1
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Li H, Ou Y, Huang K, Zhang Z, Cao Y, Zhu H. A pathogenesis-related protein, PRP1, negatively regulates root nodule symbiosis in Lotus japonicus. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3542-3556. [PMID: 38457346 DOI: 10.1093/jxb/erae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
The legume-rhizobium symbiosis represents a unique model within the realm of plant-microbe interactions. Unlike typical cases of pathogenic invasion, the infection of rhizobia and their residence within symbiotic cells do not elicit a noticeable immune response in plants. Nevertheless, there is still much to uncover regarding the mechanisms through which plant immunity influences rhizobial symbiosis. In this study, we identify an important player in this intricate interplay: Lotus japonicus PRP1, which serves as a positive regulator of plant immunity but also exhibits the capacity to decrease rhizobial colonization and nitrogen fixation within nodules. The PRP1 gene encodes an uncharacterized protein and is named Pathogenesis-Related Protein1, owing to its orthologue in Arabidopsis thaliana, a pathogenesis-related family protein (At1g78780). The PRP1 gene displays high expression levels in nodules compared to other tissues. We observed an increase in rhizobium infection in the L. japonicus prp1 mutants, whereas PRP1-overexpressing plants exhibited a reduction in rhizobium infection compared to control plants. Intriguingly, L. japonicus prp1 mutants produced nodules with a pinker colour compared to wild-type controls, accompanied by elevated levels of leghaemoglobin and an increased proportion of infected cells within the prp1 nodules. The transcription factor Nodule Inception (NIN) can directly bind to the PRP1 promoter, activating PRP1 gene expression. Furthermore, we found that PRP1 is a positive mediator of innate immunity in plants. In summary, our study provides clear evidence of the intricate relationship between plant immunity and symbiosis. PRP1, acting as a positive regulator of plant immunity, simultaneously exerts suppressive effects on rhizobial infection and colonization within nodules.
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Affiliation(s)
- Hao Li
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yajuan Ou
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Kui Huang
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongming Zhang
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangrong Cao
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui Zhu
- National Key Lab of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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2
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Berrabah F, Benaceur F, Yin C, Xin D, Magne K, Garmier M, Gruber V, Ratet P. Defense and senescence interplay in legume nodules. PLANT COMMUNICATIONS 2024; 5:100888. [PMID: 38532645 PMCID: PMC11009364 DOI: 10.1016/j.xplc.2024.100888] [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: 10/03/2023] [Revised: 02/05/2024] [Accepted: 03/23/2024] [Indexed: 03/28/2024]
Abstract
Immunity and senescence play a crucial role in the functioning of the legume symbiotic nodules. The miss-regulation of one of these processes compromises the symbiosis leading to death of the endosymbiont and the arrest of the nodule functioning. The relationship between immunity and senescence has been extensively studied in plant organs where a synergistic response can be observed. However, the interplay between immunity and senescence in the symbiotic organ is poorly discussed in the literature and these phenomena are often mixed up. Recent studies revealed that the cooperation between immunity and senescence is not always observed in the nodule, suggesting complex interactions between these two processes within the symbiotic organ. Here, we discuss recent results on the interplay between immunity and senescence in the nodule and the specificities of this relationship during legume-rhizobium symbiosis.
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Affiliation(s)
- Fathi Berrabah
- Faculty of Sciences, University Amar Telidji, 03000 Laghouat, Algeria; Research Unit of Medicinal Plants (RUMP), National Center of Biotechnology Research, CRBt, 25000 Constantine, Algeria.
| | - Farouk Benaceur
- Faculty of Sciences, University Amar Telidji, 03000 Laghouat, Algeria; Research Unit of Medicinal Plants (RUMP), National Center of Biotechnology Research, CRBt, 25000 Constantine, Algeria
| | - Chaoyan Yin
- Université Paris-Saclay, CNRS, INRAE, University of Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Dawei Xin
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Kévin Magne
- Université Paris-Saclay, CNRS, INRAE, University of Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Marie Garmier
- Université Paris-Saclay, CNRS, INRAE, University of Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Véronique Gruber
- Université Paris-Saclay, CNRS, INRAE, University of Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, University of Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
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3
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Lee T, Orvosova M, Batzenschlager M, Bueno Batista M, Bailey PC, Mohd-Radzman NA, Gurzadyan A, Stuer N, Mysore KS, Wen J, Ott T, Oldroyd GED, Schiessl K. Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula. Curr Biol 2024; 34:825-840.e7. [PMID: 38301650 DOI: 10.1016/j.cub.2024.01.018] [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: 08/16/2023] [Revised: 09/29/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting nitrogen-fixing bacteria. We have previously shown that a lateral root program underpins nodule initiation, but there must be additional developmental regulators that confer nodule identity. Here, we show two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity and organ boundaries, function as regulators of nodule organ identity. In parallel to the root initiation program, LSH1/LSH2 recruit a program into the root cortex that mediates the divergence into nodules, in particular with cell divisions in the mid-cortex. This includes regulation of auxin and cytokinin, promotion of NODULE ROOT1/2 and Nuclear Factor YA1, and suppression of the lateral root program. A principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a key feature unique to nodules.
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Affiliation(s)
- Tak Lee
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Martina Orvosova
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | | | - Marcelo Bueno Batista
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul C Bailey
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Nadia A Mohd-Radzman
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Aram Gurzadyan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Naomi Stuer
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Kirankumar S Mysore
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jiangqi Wen
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Thomas Ott
- University of Freiburg, Faculty of Biology, Schänzlestrasse, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, Schänzlestrasse, 79104 Freiburg, Germany
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Crop Science Centre, Department of Plant Sciences, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK.
| | - Katharina Schiessl
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
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4
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Geurts R, Huisman R. Innovations in two genes kickstarted the evolution of nitrogen-fixing nodules. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102446. [PMID: 37696726 DOI: 10.1016/j.pbi.2023.102446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023]
Abstract
The root nodule symbiosis between plants and nitrogen-fixing bacteria is a fascinating trait limited to several plant species. Given the agronomic potential of transferring this symbiosis to nonleguminous crops, the symbiosis has attracted researchers' attention for over a century. The origins of this symbiosis can be traced back to a single ancestor, around 110 million years ago. Recent findings have uncovered that adaptations in a receptor complex and the recruitment of the transcription factor Nodule Inception (NIN) are among the first genetic adaptations that allowed this ancestor to respond to its microsymbiont. Understanding the consequences of recruiting these genes provides insights into the start of this complex genetic trait.
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Affiliation(s)
- Rene Geurts
- Laboratory of Molecular Biology, Plant Science Group, Wageningen University Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
| | - Rik Huisman
- Laboratory of Molecular Biology, Plant Science Group, Wageningen University Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
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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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Yan D, Nambara E. Conserved and unique functions of NIN-like proteins in nitrate sensing and signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111842. [PMID: 37633494 DOI: 10.1016/j.plantsci.2023.111842] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Nitrogen is the most abundant element in the atmosphere and serves as the foundation block of life, including plants on earth. Unlike carbon fixation through photosynthesis, plants rely heavily on external supports to acquire nitrogen. To this end, plants have adapted various strategies such as forming mutualistic relationships with nitrogen-fixing bacteria and evolving a large regulatory network that includes multiple transporters, sensors, and transcription factors for fine-tuning nitrate sensing and signaling. Nodule Inception (NIN) and NIN-like protein (NLP) are central in this network by executing multiple functions such as initiating and regulating the nodule symbiosis for nitrogen fixation, acting as the intracellular sensor to monitor the nitrate fluctuations in the environment, and activating the transcription of nitrate-responsive genes for optimal nitrogen uptake, assimilation, and usage. The involvement of NLPs in intracellular nitrate binding and early nitrate responses highlight their pivotal role in the primary nitrate response (PNR). Genome-wide reprogramming in response to nitrate by NLP is highly transient and rapid, requiring regulation in a precise and dynamic manner. This review aims to summarize recent progress in the study of NIN/NLP for a better understanding of the molecular basis of their roles and regulations in nitrate sensing and signaling, with the hope of shedding light on increasing biological nitrogen fixation and improving nitrogen use efficiency (NUE) to minimize fertilizer input in agriculture.
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Affiliation(s)
- Dawei Yan
- Department of Cell & Systems Biology, University of Toronto, Toronto M5S3B2, Ontario, Canada.
| | - Eiji Nambara
- Department of Cell & Systems Biology, University of Toronto, Toronto M5S3B2, Ontario, Canada
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7
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Van Dingenen J, De Keyser A, Desmet S, Clarysse A, Beullens S, Michiels J, Planque M, Goormachtig S. Strigolactones repress nodule development and senescence in pea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:7-22. [PMID: 37608631 DOI: 10.1111/tpj.16421] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/21/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023]
Abstract
Strigolactones are a class of phytohormones that are involved in many different plant developmental processes, including the rhizobium-legume nodule symbiosis. Although both positive and negative effects of strigolactones on the number of nodules have been reported, the influence of strigolactones on nodule development is still unknown. Here, by means of the ramosus (rms) mutants of Pisum sativum (pea) cv Terese, we investigated the impact of strigolactone biosynthesis (rms1 and rms5) and signaling (rms3 and rms4) mutants on nodule growth. The rms mutants had more red, that is, functional, and larger nodules than the wild-type plants. Additionally, the increased nitrogen fixation and senescence zones with consequently reduced meristematic and infection zones indicated that the rms nodules developed faster than the wild-type nodules. An enhanced expression of the nodule zone-specific molecular markers for meristem activity and senescence supported the enlarged, fast maturing nodules. Interestingly, the master nodulation regulator, NODULE INCEPTION, NIN, was strongly induced in nodules of all rms mutants but not prior to inoculation. Determination of sugar levels with both bulk and spatial metabolomics in roots and nodules, respectively, hints at slightly increased malic acid levels early during nodule primordia formation and reduced sugar levels at later stages, possibly the consequence of an increased carbon usage of the enlarged nodules, contributing to the enhanced senescence. Taken together, these results suggest that strigolactones regulate the development of nodules, which is probably mediated through NIN, and available plant sugars.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- VIB Metabolomics Core, VIB, Technologiepark 71, 9052, Ghent, Belgium
| | - Alexander Clarysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Serge Beullens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Mélanie Planque
- Spatial Metabolomics Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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8
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Yu H, Xiao A, Wu J, Li H, Duan Y, Chen Q, Zhu H, Cao Y. GmNAC039 and GmNAC018 activate the expression of cysteine protease genes to promote soybean nodule senescence. THE PLANT CELL 2023; 35:2929-2951. [PMID: 37177994 PMCID: PMC10396383 DOI: 10.1093/plcell/koad129] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 04/03/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Root nodules are major sources of nitrogen for soybean (Glycine max (L.) Merr.) growth, development, production, and seed quality. Symbiotic nitrogen fixation is time-limited, as the root nodule senesces during the reproductive stage of plant development, specifically during seed development. Nodule senescence is characterized by the induction of senescence-related genes, such as papain-like cysteine proteases (CYPs), which ultimately leads to the degradation of both bacteroids and plant cells. However, how nodule senescence-related genes are activated in soybean is unknown. Here, we identified 2 paralogous NAC transcription factors, GmNAC039 and GmNAC018, as master regulators of nodule senescence. Overexpression of either gene induced soybean nodule senescence with increased cell death as detected using a TUNEL assay, whereas their knockout delayed senescence and increased nitrogenase activity. Transcriptome analysis and nCUT&Tag-qPCR assays revealed that GmNAC039 directly binds to the core motif CAC(A)A and activates the expression of 4 GmCYP genes (GmCYP35, GmCYP37, GmCYP39, and GmCYP45). Similar to GmNAC039 and GmNAC018, overexpression or knockout of GmCYP genes in nodules resulted in precocious or delayed senescence, respectively. These data provide essential insights into the regulatory mechanisms of nodule senescence, in which GmNAC039 and GmNAC018 directly activate the expression of GmCYP genes to promote nodule senescence.
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Affiliation(s)
- Haixiang Yu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Aifang Xiao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jiashan Wu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Haoxing Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yan Duan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qingshan Chen
- Key Laboratory of Soybean Biology of Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, Heilongjiang 150038, China
| | - Hui Zhu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yangrong Cao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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9
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Lagunas B, Richards L, Sergaki C, Burgess J, Pardal AJ, Hussain RMF, Richmond BL, Baxter L, Roy P, Pakidi A, Stovold G, Vázquez S, Ott S, Schäfer P, Gifford ML. Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth. MICROBIOME 2023; 11:146. [PMID: 37394496 DOI: 10.1186/s40168-023-01592-0] [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: 12/31/2022] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Despite the knowledge that the soil-plant-microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant-microbe interaction during nodulation. RESULTS The outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant-soil-rhizobia strain combinations. CONCLUSIONS The microbiome-soil-rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant-rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community. Video Abstract.
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Affiliation(s)
- Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Luke Richards
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jamie Burgess
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Rana M F Hussain
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Laura Baxter
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Anastasia Pakidi
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Gina Stovold
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Saúl Vázquez
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Present Address: Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392, Germany.
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV47AL, UK.
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10
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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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11
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Wang L, Yang J, Tan W, Guo Y, Li J, Duan C, Wei G, Chou M. Macrophage migration inhibitory factor MtMIF3 prevents the premature aging of Medicago truncatula nodules. PLANT, CELL & ENVIRONMENT 2023; 46:1004-1017. [PMID: 36515398 DOI: 10.1111/pce.14515] [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: 05/13/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine involved in immune response in animals. However, the role of MIFs in plants such as Medicago truncatula, particularly in symbiotic nitrogen fixation, remains unclear. An investigation of M. truncatula-Sinorhizobium meliloti symbiosis revealed that MtMIF3 was mainly expressed in the nitrogen-fixing zone of the nodules. Silencing MtMIF3 using RNA interference (Ri) technology resulted in increased nodule numbers but higher levels of bacteroid degradation in the infected cells of the nitrogen-fixing zone, suggesting that premature aging was induced in MtMIF3-Ri nodules. In agreement with this conclusion, the activities of nitrogenase, superoxide dismutase and catalase were lower than those in controls, but cysteine proteinase activity was increased in nodulated roots at 28 days postinoculation. In contrast, the overexpression of MtMIF3 inhibited nodule senescence. MtMIF3 is localized in the plasma membrane, nucleus, and cytoplasm, where it interacts with methionine sulfoxide reductase B (MsrB), which is also localized in the chloroplasts of tobacco leaf cells. Taken together, these results suggest that MtMIF3 prevents premature nodule aging and protects against oxidation by interacting with MtMsrB.
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Affiliation(s)
- Li Wang
- 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, People's Republic of China
| | - Jieyu Yang
- 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, People's Republic of China
| | - Wenjun Tan
- 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, People's Republic of China
| | - Yile Guo
- 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, People's Republic of China
| | - Jiaqi Li
- 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, People's Republic of China
| | - Chuntao Duan
- 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, People's Republic of 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, People's Republic of 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, People's Republic of China
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12
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Rapid Changes to Endomembrane System of Infected Root Nodule Cells to Adapt to Unusual Lifestyle. Int J Mol Sci 2023; 24:ijms24054647. [PMID: 36902077 PMCID: PMC10002930 DOI: 10.3390/ijms24054647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Symbiosis between leguminous plants and soil bacteria rhizobia is a refined type of plant-microbial interaction that has a great importance to the global balance of nitrogen. The reduction of atmospheric nitrogen takes place in infected cells of a root nodule that serves as a temporary shelter for thousands of living bacteria, which, per se, is an unusual state of a eukaryotic cell. One of the most striking features of an infected cell is the drastic changes in the endomembrane system that occur after the entrance of bacteria to the host cell symplast. Mechanisms for maintaining intracellular bacterial colony represent an important part of symbiosis that have still not been sufficiently clarified. This review focuses on the changes that occur in an endomembrane system of infected cells and on the putative mechanisms of infected cell adaptation to its unusual lifestyle.
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13
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Singh J, Valdés‐López O. Discovering the genetic modules controlling root nodule symbiosis under abiotic stresses: salinity as a case study. THE NEW PHYTOLOGIST 2023; 237:1082-1085. [PMID: 36401792 PMCID: PMC10107258 DOI: 10.1111/nph.18627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Legumes form a symbiotic association with rhizobia and fix atmospheric nitrogen in specialized root organs known as nodules. It is well known that salt stress inhibits root nodule symbiosis by decreasing rhizobial growth, rhizobial infection, nodule number, and nitrogenase activity in diverse legumes. Despite this knowledge, the genetic and molecular mechanisms governing salt stress's inhibition of nodulation and nitrogen fixation are still elusive. In this Viewpoint, we summarize the most recent knowledge of the genetic mechanisms that shape this symbiosis according to the salt levels in the soil. We emphasize the relevance of modulating the activity of the transcription factor Nodule Inception to properly shape the symbiosis with rhizobia accordingly. We also highlight the knowledge gaps that are critical for gaining a deeper understanding of the molecular mechanisms underlying the adaptation of the root nodule symbiosis to salt-stress conditions. We consider that filling these gaps can help to improve legume nodulation and harness its ecological benefits even under salt-stress conditions.
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Affiliation(s)
- Jawahar Singh
- Facultad de Estudios Superiores Iztacala, Laboratorio de Genómica Funcional de LeguminosasUniversidad Nacional Autónoma de MéxicoTlalnepantlaEstado de México54090Mexico
| | - Oswaldo Valdés‐López
- Facultad de Estudios Superiores Iztacala, Laboratorio de Genómica Funcional de LeguminosasUniversidad Nacional Autónoma de MéxicoTlalnepantlaEstado de México54090Mexico
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14
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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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15
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Vlk D, Trněný O, Řepková J. Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover ( Trifolium pratense L.). LIFE (BASEL, SWITZERLAND) 2022; 12:life12121975. [PMID: 36556339 PMCID: PMC9785344 DOI: 10.3390/life12121975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Commonly studied in the context of legume-rhizobia symbiosis, biological nitrogen fixation (BNF) is a key component of the nitrogen cycle in nature. Despite its potential in plant breeding and many years of research, information is still lacking as to the regulation of hundreds of genes connected with plant-bacteria interaction, nodulation, and nitrogen fixation. Here, we compared root nodule transcriptomes of red clover (Trifolium pratense L.) genotypes with contrasting nitrogen fixation efficiency, and we found 491 differentially expressed genes (DEGs) between plants with high and low BNF efficiency. The annotation of genes expressed in nodules revealed more than 800 genes not yet experimentally confirmed. Among genes mediating nodule development, four nod-ule-specific cysteine-rich (NCR) peptides were confirmed in the nodule transcriptome. Gene duplication analyses revealed that genes originating from tandem and dispersed duplication are significantly over-represented among DEGs. Weighted correlation network analysis (WGCNA) organized expression profiles of the transcripts into 16 modules linked to the analyzed traits, such as nitrogen fixation efficiency or sample-specific modules. Overall, the results obtained broaden our knowledge about transcriptomic landscapes of red clover's root nodules and shift the phenotypic description of BNF efficiency on the level of gene expression in situ.
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Affiliation(s)
- David Vlk
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
| | - Oldřich Trněný
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
- Correspondence: ; Tel.: +420-549-49-6895
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16
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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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17
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Irving TB, Chakraborty S, Maia LGS, Knaack S, Conde D, Schmidt HW, Triozzi PM, Simmons CH, Roy S, Kirst M, Ané JM. An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp. PLANT PHYSIOLOGY 2022; 190:1699-1714. [PMID: 35929094 PMCID: PMC9614479 DOI: 10.1093/plphys/kiac356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
The transcription factor NODULE INCEPTION (NIN) has been studied extensively for its multiple roles in root nodule symbiosis within plants of the nitrogen-fixing clade (NFC) that associate with soil bacteria, such as rhizobia and Frankia. However, NIN homologs are present in plants outside the NFC, suggesting a role in other developmental processes. Here, we show that the biofuel crop Populus sp., which is not part of the NFC, contains eight copies of NIN with diversified protein sequence and expression patterns. Lipo-chitooligosaccharides (LCOs) are produced by rhizobia and a wide range of fungi, including mycorrhizal ones, and act as symbiotic signals that promote lateral root formation. RNAseq analysis of Populus sp. treated with purified LCO showed induction of the PtNIN2 subfamily. Moreover, the expression of PtNIN2b correlated with the formation of lateral roots and was suppressed by cytokinin treatment. Constitutive expression of PtNIN2b overcame the inhibition of lateral root development by cytokinin under high nitrate conditions. Lateral root induction in response to LCOs likely represents an ancestral function of NIN retained and repurposed in nodulating plants, as we demonstrate that the role of NIN in LCO-induced root branching is conserved in both Populus sp. and legumes. We further established a visual marker of LCO perception in Populus sp. roots, the putative sulfotransferase PtSS1 that can be used to study symbiotic interactions with the bacterial and fungal symbionts of Populus sp.
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Affiliation(s)
| | | | - Lucas Gontijo Silva Maia
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Sara Knaack
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Daniel Conde
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Henry W Schmidt
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Paolo M Triozzi
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Carl H Simmons
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
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18
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Sauviac L, Rémy A, Huault E, Dalmasso M, Kazmierczak T, Jardinaud MF, Legrand L, Moreau C, Ruiz B, Cazalé AC, Valière S, Gourion B, Dupont L, Gruber V, Boncompagni E, Meilhoc E, Frendo P, Frugier F, Bruand C. A dual legume-rhizobium transcriptome of symbiotic nodule senescence reveals coordinated plant and bacterial responses. PLANT, CELL & ENVIRONMENT 2022; 45:3100-3121. [PMID: 35781677 DOI: 10.1111/pce.14389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Senescence determines plant organ lifespan depending on aging and environmental cues. During the endosymbiotic interaction with rhizobia, legume plants develop a specific organ, the root nodule, which houses nitrogen (N)-fixing bacteria. Unlike earlier processes of the legume-rhizobium interaction (nodule formation, N fixation), mechanisms controlling nodule senescence remain poorly understood. To identify nodule senescence-associated genes, we performed a dual plant-bacteria RNA sequencing approach on Medicago truncatula-Sinorhizobium meliloti nodules having initiated senescence either naturally (aging) or following an environmental trigger (nitrate treatment or salt stress). The resulting data allowed the identification of hundreds of plant and bacterial genes differentially regulated during nodule senescence, thus providing an unprecedented comprehensive resource of new candidate genes associated with this process. Remarkably, several plant and bacterial genes related to the cell cycle and stress responses were regulated in senescent nodules, including the rhizobial RpoE2-dependent general stress response. Analysis of selected core nodule senescence plant genes allowed showing that MtNAC969 and MtS40, both homologous to leaf senescence-associated genes, negatively regulate the transition between N fixation and senescence. In contrast, overexpression of a gene involved in the biosynthesis of cytokinins, well-known negative regulators of leaf senescence, may promote the transition from N fixation to senescence in nodules.
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Affiliation(s)
- Laurent Sauviac
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Antoine Rémy
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Emeline Huault
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | | | - Théophile Kazmierczak
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | - Marie-Françoise Jardinaud
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Ludovic Legrand
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Corentin Moreau
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Anne-Claire Cazalé
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | | | - Benjamin Gourion
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | | | - Véronique Gruber
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | | | - Eliane Meilhoc
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Pierre Frendo
- Université Côte d'Azur, INRAE, CNRS, ISA, Nice, France
| | - Florian Frugier
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | - Claude Bruand
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
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19
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Wang X, Chen K, Zhou M, Gao Y, Huang H, Liu C, Fan Y, Fan Z, Wang Y, Li X. GmNAC181 promotes symbiotic nodulation and salt tolerance of nodulation by directly regulating GmNINa expression in soybean. THE NEW PHYTOLOGIST 2022; 236:656-670. [PMID: 35751548 DOI: 10.1111/nph.18343] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Soybean (Glycine max) is one of the most important crops world-wide. Under low nitrogen (N) condition, soybean can form a symbiotic relationship with rhizobia to acquire sufficient N for their growth and production. Nodulation signaling controls soybean symbiosis with rhizobia. The soybean Nodule Inception (GmNINa) gene is a central regulator of soybean nodulation. However, the transcriptional regulation of GmNINa remains largely unknown. Nodulation is sensitive to salt stress, but the underlying mechanisms are unclear. Here, we identified an NAC transcription factor designated GmNAC181 (also known as GmNAC11) as the interacting protein of GmNSP1a. GmNAC181 overexpression or knockdown in soybean resulted in increased or decreased numbers of nodules, respectively. Accordingly, the expression of GmNINa was greatly up- and downregulated, respectively. Furthermore, we showed that GmNAC181 can directly bind to the GmNINa promoter to activate its gene expression. Intriguingly, GmNAC181 was highly induced by salt stress during nodulation and promoted symbiotic nodulation under salt stress. We identified a new transcriptional activator of GmNINa in the nodulation pathway and revealed a mechanism by which GmNAC181 acts as a network node orchestrating the expression of GmNINa and symbiotic nodulation under salt stress conditions.
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Affiliation(s)
- Xiaodi Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, Guangdong, 510642, China
| | - Kuan Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Miaomiao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongkang Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huimei Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuanyuan Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zihui Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Youning Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, Guangdong, 510642, China
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20
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Quilbé J, Nouwen N, Pervent M, Guyonnet R, Cullimore J, Gressent F, Araújo NH, Gully D, Klopp C, Giraud E, Arrighi JF. A mutant-based analysis of the establishment of Nod-independent symbiosis in the legume Aeschynomene evenia. PLANT PHYSIOLOGY 2022; 190:1400-1417. [PMID: 35876558 PMCID: PMC9516736 DOI: 10.1093/plphys/kiac325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Intensive research on nitrogen-fixing symbiosis in two model legumes has uncovered the molecular mechanisms, whereby rhizobial Nod factors activate a plant symbiotic signaling pathway that controls infection and nodule organogenesis. In contrast, the so-called Nod-independent symbiosis found between Aeschynomene evenia and photosynthetic bradyrhizobia, which does not involve Nod factor recognition nor infection thread formation, is less well known. To gain knowledge on how Nod-independent symbiosis is established, we conducted a phenotypic and molecular characterization of A. evenia lines carrying mutations in different nodulation genes. Besides investigating the effect of the mutations on rhizobial symbiosis, we examined their consequences on mycorrhizal symbiosis and in nonsymbiotic conditions. Analyzing allelic mutant series for AePOLLUX, Ca2+/calmodulin dependent kinase, AeCYCLOPS, nodulation signaling pathway 2 (AeNSP2), and nodule inception demonstrated that these genes intervene at several stages of intercellular infection and during bacterial accommodation. We provide evidence that AeNSP2 has an additional nitrogen-dependent regulatory function in the formation of axillary root hairs at lateral root bases, which are rhizobia-colonized infection sites. Our investigation of the recently discovered symbiotic actor cysteine-rich receptor-like kinase specified that it is not involved in mycorrhization; however, it is essential for both symbiotic signaling and early infection during nodulation. These findings provide important insights on the modus operandi of Nod-independent symbiosis and contribute to the general understanding of how rhizobial-legume symbioses are established by complementing the information acquired in model legumes.
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Affiliation(s)
| | | | | | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
| | - Julie Cullimore
- Laboratory of Plant-Microbe Interactions and Environment (LIPME), University Toulouse III, INRAE, CNRS, Castanet-Tolosan, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
| | - Natasha Horta Araújo
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J-Campus de Baillarguet, Montpellier 34398, France
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, TA-A82/J – Campus de Baillarguet, Montpellier 34398, France
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21
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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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22
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Jardinaud MF, Fromentin J, Auriac MC, Moreau S, Pecrix Y, Taconnat L, Cottret L, Aubert G, Balzergue S, Burstin J, Carrere S, Gamas P. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development. PLANT PHYSIOLOGY 2022; 189:1587-1607. [PMID: 35471237 PMCID: PMC9237690 DOI: 10.1093/plphys/kiac177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2022] [Indexed: 05/31/2023]
Abstract
Rhizobium-legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
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Affiliation(s)
| | | | | | - Sandra Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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23
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Wang D, Dong W, Murray J, Wang E. Innovation and appropriation in mycorrhizal and rhizobial Symbioses. THE PLANT CELL 2022; 34:1573-1599. [PMID: 35157080 PMCID: PMC9048890 DOI: 10.1093/plcell/koac039] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/21/2022] [Indexed: 05/20/2023]
Abstract
Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.
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Affiliation(s)
- Dapeng Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wentao Dong
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Ertao Wang
- Authors for correspondence: (E.W) and (J.M.)
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24
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Rudaya ES, Kozyulina PY, Pavlova OA, Dolgikh AV, Ivanova AN, Dolgikh EA. Regulation of the Later Stages of Nodulation Stimulated by IPD3/CYCLOPS Transcription Factor and Cytokinin in Pea Pisum sativum L. PLANTS (BASEL, SWITZERLAND) 2021; 11:56. [PMID: 35009060 PMCID: PMC8747635 DOI: 10.3390/plants11010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022]
Abstract
The IPD3/CYCLOPS transcription factor was shown to be involved in the regulation of nodule primordia development and subsequent stages of nodule differentiation. In contrast to early stages, the stages related to nodule differentiation remain less studied. Recently, we have shown that the accumulation of cytokinin at later stages may significantly impact nodule development. This conclusion was based on a comparative analysis of cytokinin localization between pea wild type and ipd3/cyclops mutants. However, the role of cytokinin at these later stages of nodulation is still far from understood. To determine a set of genes involved in the regulation of later stages of nodule development connected with infection progress, intracellular accommodation, as well as plant tissue and bacteroid differentiation, the RNA-seq analysis of pea mutant SGEFix--2 (sym33) nodules impaired in these processes compared to wild type SGE nodules was performed. To verify cytokinin's influence on late nodule development stages, the comparative RNA-seq analysis of SGEFix--2 (sym33) mutant plants treated with cytokinin was also conducted. Findings suggest a significant role of cytokinin in the regulation of later stages of nodule development.
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Affiliation(s)
- Elizaveta S. Rudaya
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Polina Yu. Kozyulina
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Olga A. Pavlova
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Alexandra V. Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Alexandra N. Ivanova
- Komarov Botanical Institute RAS, Prof. Popov St., 2, 197376 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, Universitetskaya Emb. 7-9, 199034 St. Petersburg, Russia
| | - Elena A. Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
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25
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Kovacs S, Fodor L, Domonkos A, Ayaydin F, Laczi K, Rákhely G, Kalo P. Amino Acid Polymorphisms in the VHIID Conserved Motif of Nodulation Signaling Pathways 2 Distinctly Modulate Symbiotic Signaling and Nodule Morphogenesis in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:709857. [PMID: 34966395 PMCID: PMC8711286 DOI: 10.3389/fpls.2021.709857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
Legumes establish an endosymbiotic association with nitrogen-fixing soil bacteria. Following the mutual recognition of the symbiotic partner, the infection process is controlled by the induction of the signaling pathway and subsequent activation of symbiosis-related host genes. One of the protein complexes regulating nitrogen-fixing root nodule symbiosis is formed by GRAS domain regulatory proteins Nodulation Signaling Pathways 1 and 2 (NSP1 and NSP2) that control the expression of several early nodulation genes. Here, we report on a novel point mutant allele (nsp2-6) affecting the function of the NSP2 gene and compared the mutant with the formerly identified nsp2-3 mutant. Both mutants carry a single amino acid substitution in the VHIID motif of the NSP2 protein. We found that the two mutant alleles show dissimilar root hair response to bacterial infection. Although the nsp2-3 mutant developed aberrant infection threads, rhizobia were able to colonize nodule cells in this mutant. The encoded NSP2 proteins of the nsp2-3 and the novel nsp2 mutants interact with NSP1 diversely and, as a consequence, the activation of early nodulin genes and nodule organogenesis are arrested in the new nsp2 allele. The novel mutant with amino acid substitution D244H in NSP2 shows similar defects in symbiotic responses as a formerly identified nsp2-2 mutant carrying a deletion in the NSP2 gene. Additionally, we found that rhizobial strains induce delayed nodule formation on the roots of the ns2-3 weak allele. Our study highlights the importance of a conserved Asp residue in the VHIID motif of NSP2 that is required for the formation of a functional NSP1-NSP2 signaling module. Furthermore, our results imply the involvement of NSP2 during differentiation of symbiotic nodule cells.
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Affiliation(s)
- Szilárd Kovacs
- Institute of Plant Biology, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
| | - Lili Fodor
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllö, Hungary
| | - Agota Domonkos
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllö, Hungary
| | - Ferhan Ayaydin
- Hungarian Centre of Excellence for Molecular Medicine (HCEMM) Nonprofit Ltd., Szeged, Hungary
- Cellular Imaging Laboratory, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
| | - Krisztián Laczi
- Institute of Plant Biology, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
| | - Péter Kalo
- Institute of Plant Biology, Biological Research Center, Eötvös Lóránd Research Network, Szeged, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllö, Hungary
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26
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Feng J, Lee T, Schiessl K, Oldroyd GED. Processing of NODULE INCEPTION controls the transition to nitrogen fixation in root nodules. Science 2021; 374:629-632. [PMID: 34709900 DOI: 10.1126/science.abg2804] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jian Feng
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Tak Lee
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Katharina Schiessl
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge CB3 0LE, UK
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27
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Ayra L, Reyero-Saavedra MDR, Isidra-Arellano MC, Lozano L, Ramírez M, Leija A, Fuentes SI, Girard L, Valdés-López O, Hernández G. Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors. FRONTIERS IN PLANT SCIENCE 2021; 12:679463. [PMID: 34163511 PMCID: PMC8216239 DOI: 10.3389/fpls.2021.679463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 05/25/2023]
Abstract
Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.
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Affiliation(s)
- Litzy Ayra
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María del Rocio Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Luis Lozano
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramírez
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alfonso Leija
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara-Isabel Fuentes
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Georgina Hernández
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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