specific pectin methyl esterases (SyPME1) and the nodulation pectate lyase (NPL) at the infection thread and transcellular passage sites. Their coordinated function mediates spatially confined pectin alterations in the cell-cell interface that result in the establishment of an apoplastic compartment where bacteria are temporarily released into and taken up from the subjacent cell. This process allows successful intracellular progression of infection threads through the entire root cortical tissue.
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Affiliation(s)
- Chao Su
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.
| | - Guofeng Zhang
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Rosula Hinnenberg
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jenny Wietschorke
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Pengbo Liang
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; State Key Laboratory of Plant Physiology and Biochemistry, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing 100193, P.R. China
| | - Wei Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan 430070, Hubei, P.R. China
| | - Leonard Uhler
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Hongshan District, Wuhan 430070, Hubei, P.R. China
| | - Thomas Ott
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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20
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Li X, Liu M, Cai M, Chiasson D, Groth M, Heckmann AB, Wang TL, Parniske M, Downie JA, Xie F. RPG interacts with E3-ligase CERBERUS to mediate rhizobial infection in Lotus japonicus. PLoS Genet 2023; 19:e1010621. [PMID: 36735729 PMCID: PMC9931111 DOI: 10.1371/journal.pgen.1010621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/15/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Symbiotic interactions between rhizobia and legumes result in the formation of root nodules, which fix nitrogen that can be used for plant growth. Rhizobia usually invade legume roots through a plant-made tunnel-like structure called an infection thread (IT). RPG (Rhizobium-directed polar growth) encodes a coiled-coil protein that has been identified in Medicago truncatula as required for root nodule infection, but the function of RPG remains poorly understood. In this study, we identified and characterized RPG in Lotus japonicus and determined that it is required for IT formation. RPG was induced by Mesorhizobium loti or purified Nodulation factor and displayed an infection-specific expression pattern. Nodule inception (NIN) bound to the RPG promoter and induced its expression. We showed that RPG displayed punctate subcellular localization in L. japonicus root protoplasts and in root hairs infected by M. loti. The N-terminal predicted C2 lipid-binding domain of RPG was not required for this subcellular localization or for function. CERBERUS, a U-box E3 ligase which is also required for rhizobial infection, was found to be localized similarly in puncta. RPG co-localized and directly interacted with CERBERUS in the early endosome (TGN/EE) compartment and near the nuclei in root hairs after rhizobial inoculation. Our study sheds light on an RPG-CERBERUS protein complex that is involved in an exocytotic pathway mediating IT elongation.
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Affiliation(s)
- Xiaolin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Miaoxia Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Min Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - David Chiasson
- Faculty of Biology, University of Munich, Großhaderner Straße 2–4, Planegg-Martinsried, Germany
| | - Martin Groth
- Faculty of Biology, University of Munich, Großhaderner Straße 2–4, Planegg-Martinsried, Germany
| | - Anne B. Heckmann
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Trevor L. Wang
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2–4, Planegg-Martinsried, Germany
| | - J. Allan Downie
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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21
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Liu M, Kameoka H, Oda A, Maeda T, Goto T, Yano K, Soyano T, Kawaguchi M. The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2023; 13:995589. [PMID: 36733592 PMCID: PMC9888413 DOI: 10.3389/fpls.2022.995589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.
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Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Akiko Oda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Goto
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
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22
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Cervantes-Pérez SA, Thibivilliers S, Laffont C, Farmer AD, Frugier F, Libault M. Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume. MOLECULAR PLANT 2022; 15:1868-1888. [PMID: 36321199 DOI: 10.1016/j.molp.2022.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell types, showing the strongest differential regulation in response to a short-term (48 h) rhizobium inoculation, revealed not only known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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23
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Bhattacharjee O, Raul B, Ghosh A, Bhardwaj A, Bandyopadhyay K, Sinharoy S. Nodule INception-independent epidermal events lead to bacterial entry during nodule development in peanut (Arachis hypogaea). THE NEW PHYTOLOGIST 2022; 236:2265-2281. [PMID: 36098671 DOI: 10.1111/nph.18483] [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: 04/27/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Legumes can host nitrogen-fixing rhizobia inside root nodules. In model legumes, rhizobia enter via infection threads (ITs) and develop nodules in which the infection zone contains a mixture of infected and uninfected cells. Peanut (Arachis hypogaea) diversified from model legumes c. 50-55 million years ago. Rhizobia enter through 'cracks' to form nodules in peanut roots where cells of the infection zone are uniformly infected. Phylogenomic studies have indicated symbiosis as a labile trait in peanut. These atypical features prompted us to investigate the molecular mechanism of peanut nodule development. Combining cell biology, genetics and genomic tools, we visualized the status of hormonal signaling in peanut nodule primordia. Moreover, we dissected the signaling modules of Nodule INception (NIN), a master regulator of both epidermal infection and cortical organogenesis. Cytokinin signaling operates in a broad zone, from the epidermis to the pericycle inside nodule primordia, while auxin signaling is narrower and focused. Nodule INception is involved in nodule organogenesis, but not in crack entry. Nodulation Pectate Lyase, which remodels cell walls during IT formation, is not required. By contrast, Nodule enhanced Glycosyl Hydrolases (AhNGHs) are recruited for cell wall modification during crack entry. While hormonal regulation is conserved, the function of the NIN signaling modules is diversified in peanut.
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Affiliation(s)
- Oindrila Bhattacharjee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Amity University Haryana, Amity Education Valley, Panchgaon, Manesar, Haryana, 122412, India
| | - Bikash Raul
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Amit Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Akanksha Bhardwaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kaustav Bandyopadhyay
- Amity University Haryana, Amity Education Valley, Panchgaon, Manesar, Haryana, 122412, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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24
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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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25
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Chakraborty S, Valdés-López O, Stonoha-Arther C, Ané JM. Transcription Factors Controlling the Rhizobium-Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment. PLANT & CELL PHYSIOLOGY 2022; 63:1326-1343. [PMID: 35552446 DOI: 10.1093/pcp/pcac063] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium-legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium-legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium-legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium-legume symbiosis.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin, Microbial Sciences Building, 1550 Linden Dr, Madison, WI 53706, USA
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Estado de México 54090, México
| | - Christina Stonoha-Arther
- Department of Bacteriology, University of Wisconsin, Microbial Sciences Building, 1550 Linden Dr, Madison, WI 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin, Microbial Sciences Building, 1550 Linden Dr, Madison, WI 53706, USA
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI 53706, USA
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26
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Dinkins RD, Hancock JA, Bickhart DM, Sullivan ML, Zhu H. Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover. PLANTS (BASEL, SWITZERLAND) 2022; 11:2888. [PMID: 36365339 PMCID: PMC9655500 DOI: 10.3390/plants11212888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Red clover (Trifolium pratense L.) is an important forage crop and serves as a major contributor of nitrogen input in pasture settings because of its ability to fix atmospheric nitrogen. During the legume-rhizobial symbiosis, the host plant undergoes a large number of gene expression changes, leading to development of root nodules that house the rhizobium bacteria as they are converted into nitrogen-fixing bacteroids. Many of the genes involved in symbiosis are conserved across legume species, while others are species-specific with little or no homology across species and likely regulate the specific plant genotype/symbiont strain interactions. Red clover has not been widely used for studying symbiotic nitrogen fixation, primarily due to its outcrossing nature, making genetic analysis rather complicated. With the addition of recent annotated genomic resources and use of RNA-seq tools, we annotated and characterized a number of genes that are expressed only in nodule forming roots. These genes include those encoding nodule-specific cysteine rich peptides (NCRs) and nodule-specific Polycystin-1, Lipoxygenase, Alpha toxic (PLAT) domain proteins (NPDs). Our results show that red clover encodes one of the highest number of NCRs and ATS3-like/NPDs, which are postulated to increase nitrogen fixation efficiency, in the Inverted-Repeat Lacking Clade (IRLC) of legumes. Knowledge of the variation and expression of these genes in red clover will provide more insights into the function of these genes in regulating legume-rhizobial symbiosis and aid in breeding of red clover genotypes with increased nitrogen fixation efficiency.
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Affiliation(s)
- Randy D. Dinkins
- Forage-Animal Production Research Unit, USDA-ARS, Lexington, KY 40506, USA
| | - Julie A. Hancock
- College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40508, USA
| | | | | | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
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27
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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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28
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Upadhyay SK, Srivastava AK, Rajput VD, Chauhan PK, Bhojiya AA, Jain D, Chaubey G, Dwivedi P, Sharma B, Minkina T. Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production. Front Microbiol 2022; 13:916488. [PMID: 35910633 PMCID: PMC9329127 DOI: 10.3389/fmicb.2022.916488] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022] Open
Abstract
The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.
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Affiliation(s)
- Sudhir K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | | | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Prabhat K. Chauhan
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | - Ali Asger Bhojiya
- Department of Agriculture and Veterinary Sciences, Mewar University, Chittorgarh, India
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Padmanabh Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Bechan Sharma
- Department of Biochemistry, Faculty of Science, University of Allahabad, Allahabad, India
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
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29
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Chakraborty S, Harris JM. At the Crossroads of Salinity and Rhizobium-Legume Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:540-553. [PMID: 35297650 DOI: 10.1094/mpmi-09-21-0231-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, U.S.A
| | - Jeanne M Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, U.S.A
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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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Kovács S, Kiss E, Jenei S, Fehér-Juhász E, Kereszt A, Endre G. The Medicago truncatula IEF Gene Is Crucial for the Progression of Bacterial Infection During Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:401-415. [PMID: 35171648 DOI: 10.1094/mpmi-11-21-0279-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Legumes are able to meet their nitrogen need by establishing nitrogen-fixing symbiosis with rhizobia. Nitrogen fixation is performed by rhizobia, which has been converted to bacteroids, in newly formed organs, the root nodules. In the model legume Medicago truncatula, nodule cells are invaded by rhizobia through transcellular tubular structures called infection threads (ITs) that are initiated at the root hairs. Here, we describe a novel M. truncatula early symbiotic mutant identified as infection-related epidermal factor (ief), in which the formation of ITs is blocked in the root hair cells and only nodule primordia are formed. We show that the function of MtIEF is crucial for the bacterial infection in the root epidermis but not required for the nodule organogenesis. The IEF gene that appears to have been recruited for a symbiotic function after the duplication of a flower-specific gene is activated by the ERN1-branch of the Nod factor signal transduction pathway and independent of the NIN activity. The expression of MtIEF is induced transiently in the root epidermal cells by the rhizobium partner or Nod factors. Although its expression was not detectable at later stages of symbiosis, complementation experiments indicate that MtIEF is also required for the proper invasion of the nodule cells by rhizobia. The gene encodes an intracellular protein of unknown function possessing a coiled-coil motif and a plant-specific DUF761 domain. The IEF protein interacts with RPG, another symbiotic protein essential for normal IT development, suggesting that combined action of these proteins plays a role in nodule infection.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Szilárd Kovács
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ernő Kiss
- Biological Research Centre, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Sándor Jenei
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erzsébet Fehér-Juhász
- Biological Research Centre, Institute of Genetics, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Attila Kereszt
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gabriella Endre
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
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32
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Castaingts M, Kirolinko C, Rivero C, Artunian J, Mancini Villagra U, Blanco FA, Zanetti ME. Identification of conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris-Rhizobium etli symbiosis through differential analysis of host small RNAs. THE NEW PHYTOLOGIST 2022; 234:1430-1447. [PMID: 35203109 DOI: 10.1111/nph.18055] [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: 01/15/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Phaseolus vulgaris plants from the Mesoamerican centre of genetic diversification establish a preferential and more efficient root nodule symbiosis with sympatric Rhizobium etli strains. This is mediated by changes in host gene expression, which might occur either at the transcriptional or at the post-transcriptional level. However, the implication of small RNA (sRNA)-mediated control of gene expression in strain selectivity has remained elusive. sRNA sequencing was used to identify host microRNAs (miRNAs) differentially regulated in roots at an early stage of the symbiotic interaction, which were further characterized by applying a reverse genetic approach. In silico analysis identified known and new miRNAs that accumulated to a greater extent in the preferential and more efficient interaction. One of them, designated as Pvu-miR5924, participates in the mechanisms that determine the selection of R. etli strains that will colonize the nodules. In addition, the functional analysis of Pvu-miR390b verified that this miRNA is a negative modulator of nodule formation and bacterial infection. This study not only extended the list of miRNAs identified in P. vulgaris but also enabled the identification of miRNAs that play relevant functions in nodule formation, rhizobial infection and the selection of the rhizobial strains that will occupy the nodule.
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Affiliation(s)
- Melisse Castaingts
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Cristina Kirolinko
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Claudio Rivero
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Jennifer Artunian
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Ulises Mancini Villagra
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Flavio Antonio Blanco
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - María Eugenia Zanetti
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
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Darrington M, Leftwich PT, Holmes NA, Friend LA, Clarke NVE, Worsley SF, Margaritopolous JT, Hogenhout SA, Hutchings MI, Chapman T. Characterisation of the symbionts in the Mediterranean fruit fly gut. Microb Genom 2022; 8. [PMID: 35446250 PMCID: PMC9453069 DOI: 10.1099/mgen.0.000801] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Symbioses between bacteria and their insect hosts can range from loose associations through to obligate interdependence. While fundamental evolutionary insights have been gained from the in-depth study of obligate mutualisms, there is increasing interest in the evolutionary potential of flexible symbiotic associations between hosts and their gut microbiomes. Understanding relationships between microbes and hosts also offers the potential for exploitation for insect control. Here, we investigate the gut microbiome of a global agricultural pest, the Mediterranean fruit fly (Ceratitis capitata). We used 16S rRNA profiling to compare the gut microbiomes of laboratory and wild strains raised on different diets and from flies collected from various natural plant hosts. The results showed that medfly guts harbour a simple microbiome that is primarily determined by the larval diet. However, regardless of the laboratory diet or natural plant host on which flies were raised, Klebsiella spp. dominated medfly microbiomes and were resistant to removal by antibiotic treatment. We sequenced the genome of the dominant putative Klebsiella spp. (‘Medkleb’) isolated from the gut of the Toliman wild-type strain. Genome-wide ANI analysis placed Medkleb within the K. oxytoca / michiganensis group. Species level taxonomy for Medkleb was resolved using a mutli-locus phylogenetic approach - and molecular, sequence and phenotypic analyses all supported its identity as K. michiganensis. Medkleb has a genome size (5825435 bp) which is 1.6 standard deviations smaller than the mean genome size of free-living Klebsiella spp. Medkleb also lacks some genes involved in environmental sensing. Moreover, the Medkleb genome contains at least two recently acquired unique genomic islands as well as genes that encode pectinolytic enzymes capable of degrading plant cell walls. This may be advantageous given that the medfly diet includes unripe fruits containing high proportions of pectin. The results suggest that the medfly harbours a commensal gut bacterium that may have developed a mutualistic association with its host and provide nutritional benefits.
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Affiliation(s)
- Mike Darrington
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Neil A Holmes
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Lucy A Friend
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Naomi V E Clarke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John T Margaritopolous
- Department of Plant Protection, Institute of Industrial and Fodder Crops, Hellenic Agricultural Organization-DEMETER, Volos, Greece
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, NR4 7UH, Norwich, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Yun J, Sun Z, Jiang Q, Wang Y, Wang C, Luo Y, Zhang F, Li X. The miR156b-GmSPL9d module modulates nodulation by targeting multiple core nodulation genes in soybean. THE NEW PHYTOLOGIST 2022; 233:1881-1899. [PMID: 34862970 PMCID: PMC9303946 DOI: 10.1111/nph.17899] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/27/2021] [Indexed: 05/25/2023]
Abstract
Symbiotic nodulation is initiated in the roots of legumes in response to low nitrogen and rhizobial signal molecules and is dynamically regulated by a complex regulatory network that coordinates rhizobial infection and nodule organogenesis. It has been shown that the miR156-SPL module mediates nodulation in legumes; however, conclusive evidence of how this module exerts its function during nodulation remains elusive. Here, we report that the miR156b-GmSPL9d module regulates symbiotic nodulation by targeting multiple key regulatory genes in the nodulation signalling pathway of soybean. miR156 family members are differentially expressed during nodulation, and miR156b negatively regulates nodulation by mainly targeting soybean SQUAMOSA promoter-binding protein-like 9d (GmSPL9d), a positive regulator of soybean nodulation. GmSPL9d directly binds to the miR172c promoter and activates its expression, suggesting a conserved role of GmSPL9d. Furthermore, GmSPL9d was coexpressed with the soybean nodulation marker genes nodule inception a (GmNINa) and GmENOD40-1 during nodule formation and development. Intriguingly, GmSPL9d can bind to the promoters of GmNINa and GmENOD40-1 and regulate their expression. Our data demonstrate that the miR156b-GmSPL9d module acts as an upstream master regulator of soybean nodulation, which coordinates multiple marker genes involved in soybean nodulation.
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Affiliation(s)
- Jinxia Yun
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Zhengxi Sun
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in JiangsuCollege of AgricultureYangzhou UniversityYangzhou225009China
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Qiong Jiang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetic and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Youning Wang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Can Wang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Yuanqing Luo
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Fengrong Zhang
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Xia Li
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
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Raul B, Bhattacharjee O, Ghosh A, Upadhyay P, Tembhare K, Singh A, Shaheen T, Ghosh AK, Torres-Jerez I, Krom N, Clevenger J, Udvardi M, Scheffler BE, Ozias-Akins P, Sharma RD, Bandyopadhyay K, Gaur V, Kumar S, Sinharoy S. Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:131-145. [PMID: 34689599 DOI: 10.1094/mpmi-05-21-0122-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: 06/13/2023]
Abstract
Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.[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)
- Bikash Raul
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Oindrila Bhattacharjee
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Amit Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Priya Upadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kunal Tembhare
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ajeet Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tarannum Shaheen
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Asim Kumar Ghosh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Nick Krom
- Noble Research Institute, 2510 Sam Noble Pkwy, Ardmore, OK 73401, U.S.A
| | - Josh Clevenger
- University of Georgia, Institute of Plant Breeding, Genetics and Genomics and Department of Horticulture, Tifton, GA 31793, U.S.A
| | - Michael Udvardi
- Noble Research Institute, 2510 Sam Noble Pkwy, Ardmore, OK 73401, U.S.A
| | - Brian E Scheffler
- United States Department of Agriculture-Agricultural Research Service Jamie Whitten Delta States Research Center (JWDSRC) Stoneville, JWDSRC, Bldg.1, Room 229, Experiment Station Road, PO Box 36, Stoneville, MS 38776-0036, U.S.A
| | - Peggy Ozias-Akins
- University of Georgia, Institute of Plant Breeding, Genetics and Genomics and Department of Horticulture, Tifton, GA 31793, U.S.A
| | - Ravi Datta Sharma
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Kaustav Bandyopadhyay
- Amity University Haryana, Amity Education Valley, Manesar, Panchgaon, Haryana 122412, India
| | - Vineet Gaur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Fu M, Sun J, Li X, Guan Y, Xie F. Asymmetric redundancy of soybean Nodule Inception (NIN) genes in root nodule symbiosis. PLANT PHYSIOLOGY 2022; 188:477-489. [PMID: 34633461 PMCID: PMC8774708 DOI: 10.1093/plphys/kiab473] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/10/2021] [Indexed: 05/21/2023]
Abstract
Nodule Inception (NIN) is one of the most important root nodule symbiotic genes as it is required for both infection and nodule organogenesis in legumes. Unlike most legumes with a sole NIN gene, there are four putative orthologous NIN genes in soybean (Glycine max). Whether and how these NIN genes contribute to soybean-rhizobia symbiotic interaction remain unknown. In this study, we found that all four GmNIN genes are induced by rhizobia and that conserved CE and CYC binding motifs in their promoter regions are required for their expression in the nodule formation process. By generation of multiplex Gmnin mutants, we found that the Gmnin1a nin2a nin2b triple mutant and Gmnin1a nin1b nin2a nin2b quadruple mutant displayed similar defects in rhizobia infection and root nodule formation, Gmnin2a nin2b produced fewer nodules but displayed a hyper infection phenotype compared to wild type (WT), while the Gmnin1a nin1b double mutant nodulated similar to WT. Overexpression of GmNIN1a, GmNIN1b, GmNIN2a, and GmNIN2b reduced nodule numbers after rhizobia inoculation, with GmNIN1b overexpression having the weakest effect. In addition, overexpression of GmNIN1a, GmNIN2a, or GmNIN2b, but not GmNIN1b, produced malformed pseudo-nodule-like structures without rhizobia inoculation. In conclusion, GmNIN1a, GmNIN2a, and GmNIN2b play functionally redundant yet complicated roles in soybean nodulation. GmNIN1b, although expressed at a comparable level with the other homologs, plays a minor role in root nodule symbiosis. Our work provides insight into the understanding of the asymmetrically redundant function of GmNIN genes in soybean.
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MESH Headings
- Crops, Agricultural/genetics
- Crops, Agricultural/growth & development
- Crops, Agricultural/metabolism
- Crops, Agricultural/microbiology
- Gene Expression Regulation, Plant
- Genes, Plant
- Genetic Variation
- Genotype
- Rhizobium
- Root Nodules, Plant/genetics
- Root Nodules, Plant/growth & development
- Root Nodules, Plant/metabolism
- Root Nodules, Plant/microbiology
- Glycine max/genetics
- Glycine max/growth & development
- Glycine max/metabolism
- Glycine max/microbiology
- Symbiosis/genetics
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Affiliation(s)
- Mengdi Fu
- 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 200032, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jiafeng Sun
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiaolin Li
- 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 200032, China
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, 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 200032, China
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Lebedeva M, Azarakhsh M, Sadikova D, Lutova L. At the Root of Nodule Organogenesis: Conserved Regulatory Pathways Recruited by Rhizobia. PLANTS (BASEL, SWITZERLAND) 2021; 10:2654. [PMID: 34961125 PMCID: PMC8705049 DOI: 10.3390/plants10122654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 05/13/2023]
Abstract
The interaction between legume plants and soil bacteria rhizobia results in the formation of new organs on the plant roots, symbiotic nodules, where rhizobia fix atmospheric nitrogen. Symbiotic nodules represent a perfect model to trace how the pre-existing regulatory pathways have been recruited and modified to control the development of evolutionary "new" organs. In particular, genes involved in the early stages of lateral root development have been co-opted to regulate nodule development. Other regulatory pathways, including the players of the KNOX-cytokinin module, the homologues of the miR172-AP2 module, and the players of the systemic response to nutrient availability, have also been recruited to a unique regulatory program effectively governing symbiotic nodule development. The role of the NIN transcription factor in the recruitment of such regulatory modules to nodulation is discussed in more details.
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Affiliation(s)
- Maria Lebedeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Mahboobeh Azarakhsh
- Cell and Molecular Biology Department, Kosar University of Bojnord, 9415615458 Bojnord, Iran;
| | - Darina Sadikova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Lyudmila Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, 199034 Saint Petersburg, Russia; (D.S.); (L.L.)
- Center for Genetic Technologies, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
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38
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Qu Z, Zhang H, Wang Q, Zhao H, Liu X, Fu Y, Lin Y, Xie J, Cheng J, Li B, Jiang D. Exploring the Symbiotic Mechanism of a Virus-Mediated Endophytic Fungus in Its Host by Dual Unique Molecular Identifier-RNA Sequencing. mSystems 2021; 6:e0081421. [PMID: 34519518 PMCID: PMC8547468 DOI: 10.1128/msystems.00814-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
The symbiosis of endophytes and plants is universal in nature. However, how endophytes grow in plants is not entirely clear. Previously, we reported that a virus-infected fungal pathogen could grow in plants as an endophyte. In this study, we utilized Sclerotinia sclerotiorum strain DT-8, a virus-mediated endophyte, to investigate the mechanism of symbiosis with rapeseed by dual unique molecular identifier-RNA sequencing (dual-UMI RNA-seq). We found that the expressions of genes encoding S. sclerotiorum amylase/glucoamylase, glucose transporters, and rapeseed sugars will eventually be exported transporter 11 (SWEET11) were upregulated. It suggested that strain DT-8 might utilize plant starch as a nutrient. The defense systems of rapeseed were also activated, such as production of reactive oxygen species, phenylpropanoids, and brassinin, to control the growth of strain DT-8, while strain DT-8 counteracted host suppression by producing effector-like proteins, detoxification enzymes, and antioxidant components. Moreover, rapeseed also upregulated pectate lyase and pectinesterase genes to facilitate the colonization by strain DT-8. Our findings provide novel insights into the interaction of virus-mediated endophytes and their hosts that warrant further study. IMPORTANCE Although endophytes are widespread in nature, the interactions between endophytes and their hosts are still not fully understood. Members of a unique class of endophytes, the virus-mediated endophytic fungi, are continuously being discovered and have received wide attention. In this study, we investigated the interaction between a mycovirus-mediated endophytic fungus and its host rapeseed by using dual-UMI RNA-seq. According to the dual-UMI RNA-seq results, an aerial view of symbiotic mechanism under balanced regulation was suggested. This research expands our understanding of the symbiotic mechanisms of virus-fungus-plant interactions and could establish a foundation for the further development of practical application with virus-mediated hypovirulent fungi.
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Affiliation(s)
- Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Hongxiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Huizhang Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Xiaofan Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Hubei Province, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Zhou T, Liu H, Huang Y, Wang Z, Shan Y, Yue Y, Xia Z, Liang Y, An M, Wu Y. ε-poly- L-lysine Affects the Vegetative Growth, Pathogenicity and Expression Regulation of Necrotrophic Pathogen Sclerotinia sclerotiorum and Botrytis cinerea. J Fungi (Basel) 2021; 7:jof7100821. [PMID: 34682242 PMCID: PMC8540936 DOI: 10.3390/jof7100821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 02/04/2023] Open
Abstract
Microbial secondary metabolites produced by Streptomyces are applied to control plant diseases. The metabolite, ε-poly-l-lysine (ε-PL), is a non-toxic food preservative, but the potential application of this compound as a microbial fungicide in agriculture is rarely reported. In this study, the effect and mode of action of ε-PL on two necrotrophic pathogenic fungi, Sclerotinia sclerotiorum and Botrytis cinerea, were investigated. The results showed that ε-PL effectively inhibited the mycelial growth of S. sclerotiorum and B. cinerea with EC50 values of 283 μg/mL and 281 μg/mL, respectively. In addition, ε-PL at the dose of 150 and 300 μg/mL reduced S. sclerotiorum sclerotia formation. The results of the RNA-seq and RT-qPCR validation indicated that ε-PL significantly regulated the gene expression of critical differential expressed genes (DEGs) involved in fungal growth, metabolism, pathogenicity, and induced an increase in the expression of the fungal stress responses and the detoxification genes. These results provided new insights for understanding the modes of action of ε-PL on S. sclerotiorum and B. cinerea and improved the sustainable management of these plant diseases.
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40
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Karas BJ, Ross L, Novero M, Amyot L, Shrestha A, Inada S, Nakano M, Sakai T, Bonetta D, Sato S, Murray JD, Bonfante P, Szczyglowski K. Intragenic complementation at the Lotus japonicus CELLULOSE SYNTHASE-LIKE D1 locus rescues root hair defects. PLANT PHYSIOLOGY 2021; 186:2037-2050. [PMID: 34618101 PMCID: PMC8331140 DOI: 10.1093/plphys/kiab204] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
Root hair cells form the primary interface of plants with the soil environment, playing key roles in nutrient uptake and plant defense. In legumes, they are typically the first cells to become infected by nitrogen-fixing soil bacteria during root nodule symbiosis. Here, we report a role for the CELLULOSE SYNTHASE-LIKE D1 (CSLD1) gene in root hair development in the legume species Lotus japonicus. CSLD1 belongs to the cellulose synthase protein family that includes cellulose synthases and cellulose synthase-like proteins, the latter thought to be involved in the biosynthesis of hemicellulose. We describe 11 Ljcsld1 mutant alleles that impose either short (Ljcsld1-1) or variable (Ljcsld1-2 to 11) root hair length phenotypes. Examination of Ljcsld1-1 and one variable-length root hair mutant, Ljcsld1-6, revealed increased root hair cell wall thickness, which in Ljcsld1-1 was significantly more pronounced and also associated with a strong defect in root nodule symbiosis. Lotus japonicus plants heterozygous for Ljcsld1-1 exhibited intermediate root hair lengths, suggesting incomplete dominance. Intragenic complementation was observed between alleles with mutations in different CSLD1 domains, suggesting CSLD1 function is modular and that the protein may operate as a homodimer or multimer during root hair development.
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Affiliation(s)
- Bogumil J Karas
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5C1
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada, N5V 4T3
| | - Loretta Ross
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada, N5V 4T3
| | - Mara Novero
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada, N5V 4T3
| | - Arina Shrestha
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5C1
| | - Sayaka Inada
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michiharu Nakano
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tatsuya Sakai
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-nino-cho, Nishiku, Niigata 950-2181, Japan
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Sushei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Jeremy D Murray
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada, N5V 4T3
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), CAS Center for Excellence in Molecular and Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Krzysztof Szczyglowski
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada, N5V 4T3
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7 Canada
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Chakraborty S, Driscoll HE, Abrahante JE, Zhang F, Fisher RF, Harris JM. Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:904-921. [PMID: 33819071 PMCID: PMC8578154 DOI: 10.1094/mpmi-01-21-0019-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sanhita Chakraborty
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heather E. Driscoll
- Vermont Biomedical Research Network (VBRN), Department of Biology, Norwich University, Northfield, Vermont 05663, USA
| | - Juan E. Abrahante
- University of Minnesota Informatics Institute (UMII) (CCRB 1-210C), 2231 6th Street SE, Minneapolis, MN 55455, USA
| | - Fan Zhang
- Vermont Biomedical Research Network (VBRN), Department of Biology, University of Vermont, Burlington, Vermont 05405, USA
- Institute for Translational Research and Department of family medicine, University of North Texas Health Science Center, Fort Worth, TX, 76107
| | - Robert F. Fisher
- Stanford University, Department of Biology, 371 Serra Mall, Stanford, California 94305-5020, USA
| | - Jeanne M. Harris
- Department of Plant Biology, University of Vermont, Burlington, VT 05405, USA
- Corresponding author: Jeanne M. Harris ()
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42
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Translational regulation in pathogenic and beneficial plant-microbe interactions. Biochem J 2021; 478:2775-2788. [PMID: 34297042 DOI: 10.1042/bcj20210066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/17/2022]
Abstract
Plants are surrounded by a vast diversity of microorganisms. Limiting pathogenic microorganisms is crucial for plant survival. On the other hand, the interaction of plants with beneficial microorganisms promotes their growth or allows them to overcome nutrient deficiencies. Balancing the number and nature of these interactions is crucial for plant growth and development, and thus, for crop productivity in agriculture. Plants use sophisticated mechanisms to recognize pathogenic and beneficial microorganisms and genetic programs related to immunity or symbiosis. Although most research has focused on characterizing changes in the transcriptome during plant-microbe interactions, the application of techniques such as Translating Ribosome Affinity Purification (TRAP) and Ribosome profiling allowed examining the dynamic association of RNAs to the translational machinery, highlighting the importance of the translational level of control of gene expression in both pathogenic and beneficial interactions. These studies revealed that the transcriptional and the translational responses are not always correlated, and that translational control operates at cell-specific level. In addition, translational control is governed by cis-elements present in the 5'mRNA leader of regulated mRNAs, e.g. upstream open reading frames (uORFs) and sequence-specific motifs. In this review, we summarize and discuss the recent advances made in the field of translational control during pathogenic and beneficial plant-microbe interactions.
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43
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Furuta KM, Xiang L, Cui S, Yoshida S. Molecular dissection of haustorium development in Orobanchaceae parasitic plants. PLANT PHYSIOLOGY 2021; 186:1424-1434. [PMID: 33783524 PMCID: PMC8260117 DOI: 10.1093/plphys/kiab153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Characterizing molecular aspects of haustorium development by parasitic plants in the Orobanchaceae family has identified hormone signaling/transport and specific genes as major players.
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Affiliation(s)
- Kaori Miyashima Furuta
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Lei Xiang
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Songkui Cui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Satoko Yoshida
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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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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45
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Huo H, Wang X, Liu Y, Chen J, Wei G. A Nod factor- and type III secretion system-dependent manner for Robinia pseudoacacia to establish symbiosis with Mesorhizobium amorphae CCNWGS0123. TREE PHYSIOLOGY 2021; 41:817-835. [PMID: 33219377 DOI: 10.1093/treephys/tpaa160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/15/2020] [Indexed: 06/11/2023]
Abstract
Under nitrogen-limiting conditions, symbiotic nodulation promotes the growth of legume plants via the fixation of atmospheric nitrogen to ammonia by rhizobia in root nodules. The rhizobial Nod factor (NF) and type III secretion system (T3SS) are two key signaling pathways for establishing the legume-rhizobium symbiosis. However, whether NF signaling is involved in the nodulation of Robinia pseudoacacia and Mesorhizobium amorphae CCNWGS0123, and its symbiotic differences compared with T3SS signaling remain unclear. Therefore, to elucidate the function of NF signaling in nodulation, we mutated nodC in M. amorphae CCNWGS0123, which aborted NF synthesis. Compared with the plants inoculated with the wild type strain, the plants inoculated with the NF-deficient strain exhibited shorter shoots with etiolated leaves. These phenotypic characteristics were similar to those of the plants inoculated with the T3SS-deficient strain, which served as a Nod- (non-effective nodulation) control. The plants inoculated with both the NF- and T3SS-deficient strains formed massive root hair swellings, but no normal infection threads were detected. Sections of the nodules showed that inoculation with the NF- and T3SS-deficient strains induced small, white bumps without any rhizobia inside. Analyzing the accumulation of 6 plant hormones and the expression of 10 plant genes indicated that the NF- and T3SS-deficient strains activated plant defense reactions while suppressing plant symbiotic signaling during the perception and nodulation processes. The requirement for NF signaling appeared to be conserved in two other leguminous trees that can establish symbiosis with M. amorphae CCNWGS0123. In contrast, the function of the T3SS might differ among species, even within the same subfamily (Faboideae). Overall, this work demonstrated that nodulation of R. pseudoacacia and M. amorphae CCNWGS0123 was both NF and T3SS dependent.
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Affiliation(s)
- Haibo Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Xinye Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Yao Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Juan Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water conservation, Northwest A&F University, 26 Xinong Road, Yangling 712100, Shaanxi, People's Republic of China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People's Republic of China
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Liu D, Luo Y, Zheng X, Wang X, Chou M, Wei G. TRAPPC13 Is a Novel Target of Mesorhizobium amorphae Type III Secretion System Effector NopP. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:511-523. [PMID: 33630651 DOI: 10.1094/mpmi-12-20-0354-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Similar to pathogenic bacteria, rhizobia can inject effector proteins into host cells directly to promote infection via the type III secretion system (T3SS). Nodulation outer protein P (NopP), a specific T3SS effector of rhizobia, plays different roles in the establishment of multiple rhizobia-legume symbiotic systems. Mesorhizobium amorphae CCNWGS0123 (GS0123), which infects Robinia pseudoacacia specifically, secretes several T3SS effectors, including NopP. Here, we demonstrate that NopP is secreted through T3SS-I of GS0123 during the early stages of infection, and its deficiency decreases nodule nitrogenase activity of R. pseudoacacia nodules. A trafficking protein particle complex subunit 13-like protein (TRAPPC13) has been identified as a NopP target protein in R. pseudoacacia roots by screening a yeast two-hybrid library. The physical interaction between NopP and TRAPPC13 is verified by bimolecular fluorescence complementation and coimmunoprecipitation assays. In addition, subcellular localization analysis reveals that both NopP and its target, TRAPPC13, are colocalized on the plasma membrane. Compared with GS0123-inoculated R. pseudoacacia roots, some genes associated with cell wall remodeling and plant innate immunity down-regulated in ΔnopP-inoculated roots at 36 h postinoculation. The results suggest that NopP in M. amorphae CCNWGS0123 acts in multiple processes in R. pseudoacacia during the early stages of infection, and TRAPPC13 could participate in the process as a NopP target.[Formula: see text] Copyright © 2021 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)
- 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 712100, China
| | - 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 712100, China
| | - Xiaofeng Zheng
- Shaanxi Hydrogeology Engineering Geology and Environmental Geology Survey Center, Shaanxi Institute of Geological Survey, Xi'an, Shaanxi 710054, China
| | - Xinye Wang
- Moutai Institute, Renhuai, Guizhou 564500, China
| | - Minxia Chou
- 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 712100, 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 712100, China
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47
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Xu Y, Wang H, Lu Z, Wen L, Gu Z, Zhang X, Yu G, Wang H, Zhou C, Han L. Developmental Analysis of the GATA Factor HANABA TARANU Mutants in Medicago truncatula Reveals Their Roles in Nodule Formation. FRONTIERS IN PLANT SCIENCE 2021; 12:616776. [PMID: 33995430 PMCID: PMC8118203 DOI: 10.3389/fpls.2021.616776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Formation of nodules on legume roots results from symbiosis with rhizobial bacteria. Here, we identified two GATA transcription factors, MtHAN1 and MtHAN2, in Medicago truncatula, which are the homologs of HANABA TARANU (HAN) and HANABA TARANU LIKE in Arabidopsis thaliana. Our analysis revealed that MtHAN1 and MtHAN2 are expressed in roots and shoots including the root tip and nodule apex. We further show that MtHAN1 and MtHAN2 localize to the nucleus where they interact and that single and double loss-of-function mutants of MtHAN1 and MtHAN2 did not show any obvious phenotype in flower development, suggesting their role is different than their closest Arabidopsis homologues. Investigation of their symbiotic phenotypes revealed that the mthan1 mthan2 double mutant develop twice as many nodules as wild type, revealing a novel biological role for GATA transcription factors. We found that HAN1/2 transcript levels respond to nitrate treatment like their Arabidopsis counterparts. Global gene transcriptional analysis by RNA sequencing revealed different expression genes enriched for several pathways important for nodule development including flavonoid biosynthesis and phytohormones. In addition, further studies suggest that MtHAN1 and MtHAN2 are required for the expression of several nodule-specific cysteine-rich genes, which they may activate directly, and many peptidase and peptidase inhibitor genes. This work expands our knowledge of the functions of MtHANs in plants by revealing an unexpected role in legume nodulation.
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Affiliation(s)
- Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhichao Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Lizhu Wen
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhiqun Gu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xue Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
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48
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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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49
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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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Liu J, Rasing M, Zeng T, Klein J, Kulikova O, Bisseling T. NIN is essential for development of symbiosomes, suppression of defence and premature senescence in Medicago truncatula nodules. THE NEW PHYTOLOGIST 2021; 230:290-303. [PMID: 33471433 PMCID: PMC7986424 DOI: 10.1111/nph.17215] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/30/2020] [Indexed: 05/29/2023]
Abstract
NIN (NODULE INCEPTION) is a transcription factor that plays a key role during root nodule initiation. However, its role in later nodule developmental stages is unclear. Both NIN mRNA and protein accumulated at the highest level in the proximal part of the infection zone in Medicago truncatula nodules. Two nin weak allele mutants, nin-13/16, form a rather normal nodule infection zone, whereas a fixation zone is not formed. Instead, a zone with defence responses and premature senescence occurred and symbiosome development gets arrested. Mutations in nin-13/16 resulted in a truncated NIN lacking the conserved PB1 domain. However, this did not cause the nodule phenotype as nin mutants expressing NINΔPB1 formed wild-type-like nodule. The phenotype is likely to be caused by reduced NIN mRNA levels in the cytoplasm. Transcriptome analyses of nin-16 nodules showed that expression levels of defence/senescence-related genes are markedly increased, whereas the levels of defence suppressing genes are reduced. Although defence/senescence seems well suppressed in the infection zone, the transcriptome is already markedly changed in the proximal part of infection zone. In addition to its function in infection and nodule organogenesis, NIN also plays a major role at the transition from infection to fixation zone in establishing a functional symbiosis.
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Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular BiologyDepartment of Plant SciencesGraduate School Experimental Plant SciencesWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Menno Rasing
- Laboratory of Molecular BiologyDepartment of Plant SciencesGraduate School Experimental Plant SciencesWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Tian Zeng
- Laboratory of Molecular BiologyDepartment of Plant SciencesGraduate School Experimental Plant SciencesWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Joël Klein
- Laboratory of Molecular BiologyDepartment of Plant SciencesGraduate School Experimental Plant SciencesWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Olga Kulikova
- Laboratory of Molecular BiologyDepartment of Plant SciencesGraduate School Experimental Plant SciencesWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Ton Bisseling
- Laboratory of Molecular BiologyDepartment of Plant SciencesGraduate School Experimental Plant SciencesWageningen University & ResearchWageningen6708 PBthe Netherlands
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206China
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