51
|
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.
Collapse
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 ()
| |
Collapse
|
52
|
Plett KL, Bithell SL, Dando A, Plett JM. Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories. BMC PLANT BIOLOGY 2021; 21:310. [PMID: 34210277 PMCID: PMC8247157 DOI: 10.1186/s12870-021-03102-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 05/20/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with Mesorhizobium ciceri is of critical importance in supporting growth and grain production. A number of factors can affect this symbiotic relationship including abiotic conditions, plant genotype, and disruptions to host signalling/perception networks. In order to support improved nodule formation in chickpea, we investigated how plant genotype and soil nutrient availability affect chickpea nodule formation and nitrogen fixation. Further, using transcriptomic profiling, we sought to identify gene expression patterns that characterize highly nodulated genotypes. RESULTS A study involving six chickpea varieties demonstrated large genotype by soil nitrogen interaction effects on nodulation and further identified agronomic traits of genotypes (such as shoot weight) associated with high nodulation. We broadened our scope to consider 29 varieties and breeding lines to examine the relationship between soilborne disease resistance and the number of nodules developed and real-time nitrogen fixation. Results of this larger study supported the earlier genotype specific findings, however, disease resistance did not explain differences in nodulation across genotypes. Transcriptional profiling of six chickpea genotypes indicates that genes associated with signalling, N transport and cellular localization, as opposed to genes associated with the classical nodulation pathway, are more likely to predict whether a given genotype will exhibit high levels of nodule formation. CONCLUSIONS This research identified a number of key abiotic and genetic factors affecting chickpea nodule development and nitrogen fixation. These findings indicate that an improved understanding of genotype-specific factors affecting chickpea nodule induction and function are key research areas necessary to improving the benefits of rhizobial symbiosis in chickpea.
Collapse
Affiliation(s)
- Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Sean L Bithell
- New South Wales Department of Primary Industries, Tamworth, NSW, Australia
| | - Adrian Dando
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
| |
Collapse
|
53
|
Gühl K, Holmer R, Xiao TT, Shen D, Wardhani TAK, Geurts R, van Zeijl A, Kohlen W. The Effect of Exogenous Nitrate on LCO Signalling, Cytokinin Accumulation, and Nodule Initiation in Medicago truncatula. Genes (Basel) 2021; 12:genes12070988. [PMID: 34203444 PMCID: PMC8305252 DOI: 10.3390/genes12070988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/21/2023] Open
Abstract
Nitrogen fixation by rhizobia is a highly energy-demanding process. Therefore, nodule initiation in legumes is tightly regulated. Environmental nitrate is a potent inhibitor of nodulation. However, the precise mechanism by which this agent (co)regulates the inhibition of nodulation is not fully understood. Here, we demonstrate that in Medicago truncatula the lipo-chitooligosaccharide-induced accumulation of cytokinins is reduced in response to the application of exogenous nitrate. Under permissive nitrate conditions, perception of rhizobia-secreted signalling molecules leads to an increase in the level of four cytokinins (i.e., iP, iPR, tZ, and tZR). However, under high-nitrate conditions, this increase in cytokinins is reduced. The ethylene-insensitive mutant Mtein2/sickle, as well as wild-type plants grown in the presence of the ethylene biosynthesis inhibitor 2-aminoethoxyvinyl glycine (AVG), is resistant to the inhibition of nodulation by nitrate. This demonstrates that ethylene biosynthesis and perception are required to inhibit nodule organogenesis under high-nitrate conditions.
Collapse
Affiliation(s)
- Kerstin Gühl
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
| | - Rens Holmer
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ting Ting Xiao
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
| | - Defeng Shen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
| | - Titis A. K. Wardhani
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
| | - René Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
| | - Arjan van Zeijl
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (K.G.); (R.H.); (T.T.X.); (D.S.); (T.A.K.W.); (R.G.); (A.v.Z.)
- Correspondence:
| |
Collapse
|
54
|
Liang P, Schmitz C, Lace B, Ditengou FA, Su C, Schulze E, Knerr J, Grosse R, Keller J, Libourel C, Delaux PM, Ott T. Formin-mediated bridging of cell wall, plasma membrane, and cytoskeleton in symbiotic infections of Medicago truncatula. Curr Biol 2021; 31:2712-2719.e5. [PMID: 33930305 PMCID: PMC8231094 DOI: 10.1016/j.cub.2021.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 02/01/2021] [Accepted: 04/01/2021] [Indexed: 12/25/2022]
Abstract
Legumes have maintained the ability to associate with rhizobia to sustain the nitrogen-fixing root nodule symbiosis (RNS). In Medicago truncatula, the Nod factor (NF)-dependent intracellular root colonization by Sinorhizobium meliloti initiates from young, growing root hairs. They form rhizobial traps by physically curling around the symbiont.1,2 Although alterations in root hair morphology like branching and swelling have been observed in other plants in response to drug treatments3 or genetic perturbations,4, 5, 6 full root hair curling represents a rather specific invention in legumes. The entrapment of the symbiont completes with its full enclosure in a structure called the “infection chamber” (IC),1,2,7,8 from which a tube-like membrane channel, the “infection thread” (IT), initiates.1,2,9 All steps of rhizobium-induced root hair alterations are aided by a tip-localized cytosolic calcium gradient,10,11 global actin re-arrangements, and dense subapical fine actin bundles that are required for the delivery of Golgi-derived vesicles to the root hair tip.7,12, 13, 14 Altered actin dynamics during early responses to NFs or rhizobia have mostly been shown in mutants that are affected in the actin-related SCAR/WAVE complex.15, 16, 17, 18 Here, we identified a polarly localized SYMBIOTIC FORMIN 1 (SYFO1) to be required for NF-dependent alterations in membrane organization and symbiotic root hair responses. We demonstrate that SYFO1 mediates a continuum between the plasma membrane and the cell wall that is required for the onset of rhizobial infections. The SYMBIOTIC FORMIN 1 (SYFO1) specifically regulates symbiotic root hair curling SYFO1 directly binds actin and polarizes in responding root hairs SYFO1 induces membrane protrusions in cell-wall-devoid protoplasts Cell wall association of SYFO1 is indispensable for its function in root hairs
Collapse
Affiliation(s)
- Pengbo Liang
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Clara Schmitz
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Beatrice Lace
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Franck Anicet Ditengou
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Chao Su
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Eija Schulze
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Julian Knerr
- University of Freiburg, Medical Faculty, Institute of Pharmacology, Albertstr. 25, 79104 Freiburg, Germany
| | - Robert Grosse
- University of Freiburg, Medical Faculty, Institute of Pharmacology, Albertstr. 25, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, Schänzlestr. 8, 79104 Freiburg, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24, chemin de Borde-Rouge, 31326 Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24, chemin de Borde-Rouge, 31326 Castanet-Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24, chemin de Borde-Rouge, 31326 Castanet-Tolosan, France
| | - Thomas Ott
- University of Freiburg, Faculty of Biology, Cell Biology, Schänzlestr. 1, 79104 Freiburg, Germany; CIBSS - Centre of Integrative Biological Signalling Studies, University of Freiburg, Schänzlestr. 8, 79104 Freiburg, Germany.
| |
Collapse
|
55
|
Jarzyniak K, Banasiak J, Jamruszka T, Pawela A, Di Donato M, Novák O, Geisler M, Jasiński M. Early stages of legume-rhizobia symbiosis are controlled by ABCG-mediated transport of active cytokinins. NATURE PLANTS 2021; 7:428-436. [PMID: 33753904 DOI: 10.1038/s41477-021-00873-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
Growing evidence has highlighted the essential role of plant hormones, notably, cytokinins (CKs), in nitrogen-fixing symbiosis, both at early and late nodulation stages1,2. Despite numerous studies showing the central role of CK in nodulation, the importance of CK transport in the symbiosis is unknown. Here, we show the role of ABCG56, a full-size ATP-binding cassette (ABC) transporter in the early stages of the nodulation. MtABCG56 is expressed in roots and nodules and its messenger RNA levels increase upon treatment with symbiotic bacteria, isolated Nod factor and CKs, accumulating within the epidermis and root cortex. MtABCG56 exports bioactive CKs in an ATP-dependent manner over the plasma membrane and its disruption results in an impairment of nodulation. Our data indicate that ABCG-mediated cytokinin transport is important for proper establishment of N-fixing nodules.
Collapse
Affiliation(s)
- Karolina Jarzyniak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
| | - Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Jamruszka
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Aleksandra Pawela
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Martin Di Donato
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, Czech Republic
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland.
| |
Collapse
|
56
|
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.
Collapse
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
| |
Collapse
|
57
|
Soyano T, Liu M, Kawaguchi M, Hayashi M. Leguminous nodule symbiosis involves recruitment of factors contributing to lateral root development. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:102000. [PMID: 33454544 DOI: 10.1016/j.pbi.2020.102000] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 05/27/2023]
Abstract
Legumes and several plant species in the monophyletic nitrogen-fixing clade produce root nodules that function as symbiotic organs and establish mutualistic relationships with nitrogen-fixing bacteria. The modes of nodule organogenesis are distinct from those of lateral root development and also differ among different types of nodules formed in legumes and actinorhizal plants. It is considered that the evolution of new organs occurs through rearrangement of molecular networks interposed by certain neo-functionalized factors. Accumulating evidence has suggested that root nodule organogenesis involves root or lateral root developmental pathways. This review describes the current knowledge about the factors/pathways acquired by the common ancestor of the nitrogen-fixing clade in order to control nodule organogenesis.
Collapse
Affiliation(s)
- Takashi Soyano
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (the Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan.
| | - Meng Liu
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (the Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, 444-8585 Aichi, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
| |
Collapse
|
58
|
Shrestha A, Zhong S, Therrien J, Huebert T, Sato S, Mun T, Andersen SU, Stougaard J, Lepage A, Niebel A, Ross L, Szczyglowski K. Lotus japonicus Nuclear Factor YA1, a nodule emergence stage-specific regulator of auxin signalling. THE NEW PHYTOLOGIST 2021; 229:1535-1552. [PMID: 32978812 PMCID: PMC7984406 DOI: 10.1111/nph.16950] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/05/2020] [Indexed: 05/07/2023]
Abstract
Organogenesis of legume root nodules begins with the nodulation factor-dependent stimulation of compatible root cells to initiate divisions, signifying an early nodule primordium formation event. This is followed by cellular differentiation, including cell expansion and vascular bundle formation, and we previously showed that Lotus japonicus NF-YA1 is essential for this process, presumably by regulating three members of the SHORT INTERNODES/STYLISH (STY) transcription factor gene family. In this study, we used combined genetics, genomics and cell biology approaches to characterize the role of STY genes during root nodule formation and to test a hypothesis that they mediate nodule development by stimulating auxin signalling. We show here that L. japonicus STYs are required for nodule emergence. This is attributed to the NF-YA1-dependent regulatory cascade, comprising STY genes and their downstream targets, YUCCA1 and YUCCA11, involved in a local auxin biosynthesis at the post-initial cell division stage. An analogous NF-YA1/STY regulatory module seems to operate in Medicago truncatula in association with the indeterminate nodule patterning. Our data define L. japonicus and M. truncatula NF-YA1 genes as important nodule emergence stage-specific regulators of auxin signalling while indicating that the inductive stage and subsequent formation of early nodule primordia are mediated through an independent mechanism(s).
Collapse
Affiliation(s)
- Arina Shrestha
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Sihui Zhong
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Jasmine Therrien
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Terry Huebert
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Shusei Sato
- Graduate School of Life SciencesTohoku University2‐1‐1 KatahiraSendai980‐8577Japan
| | - Terry Mun
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Stig U. Andersen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Agnes Lepage
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Loretta Ross
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Krzysztof Szczyglowski
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| |
Collapse
|
59
|
Ma Y, Chen R. Nitrogen and Phosphorus Signaling and Transport During Legume-Rhizobium Symbiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:683601. [PMID: 34239527 PMCID: PMC8258413 DOI: 10.3389/fpls.2021.683601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 05/11/2023]
Abstract
Nitrogen (N) and phosphorus (P) are the two predominant mineral elements, which are not only essential for plant growth and development in general but also play a key role in symbiotic N fixation in legumes. Legume plants have evolved complex signaling networks to respond to both external and internal levels of these macronutrients to optimize symbiotic N fixation in nodules. Inorganic phosphate (Pi) and nitrate (NO3 -) are the two major forms of P and N elements utilized by plants, respectively. Pi starvation and NO3 - application both reduce symbiotic N fixation via similar changes in the nodule gene expression and invoke local and long-distance, systemic responses, of which N-compound feedback regulation of rhizobial nitrogenase activity appears to operate under both conditions. Most of the N and P signaling and transport processes have been investigated in model organisms, such as Medicago truncatula, Lotus japonicus, Glycine max, Phaseolus vulgaris, Arabidopsis thaliana, Oryza sativa, etc. We attempted to discuss some of these processes wherever appropriate, to serve as references for a better understanding of the N and P signaling and transport during symbiosis.
Collapse
Affiliation(s)
- Yanlin Ma
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rujin Chen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
- *Correspondence: Rujin Chen,
| |
Collapse
|
60
|
An SHR-SCR module specifies legume cortical cell fate to enable nodulation. Nature 2020; 589:586-590. [PMID: 33299183 DOI: 10.1038/s41586-020-3016-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/19/2020] [Indexed: 11/08/2022]
Abstract
Legumes, unlike other plants, have the ability to establish symbiosis with nitrogen-fixing rhizobia. It has been theorized that a unique property of legume root cortical cells enabled the initial establishment of rhizobial symbiosis1-3. Here we show that a SHORTROOT-SCARECROW (SHR-SCR) stem cell program in cortical cells of the legume Medicago truncatula specifies their distinct fate. Regulatory elements drive the cortical expression of SCR, and stele-expressed SHR protein accumulates in cortical cells of M. truncatula but not Arabidopsis thaliana. The cortical SHR-SCR network is conserved across legume species, responds to rhizobial signals, and initiates legume-specific cortical cell division for de novo nodule organogenesis and accommodation of rhizobia. Ectopic activation of SHR and SCR in legumes is sufficient to induce root cortical cell division. Our work suggests that acquisition of the cortical SHR-SCR module enabled cell division coupled to rhizobial infection in legumes. We propose that this event was central to the evolution of rhizobial endosymbiosis.
Collapse
|
61
|
Tsyganov VE, Tsyganova AV. Symbiotic Regulatory Genes Controlling Nodule Development in Pisum sativum L. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1741. [PMID: 33317178 PMCID: PMC7764586 DOI: 10.3390/plants9121741] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Analyses of natural variation and the use of mutagenesis and molecular-biological approaches have revealed 50 symbiotic regulatory genes in pea (Pisum sativum L.). Studies of genomic synteny using model legumes, such as Medicago truncatula Gaertn. and Lotus japonicus (Regel) K. Larsen, have identified the sequences of 15 symbiotic regulatory genes in pea. These genes encode receptor kinases, an ion channel, a calcium/calmodulin-dependent protein kinase, transcription factors, a metal transporter, and an enzyme. This review summarizes and describes mutant alleles, their phenotypic manifestations, and the functions of all identified symbiotic regulatory genes in pea. Some examples of gene interactions are also given. In the review, all mutant alleles in genes with identified sequences are designated and still-unidentified symbiotic regulatory genes of great interest are considered. The identification of these genes will help elucidate additional components involved in infection thread growth, nodule primordium development, bacteroid differentiation and maintenance, and the autoregulation of nodulation. The significance of symbiotic mutants of pea as extremely fruitful genetic models for studying nodule development and for comparative cell biology studies of legume nodules is clearly demonstrated. Finally, it is noted that many more sequences of symbiotic regulatory genes remain to be identified. Transcriptomics approaches and genome-wide sequencing could help address this challenge.
Collapse
Affiliation(s)
- Viktor E. Tsyganov
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin 8, 196608 Saint Petersburg, Russia;
| | | |
Collapse
|
62
|
Walker L, Lagunas B, Gifford ML. Determinants of Host Range Specificity in Legume-Rhizobia Symbiosis. Front Microbiol 2020; 11:585749. [PMID: 33329456 PMCID: PMC7728800 DOI: 10.3389/fmicb.2020.585749] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/06/2020] [Indexed: 01/24/2023] Open
Abstract
Leguminous plants possess the almost unique ability to enter symbiosis with soil-resident, nitrogen fixing bacteria called rhizobia. During this symbiosis, the bacteria physically colonize specialized organs on the roots of the host plant called nodules, where they reduce atmospheric nitrogen into forms that can be assimilated by the host plant and receive photosynthates in return. In order for nodule development to occur, there is extensive chemical cross-talk between both parties during the formative stages of the symbiosis. The vast majority of the legume family are capable of forming root nodules and typically rhizobia are only able to fix nitrogen within the context of this symbiotic association. However, many legume species only enter productive symbiosis with a few, or even single rhizobial species or strains, and vice-versa. Permitting symbiosis with only rhizobial strains that will be able to fix nitrogen with high efficiency is a crucial strategy for the host plant to prevent cheating by rhizobia. This selectivity is enforced at all stages of the symbiosis, with partner choice beginning during the initial communication between the plant and rhizobia. However, it can also be influenced even once nitrogen-fixing nodules have developed on the root. This review sets out current knowledge about the molecular mechanisms employed by both parties to influence host range during legume-rhizobia symbiosis.
Collapse
Affiliation(s)
- Liam Walker
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| |
Collapse
|
63
|
Lin J, Frank M, Reid D. No Home without Hormones: How Plant Hormones Control Legume Nodule Organogenesis. PLANT COMMUNICATIONS 2020; 1:100104. [PMID: 33367261 PMCID: PMC7747975 DOI: 10.1016/j.xplc.2020.100104] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 05/08/2023]
Abstract
The establishment of symbiotic nitrogen fixation requires the coordination of both nodule development and infection events. Despite the evolution of a variety of anatomical structures, nodule organs serve a common purpose in establishing a localized area that facilitates efficient nitrogen fixation. As in all plant developmental processes, the establishment of a new nodule organ is regulated by plant hormones. During nodule initiation, regulation of plant hormone signaling is one of the major targets of symbiotic signaling. We review the role of major developmental hormones in the initiation of the nodule organ and argue that the manipulation of plant hormones is a key requirement for engineering nitrogen fixation in non-legumes as the basis for improved food security and sustainability.
Collapse
Affiliation(s)
- Jieshun Lin
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Manuel Frank
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Corresponding author
| |
Collapse
|
64
|
Isidra-Arellano MC, Pozas-Rodríguez EA, Del Rocío Reyero-Saavedra M, Arroyo-Canales J, Ferrer-Orgaz S, Del Socorro Sánchez-Correa M, Cardenas L, Covarrubias AA, Valdés-López O. Inhibition of legume nodulation by Pi deficiency is dependent on the autoregulation of nodulation (AON) pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1125-1139. [PMID: 32344464 DOI: 10.1111/tpj.14789] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 05/26/2023]
Abstract
Inhibition of nodule development is one of the main adverse effects of phosphate (Pi) deficiency in legumes. Despite all of the efforts made over the last decades to understand how root nodules cope with Pi deficiency, the molecular mechanisms leading to the reduction in nodule number under Pi deficiency remain elusive. In the present study, we provide experimental evidence indicating that Pi deficiency activates the autoregulation of nodulation (AON) pathway, leading to a reduction in nodule numbers in both common bean and soybean. A transcriptional profile analysis revealed that the expression of the AON-related genes PvNIN, PvRIC1, PvRIC2, and PvTML is upregulated under Pi deficiency conditions. The downregulation of the MYB transcription factor PvPHR1 in common bean roots significantly reduced the expression of these four AON-related genes. Physiological analyses indicated that Pi deficiency does not affect the establishment of the root nodule symbiosis in the supernodulation mutant lines Pvnark and Gmnark. Reciprocal grafting and split-roots analyses determined that the activation of the AON pathway was required for the inhibitory effect of Pi deficiency. Altogether, these data improve our understanding of the genetic mechanisms controlling the establishment of the root nodule symbiosis under Pi deficiency.
Collapse
Affiliation(s)
- Mariel C Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autonoma de Mexico, Coyoacan, Mexico City, 04510, Mexico
| | - Eithan A Pozas-Rodríguez
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - María Del Rocío Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - Jazmin Arroyo-Canales
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - Susana Ferrer-Orgaz
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - María Del Socorro Sánchez-Correa
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| | - Luis Cardenas
- Departamento de Biologia Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biologia Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autonoma de Mexico, Tlalnepantla, 54090, México
| |
Collapse
|
65
|
Liu J, Bisseling T. Evolution of NIN and NIN-like Genes in Relation to Nodule Symbiosis. Genes (Basel) 2020; 11:E777. [PMID: 32664480 PMCID: PMC7397163 DOI: 10.3390/genes11070777] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/26/2020] [Accepted: 07/09/2020] [Indexed: 01/06/2023] Open
Abstract
Legumes and actinorhizal plants are capable of forming root nodules symbiosis with rhizobia and Frankia bacteria. All these nodulating species belong to the nitrogen fixation clade. Most likely, nodulation evolved once in the last common ancestor of this clade. NIN (NODULE INCEPTION) is a transcription factor that is essential for nodulation in all studied species. Therefore, it seems probable that it was recruited at the start when nodulation evolved. NIN is the founding member of the NIN-like protein (NLP) family. It arose by duplication, and this occurred before nodulation evolved. Therefore, several plant species outside the nitrogen fixation clade have NLP(s), which is orthologous to NIN. In this review, we discuss how NIN has diverged from the ancestral NLP, what minimal changes would have been essential for it to become a key transcription controlling nodulation, and which adaptations might have evolved later.
Collapse
Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
| |
Collapse
|
66
|
Costa SR, Chin S, Mathesius U. Infection of Medicago truncatula by the Root-Knot Nematode Meloidogyne javanica Does Not Require Early Nodulation Genes. FRONTIERS IN PLANT SCIENCE 2020; 11:1050. [PMID: 32733526 PMCID: PMC7363973 DOI: 10.3389/fpls.2020.01050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/25/2020] [Indexed: 05/27/2023]
Abstract
Because of the developmental similarities between root nodules induced by symbiotic rhizobia and root galls formed by parasitic nematodes, we investigated the involvement of nodulation genes in the infection of Medicago truncatula by the root knot nematode (RKN), Meloidogyne javanica. We found that gall formation, including giant cell formation, pericycle and cortical cell division, as well as egg laying, occurred successfully in the non-nodulating mutants nfp1 (nod factor perception1), nin1 (nodule inception1) and nsp2 (nodulation signaling pathway2) and the cytokinin perception mutant cre1 (cytokinin receptor1). Gall and egg formation were significantly reduced in the ethylene insensitive, hypernodulating mutant skl (sickle), and to a lesser extent, in the low nodulation, abscisic acid insensitive mutant latd/nip (lateral root-organ defective/numerous infections and polyphenolics). Despite its supernodulation phenotype, the sunn4 (super numeric nodules4) mutant, which has lost the ability to autoregulate nodule numbers, did not form excessive numbers of galls. Co-inoculation of roots with nematodes and rhizobia significantly reduced nodule numbers compared to rhizobia-only inoculated roots, but only in the hypernodulation mutant skl. Thus, this effect is likely to be influenced by ethylene signaling, but is not likely explained by resource competition between galls and nodules. Co-inoculation with rhizobia also reduced gall numbers compared to nematode-only infected roots, but only in the wild type. Therefore, the protective effect of rhizobia on nematode infection does not clearly depend on nodule number or on Nod factor signaling. Our study demonstrates that early nodulation genes that are essential for successful nodule development are not necessary for nematode-induced gall formation, that gall formation is not under autoregulation of nodulation control, and that ethylene signaling plays a positive role in successful RKN parasitism in M. truncatula.
Collapse
Affiliation(s)
- Sofia R. Costa
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia
- CBMA—Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Sabrina Chin
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia
| |
Collapse
|
67
|
Xiao A, Yu H, Fan Y, Kang H, Ren Y, Huang X, Gao X, Wang C, Zhang Z, Zhu H, Cao Y. Transcriptional regulation of NIN expression by IPN2 is required for root nodule symbiosis in Lotus japonicus. THE NEW PHYTOLOGIST 2020; 227:513-528. [PMID: 32187696 DOI: 10.1111/nph.16553] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/09/2020] [Indexed: 05/14/2023]
Abstract
Expression of Nodule Inception (NIN) is essential for initiation of legume-rhizobial symbiosis. An existing model regarding the regulation of NIN expression involves two GRAS transcription factors - NSP1 (Nodulation Signaling Pathway 1) and NSP2. NSP2 forms a complex with NSP1 to directly bind to NIN promoter. However, rhizobial treatment-induced NIN expression could still be detected in the nsp1 mutant plants, suggesting that other proteins must be involved in the regulation of NIN expression. A combination of molecular, biochemical and genetic analyses was used to investigate the molecular basis of IPN2 in regulating root development and NIN expression in Lotus japonicus. In this study, we identified that IPN2 is a close homolog of Arabidopsis APL (ALTERED PHLOEM DEVELOPMENT) with essential function in root development. However, Lotus IPN2 has a different expression pattern compared with the Arabidopsis APL gene. IPN2 binds to the IPN2-responsive cis element (IPN2-RE) of NIN promoter and activates NIN expression. IPN2, NSP1 and NSP2 form a protein complex to directly target NIN promoter and activate NIN expression in the legume-rhizobial symbiosis. Our data refine the regulatory model of NIN expression that NSP2 works together with NSP1 and IPN2 to activate the NIN gene allowing nodulation in L. japonicus.
Collapse
Affiliation(s)
- Aifang Xiao
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haixiang Yu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqian Fan
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Heng Kang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yaping Ren
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqin Huang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiumei Gao
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao Wang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongming Zhang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hui Zhu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangrong Cao
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
68
|
Laffont C, Ivanovici A, Gautrat P, Brault M, Djordjevic MA, Frugier F. The NIN transcription factor coordinates CEP and CLE signaling peptides that regulate nodulation antagonistically. Nat Commun 2020; 11:3167. [PMID: 32576831 PMCID: PMC7311451 DOI: 10.1038/s41467-020-16968-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/31/2020] [Indexed: 12/14/2022] Open
Abstract
Legumes tightly regulate nodule number to balance the cost of supporting symbiotic rhizobia with the benefits of nitrogen fixation. C-terminally Encoded Peptides (CEPs) and CLAVATA3-like (CLE) peptides positively and negatively regulate nodulation, respectively, through independent systemic pathways, but how these regulations are coordinated remains unknown. Here, we show that rhizobia, Nod Factors, and cytokinins induce a symbiosis-specific CEP gene, MtCEP7, which positively regulates rhizobial infection. Via grafting and split root studies, we reveal that MtCEP7 increases nodule number systemically through the MtCRA2 receptor. MtCEP7 and MtCLE13 expression in rhizobia-inoculated roots rely on the MtCRE1 cytokinin receptor and on the MtNIN transcription factor. MtNIN binds and transactivates MtCEP7 and MtCLE13, and a NIN Binding Site (NBS) identified within the proximal MtCEP7 promoter is required for its symbiotic activation. Overall, these results demonstrate that a cytokinin-MtCRE1-MtNIN regulatory module coordinates the expression of two antagonistic, symbiosis-related, peptide hormones from different families to fine-tune nodule number. CLE and CEP peptides regulate rhizobial symbiosis in legumes to balance the benefits of nitrogen fixation with the metabolic costs of nodule production. Here Laffont et al. show that cytokinin and bacterial Nod factors induce Medicago CEP7 which acts antagonistically to CLE13 to fine-tune nodulation.
Collapse
Affiliation(s)
- Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Pierre Gautrat
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mathias Brault
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France
| | - Michael Anthony Djordjevic
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ d'Evry, Université de Paris; Université Paris-Saclay, Gif-sur-Yvette, France.
| |
Collapse
|
69
|
Dolgikh EA, Kusakin PG, Kitaeva AB, Tsyganova AV, Kirienko AN, Leppyanen IV, Dolgikh AV, Ilina EL, Demchenko KN, Tikhonovich IA, Tsyganov VE. Mutational analysis indicates that abnormalities in rhizobial infection and subsequent plant cell and bacteroid differentiation in pea (Pisum sativum) nodules coincide with abnormal cytokinin responses and localization. ANNALS OF BOTANY 2020; 125:905-923. [PMID: 32198503 PMCID: PMC7218816 DOI: 10.1093/aob/mcaa022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Recent findings indicate that Nod factor signalling is tightly interconnected with phytohormonal regulation that affects the development of nodules. Since the mechanisms of this interaction are still far from understood, here the distribution of cytokinin and auxin in pea (Pisum sativum) nodules was investigated. In addition, the effect of certain mutations blocking rhizobial infection and subsequent plant cell and bacteroid differentiation on cytokinin distribution in nodules was analysed. METHODS Patterns of cytokinin and auxin in pea nodules were profiled using both responsive genetic constructs and antibodies. KEY RESULTS In wild-type nodules, cytokinins were found in the meristem, infection zone and apical part of the nitrogen fixation zone, whereas auxin localization was restricted to the meristem and peripheral tissues. We found significantly altered cytokinin distribution in sym33 and sym40 pea mutants defective in IPD3/CYCLOPS and EFD transcription factors, respectively. In the sym33 mutants impaired in bacterial accommodation and subsequent nodule differentiation, cytokinin localization was mostly limited to the meristem. In addition, we found significantly decreased expression of LOG1 and A-type RR11 as well as KNOX3 and NIN genes in the sym33 mutants, which correlated with low cellular cytokinin levels. In the sym40 mutant, cytokinins were detected in the nodule infection zone but, in contrast to the wild type, they were absent in infection droplets. CONCLUSIONS In conclusion, our findings suggest that enhanced cytokinin accumulation during the late stages of symbiosis development may be associated with bacterial penetration into the plant cells and subsequent plant cell and bacteroid differentiation.
Collapse
Affiliation(s)
- Elena A Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Pyotr G Kusakin
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Anna B Kitaeva
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Anna V Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Anna N Kirienko
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Irina V Leppyanen
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
| | - Aleksandra V Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
- Saint Petersburg State University, Department of Genetics and Biotechnology, Universitetskaya embankment 7–9, Saint Petersburg, Russia
| | - Elena L Ilina
- Komarov Botanical Institute, Russian Academy of Sciences, Laboratory of Cellular and Molecular Mechanisms of Plant Development, Saint Petersburg, Russia
| | - Kirill N Demchenko
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
- Komarov Botanical Institute, Russian Academy of Sciences, Laboratory of Cellular and Molecular Mechanisms of Plant Development, Saint Petersburg, Russia
| | - Igor A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
- Saint Petersburg State University, Department of Genetics and Biotechnology, Universitetskaya embankment 7–9, Saint Petersburg, Russia
| | - Viktor E Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Laboratory of Molecular and Cellular Biology, Saint Petersburg, Russia
- Saint Petersburg Scientific Center Russian Academy of Sciences, Universitetskaya embankment 5, Saint Petersburg, Russia
| |
Collapse
|
70
|
Bu F, Rutten L, Roswanjaya YP, Kulikova O, Rodriguez‐Franco M, Ott T, Bisseling T, van Zeijl A, Geurts R. Mutant analysis in the nonlegume Parasponia andersonii identifies NIN and NF-YA1 transcription factors as a core genetic network in nitrogen-fixing nodule symbioses. THE NEW PHYTOLOGIST 2020; 226:541-554. [PMID: 31863481 PMCID: PMC7154530 DOI: 10.1111/nph.16386] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/04/2019] [Indexed: 05/13/2023]
Abstract
●Nitrogen-fixing nodulation occurs in 10 taxonomic lineages, with either rhizobia or Frankia bacteria. To establish such an endosymbiosis, two processes are essential: nodule organogenesis and intracellular bacterial infection. In the legume-rhizobium endosymbiosis, both processes are guarded by the transcription factor NODULE INCEPTION (NIN) and its downstream target genes of the NUCLEAR FACTOR Y (NF-Y) complex. ●It is hypothesized that nodulation has a single evolutionary origin c. 110 Ma, followed by many independent losses. Despite a significant body of knowledge of the legume-rhizobium symbiosis, it remains elusive which signalling modules are shared between nodulating species in different taxonomic clades. We used Parasponia andersonii to investigate the role of NIN and NF-YA genes in rhizobium nodulation in a nonlegume system. ●Consistent with legumes, P. andersonii PanNIN and PanNF-YA1 are coexpressed in nodules. By analyzing single, double and higher-order CRISPR-Cas9 knockout mutants, we show that nodule organogenesis and early symbiotic expression of PanNF-YA1 are PanNIN-dependent and that PanNF-YA1 is specifically required for intracellular rhizobium infection. ●This demonstrates that NIN and NF-YA1 have conserved symbiotic functions. As Parasponia and legumes diverged soon after the birth of the nodulation trait, we argue that NIN and NF-YA1 represent core transcriptional regulators in this symbiosis.
Collapse
Affiliation(s)
- Fengjiao Bu
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Luuk Rutten
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Yuda Purwana Roswanjaya
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
- Center of Technology for Agricultural ProductionAgency for the Assessment and Application of Technology (BPPT)10340JakartaIndonesia
| | - Olga Kulikova
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | | | - Thomas Ott
- Cell BiologyFaculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Ton Bisseling
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Arjan van Zeijl
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Rene Geurts
- Laboratory of Molecular BiologyDepartment of Plant ScienceWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| |
Collapse
|
71
|
Wang Z, Wang L, Wang Y, Li X. The NMN Module Conducts Nodule Number Orchestra. iScience 2020; 23:100825. [PMID: 31978752 PMCID: PMC6976932 DOI: 10.1016/j.isci.2020.100825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/12/2019] [Accepted: 01/06/2020] [Indexed: 01/08/2023] Open
Abstract
Legumes control nodule number through nodulation and autoregulation of nodulation (AON) pathways. Nodule Inception (NIN) is essential for rhizobial infection and nodule organogenesis in legumes. The GmNINa-miR172c-NNC1 (NMN) module, which consists of two positive regulators, GmNINa and miR172c, and a suppressor, NNC1, integrates both pathways. GmNINa activates miR172c to downregulate NNC1, leading to nodulation, while NNC1 inhibits miR172c expression, forming a negative feedback loop. GmNINa and NNC1 interact with each other and antagonistically fine-tune GmRIC1/RIC2 expression, turning AON on and off. Conversely, activation of AON inhibits GmNINa and miR172c expression, thereby reducing their inhibitory effects on NNC1 to attenuate both nodulation signaling and AON. The NMN module functions not only as an “accelerator” of the nodulation signal to promote nodulation but also as a “brake” on the signal by activating AON to orchestrate nodule number.
Collapse
Affiliation(s)
- Zhijuan Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China; Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yongliang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
| |
Collapse
|
72
|
Traubenik S, Reynoso MA, Hobecker K, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco F, Zanetti ME. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs. THE PLANT CELL 2020; 32:352-373. [PMID: 31748328 PMCID: PMC7008484 DOI: 10.1105/tpc.19.00647] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied translating ribosome affinity purification combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen-fixing symbiosis established between Medicago truncatula and Sinorhizobium meliloti Our analysis revealed a poor correlation between transcriptional and translational changes and identified hundreds of regulated protein-coding and long noncoding RNAs (lncRNAs), some of which are regulated in specific cell types. We demonstrated that a short variant of the lncRNA Trans-acting small interference RNA3 (TAS3) increased its association to the translational machinery in response to rhizobia. Functional analysis revealed that this short variant of TAS3 might act as a target mimic that captures microRNA390, contributing to reduce trans acting small interference Auxin Response Factor production and modulating nodule formation and rhizobial infection. The analysis of alternative transcript variants identified a translationally upregulated mRNA encoding subunit 3 of the SUPERKILLER complex (SKI3), which participates in mRNA decay. Knockdown of SKI3 decreased nodule initiation and development, as well as the survival of bacteria within nodules. Our results highlight the importance of translational control and mRNA decay pathways for the successful establishment of the nitrogen-fixing symbiosis.
Collapse
Affiliation(s)
- Soledad Traubenik
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Mauricio Alberto Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Marcos Lancia
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Maureen Hummel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | | | | | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| |
Collapse
|
73
|
Huisman R, Geurts R. A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis. PLANT COMMUNICATIONS 2020; 1:100019. [PMID: 33404552 PMCID: PMC7748023 DOI: 10.1016/j.xplc.2019.100019] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 05/26/2023]
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
Collapse
Affiliation(s)
- Rik Huisman
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Rene Geurts
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| |
Collapse
|
74
|
Mergaert P, Kereszt A, Kondorosi E. Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants. THE PLANT CELL 2020; 32:42-68. [PMID: 31712407 PMCID: PMC6961632 DOI: 10.1105/tpc.19.00494] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/08/2019] [Indexed: 05/06/2023]
Abstract
Root nodules formed by plants of the nitrogen-fixing clade (NFC) are symbiotic organs that function in the maintenance and metabolic integration of large populations of nitrogen-fixing bacteria. These organs feature unique characteristics and processes, including their tissue organization, the presence of specific infection structures called infection threads, endocytotic uptake of bacteria, symbiotic cells carrying thousands of intracellular bacteria without signs of immune responses, and the integration of symbiont and host metabolism. The early stages of nodulation are governed by a few well-defined functions, which together constitute the common symbiosis-signaling pathway (CSSP). The CSSP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection. The later stages of nodule development require the activation of hundreds to thousands of genes, mostly expressed in symbiotic cells. Many of these genes are only active in symbiotic cells, reflecting the unique nature of nodules as plant structures. Although how the nodule-specific transcriptome is activated and connected to early CSSP-signaling is poorly understood, candidate TFs have been identified using transcriptomic approaches, and the importance of epigenetic and chromatin-based regulation has been demonstrated. We discuss how gene regulation analyses have advanced our understanding of nodule organogenesis, the functioning of symbiotic cells, and the evolution of symbiosis in the NFC.
Collapse
Affiliation(s)
- Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Attila Kereszt
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| | - Eva Kondorosi
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary
| |
Collapse
|
75
|
Roy S, Liu W, Nandety RS, Crook A, Mysore KS, Pislariu CI, Frugoli J, Dickstein R, Udvardi MK. Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation. THE PLANT CELL 2020; 32:15-41. [PMID: 31649123 PMCID: PMC6961631 DOI: 10.1105/tpc.19.00279] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/17/2019] [Accepted: 10/24/2019] [Indexed: 05/13/2023]
Abstract
Since 1999, various forward- and reverse-genetic approaches have uncovered nearly 200 genes required for symbiotic nitrogen fixation (SNF) in legumes. These discoveries advanced our understanding of the evolution of SNF in plants and its relationship to other beneficial endosymbioses, signaling between plants and microbes, the control of microbial infection of plant cells, the control of plant cell division leading to nodule development, autoregulation of nodulation, intracellular accommodation of bacteria, nodule oxygen homeostasis, the control of bacteroid differentiation, metabolism and transport supporting symbiosis, and the control of nodule senescence. This review catalogs and contextualizes all of the plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean). We also briefly consider the future of SNF genetics in the era of pan-genomics and genome editing.
Collapse
Affiliation(s)
- Sonali Roy
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Wei Liu
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Ashley Crook
- College of Science, Clemson University, Clemson, South Carolina 29634
| | | | | | - Julia Frugoli
- College of Science, Clemson University, Clemson, South Carolina 29634
| | - Rebecca Dickstein
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton Texas 76203
| | | |
Collapse
|
76
|
Shen D, Kulikova O, Guhl K, Franssen H, Kohlen W, Bisseling T, Geurts R. The Medicago truncatula nodule identity gene MtNOOT1 is required for coordinated apical-basal development of the root. BMC PLANT BIOLOGY 2019; 19:571. [PMID: 31856724 PMCID: PMC6923920 DOI: 10.1186/s12870-019-2194-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 12/10/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND Legumes can utilize atmospheric nitrogen by hosting nitrogen-fixing bacteria in special lateral root organs, called nodules. Legume nodules have a unique ontology, despite similarities in the gene networks controlling nodule and lateral root development. It has been shown that Medicago truncatula NODULE ROOT1 (MtNOOT1) is required for the maintenance of nodule identity, preventing the conversion to lateral root development. MtNOOT1 and its orthologs in other plant species -collectively called the NOOT-BOP-COCH-LIKE (NBCL) family- specify boundary formation in various aerial organs. However, MtNOOT1 is not only expressed in nodules and aerial organs, but also in developing roots, where its function remains elusive. RESULTS We show that Mtnoot1 mutant seedlings display accelerated root elongation due to an enlarged root apical meristem. Also, Mtnoot1 mutant roots are thinner than wild-type and are delayed in xylem cell differentiation. We provide molecular evidence that the affected spatial development of Mtnoot1 mutant roots correlates with delayed induction of genes involved in xylem cell differentiation. This coincides with a basipetal shift of the root zone that is susceptible to rhizobium-secreted symbiotic signal molecules. CONCLUSIONS Our data show that MtNOOT1 regulates the size of the root apical meristem and vascular differentiation. Our data demonstrate that MtNOOT1 not only functions as a homeotic gene in nodule development but also coordinates the spatial development of the root.
Collapse
Affiliation(s)
- Defeng Shen
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kerstin Guhl
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Henk Franssen
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - René Geurts
- Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
77
|
Schiessl K, Lilley JLS, Lee T, Tamvakis I, Kohlen W, Bailey PC, Thomas A, Luptak J, Ramakrishnan K, Carpenter MD, Mysore KS, Wen J, Ahnert S, Grieneisen VA, Oldroyd GED. NODULE INCEPTION Recruits the Lateral Root Developmental Program for Symbiotic Nodule Organogenesis in Medicago truncatula. Curr Biol 2019; 29:3657-3668.e5. [PMID: 31543454 PMCID: PMC6839406 DOI: 10.1016/j.cub.2019.09.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/02/2019] [Accepted: 09/02/2019] [Indexed: 01/18/2023]
Abstract
To overcome nitrogen deficiencies in the soil, legumes enter symbioses with rhizobial bacteria that convert atmospheric nitrogen into ammonium. Rhizobia are accommodated as endosymbionts within lateral root organs called nodules that initiate from the inner layers of Medicago truncatula roots in response to rhizobial perception. In contrast, lateral roots emerge from predefined founder cells as an adaptive response to environmental stimuli, including water and nutrient availability. CYTOKININ RESPONSE 1 (CRE1)-mediated signaling in the pericycle and in the cortex is necessary and sufficient for nodulation, whereas cytokinin is antagonistic to lateral root development, with cre1 showing increased lateral root emergence and decreased nodulation. To better understand the relatedness between nodule and lateral root development, we undertook a comparative analysis of these two root developmental programs. Here, we demonstrate that despite differential induction, lateral roots and nodules share overlapping developmental programs, with mutants in LOB-DOMAIN PROTEIN 16 (LBD16) showing equivalent defects in nodule and lateral root initiation. The cytokinin-inducible transcription factor NODULE INCEPTION (NIN) allows induction of this program during nodulation through activation of LBD16 that promotes auxin biosynthesis via transcriptional induction of STYLISH (STY) and YUCCAs (YUC). We conclude that cytokinin facilitates local auxin accumulation through NIN promotion of LBD16, which activates a nodule developmental program overlapping with that induced during lateral root initiation.
Collapse
Affiliation(s)
- Katharina Schiessl
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jodi L S Lilley
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Tak Lee
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Ioannis Tamvakis
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Wouter Kohlen
- Laboratory for Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Paul C Bailey
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Aaron Thomas
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jakub Luptak
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Karunakaran Ramakrishnan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Matthew D Carpenter
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | | | - Jiangqi Wen
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Sebastian Ahnert
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | - Veronica A Grieneisen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Giles E D Oldroyd
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
| |
Collapse
|
78
|
Poehlman WL, Schnabel EL, Chavan SA, Frugoli JA, Feltus FA. Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-Expression Network Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1409. [PMID: 31737022 PMCID: PMC6836625 DOI: 10.3389/fpls.2019.01409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Root nodulation results from a symbiotic relationship between a plant host and Rhizobium bacteria. Synchronized gene expression patterns over the course of rhizobial infection result in activation of pathways that are unique but overlapping with the highly conserved pathways that enable mycorrhizal symbiosis. We performed RNA sequencing of 30 Medicago truncatula root maturation zone samples at five distinct time points. These samples included plants inoculated with Sinorhizobium medicae and control plants that did not receive any Rhizobium. Following gene expression quantification, we identified 1,758 differentially expressed genes at various time points. We constructed a gene co-expression network (GCN) from the same data and identified link community modules (LCMs) that were comprised entirely of differentially expressed genes at specific time points post-inoculation. One LCM included genes that were up-regulated at 24 h following inoculation, suggesting an activation of allergen family genes and carbohydrate-binding gene products in response to Rhizobium. We also identified two LCMs that were comprised entirely of genes that were down regulated at 24 and 48 h post-inoculation. The identity of the genes in these modules suggest that down-regulating specific genes at 24 h may result in decreased jasmonic acid production with an increase in cytokinin production. At 48 h, coordinated down-regulation of a specific set of genes involved in lipid biosynthesis may play a role in nodulation. We show that GCN-LCM analysis is an effective method to preliminarily identify polygenic candidate biomarkers of root nodulation and develop hypotheses for future discovery.
Collapse
|
79
|
Mu X, Luo J. Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling. Cell Mol Life Sci 2019; 76:3753-3764. [PMID: 31161283 PMCID: PMC11105697 DOI: 10.1007/s00018-019-03164-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022]
Abstract
Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca2+-Ca2+ sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.
Collapse
Affiliation(s)
- Xiaohuan Mu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jie Luo
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
80
|
Li X, Zheng Z, Kong X, Xu J, Qiu L, Sun J, Reid D, Jin H, Andersen SU, Oldroyd GED, Stougaard J, Downie JA, Xie F. Atypical Receptor Kinase RINRK1 Required for Rhizobial Infection But Not Nodule Development in Lotus japonicus. PLANT PHYSIOLOGY 2019; 181:804-816. [PMID: 31409696 PMCID: PMC6776872 DOI: 10.1104/pp.19.00509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/01/2019] [Indexed: 05/21/2023]
Abstract
During the legume-rhizobium symbiotic interaction, rhizobial invasion of legumes is primarily mediated by a plant-made tubular invagination called an infection thread (IT). Here, we identify a gene in Lotus japonicus encoding a Leu-rich repeat receptor-like kinase (LRR-RLK), RINRK1 (Rhizobial Infection Receptor-like Kinase1), that is induced by Nod factors (NFs) and is involved in IT formation but not nodule organogenesis. A paralog, RINRK2, plays a relatively minor role in infection. RINRK1 is required for full induction of early infection genes, including Nodule Inception (NIN), encoding an essential nodulation transcription factor. RINRK1 displayed an infection-specific expression pattern, and NIN bound to the RINRK1 promoter, inducing its expression. RINRK1 was found to be an atypical kinase localized to the plasma membrane and did not require kinase activity for rhizobial infection. We propose RINRK1 is an infection-specific RLK, which may specifically coordinate output from NF signaling or perceive an unknown signal required for rhizobial infection.
Collapse
Affiliation(s)
- 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
| | - Zhiqiong Zheng
- 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 100049, China
| | - Xiangxiao Kong
- 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 100049, China
| | - Ji Xu
- 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
| | - Liping Qiu
- 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
| | - Jongho Sun
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000 C, Denmark
| | - J Allan Downie
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - 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
| |
Collapse
|
81
|
Wang L, Sun Z, Su C, Wang Y, Yan Q, Chen J, Ott T, Li X. A GmNINa-miR172c-NNC1 Regulatory Network Coordinates the Nodulation and Autoregulation of Nodulation Pathways in Soybean. MOLECULAR PLANT 2019; 12:1211-1226. [PMID: 31201867 DOI: 10.1016/j.molp.2019.06.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 05/25/2023]
Abstract
Symbiotic root nodules are root lateral organs of plants in which nitrogen-fixing bacteria (rhizobia) convert atmospheric nitrogen to ammonia. The formation and number of nodules in legumes are precisely controlled by a rhizobia-induced signal cascade and host-controlled autoregulation of nodulation (AON). However, how these pathways are integrated and their underlying mechanisms are unclear. Here, we report that microRNA172c (miR172c) activates soybean (Glycine max) Rhizobia-Induced CLE1 (GmRIC1) and GmRIC2 by removing the transcriptional repression of these genes by Nodule Number Control 1 (NNC1), leading to the activation of the AON pathway. NNC1 interacts with GmNINa, the soybean ortholog of Lotus NODULE INCEPTION (NIN), and hampers its transcriptional activation of GmRIC1 and GmRIC2. Importantly, GmNINa acts as a transcriptional activator of miR172c. Intriguingly, NNC1 can transcriptionally repress miR172c expression, adding a negative feedback loop into the NNC1 regulatory network. Moreover, GmNINa interacts with NNC1 and can relieve the NNC1-mediated repression of miR172c transcription. Thus, the GmNINa-miR172c-NNC1 network is a master switch that coordinately regulates and optimizes NF and AON signaling, supporting the balance between nodulation and AON in soybean.
Collapse
Affiliation(s)
- Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China; College of Biological Science and Engineering, Panzhihua University, No. 10 Airport Road, Eastern District, Panzhihua, Sichuan, China
| | - Zhengxi Sun
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Chao Su
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China; University of Freiburg, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yongliang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Qiqi Yan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Jiahuan Chen
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China
| | - Thomas Ott
- University of Freiburg, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, Hubei 430070, P.R. China.
| |
Collapse
|
82
|
Liu M, Soyano T, Yano K, Hayashi M, Kawaguchi M. ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus. JOURNAL OF PLANT RESEARCH 2019; 132:641-653. [PMID: 31313020 DOI: 10.1007/s10265-019-01122-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Legumes engage in symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia, under nitrogen-limited conditions. In many legumes, the root invasion of rhizobia is mediated by infection threads (ITs), tubular invaginations of the host cell wall and plasma membrane, developed from infection foci of deformed root hairs. IT formation is regulated by a series of signal transduction in host root. Nodulation signals activate the host transcription factor (TF), CYCLOPS, which directly induces expression of two TF genes, ERF REQUIRED FOR NODULATION1 (ERN1) and NODULE INCEPTION (NIN), essential for IT development. Here, we explored the relationship among these three symbiotic TF genes in the model legume Lotus japonicus and examined how their interplay contributes to IT formation. qRT-PCR analysis showed that NIN expression induced by rhizobial infection was attenuated in ern1-1, and further declined in cyclops-3 ern1-1. ERN1 overexpression led to induction of NIN expression in cyclops-3 ern1-1 in the presence of rhizobia. Thus, in addition to CYCLOPS, ERN1 is able to increase the NIN expression level depending on infection. Furthermore, consistent with this transcriptional hierarchy, ectopic expression of ERN1 as well as NIN suppressed the IT-deficient cyclops-3 phenotype, but ERN1 failed to confer ITs in the nin-2 root. However, the ern1-1 symbiotic epidermal phenotype was not suppressed by the NIN ectopic expression. The cyclops-3 ern1-1 double mutant was less sensitive to rhizobial infection than the single mutants and defective in the symbiotic root hair response at earlier stages. This more severe phenotype of the double mutant suggests a role for ERN1 that independent of the CYCLOPS-mediated transcriptional regulation. We conclude that ERN1 is involved in regulating NIN expression in addition to CYCLOPS, and these TFs coordinately promote the symbiotic root hair response and IT development. Our data help to reveal the extensive role of ERN1 in root nodule symbiosis signaling.
Collapse
Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan.
| |
Collapse
|
83
|
Zou H, Zhang NN, Pan Q, Zhang JH, Chen J, Wei GH. Hydrogen Sulfide Promotes Nodulation and Nitrogen Fixation in Soybean-Rhizobia Symbiotic System. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:972-985. [PMID: 31204904 DOI: 10.1094/mpmi-01-19-0003-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The rhizobium-legume symbiotic system is crucial for nitrogen cycle balance in agriculture. Hydrogen sulfide (H2S), a gaseous signaling molecule, may regulate various physiological processes in plants. However, whether H2S has regulatory effect in this symbiotic system remains unknown. Herein, we investigated the possible role of H2S in the symbiosis between soybean (Glycine max) and rhizobium (Sinorhizobium fredii). Our results demonstrated that an exogenous H2S donor (sodium hydrosulfide [NaHS]) treatment promoted soybean growth, nodulation, and nitrogenase (Nase) activity. Western blotting analysis revealed that the abundance of Nase component nifH was increased by NaHS treatment in nodules. Quantitative real-time polymerase chain reaction data showed that NaHS treatment upregulated the expressions of symbiosis-related genes nodA, nodC, and nodD of S. fredii. In addition, expression of soybean nodulation marker genes, including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN), nodulation signaling pathway 2b (GmNSP2b), and nodulation inception genes (GmNIN1a, GmNIN2a, and GmNIN2b), were upregulated. Moreover, the expressions of glutamate synthase (GmGOGAT), asparagine synthase (GmAS), nitrite reductase (GmNiR), ammonia transporter (GmSAT1), leghemoglobin (GmLb), and nifH involved in nitrogen metabolism were upregulated in NaHS-treated soybean roots and nodules. Together, our results suggested that H2S may act as a positive signaling molecule in the soybean-rhizobia symbiotic system and enhance the system's nitrogen fixation ability.
Collapse
Affiliation(s)
- Hang Zou
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, PR China
| | - Ni-Na Zhang
- 3State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Qing Pan
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, PR China
| | - Jian-Hua Zhang
- 4School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong
- 5Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Juan Chen
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
- 3State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
- 4School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong
| | - Ge-Hong Wei
- 1State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
- 2Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, PR China
| |
Collapse
|
84
|
Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML. Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. MOLECULAR PLANT 2019; 12:833-846. [PMID: 30953787 PMCID: PMC6557310 DOI: 10.1016/j.molp.2019.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 05/29/2023]
Abstract
Understanding how plants respond to nitrogen in their environment is crucial for determining how they use it and how the nitrogen use affects other processes related to plant growth and development. Under nitrogen limitation the activity and affinity of uptake systems is increased in roots, and lateral root formation is regulated in order to adapt to low nitrogen levels and scavenge from the soil. Plants in the legume family can form associations with rhizobial nitrogen-fixing bacteria, and this association is tightly regulated by nitrogen levels. The effect of nitrogen on nodulation has been extensively investigated, but the effects of nodulation on plant nitrogen responses remain largely unclear. In this study, we integrated molecular and phenotypic data in the legume Medicago truncatula and determined that genes controlling nitrogen influx are differently expressed depending on whether plants are mock or rhizobia inoculated. We found that a functional autoregulation of nodulation pathway is required for roots to perceive, take up, and mobilize nitrogen as well as for normal root development. Our results together revealed that autoregulation of nodulation, root development, and the location of nitrogen are processes balanced by the whole plant system as part of a resource-partitioning mechanism.
Collapse
Affiliation(s)
- Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Mingkee Achom
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Alonso J Pardal
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Saúl Vázquez
- Gateway Building, Sutton Bonington Campus, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sascha Ott
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK
| | - John Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, UK; Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| |
Collapse
|
85
|
Miri M, Janakirama P, Huebert T, Ross L, McDowell T, Orosz K, Markmann K, Szczyglowski K. Inside out: root cortex-localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti. THE NEW PHYTOLOGIST 2019; 222:1523-1537. [PMID: 30636324 DOI: 10.1111/nph.15683] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/03/2019] [Indexed: 05/27/2023]
Abstract
During Lotus japonicus-Mesorhizobium loti symbiosis, the LOTUS HISTIDINE KINASE1 (LHK1) cytokinin receptor regulates both the initiation of nodule formation and the scope of root infection. However, the exact spatiotemporal mechanism by which this receptor exerts its symbiotic functions has remained elusive. In this study, we performed cell type-specific complementation experiments in the hyperinfected lhk1-1 mutant background, targeting LHK1 to either the root epidermis or the root cortex. We also utilized various genetic backgrounds to characterize expression of several genes regulating symbiotic infection. We show here that expression of LHK1 in the root cortex is required and sufficient to regulate both nodule formation and epidermal infections. The LHK1-dependent signalling that restricts subsequent infection events is triggered before initial cell divisions for nodule primordium formation. We also demonstrate that AHK4, the Arabidopsis orthologue of LHK1, is able to regulate M. loti infection in L. japonicus, suggesting that an endogenous cytokinin receptor could be sufficient for engineering nitrogen-fixing root nodule symbiosis in nonlegumes. Our data provide experimental evidence for the existence of an LHK1-dependent root cortex-to-epidermis feedback mechanism regulating rhizobial infection. This root-localized regulatory module functionally links with the systemic autoregulation of nodulation (AON) to maintain the homeostasis of symbiotic infection.
Collapse
Affiliation(s)
- Mandana Miri
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5BF, Canada
| | - Preetam Janakirama
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Terry Huebert
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Loretta Ross
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
| | - Kathleen Orosz
- Fanshawe College, 1001 Fanshawe College Boulevard, London, ON, N5Y 5R6, Canada
| | - Katharina Markmann
- The Center for Plant Molecular Biology, Tübingen University, 72076, Tübingen, Germany
| | - Krzysztof Szczyglowski
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5BF, Canada
| |
Collapse
|
86
|
Hossain MS, Hoang NT, Yan Z, Tóth K, Meyers BC, Stacey G. Characterization of the Spatial and Temporal Expression of Two Soybean miRNAs Identifies SCL6 as a Novel Regulator of Soybean Nodulation. FRONTIERS IN PLANT SCIENCE 2019; 10:475. [PMID: 31057581 PMCID: PMC6477095 DOI: 10.3389/fpls.2019.00475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/28/2019] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) control expression of endogenous target genes through transcript cleavage or translational inhibition. Legume plants can form a specialized organ, the nodule, through interaction with nitrogen fixing soil bacteria. To understand the regulatory roles of miRNAs in the nodulation process, we functionally validated gma-miR171o and gma-miR171q and their target genes in soybean. These two miRNA sequences are identical in sequence but their miRNA genes are divergent and show unique, tissue-specific expression patterns. The expression levels of the two miRNAs are negatively correlated with that of their target genes. Ectopic expression of these miRNAs in transgenic hairy roots resulted in a significant reduction in nodule formation. Both gma-miR171o and gma-miR171q target members of the GRAS transcription factor superfamily, namely GmSCL-6 and GmNSP2. Transient interaction of miRNAs and their target genes in tobacco cells further confirmed their cleavage activity. The results suggest that gma-miR171o and gma-miR171q regulate GmSCL-6 and GmNSP2, which in turn, influence expression of the Nodule inception (NIN), Early Nodulin 40 (ENOD40), and Ethylene Response Factor Required for Nodulation (ERN) genes during the Bradyrhizobium japonicum-soybean nodulation process. Collectively, our data suggest a role for two miRNAs, gma-miR171o and gma-miR171q, in regulating the spatial and temporal aspects of soybean nodulation.
Collapse
Affiliation(s)
- Md Shakhawat Hossain
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nhung T. Hoang
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Zhe Yan
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Katalin Tóth
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Gary Stacey
- C.S. Bond Life Science Center, Divisions of Plant Sciences and Biochemistry, University of Missouri, Columbia, MO, United States
| |
Collapse
|
87
|
Liu CW, Breakspear A, Guan D, Cerri MR, Jackson K, Jiang S, Robson F, Radhakrishnan GV, Roy S, Bone C, Stacey N, Rogers C, Trick M, Niebel A, Oldroyd GED, de Carvalho-Niebel F, Murray JD. NIN Acts as a Network Hub Controlling a Growth Module Required for Rhizobial Infection. PLANT PHYSIOLOGY 2019; 179:1704-1722. [PMID: 30710053 PMCID: PMC6446755 DOI: 10.1104/pp.18.01572] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/20/2019] [Indexed: 05/22/2023]
Abstract
The symbiotic infection of root cells by nitrogen-fixing rhizobia during nodulation requires the transcription factor Nodule Inception (NIN). Our root hair transcriptomic study extends NIN's regulon to include Rhizobium Polar Growth and genes involved in cell wall modification, gibberellin biosynthesis, and a comprehensive group of nutrient (N, P, and S) uptake and assimilation genes, suggesting that NIN's recruitment to nodulation was based on its role as a growth module, a role shared with other NIN-Like Proteins. The expression of jasmonic acid genes in nin suggests the involvement of NIN in the resolution of growth versus defense outcomes. We find that the regulation of the growth module component Nodulation Pectate Lyase by NIN, and its function in rhizobial infection, are conserved in hologalegina legumes, highlighting its recruitment as a major event in the evolution of nodulation. We find that Nodulation Pectate Lyase is secreted to the infection chamber and the lumen of the infection thread. Gene network analysis using the transcription factor mutants for ERF Required for Nodulation1 and Nuclear Factor-Y Subunit A1 confirms hierarchical control of NIN over Nuclear Factor-Y Subunit A1 and shows that ERF Required for Nodulation1 acts independently to control infection. We conclude that while NIN shares functions with other NIN-Like Proteins, the conscription of key infection genes to NIN's control has made it a central regulatory hub for rhizobial infection.
Collapse
Affiliation(s)
- Cheng-Wu Liu
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andrew Breakspear
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Dian Guan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marion R Cerri
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Kirsty Jackson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Suyu Jiang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Centre of Excellence for Plant and Microbial Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fran Robson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Guru V Radhakrishnan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sonali Roy
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Caitlin Bone
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Nicola Stacey
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Christian Rogers
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andreas Niebel
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giles E D Oldroyd
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Fernanda de Carvalho-Niebel
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Jeremy D Murray
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Centre of Excellence for Plant and Microbial Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
88
|
Sun Y, Wu Z, Wang Y, Yang J, Wei G, Chou M. Identification of Phytocyanin Gene Family in Legume Plants and their Involvement in Nodulation of Medicago truncatula. PLANT & CELL PHYSIOLOGY 2019; 60:900-915. [PMID: 30649463 DOI: 10.1093/pcp/pcz007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
The establishment of symbiosis between legume and rhizobium results in the formation of nodule. Phytocyanins (PCs) are a class of plant-specific blue copper proteins, playing critical roles in plant development including nodule formation. Although a few PC genes have been isolated from nodules, their functions are still unclear. Here, we performed a genome-wide identification of PC family in seven sequenced legume species (Medicago truncatula, Glycine max, Cicer arietinum, Cajanus cajan, Lotus japonicus, Vigna angularis and Phaseolus vulgaris) and found PCs experienced a remarkable expansion in M. truncatula and G. max. Further, we conducted an in-depth analysis of PC family in the model legume M. truncatula. Briefly, 82 MtPCs were divided into four subfamilies and clustered into seven clades, with a large proportion of tandem duplications and various cross-tissues expression patterns. Importantly, some PCs, such as MtPLC1, MtENODL27 and MtENODL28 were preferentially expressed in nodules. Further, RNA interference (RNAi) experiment revealed the knockdown of MtENDOL27 and MtENDOL28 impaired rhizobia infection, nodule numbers and nitrogenase activity. Moreover, in the MtENODL27-RNAi nodules, the infected cells were reduced and the symbiosomes did not reach the elongated stage, indicating MtENDOL27 is required for rhizobia infection and nodule development. In addition, co-expression analysis showed MtPLC1, MtENODL27 and MtENODL28 were grouped into two different functional modules and co-expressed with the known symbiotic nitrogen fixation-related genes, suggesting that they might participate in nodulation via different ways. In summary, this study provides a useful resource for future researches on the structure and function of PCs in nodulation.
Collapse
Affiliation(s)
- Yali Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Zefeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Yujie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Jieyu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Minxia Chou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| |
Collapse
|
89
|
Suzaki T, Takeda N, Nishida H, Hoshino M, Ito M, Misawa F, Handa Y, Miura K, Kawaguchi M. LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus. PLoS Genet 2019; 15:e1007865. [PMID: 30605473 PMCID: PMC6317779 DOI: 10.1371/journal.pgen.1007865] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/30/2018] [Indexed: 11/19/2022] Open
Abstract
Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells. In model legumes such as Lotus japonicus and Medicago truncatula, rhizobia enter into roots through an intracellular invasion system that depends on the formation of a root-hair infection thread (IT). While IT-mediated intracellular rhizobia invasion is thought to be the most evolutionarily derived invasion system, some studies have indicated that a basal intercellular invasion system can replace it when some nodulation-related factors are genetically modified. In addition, intracellular rhizobia accommodation is suggested to have a similar mechanism as AMF accommodation. Nevertheless, our understanding of the underlying genetic mechanisms is incomplete. Here we identify a L. japonicus nodulation-deficient mutant, with a mutation in the LACK OF SYMBIONT ACCOMMODATION (LAN) gene, in which root-hair IT formation is strongly reduced, but intercellular rhizobial invasion eventually results in functional nodule formation. LjLAN encodes a protein that is homologous to Arabidopsis MEDIATOR 2/29/32 possibly acting as a subunit of a Mediator complex, a multiprotein complex required for gene transcription. We also show that LjLAN acts in parallel with a signaling pathway including LjCYCLOPS. In addition, the lan mutation drastically reduces the colonization levels of AMF. Taken together, our data provide a new factor that has a common role in symbiont accommodation process during root nodule and AM symbiosis. Symbiosis between plants and beneficial microbes such as nitrogen-fixing bacteria and arbuscular mycorrhizal fungi has enabled plant colonization of new environments. Root nodule symbiosis with nitrogen-fixing rhizobia enables sessile plants to survive in a nitrogen-deficient environment. To establish the symbiosis, host plant cells need to accommodate rhizobia during nodule development, a process mediated by a plant-derived intracellular structure called the infection thread (IT). In this study, we show that LACK OF SYMBIONT ACCOMMODATION (LAN) is involved in intracellular rhizobia accommodation in the model leguminous plant Lotus japonicus. LjLAN encodes a putative subunit of Mediator complex, a multiprotein complex that has a fundamental role as an activator of gene transcription. Mutation analysis suggests that LjLAN is required for root hair IT formation, which enables swift and efficient rhizobial accommodation. Moreover, we show that LjLAN is required for symbiosis with arbuscular mycorrhizal fungi. These data add a new component to the molecular mechanism relevant to the establishment of root nodule and arbuscular mycorrhizal symbiosis.
Collapse
Affiliation(s)
- Takuya Suzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Naoya Takeda
- Graduate School of Science and Technology, Kwansei Gakuin University, Mita, Hyogo, Japan
| | - Hanna Nishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Motomi Hoshino
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Momoyo Ito
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Fumika Misawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| |
Collapse
|
90
|
van Velzen R, Doyle JJ, Geurts R. A Resurrected Scenario: Single Gain and Massive Loss of Nitrogen-Fixing Nodulation. TRENDS IN PLANT SCIENCE 2019; 24:49-57. [PMID: 30409687 DOI: 10.1016/j.tplants.2018.10.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/28/2018] [Accepted: 10/12/2018] [Indexed: 05/26/2023]
Abstract
Root nodule endosymbiosis with nitrogen-fixing bacteria provides plants with unlimited access to fixed nitrogen, but at a significant energetic cost. Nodulation is generally considered to have originated in parallel in different lineages, but this hypothesis downplays the genetic complexity of nodulation and requires independent recruitment of many common features across lineages. Recent phylogenomic studies revealed that genes that function in establishing or maintaining nitrogen-fixing nodules are independently lost in non-nodulating relatives of nitrogen-fixing plants. In our opinion, these data are best explained by a scenario of a single gain followed by massively parallel loss of nitrogen-fixing root nodules triggered by events at geological scale.
Collapse
Affiliation(s)
- Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708PB, Wageningen, The Netherlands
| | - Jeff J Doyle
- School of Integrative Plant Science, Section of Plant Breeding & Genetics and Section of Plant Biology, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, 6708PB, Wageningen, The Netherlands.
| |
Collapse
|
91
|
Liu J, Rutten L, Limpens E, van der Molen T, van Velzen R, Chen R, Chen Y, Geurts R, Kohlen W, Kulikova O, Bisseling T. A Remote cis-Regulatory Region Is Required for NIN Expression in the Pericycle to Initiate Nodule Primordium Formation in Medicago truncatula. THE PLANT CELL 2019; 31:68-83. [PMID: 30610167 PMCID: PMC6391699 DOI: 10.1105/tpc.18.00478] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/13/2018] [Accepted: 01/04/2019] [Indexed: 05/22/2023]
Abstract
The legume-rhizobium symbiosis results in nitrogen-fixing root nodules, and their formation involves both intracellular infection initiated in the epidermis and nodule organogenesis initiated in inner root cell layers. NODULE INCEPTION (NIN) is a nodule-specific transcription factor essential for both processes. These NIN-regulated processes occur at different times and locations in the root, demonstrating a complex pattern of spatiotemporal regulation. We show that regulatory sequences sufficient for the epidermal infection process are located within a 5 kb region directly upstream of the NIN start codon in Medicago truncatula Furthermore, we identify a remote upstream cis-regulatory region required for the expression of NIN in the pericycle, and we show that this region is essential for nodule organogenesis. This region contains putative cytokinin response elements and is conserved in eight more legume species. Both the cytokinin receptor 1, which is essential for nodule primordium formation, and the B-type response regulator RR1 are expressed in the pericycle in the susceptible zone of the uninoculated root. This, together with the identification of the cytokinin-responsive elements in the NIN promoter, strongly suggests that NIN expression is initially triggered by cytokinin signaling in the pericycle to initiate nodule primordium formation.
Collapse
Affiliation(s)
- Jieyu Liu
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Tjitse van der Molen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Rujin Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Yuhui Chen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
92
|
Gaudioso-Pedraza R, Beck M, Frances L, Kirk P, Ripodas C, Niebel A, Oldroyd GED, Benitez-Alfonso Y, de Carvalho-Niebel F. Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development. Curr Biol 2018; 28:3562-3577.e6. [PMID: 30416059 DOI: 10.1016/j.cub.2018.09.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/27/2018] [Accepted: 09/13/2018] [Indexed: 01/08/2023]
Abstract
The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula β-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing β-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.
Collapse
Affiliation(s)
| | - Martina Beck
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Lisa Frances
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Philip Kirk
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carolina Ripodas
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, 31326 Castanet-Tolosan, France
| | - Giles E D Oldroyd
- Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge CB2 1LR, UK
| | | | | |
Collapse
|
93
|
Lin JS, Li X, Luo Z, Mysore KS, Wen J, Xie F. NIN interacts with NLPs to mediate nitrate inhibition of nodulation in Medicago truncatula. NATURE PLANTS 2018; 4:942-952. [PMID: 30297831 DOI: 10.1038/s41477-018-0261-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 08/21/2018] [Indexed: 05/21/2023]
Abstract
Legume plants can assimilate inorganic nitrogen and have access to fixed nitrogen through symbiotic interaction with diazotrophic bacteria called rhizobia. Symbiotic nitrogen fixation is an energy-consuming process and is strongly inhibited when sufficient levels of fixed nitrogen are available, but the molecular mechanisms governing this regulation are largely unknown. The transcription factor nodule inception (NIN) is strictly required for nodulation and belongs to a family of NIN-like proteins (NLPs), which have been implicated in the regulation of nitrogen homeostasis in Arabidopsis. Here, we show that mutation or downregulation of NLP genes prevents nitrate inhibition of infection, nodule formation and nitrogen fixation. We find that NIN and NLPs physically interact through their carboxy-terminal PB1 domains. Furthermore, we find that NLP1 is required for the expression of nitrate-responsive genes and that nitrate triggers NLP1 re-localization from the cytosol to the nucleus. Finally, we show that NLP1 can suppress NIN activation of CRE1 expression in Nicotiana benthamiana and Medicago truncatula. Our findings highlight a central role for NLPs in the suppression of nodulation by nitrate.
Collapse
Affiliation(s)
- Jie-Shun Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - 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, China
| | - Zhenpeng Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | | | - Jiangqi Wen
- Noble Research Institute, LLC, Ardmore, OK, USA
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
94
|
Nishida H, Suzaki T. Nitrate-mediated control of root nodule symbiosis. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:129-136. [PMID: 29684704 DOI: 10.1016/j.pbi.2018.04.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 05/14/2023]
Abstract
Nitrogen is an indispensable inorganic nutrient that is required by plants throughout their life. Root nodule symbiosis (RNS) is an important strategy mainly adopted by legumes to enhance nitrogen acquisition, where several key processes required for the establishment of the symbiosis, are pleiotropically controlled by nitrate availability in soil. Although the autoregulation of nodulation (AON), a systemic long-range signaling, has been suggested to be implicated in nitrate-induced control of RNS, AON alone is insufficient to fully explain the pleiotropic regulation that is induced by nitrate. A recent elucidation of the function of a NIN-LIKE PROTEIN transcription factor has provided greater insights into the genetic mechanisms underlying nitrate-induced control of RNS in varying nitrate environments.
Collapse
Affiliation(s)
- Hanna Nishida
- National Institute for Basic Biology, Okazaki, Aichi, Japan; School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takuya Suzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| |
Collapse
|
95
|
Murakami E, Cheng J, Gysel K, Bozsoki Z, Kawaharada Y, Hjuler CT, Sørensen KK, Tao K, Kelly S, Venice F, Genre A, Thygesen MB, de Jong N, Vinther M, Jensen DB, Jensen KJ, Blaise M, Madsen LH, Andersen KR, Stougaard J, Radutoiu S. Epidermal LysM receptor ensures robust symbiotic signalling in Lotus japonicus. eLife 2018; 7:e33506. [PMID: 29957177 PMCID: PMC6025957 DOI: 10.7554/elife.33506] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 06/05/2018] [Indexed: 02/04/2023] Open
Abstract
Recognition of Nod factors by LysM receptors is crucial for nitrogen-fixing symbiosis in most legumes. The large families of LysM receptors in legumes suggest concerted functions, yet only NFR1 and NFR5 and their closest homologs are known to be required. Here we show that an epidermal LysM receptor (NFRe), ensures robust signalling in L. japonicus. Mutants of Nfre react to Nod factors with increased calcium spiking interval, reduced transcriptional response and fewer nodules in the presence of rhizobia. NFRe has an active kinase capable of phosphorylating NFR5, which in turn, controls NFRe downstream signalling. Our findings provide evidence for a more complex Nod factor signalling mechanism than previously anticipated. The spatio-temporal interplay between Nfre and Nfr1, and their divergent signalling through distinct kinases suggests the presence of an NFRe-mediated idling state keeping the epidermal cells of the expanding root system attuned to rhizobia.
Collapse
Affiliation(s)
- Eiichi Murakami
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Jeryl Cheng
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Kira Gysel
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Zoltan Bozsoki
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | | | | | - Ke Tao
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Simon Kelly
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Francesco Venice
- Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
| | - Andrea Genre
- Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
| | | | - Noor de Jong
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Maria Vinther
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | | | - Michael Blaise
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | | | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Simona Radutoiu
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| |
Collapse
|
96
|
Trevaskis B. Developmental Pathways Are Blueprints for Designing Successful Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:745. [PMID: 29922318 PMCID: PMC5996307 DOI: 10.3389/fpls.2018.00745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/15/2018] [Indexed: 05/29/2023]
Abstract
Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.
Collapse
Affiliation(s)
- Ben Trevaskis
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| |
Collapse
|
97
|
Tsyganova AV, Tsyganov VE. Plant Genetic Control over Infection Thread Development during Legume-Rhizobium Symbiosis. Symbiosis 2018. [DOI: 10.5772/intechopen.70689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
98
|
van Velzen R, Holmer R, Bu F, Rutten L, van Zeijl A, Liu W, Santuari L, Cao Q, Sharma T, Shen D, Roswanjaya Y, Wardhani TAK, Kalhor MS, Jansen J, van den Hoogen J, Güngör B, Hartog M, Hontelez J, Verver J, Yang WC, Schijlen E, Repin R, Schilthuizen M, Schranz ME, Heidstra R, Miyata K, Fedorova E, Kohlen W, Bisseling T, Smit S, Geurts R. Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. Proc Natl Acad Sci U S A 2018; 115:E4700-E4709. [PMID: 29717040 PMCID: PMC5960304 DOI: 10.1073/pnas.1721395115] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
Collapse
Affiliation(s)
- Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Rens Holmer
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Fengjiao Bu
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Arjan van Zeijl
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Wei Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Luca Santuari
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Qingqin Cao
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
- College of Biological Science and Engineering & Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China
| | - Trupti Sharma
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Defeng Shen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Yuda Roswanjaya
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Titis A K Wardhani
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Maryam Seifi Kalhor
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Joelle Jansen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Johan van den Hoogen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Berivan Güngör
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Marijke Hartog
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Jan Hontelez
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Jan Verver
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Wei-Cai Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Elio Schijlen
- Bioscience, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Rimi Repin
- Sabah Parks, 88806 Kota Kinabalu, Malaysia
| | - Menno Schilthuizen
- Naturalis Biodiversity Center, 2333 CR, Leiden, The Netherlands
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, 88999 Kota Kinabalu, Malaysia
- Institute for Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Kana Miyata
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Elena Fedorova
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands;
| |
Collapse
|
99
|
Azarakhsh M, Lebedeva MA, Lutova LA. Identification and Expression Analysis of Medicago truncatula Isopentenyl Transferase Genes ( IPTs) Involved in Local and Systemic Control of Nodulation. FRONTIERS IN PLANT SCIENCE 2018; 9:304. [PMID: 29593763 PMCID: PMC5855100 DOI: 10.3389/fpls.2018.00304] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/22/2018] [Indexed: 05/26/2023]
Abstract
Cytokinins are essential for legume plants to establish a nitrogen-fixing symbiosis with rhizobia. Recently, the expression level of cytokinin biosynthesis IPTs (ISOPENTENYLTRANSFERASES) genes was shown to be increased in response to rhizobial inoculation in Lotus japonicus, Medicago truncatula and Pisum sativum. In addition to its well-established positive role in nodule primordium initiation in root cortex, cytokinin negatively regulates infection processes in the epidermis. Moreover, it was reported that shoot-derived cytokinin inhibits the subsequent nodule formation through AON (autoregulation of nodulation) pathway. In L. japonicus, LjIPT3 gene was shown to be activated in the shoot phloem via the components of AON system, negatively affecting nodulation. However, in M. truncatula, the detailed analysis of MtIPTs expression, both in roots and shoots, in response to nodulation has not been performed yet, and the link between IPTs and AON has not been studied so far. In this study, we performed an extensive analysis of MtIPTs expression levels in different organs, focusing on the possible role of MtIPTs in nodule development. MtIPTs expression dynamics in inoculated roots suggest that besides its early established role in the nodule primordia development, cytokinin may be also important for later stages of nodulation. According to expression analysis, MtIPT3, MtIPT4, and MtIPT5 are activated in the shoots in response to inoculation. Among these genes, MtIPT3 is the only one the induction of which was not observed in leaves of the sunn-3 mutant defective in CLV1-like kinase, the key component of AON, suggesting that MtIPT3 is activated in the shoots in an AON-dependent manner. Taken together, our findings suggest that MtIPTs are involved in the nodule development at different stages, both locally in inoculated roots and systemically in shoots, where their expression can be activated in an AON-dependent manner.
Collapse
|
100
|
van Zeijl A, Wardhani TAK, Seifi Kalhor M, Rutten L, Bu F, Hartog M, Linders S, Fedorova EE, Bisseling T, Kohlen W, Geurts R. CRISPR/Cas9-Mediated Mutagenesis of Four Putative Symbiosis Genes of the Tropical Tree Parasponia andersonii Reveals Novel Phenotypes. FRONTIERS IN PLANT SCIENCE 2018; 9:284. [PMID: 29559988 PMCID: PMC5845686 DOI: 10.3389/fpls.2018.00284] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/19/2018] [Indexed: 05/18/2023]
Abstract
Parasponia represents five fast-growing tropical tree species in the Cannabaceae and is the only plant lineage besides legumes that can establish nitrogen-fixing nodules with rhizobium. Comparative analyses between legumes and Parasponia allows identification of conserved genetic networks controlling this symbiosis. However, such studies are hampered due to the absence of powerful reverse genetic tools for Parasponia. Here, we present a fast and efficient protocol for Agrobacterium tumefaciens-mediated transformation and CRISPR/Cas9 mutagenesis of Parasponia andersonii. Using this protocol, knockout mutants are obtained within 3 months. Due to efficient micro-propagation, bi-allelic mutants can be studied in the T0 generation, allowing phenotypic evaluation within 6 months after transformation. We mutated four genes - PanHK4, PanEIN2, PanNSP1, and PanNSP2 - that control cytokinin, ethylene, or strigolactone hormonal networks and that in legumes commit essential symbiotic functions. Knockout mutants in Panhk4 and Panein2 displayed developmental phenotypes, namely reduced procambium activity in Panhk4 and disturbed sex differentiation in Panein2 mutants. The symbiotic phenotypes of Panhk4 and Panein2 mutant lines differ from those in legumes. In contrast, PanNSP1 and PanNSP2 are essential for nodule formation, a phenotype similar as reported for legumes. This indicates a conserved role for these GRAS-type transcriptional regulators in rhizobium symbiosis, illustrating the value of Parasponia trees as a research model for reverse genetic studies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| |
Collapse
|