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Abel NB, Nørgaard MMM, Hansen SB, Gysel K, Díez IA, Jensen ON, Stougaard J, Andersen KR. Phosphorylation of the alpha-I motif in SYMRK drives root nodule organogenesis. Proc Natl Acad Sci U S A 2024; 121:e2311522121. [PMID: 38363863 PMCID: PMC10895371 DOI: 10.1073/pnas.2311522121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/15/2023] [Indexed: 02/18/2024] Open
Abstract
Symbiosis receptor-like kinase SYMRK is required for root nodule symbiosis between legume plants and nitrogen-fixing bacteria. To understand symbiotic signaling from SYMRK, we determined the crystal structure to 1.95 Å and mapped the phosphorylation sites onto the intracellular domain. We identified four serine residues in a conserved "alpha-I" motif, located on the border between the kinase core domain and the flexible C-terminal tail, that, when phosphorylated, drives organogenesis. Substituting the four serines with alanines abolished symbiotic signaling, while substituting them with phosphorylation-mimicking aspartates induced the formation of spontaneous nodules in the absence of bacteria. These findings show that the signaling pathway controlling root nodule organogenesis is mediated by SYMRK phosphorylation, which may help when engineering this trait into non-legume plants.
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Affiliation(s)
- Nikolaj B. Abel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Malita M. M. Nørgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Simon B. Hansen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Ignacio Arribas Díez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M5230, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M5230, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Kasper R. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
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2
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García-Soto I, Andersen SU, Monroy-Morales E, Robledo-Gamboa M, Guadarrama J, Aviles-Baltazar NY, Serrano M, Stougaard J, Montiel J. A collection of novel Lotus japonicus LORE1 mutants perturbed in the nodulation program induced by the Agrobacterium pusense strain IRBG74. Front Plant Sci 2024; 14:1326766. [PMID: 38250449 PMCID: PMC10796720 DOI: 10.3389/fpls.2023.1326766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The Lotus japonicus population carrying new Lotus retrotransposon 1 (LORE1) insertions represents a valuable biological resource for genetic research. New insertions were generated by activation of the endogenous retroelement LORE1a in the germline of the G329-3 plant line and arranged in a 2-D system for reverse genetics. LORE1 mutants identified in this collection contributes substantially to characterize candidate genes involved in symbiotic association of L. japonicus with its cognate symbiont, the nitrogen-fixing bacteria Mesorhizobium loti that infects root nodules intracellularly. In this study we aimed to identify novel players in the poorly explored intercellular infection induced by Agrobacterium pusense IRBG74 sp. For this purpose, a forward screen of > 200,000 LORE1 seedlings, obtained from bulk propagation of G329-3 plants, inoculated with IRBG74 was performed. Plants with perturbed nodulation were scored and the offspring were further tested on plates to confirm the symbiotic phenotype. A total of 110 Lotus mutants with impaired nodulation after inoculation with IRBG74 were obtained. A comparative analysis of nodulation kinetics in a subset of 20 mutants showed that most of the lines were predominantly affected in nodulation by IRBG74. Interestingly, additional defects in the main root growth were observed in some mutant lines. Sequencing of LORE1 flanking regions in 47 mutants revealed that 92 Lotus genes were disrupted by novel LORE1 insertions in these lines. In the IM-S34 mutant, one of the insertions was located in the 5´UTR of the LotjaGi5g1v0179800 gene, which encodes the AUTOPHAGY9 protein. Additional mutant alleles, named atg9-2 and atg9-3, were obtained in the reverse genetic collection. Nodule formation was significantly reduced in these mutant alleles after M. loti and IRBG74 inoculation, confirming the effectiveness of the mutant screening. This study describes an effective forward genetic approach to obtain novel mutants in Lotus with a phenotype of interest and to identify the causative gene(s).
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Affiliation(s)
- Ivette García-Soto
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Elizabeth Monroy-Morales
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Mariana Robledo-Gamboa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Jesús Guadarrama
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | | | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jesús Montiel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
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3
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Ferguson S, Abel NB, Reid D, Madsen LH, Luu TB, Andersen KR, Stougaard J, Radutoiu S. A simple and efficient protocol for generating transgenic hairy roots using Agrobacterium rhizogenes. PLoS One 2023; 18:e0291680. [PMID: 37910566 PMCID: PMC10619795 DOI: 10.1371/journal.pone.0291680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/01/2023] [Indexed: 11/03/2023] Open
Abstract
For decades, Agrobacterium rhizogenes (now Rhizobium rhizogenes), the causative agent of hairy root disease, has been harnessed as an interkingdom DNA delivery tool for generating transgenic hairy roots on a wide variety of plants. One of the strategies involves the construction of transconjugant R. rhizogenes by transferring gene(s) of interest into previously constructed R. rhizogenes pBR322 acceptor strains; little has been done, however, to improve upon this system since its implementation. We developed a simplified method utilising bi-parental mating in conjunction with effective counterselection for generating R. rhizogenes transconjugants. Central to this was the construction of a new Modular Cloning (MoClo) compatible pBR322-derived integration vector (pIV101). Although this protocol remains limited to pBR322 acceptor strains, pIV101 facilitated an efficient construction of recombinant vectors, effective screening of transconjugants, and RP4-based mobilisation compatibility that enabled simplified conjugal transfer. Transconjugants from this system were tested on Lotus japonicus and found to be efficient for the transformation of transgenic hairy roots and supported infection of nodules by a rhizobia symbiont. The expedited protocol detailed herein substantially decreased both the time and labour for creating transconjugant R. rhizogenes for the subsequent transgenic hairy root transformation of Lotus, and it could readily be applied for the transformation of other plants.
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Affiliation(s)
- Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Nikolaj B. Abel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Australia
| | - Lene H. Madsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Thi-Bich Luu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kasper R. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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4
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Montiel J, García-Soto I, James EK, Reid D, Cárdenas L, Napsucialy-Mendivil S, Ferguson S, Dubrovsky JG, Stougaard J. Aromatic amino acid biosynthesis impacts root hair development and symbiotic associations in Lotus japonicus. Plant Physiol 2023; 193:1508-1526. [PMID: 37427869 PMCID: PMC10517252 DOI: 10.1093/plphys/kiad398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense strain IRBG74. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. In this study, we demonstrate that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 1 (DAHPS1), the first enzyme in the biosynthetic pathway of aromatic amino acids (AAAs), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. Two homozygous DAHPS1 mutants (dahps1-1 and dahps1-2) showed drastic alterations in root hair morphology, associated with alterations in cell wall dynamics and a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by pharmacological and genetic complementation. dahps1-1 and dahps1-2 showed significant reductions in rhizobial infection (intracellular and intercellular) and nodule organogenesis and a delay in AM colonization. RNAseq analysis of dahps1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall-related genes, and with an attenuated signaling response. Interestingly, the dahps1 mutants showed no detectable pleiotropic effects, suggesting a more selective recruitment of this gene in certain biological processes. This work provides robust evidence linking AAA metabolism to root hair development and successful symbiotic associations.
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Affiliation(s)
- Jesús Montiel
- Departamento de Genómica Funcional de Eucariotas. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
| | - Ivette García-Soto
- Departamento de Genómica Funcional de Eucariotas. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Euan K James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus DK-8000, Denmark
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5
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Kelly S, Hansen SB, Rübsam H, Saake P, Pedersen EB, Gysel K, Madland E, Wu S, Wawra S, Reid D, Sullivan JT, Blahovska Z, Vinther M, Muszynski A, Azadi P, Thygesen MB, Aachmann FL, Ronson CW, Zuccaro A, Andersen KR, Radutoiu S, Stougaard J. A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus. PLoS Biol 2023; 21:e3002127. [PMID: 37200394 DOI: 10.1371/journal.pbio.3002127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 05/31/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023] Open
Abstract
Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro, the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus. The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.
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Affiliation(s)
- Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simon B Hansen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Henriette Rübsam
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Pia Saake
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Sciences, Cologne, Germany
| | - Emil B Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eva Madland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Stephan Wawra
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Sciences, Cologne, Germany
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Zuzana Blahovska
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Maria Vinther
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Artur Muszynski
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Finn L Aachmann
- NOBIPOL (Norwegian Biopolymer Laboratory), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alga Zuccaro
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Sciences, Cologne, Germany
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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6
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Skovbjerg CK, Angra D, Robertson-Shersby-Harvie T, Kreplak J, Keeble-Gagnère G, Kaur S, Ecke W, Windhorst A, Nielsen LK, Schiemann A, Knudsen J, Gutierrez N, Tagkouli V, Fechete LI, Janss L, Stougaard J, Warsame A, Alves S, Khazaei H, Link W, Torres AM, O'Sullivan DM, Andersen SU. Genetic analysis of global faba bean diversity, agronomic traits and selection signatures. Theor Appl Genet 2023; 136:114. [PMID: 37074596 PMCID: PMC10115707 DOI: 10.1007/s00122-023-04360-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.
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Affiliation(s)
- Cathrine Kiel Skovbjerg
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark.
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | | | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Wolfgang Ecke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Alex Windhorst
- Georg-August-Universität Göttingen, DNPW, Carl-Sprengel 1, Germany
| | | | | | | | - Natalia Gutierrez
- Área de Mejora Vegetal y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo 3092, 14080, Córdoba, Spain
| | - Vasiliki Tagkouli
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Lavinia Ioana Fechete
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Ahmed Warsame
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Sheila Alves
- Crops Research, Teagasc, Oak Park, Carlow, Ireland
| | - Hamid Khazaei
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Wolfgang Link
- Georg-August-Universität Göttingen, DNPW, Carl-Sprengel 1, Germany
| | - Ana Maria Torres
- Área de Mejora Vegetal y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo 3092, 14080, Córdoba, Spain
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7
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Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature 2023; 615:652-659. [PMID: 36890232 PMCID: PMC10033403 DOI: 10.1038/s41586-023-05791-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/03/2023] [Indexed: 03/10/2023]
Abstract
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
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Affiliation(s)
- Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Agnieszka A Golicz
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Lavinia I Fechete
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Elesandro Bornhofen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, Denmark
| | - Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Raphaël Boussageon
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kwok Cheung
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Asis Hallab
- IBG-4 Bioinformatics Forschungszentrum Jülich, Jülich, Germany
- Bingen Technical University of Applied Sciences, Bingen, Germany
| | - Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | | | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Lucie Kobrlová
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Troels W Mouritzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | | | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Laura Ávila Robledillo
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | | | | | - Petri Törönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ahmed O Warsame
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Liisa U Holm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Luc L Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, Denmark
| | - Hamid Khazaei
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Córdoba, Spain
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Ana M Torres
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Área de Mejora y Biotecnología, Centro Alameda del Obispo, Córdoba, Spain
| | - Björn Usadel
- IBG-4 Bioinformatics Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Alan H Schulman
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Córdoba, Spain.
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8
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Rübsam H, Krönauer C, Abel NB, Ji H, Lironi D, Hansen SB, Nadzieja M, Kolte MV, Abel D, de Jong N, Madsen LH, Liu H, Stougaard J, Radutoiu S, Andersen KR. Nanobody-driven signaling reveals the core receptor complex in root nodule symbiosis. Science 2023; 379:272-277. [PMID: 36656954 DOI: 10.1126/science.ade9204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding the composition and activation of multicomponent receptor complexes is a challenge in biology. To address this, we developed a synthetic approach based on nanobodies to drive assembly and activation of cell surface receptors and apply the concept by manipulating receptors that govern plant symbiosis with nitrogen-fixing bacteria. We show that the Lotus japonicus Nod factor receptors NFR1 and NFR5 constitute the core receptor complex initiating the cortical root nodule organogenesis program as well as the epidermal program controlling infection. We find that organogenesis signaling is mediated by the intracellular kinase domains whereas infection requires functional ectodomains. Finally, we identify evolutionarily distant barley receptors that activate root nodule organogenesis, which could enable engineering of biological nitrogen-fixation into cereals.
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Affiliation(s)
- Henriette Rübsam
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Christina Krönauer
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Nikolaj B Abel
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Hongtao Ji
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.,National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Damiano Lironi
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Simon B Hansen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Marie V Kolte
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Dörte Abel
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Noor de Jong
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Lene H Madsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Huijun Liu
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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9
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Zarrabian M, Montiel J, Sandal N, Ferguson S, Jin H, Lin YY, Klingl V, Marín M, James EK, Parniske M, Stougaard J, Andersen SU. A Promiscuity Locus Confers Lotus burttii Nodulation with Rhizobia from Five Different Genera. Mol Plant Microbe Interact 2022; 35:1006-1017. [PMID: 35852471 DOI: 10.1094/mpmi-06-22-0124-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil-dwelling bacteria and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, in which the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity quantitative trait loci (QTL) to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for symbiont-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mohammad Zarrabian
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico. Cuernavaca, Mexico
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Yen-Yu Lin
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Verena Klingl
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Macarena Marín
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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10
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Fukai E, Yoshikawa M, Shah N, Sandal N, Miyao A, Ono S, Hirakawa H, Akyol TY, Umehara Y, Nonomura KI, Stougaard J, Hirochika H, Hayashi M, Sato S, Andersen SU, Okazaki K. Widespread and transgenerational retrotransposon activation in inter- and intraspecies recombinant inbred populations of Lotus japonicus. Plant J 2022; 111:1397-1410. [PMID: 35792830 DOI: 10.1111/tpj.15896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.
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Affiliation(s)
- Eigo Fukai
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Manabu Yoshikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Niraj Shah
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Akio Miyao
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Seijiro Ono
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Hideki Hirakawa
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Yosuke Umehara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Ken-Ichi Nonomura
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Hirohiko Hirochika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Makoto Hayashi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2, Oowashi, Tsukuba, Ibaraki, 305-8634, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Shusei Sato
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | | | - Keiichi Okazaki
- Graduate School of Science and Technology, Niigata University, Ikarashi-ninocho, 950-2181, Niigata, Japan
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11
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Quilbé J, Montiel J, Arrighi JF, Stougaard J. Molecular Mechanisms of Intercellular Rhizobial Infection: Novel Findings of an Ancient Process. Front Plant Sci 2022; 13:922982. [PMID: 35812902 PMCID: PMC9260380 DOI: 10.3389/fpls.2022.922982] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Establishment of the root-nodule symbiosis in legumes involves rhizobial infection of nodule primordia in the root cortex that is dependent on rhizobia crossing the root epidermal barrier. Two mechanisms have been described: either through root hair infection threads or through the intercellular passage of bacteria. Among the legume genera investigated, around 75% use root hair entry and around 25% the intercellular entry mode. Root-hair infection thread-mediated infection has been extensively studied in the model legumes Medicago truncatula and Lotus japonicus. In contrast, the molecular circuit recruited during intercellular infection, which is presumably an ancient and simpler pathway, remains poorly known. In recent years, important discoveries have been made to better understand the transcriptome response and the genetic components involved in legumes with obligate (Aeschynomene and Arachis spp.) and conditional (Lotus and Sesbania spp.) intercellular rhizobial infections. This review addresses these novel findings and briefly considers possible future research to shed light on the molecular players that orchestrate intercellular infection in legumes.
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Affiliation(s)
- Johan Quilbé
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Centre for Genomic Sciences, National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico
| | - Jean-François Arrighi
- IRD, Plant Health Institute of Montpellier (PHIM), UMR IRD/SupAgro/INRAE/UM/CIRAD, Montpellier, France
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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12
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Villar I, Rubio MC, Calvo-Begueria L, Pérez-Rontomé C, Larrainzar E, Wilson MT, Sandal N, Mur LA, Wang L, Reeder B, Duanmu D, Uchiumi T, Stougaard J, Becana M. Three classes of hemoglobins are required for optimal vegetative and reproductive growth of Lotus japonicus: genetic and biochemical characterization of LjGlb2-1. J Exp Bot 2021; 72:7778-7791. [PMID: 34387337 PMCID: PMC8664582 DOI: 10.1093/jxb/erab376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Legumes express two major types of hemoglobins, namely symbiotic (leghemoglobins) and non-symbiotic (phytoglobins), with the latter being categorized into three classes according to phylogeny and biochemistry. Using knockout mutants, we show that all three phytoglobin classes are required for optimal vegetative and reproductive development of Lotus japonicus. The mutants of two class 1 phytoglobins showed different phenotypes: Ljglb1-1 plants were smaller and had relatively more pods, whereas Ljglb1-2 plants had no distinctive vegetative phenotype and produced relatively fewer pods. Non-nodulated plants lacking LjGlb2-1 showed delayed growth and alterations in the leaf metabolome linked to amino acid processing, fermentative and respiratory pathways, and hormonal balance. The leaves of mutant plants accumulated salicylic acid and contained relatively less methyl jasmonic acid, suggesting crosstalk between LjGlb2-1 and the signaling pathways of both hormones. Based on the expression of LjGlb2-1 in leaves, the alterations of flowering and fruiting of nodulated Ljglb2-1 plants, the developmental and biochemical phenotypes of the mutant fed on ammonium nitrate, and the heme coordination and reactivity of the protein toward nitric oxide, we conclude that LjGlb2-1 is not a leghemoglobin but an unusual class 2 phytoglobin. For comparison, we have also characterized a close relative of LjGlb2-1 in Medicago truncatula, MtLb3, and conclude that this is an atypical leghemoglobin.
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Affiliation(s)
- Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Maria C Rubio
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Laura Calvo-Begueria
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Carmen Pérez-Rontomé
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Estibaliz Larrainzar
- Department of Sciences, Institute for Multidisciplinary Research in Applied Biology, Campus Arrosadía, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Michael T Wilson
- School of Life Sciences, Essex University, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Luis A Mur
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences, Aberystwyth, SY23 3DA, Wales, UK
| | - Longlong Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Brandon Reeder
- School of Life Sciences, Essex University, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
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13
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Björnsdotter E, Nadzieja M, Chang W, Escobar-Herrera L, Mancinotti D, Angra D, Xia X, Tacke R, Khazaei H, Crocoll C, Vandenberg A, Link W, Stoddard FL, O'Sullivan DM, Stougaard J, Schulman AH, Andersen SU, Geu-Flores F. VC1 catalyses a key step in the biosynthesis of vicine in faba bean. Nat Plants 2021; 7:923-931. [PMID: 34226693 DOI: 10.1101/2020.02.26.966523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/24/2021] [Indexed: 05/20/2023]
Abstract
Faba bean (Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds1. However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia (favism) in 400 million genetically predisposed individuals2. Here, we use gene-to-metabolite correlations, gene mapping and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1. Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.
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Affiliation(s)
- Emilie Björnsdotter
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Wei Chang
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Xinxing Xia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rebecca Tacke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Hamid Khazaei
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Wolfgang Link
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alan H Schulman
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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14
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Björnsdotter E, Nadzieja M, Chang W, Escobar-Herrera L, Mancinotti D, Angra D, Xia X, Tacke R, Khazaei H, Crocoll C, Vandenberg A, Link W, Stoddard FL, O'Sullivan DM, Stougaard J, Schulman AH, Andersen SU, Geu-Flores F. VC1 catalyses a key step in the biosynthesis of vicine in faba bean. Nat Plants 2021; 7:923-931. [PMID: 34226693 PMCID: PMC7611347 DOI: 10.1038/s41477-021-00950-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/24/2021] [Indexed: 05/05/2023]
Abstract
Faba bean (Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds1. However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia (favism) in 400 million genetically predisposed individuals2. Here, we use gene-to-metabolite correlations, gene mapping and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1. Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.
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Affiliation(s)
- Emilie Björnsdotter
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Wei Chang
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Xinxing Xia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rebecca Tacke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Hamid Khazaei
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Wolfgang Link
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alan H Schulman
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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15
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Kamal N, Mun T, Reid D, Lin JS, Akyol TY, Sandal N, Asp T, Hirakawa H, Stougaard J, Mayer KFX, Sato S, Andersen SU. Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence. DNA Res 2021; 27:5870829. [PMID: 32658273 PMCID: PMC7508351 DOI: 10.1093/dnares/dsaa015] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023] Open
Abstract
Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs. Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density. The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.
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Affiliation(s)
- Nadia Kamal
- Helmholtz Zentrum München, German Research Center for Environmental Health, Plant Genome and Systems Biology, 85764 Neuherberg, Germany
| | - Terry Mun
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jie-Shun Lin
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Turgut Yigit Akyol
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0816, Japan
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Klaus F X Mayer
- Helmholtz Zentrum München, German Research Center for Environmental Health, Plant Genome and Systems Biology, 85764 Neuherberg, Germany.,School of Life Sciences, Technical University Munich, Munich, Germany
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
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16
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Kawaharada Y, Sandal N, Gupta V, Jin H, Kawaharada M, Taniuchi M, Ruman H, Nadzieja M, Andersen KR, Schneeberger K, Stougaard J, Andersen SU. Natural variation identifies a Pxy gene controlling vascular organisation and formation of nodules and lateral roots in Lotus japonicus. New Phytol 2021; 230:2459-2473. [PMID: 33759450 DOI: 10.1111/nph.17356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Forward and reverse genetics using the model legumes Lotus japonicus and Medicago truncatula have been instrumental in identifying the essential genes governing legume-rhizobia symbiosis. However, little information is known about the effects of intraspecific variation on symbiotic signalling. Here, we use quantitative trait locus sequencing (QTL-seq) to investigate the genetic basis of the differentiated phenotypic responses shown by the Lotus accessions Gifu and MG20 to inoculation with the Mesorhizobium loti exoU mutant that produces truncated exopolysaccharides. We identified through genetic complementation the Pxy gene as a component of this differential exoU response. Lotus Pxy encodes a leucine-rich repeat receptor-like kinase similar to Arabidopsis thaliana PXY, which regulates stem vascular development. We show that Lotus pxy insertion mutants displayed defects in root and stem vascular organisation, as well as lateral root and nodule formation. Our work links Pxy to de novo organogenesis in the root, highlights the genetic overlap between regulation of lateral root and nodule formation, and demonstrates that natural variation in Pxy affects nodulation signalling.
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Affiliation(s)
- Yasuyuki Kawaharada
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Maya Kawaharada
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Makoto Taniuchi
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Hafijur Ruman
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate, Japan
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Korbinian Schneeberger
- Department for Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
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17
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Montiel J, Reid D, Grønbæk TH, Benfeldt CM, James EK, Ott T, Ditengou FA, Nadzieja M, Kelly S, Stougaard J. Distinct signaling routes mediate intercellular and intracellular rhizobial infection in Lotus japonicus. Plant Physiol 2021; 185:1131-1147. [PMID: 33793909 PMCID: PMC8133683 DOI: 10.1093/plphys/kiaa049] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 05/07/2023]
Abstract
Rhizobial infection of legume roots during the development of nitrogen-fixing root nodules can occur intracellularly, through plant-derived infection threads traversing cells, or intercellularly, via bacterial entry between epidermal plant cells. Although it is estimated that around 25% of all legume genera are intercellularly infected, the pathways and mechanisms supporting this process have remained virtually unexplored due to a lack of genetically amenable legumes that exhibit this form of infection. In this study, we report that the model legume Lotus japonicus is infected intercellularly by the IRBG74 strain, recently proposed to belong to the Agrobacterium clade of the Rhizobiaceae. We demonstrate that the resources available for L. japonicus enable insight into the genetic requirements and fine-tuning of the pathway governing intercellular infection in this species. Inoculation of L. japonicus mutants shows that Ethylene-responsive factor required for nodulation 1 (Ern1) and Leu-rich Repeat Receptor-Like Kinase (RinRK1) are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including nod factor receptor 5 (NFR5), symbiosis receptor-like kinase (SymRK), Ca2+/calmodulin dependent kinase (CCaMK), exopolysaccharide receptor 3 (Epr3), Cyclops, nodule inception (Nin), nodulation signaling pathway 1 (Nsp1), nodulation signaling pathway 2 (Nsp2), cystathionine-β-synthase (Cbs), and Vapyrin are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared with intracellular colonization. In particular, several cytokinin-related genes were differentially regulated. Corroborating this observation, cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74, whereas lhk1 cytokinin receptor mutants formed no nodules. These results indicate a differential requirement for cytokinin signaling during intercellular rhizobial entry and highlight distinct modalities of inter- and intracellular infection mechanisms in L. japonicus.
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Affiliation(s)
- Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Thomas H Grønbæk
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Caroline M Benfeldt
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas Ott
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Franck A Ditengou
- Cell Biology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark
- Author for ommunication:
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18
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Shrestha A, Zhong S, Therrien J, Huebert T, Sato S, Mun T, Andersen SU, Stougaard J, Lepage A, Niebel A, Ross L, Szczyglowski K. Lotus japonicus Nuclear Factor YA1, a nodule emergence stage-specific regulator of auxin signalling. New Phytol 2021; 229:1535-1552. [PMID: 32978812 PMCID: PMC7984406 DOI: 10.1111/nph.16950] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/05/2020] [Indexed: 05/07/2023]
Abstract
Organogenesis of legume root nodules begins with the nodulation factor-dependent stimulation of compatible root cells to initiate divisions, signifying an early nodule primordium formation event. This is followed by cellular differentiation, including cell expansion and vascular bundle formation, and we previously showed that Lotus japonicus NF-YA1 is essential for this process, presumably by regulating three members of the SHORT INTERNODES/STYLISH (STY) transcription factor gene family. In this study, we used combined genetics, genomics and cell biology approaches to characterize the role of STY genes during root nodule formation and to test a hypothesis that they mediate nodule development by stimulating auxin signalling. We show here that L. japonicus STYs are required for nodule emergence. This is attributed to the NF-YA1-dependent regulatory cascade, comprising STY genes and their downstream targets, YUCCA1 and YUCCA11, involved in a local auxin biosynthesis at the post-initial cell division stage. An analogous NF-YA1/STY regulatory module seems to operate in Medicago truncatula in association with the indeterminate nodule patterning. Our data define L. japonicus and M. truncatula NF-YA1 genes as important nodule emergence stage-specific regulators of auxin signalling while indicating that the inductive stage and subsequent formation of early nodule primordia are mediated through an independent mechanism(s).
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Affiliation(s)
- Arina Shrestha
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Sihui Zhong
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Jasmine Therrien
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
| | - Terry Huebert
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Shusei Sato
- Graduate School of Life SciencesTohoku University2‐1‐1 KatahiraSendai980‐8577Japan
| | - Terry Mun
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Stig U. Andersen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDK‐8000Denmark
| | - Agnes Lepage
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Andreas Niebel
- Laboratoire des Interactions Plantes‐Microorganismes (LIPM)Université de Toulouse, Institut National de la Recherche pour l’Agriculturel’Alimentation et l’Environnement (INRAE)Centre National de la Recherche Scientifique (CNRS)Castanet‐Tolosan31326France
| | - Loretta Ross
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
| | - Krzysztof Szczyglowski
- Agriculture and Agri‐Food CanadaLondon Research and Development CentreLondonONN5V 4T3Canada
- Department of BiologyUniversity of Western OntarioLondonONN6A 5BFCanada
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19
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Bozsoki Z, Gysel K, Hansen SB, Lironi D, Krönauer C, Feng F, de Jong N, Vinther M, Kamble M, Thygesen MB, Engholm E, Kofoed C, Fort S, Sullivan JT, Ronson CW, Jensen KJ, Blaise M, Oldroyd G, Stougaard J, Andersen KR, Radutoiu S. Ligand-recognizing motifs in plant LysM
receptors are major determinants of
specificity. Science 2020; 369:663-670. [DOI: 10.1126/science.abb3377] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/12/2020] [Indexed: 01/02/2023]
Abstract
Plants evolved lysine motif (LysM)
receptors to recognize and parse microbial
elicitors and drive intracellular signaling to
limit or facilitate microbial colonization. We
investigated how chitin and nodulation (Nod)
factor receptors of Lotus
japonicus initiate differential
signaling of immunity or root nodule symbiosis.
Two motifs in the LysM1 domains of these receptors
determine specific recognition of ligands and
discriminate between their in planta functions.
These motifs define the ligand-binding site and
make up the most structurally divergent regions in
cognate Nod factor receptors. An adjacent motif
modulates the specificity for Nod factor
recognition and determines the selection of
compatible rhizobial symbionts in legumes. We also
identified how binding specificities in LysM
receptors can be altered to facilitate Nod factor
recognition and signaling from a chitin receptor,
advancing the prospects of engineering rhizobial
symbiosis into nonlegumes.
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Affiliation(s)
- Zoltan Bozsoki
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Simon B. Hansen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Damiano Lironi
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Christina Krönauer
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Feng Feng
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Noor de Jong
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Maria Vinther
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Manoj Kamble
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Mikkel B. Thygesen
- Department of Chemistry, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Ebbe Engholm
- Department of Chemistry, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Christian Kofoed
- Department of Chemistry, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Sébastien Fort
- Université Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - John T. Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Clive W. Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Knud J. Jensen
- Department of Chemistry, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Mickaël Blaise
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Giles Oldroyd
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper R. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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20
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Wong JEMM, Gysel K, Birkefeldt TG, Vinther M, Muszyński A, Azadi P, Laursen NS, Sullivan JT, Ronson CW, Stougaard J, Andersen KR. Structural signatures in EPR3 define a unique class of plant carbohydrate receptors. Nat Commun 2020; 11:3797. [PMID: 32732998 PMCID: PMC7392887 DOI: 10.1038/s41467-020-17568-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/05/2020] [Indexed: 11/21/2022] Open
Abstract
Receptor-mediated perception of surface-exposed carbohydrates like lipo- and exo-polysaccharides (EPS) is important for non-self recognition and responses to microbial associated molecular patterns in mammals and plants. In legumes, EPS are monitored and can either block or promote symbiosis with rhizobia depending on their molecular composition. To establish a deeper understanding of receptors involved in EPS recognition, we determined the structure of the Lotus japonicus (Lotus) exopolysaccharide receptor 3 (EPR3) ectodomain. EPR3 forms a compact structure built of three putative carbohydrate-binding modules (M1, M2 and LysM3). M1 and M2 have unique βαββ and βαβ folds that have not previously been observed in carbohydrate binding proteins, while LysM3 has a canonical βααβ fold. We demonstrate that this configuration is a structural signature for a ubiquitous class of receptors in the plant kingdom. We show that EPR3 is promiscuous, suggesting that plants can monitor complex microbial communities though this class of receptors. Exopolysaccharides (EPS) are perceived by legumes and regulate symbiosis with rhizobia. Here the authors describe the structure of the Lotus EPS receptor, EPR3 and show that it has atypical βαββ and βαβ folds that represent a structural signature for a unique class of EPS receptors in the plant kingdom.
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Affiliation(s)
- Jaslyn E M M Wong
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.,MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Thea G Birkefeldt
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Maria Vinther
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Nick S Laursen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.
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21
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Matamoros MA, Cutrona MC, Wienkoop S, Begara-Morales JC, Sandal N, Orera I, Barroso JB, Stougaard J, Becana M. Altered Plant and Nodule Development and Protein S-Nitrosylation in Lotus japonicus Mutants Deficient in S-Nitrosoglutathione Reductases. Plant Cell Physiol 2020; 61:105-117. [PMID: 31529085 DOI: 10.1093/pcp/pcz182] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/08/2019] [Indexed: 05/11/2023]
Abstract
Nitric oxide (NO) is a crucial signaling molecule that conveys its bioactivity mainly through protein S-nitrosylation. This is a reversible post-translational modification (PTM) that may affect protein function. S-nitrosoglutathione (GSNO) is a cellular NO reservoir and NO donor in protein S-nitrosylation. The enzyme S-nitrosoglutathione reductase (GSNOR) degrades GSNO, thereby regulating indirectly signaling cascades associated with this PTM. Here, the two GSNORs of the legume Lotus japonicus, LjGSNOR1 and LjGSNOR2, have been functionally characterized. The LjGSNOR1 gene is very active in leaves and roots, whereas LjGSNOR2 is highly expressed in nodules. The enzyme activities are regulated in vitro by redox-based PTMs. Reducing conditions and hydrogen sulfide-mediated cysteine persulfidation induced both activities, whereas cysteine oxidation or glutathionylation inhibited them. Ljgsnor1 knockout mutants contained higher levels of S-nitrosothiols. Affinity chromatography and subsequent shotgun proteomics allowed us to identify 19 proteins that are differentially S-nitrosylated in the mutant and the wild-type. These include proteins involved in biotic stress, protein degradation, antioxidant protection and photosynthesis. We propose that, in the mutant plants, deregulated protein S-nitrosylation contributes to developmental alterations, such as growth inhibition, impaired nodulation and delayed flowering and fruiting. Our results highlight the importance of GSNOR function in legume biology.
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Affiliation(s)
- Manuel A Matamoros
- Departamento de Nutrici�n Vegetal, Estaci�n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient�ficas, Apartado 13034, 50080 Zaragoza, Spain
| | - Maria C Cutrona
- Departamento de Nutrici�n Vegetal, Estaci�n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient�ficas, Apartado 13034, 50080 Zaragoza, Spain
| | - Stefanie Wienkoop
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna 1090, Austria
| | - Juan C Begara-Morales
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Faculty of Experimental Sciences, Center for Advanced Studies in Olive Grove and Olive Oils, Campus Universitario "Las Lagunillas", University of Ja�n, 23071 Ja�n, Spain
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Irene Orera
- Proteomics Unit, Centro Investigaciones Biom�dicas de Arag�n, Instituto Aragon�s de Ciencias de la Salud, 50059 Zaragoza, Spain
| | - Juan B Barroso
- Group of Biochemistry and Cell Signaling in Nitric Oxide, Department of Experimental Biology, Faculty of Experimental Sciences, Center for Advanced Studies in Olive Grove and Olive Oils, Campus Universitario "Las Lagunillas", University of Ja�n, 23071 Ja�n, Spain
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Manuel Becana
- Departamento de Nutrici�n Vegetal, Estaci�n Experimental de Aula Dei, Consejo Superior de Investigaciones Cient�ficas, Apartado 13034, 50080 Zaragoza, Spain
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22
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Feike D, Korolev AV, Soumpourou E, Murakami E, Reid D, Breakspear A, Rogers C, Radutoiu S, Stougaard J, Harwood WA, Oldroyd GED, Miller J. Characterizing standard genetic parts and establishing common principles for engineering legume and cereal roots. Plant Biotechnol J 2019; 17:2234-2245. [PMID: 31022324 PMCID: PMC6835126 DOI: 10.1111/pbi.13135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 04/18/2019] [Indexed: 05/20/2023]
Abstract
Plant synthetic biology and cereal engineering depend on the controlled expression of transgenes of interest. Most engineering in plant species to date has relied heavily on the use of a few, well-established constitutive promoters to achieve high levels of expression; however, the levels of transgene expression can also be influenced by the use of codon optimization, intron-mediated enhancement and varying terminator sequences. Most of these alternative approaches for regulating transgene expression have only been tested in small-scale experiments, typically testing a single gene of interest. It is therefore difficult to interpret the relative importance of these approaches and to design engineering strategies that are likely to succeed in different plant species, particularly if engineering multigenic traits where the expression of each transgene needs to be precisely regulated. Here, we present data on the characterization of 46 promoters and 10 terminators in Medicago truncatula, Lotus japonicus, Nicotiana benthamiana and Hordeum vulgare, as well as the effects of codon optimization and intron-mediated enhancement on the expression of two transgenes in H. vulgare. We have identified a core set of promoters and terminators of relevance to researchers engineering novel traits in plant roots. In addition, we have shown that combining codon optimization and intron-mediated enhancement increases transgene expression and protein levels in barley. Based on our study, we recommend a core set of promoters and terminators for broad use and also propose a general set of principles and guidelines for those engineering cereal species.
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Affiliation(s)
- Doreen Feike
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
EMBL HeidelbergMeyerhofstraße 169117HeidelbergGermany
| | | | - Eleni Soumpourou
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Sainsbury LaboratoryUniversity of Cambridge47 Bateman StreetCambridgeCB2 1LRUK
| | - Eiichi Murakami
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
- Present address:
GRA&GREEN Inc., Incubation Center 106Nagoya UniversityFuro‐cho, Chikusa‐kuNagoya464‐0814Japan
| | - Dugald Reid
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Christian Rogers
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Sainsbury LaboratoryUniversity of Cambridge47 Bateman StreetCambridgeCB2 1LRUK
| | - Simona Radutoiu
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Jens Stougaard
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | | | - Giles E. D. Oldroyd
- John Innes CentreNorwich Research ParkNorwichUK
- Present address:
Sainsbury LaboratoryUniversity of Cambridge47 Bateman StreetCambridgeCB2 1LRUK
| | - J. Benjamin Miller
- John Innes CentreNorwich Research ParkNorwichUK
- School of Biological SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
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23
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Feng F, Sun J, Radhakrishnan GV, Lee T, Bozsóki Z, Fort S, Gavrin A, Gysel K, Thygesen MB, Andersen KR, Radutoiu S, Stougaard J, Oldroyd GED. A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula. Nat Commun 2019; 10:5047. [PMID: 31695035 PMCID: PMC6834629 DOI: 10.1038/s41467-019-12999-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/03/2019] [Indexed: 12/02/2022] Open
Abstract
Plants associate with beneficial arbuscular mycorrhizal fungi facilitating nutrient acquisition. Arbuscular mycorrhizal fungi produce chitooligosaccharides (COs) and lipo-chitooligosaccharides (LCOs), that promote symbiosis signalling with resultant oscillations in nuclear-associated calcium. The activation of symbiosis signalling must be balanced with activation of immunity signalling, which in fungal interactions is promoted by COs resulting from the chitinaceous fungal cell wall. Here we demonstrate that COs ranging from CO4-CO8 can induce symbiosis signalling in Medicago truncatula. CO perception is a function of the receptor-like kinases MtCERK1 and LYR4, that activate both immunity and symbiosis signalling. A combination of LCOs and COs act synergistically to enhance symbiosis signalling and suppress immunity signalling and receptors involved in both CO and LCO perception are necessary for mycorrhizal establishment. We conclude that LCOs, when present in a mix with COs, drive a symbiotic outcome and this mix of signals is essential for arbuscular mycorrhizal establishment.
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Affiliation(s)
- Feng Feng
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Jongho Sun
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Guru V Radhakrishnan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Tak Lee
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Zoltán Bozsóki
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000 C, Denmark
| | - Sébastien Fort
- Université de Grenoble Alpes, CNRS, CERMAV, 38000, Grenoble, France
| | - Aleksander Gavrin
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000 C, Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Frederiksberg, 1871 C, Denmark
| | | | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000 C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000 C, Denmark
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK.
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24
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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 Physiol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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25
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Wong JEMM, Nadzieja M, Madsen LH, Bücherl CA, Dam S, Sandal NN, Couto D, Derbyshire P, Uldum-Berentsen M, Schroeder S, Schwämmle V, Nogueira FCS, Asmussen MH, Thirup S, Radutoiu S, Blaise M, Andersen KR, Menke FLH, Zipfel C, Stougaard J. A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A 2019; 116:14339-14348. [PMID: 31239345 PMCID: PMC6628658 DOI: 10.1073/pnas.1815425116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The establishment of nitrogen-fixing root nodules in legume-rhizobia symbiosis requires an intricate communication between the host plant and its symbiont. We are, however, limited in our understanding of the symbiosis signaling process. In particular, how membrane-localized receptors of legumes activate signal transduction following perception of rhizobial signaling molecules has mostly remained elusive. To address this, we performed a coimmunoprecipitation-based proteomics screen to identify proteins associated with Nod factor receptor 5 (NFR5) in Lotus japonicus. Out of 51 NFR5-associated proteins, we focused on a receptor-like cytoplasmic kinase (RLCK), which we named NFR5-interacting cytoplasmic kinase 4 (NiCK4). NiCK4 associates with heterologously expressed NFR5 in Nicotiana benthamiana, and directly binds and phosphorylates the cytoplasmic domains of NFR5 and NFR1 in vitro. At the cellular level, Nick4 is coexpressed with Nfr5 in root hairs and nodule cells, and the NiCK4 protein relocates to the nucleus in an NFR5/NFR1-dependent manner upon Nod factor treatment. Phenotyping of retrotransposon insertion mutants revealed that NiCK4 promotes nodule organogenesis. Together, these results suggest that the identified RLCK, NiCK4, acts as a component of the Nod factor signaling pathway downstream of NFR5.
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Affiliation(s)
- Jaslyn E M M Wong
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lene H Madsen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Christoph A Bücherl
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Svend Dam
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Niels N Sandal
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Daniel Couto
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Mette Uldum-Berentsen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Sina Schroeder
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Fábio C S Nogueira
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Mette H Asmussen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Søren Thirup
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Mickaël Blaise
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark;
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26
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Acosta-Jurado S, Rodríguez-Navarro DN, Kawaharada Y, Rodríguez-Carvajal MA, Gil-Serrano A, Soria-Díaz ME, Pérez-Montaño F, Fernández-Perea J, Niu Y, Alias-Villegas C, Jiménez-Guerrero I, Navarro-Gómez P, López-Baena FJ, Kelly S, Sandal N, Stougaard J, Ruiz-Sainz JE, Vinardell JM. Sinorhizobium fredii HH103 nolR and nodD2 mutants gain capacity for infection thread invasion of Lotus japonicus Gifu and Lotus burttii. Environ Microbiol 2019; 21:1718-1739. [PMID: 30839140 DOI: 10.1111/1462-2920.14584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 02/01/2023]
Abstract
Sinorhizobium fredii HH103 RifR , a broad-host-range rhizobial strain, forms ineffective nodules with Lotus japonicus but induces nitrogen-fixing nodules in Lotus burttii roots that are infected by intercellular entry. Here we show that HH103 RifR nolR or nodD2 mutants gain the ability to induce infection thread formation and to form nitrogen-fixing nodules in L. japonicus Gifu. Microscopy studies showed that the mode of infection of L. burttii roots by the nodD2 and nolR mutants switched from intercellular entry to infection threads (ITs). In the presence of the isoflavone genistein, both mutants overproduced Nod-factors. Transcriptomic analyses showed that, in the presence of Lotus japonicus Gifu root exudates, genes related to Nod factors production were overexpressed in both mutants in comparison to HH103 RifR . Complementation of the nodD2 and nolR mutants provoked a decrease in Nod-factor production, the incapacity to form nitrogen-fixing nodules with L. japonicus Gifu and restored the intercellular way of infection in L. burttii. Thus, the capacity of S. fredii HH103 RifR nodD2 and nolR mutants to infect L. burttii and L. japonicus Gifu by ITs and fix nitrogen L. japonicus Gifu might be correlated with Nod-factor overproduction, although other bacterial symbiotic signals could also be involved.
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Affiliation(s)
- Sebastián Acosta-Jurado
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | | | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus, CDK-8000, Denmark.,Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate, 020-8550, Japan
| | - Miguel A Rodríguez-Carvajal
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P, 41012, Sevilla, Spain
| | - Antonio Gil-Serrano
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P, 41012, Sevilla, Spain
| | - María E Soria-Díaz
- Servicio de Espectrometría de Masas, Centro de Investigación, Tecnología e Innovación (CITIUS), Universidad de Sevilla, Sevilla, Spain
| | - Francisco Pérez-Montaño
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | - Juan Fernández-Perea
- IFAPA, Centro Las Torres-Tomejil, Apartado Oficial 41200, Alcalá del Río, Sevilla, Spain
| | - Yanbo Niu
- Department of Resources and Environmental Microbiology, Institute of Microbiology, Heilongjiang Academy of Sciences, No. 68, Zhaolin Street, Daoli District, Harbin, Heilongjiang Province, China
| | - Cynthia Alias-Villegas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | - Irene Jiménez-Guerrero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | - Pilar Navarro-Gómez
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | - Francisco Javier López-Baena
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus, CDK-8000, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus, CDK-8000, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus, CDK-8000, Denmark
| | - José E Ruiz-Sainz
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
| | - José-María Vinardell
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P., 41012, Sevilla, Spain
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27
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Koch BEV, Yang S, Lamers G, Stougaard J, Spaink HP. Author Correction: Intestinal microbiome adjusts the innate immune setpoint during colonization through negative regulation of MyD88. Nat Commun 2019; 10:526. [PMID: 30692545 PMCID: PMC6349902 DOI: 10.1038/s41467-019-08456-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Bjørn E V Koch
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.,Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Shuxin Yang
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.,Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Gerda Lamers
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Herman P Spaink
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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28
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Nadzieja M, Stougaard J, Reid D. A Toolkit for High Resolution Imaging of Cell Division and Phytohormone Signaling in Legume Roots and Root Nodules. Front Plant Sci 2019; 10:1000. [PMID: 31428118 PMCID: PMC6688427 DOI: 10.3389/fpls.2019.01000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/17/2019] [Indexed: 05/22/2023]
Abstract
Legume plants benefit from a nitrogen-fixing symbiosis in association with rhizobia hosted in specialized root nodules. Formation of root nodules is initiated by de novo organogenesis and coordinated infection of these developing lateral root organs by rhizobia. Both bacterial infection and nodule organogenesis involve cell cycle activation and regulation by auxin and cytokinin is tightly integrated in the process. To characterize the hormone dynamics and cell division patterns with cellular resolution during nodulation, sensitive and specific sensors suited for imaging of multicellular tissues are required. Here we report a modular toolkit, optimized in the model legume Lotus japonicus, for use in legume roots and root nodules. This toolkit includes synthetic transcriptional reporters for auxin and cytokinin, auxin accumulation sensors and cell cycle progression markers optimized for fluorescent and bright field microscopy. The developed vectors allow for efficient one-step assembly of multiple units using the GoldenGate cloning system. Applied together with a fluorescence-compatible clearing approach, these reporters improve imaging depth and facilitate fluorescence examination in legume roots. We additionally evaluate the utility of the dynamic gravitropic root response in altering the timing and location of auxin accumulation and nodule emergence. We show that alteration of auxin distribution in roots allows for preferential nodule emergence at the outer side of the bend corresponding to a region of high auxin signaling capacity. The presented tools and procedures open new possibilities for comparative mutant studies and for developing a more comprehensive understanding of legume-rhizobia interactions.
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29
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Liu H, Sandal N, Andersen KR, James EK, Stougaard J, Kelly S, Kawaharada Y. A genetic screen for plant mutants with altered nodulation phenotypes in response to rhizobial glycan mutants. New Phytol 2018; 220:526-538. [PMID: 29959893 DOI: 10.1111/nph.15293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/24/2018] [Indexed: 05/08/2023]
Abstract
Nodule primordia induced by rhizobial glycan mutants often remain uninfected. To identify processes involved in infection and organogenesis we used forward genetics to identify plant genes involved in perception and responses to bacterial glycans. To dissect the mechanisms underlying the negative plant responses to the Mesorhizobium loti R7AexoU and ML001cep mutants, a screen for genetic suppressors of the nodulation phenotypes was performed on a chemically mutagenized Lotus population. Two mutant lines formed infected nitrogen-fixing pink nodules, while five mutant lines developed uninfected large white nodules, presumably altered in processes controlling organogenesis. Genetic mapping identified a mutation in the cytokinin receptor Lhk1 resulting in an alanine to valine substitution adjacent to a coiled-coil motif in the juxta-membrane region of LHK1. This results in a spontaneous nodulation phenotype and increased ethylene production. The allele was renamed snf5, and segregation studies of snf5 together with complementation studies suggest that snf5 is a gain-of-function allele. This forward genetic approach to investigate the role of glycans in the pathway synchronizing infection and organogenesis shows that a combination of plant and bacterial genetics opens new possibilities to study glycan responses in plants as well as identification of mutant alleles affecting nodule organogenesis.
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Affiliation(s)
- Huijun Liu
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3-18-8-Ueda, Morioka, Iwate, Japan
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30
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Tsikou D, Yan Z, Holt DB, Abel NB, Reid DE, Madsen LH, Bhasin H, Sexauer M, Stougaard J, Markmann K. Systemic control of legume susceptibility to rhizobial infection by a mobile microRNA. Science 2018; 362:233-236. [PMID: 30166437 DOI: 10.1126/science.aat6907] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/21/2018] [Indexed: 12/30/2022]
Abstract
Nitrogen-fixing root nodules on legumes result from two developmental processes, bacterial infection and nodule organogenesis. To balance symbiosis and plant growth, legume hosts restrict nodule numbers through an inducible autoregulatory process. Here, we present a mechanism where repression of a negative regulator ensures symbiotic susceptibility of uninfected roots of the host Lotus japonicus We show that microRNA miR2111 undergoes shoot-to-root translocation to control rhizobial infection through posttranscriptional regulation of the symbiosis suppressor TOO MUCH LOVE in roots. miR2111 maintains a susceptible default status in uninfected hosts and functions as an activator of symbiosis downstream of LOTUS HISTIDINE KINASE1-mediated cytokinin perception in roots and HYPERNODULATION ABERRANT ROOT FORMATION1, a shoot factor in autoregulation. The miR2111-TML node ensures activation of feedback regulation to balance infection and nodulation events.
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Affiliation(s)
- Daniela Tsikou
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Zhe Yan
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dennis B Holt
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Nikolaj B Abel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dugald E Reid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lene H Madsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Hemal Bhasin
- Zentrum für Molekularbiologie der Pflanzen, Tübingen University, Tübingen, Germany
| | - Moritz Sexauer
- Zentrum für Molekularbiologie der Pflanzen, Tübingen University, Tübingen, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katharina Markmann
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark. .,Zentrum für Molekularbiologie der Pflanzen, Tübingen University, Tübingen, Germany
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31
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Nadzieja M, Kelly S, Stougaard J, Reid D. Epidermal auxin biosynthesis facilitates rhizobial infection in Lotus japonicus. Plant J 2018; 95:101-111. [PMID: 29676826 DOI: 10.1111/tpj.13934] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/29/2018] [Accepted: 04/05/2018] [Indexed: 05/08/2023]
Abstract
Symbiotic nitrogen fixation in legumes requires nodule organogenesis to be coordinated with infection by rhizobia. The plant hormone auxin influences symbiotic infection, but the precise timing of auxin accumulation and the genetic network governing it remain unclear. We used a Lotus japonicus optimised variant of the DII-based auxin accumulation sensor and identified a rapid accumulation of auxin in the epidermis, specifically in the root hair cells. This auxin accumulation occurs in the infected root hairs during rhizobia invasion, while Nod factor application induces this response across a broader range of root hairs. Using the DR5 auxin responsive promoter, we demonstrate that activation of auxin signalling also occurs specifically in infected root hairs. Analysis of root hair transcriptome data identified induction of an auxin biosynthesis gene of the Tryptophan Amino-transferase Related (LjTar1) family following both bacteria inoculation and Nod factor treatment. Genetic analysis showed that both expression of the LjTar1 biosynthesis gene and the auxin response requires Nod factor perception, while common symbiotic pathway transcription factors are only partially required or act redundantly to initiate auxin accumulation. Using a chemical genetics approach, we confirmed that auxin biosynthesis has a functional role in promoting symbiotic infection events in the epidermis.
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Affiliation(s)
- Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
| | - Dugald Reid
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C, 8000, Denmark
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Murakami E, Cheng J, Gysel K, Bozsoki Z, Kawaharada Y, Hjuler CT, Sørensen KK, Tao K, Kelly S, Venice F, Genre A, Thygesen MB, Jong ND, 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; 7:33506. [PMID: 29957177 PMCID: PMC6025957 DOI: 10.7554/elife.33506] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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. Microbes – whether beneficial or harmful – play an important role in all organisms, including plants. The ability to monitor the surrounding microbes is therefore crucial for the survival of a species. For example, the roots of a soil-growing plant are surrounded by a microbial-rich environment and have therefore evolved sophisticated surveillance mechanisms. Unlike most other plants, legumes, such as beans, peas or lentils, are capable of growing in nitrogen-poor soils with the help of microbes. In a mutually beneficial process called root nodule symbiosis, legumes form a new organ called the nodule, where specific soil bacteria called rhizobia are hosted. Inside the nodule, rhizobia convert atmospheric dinitrogen into ammonium and provide it to the plant, which in turn supplies the bacteria with carbon resources. The interaction between the legume plants and rhizobia is very selective. Previous research has shown that plants are able to identify specific signaling molecules produced by these bacteria. One signal in particular, called the Nod factor, is crucial for establishing the relationship between these two organisms. To do so, the legumes use specific receptor proteins that can recognize the Nod factor molecules produced by bacteria. Two well-known Nod factor receptors, NFR1 and NFR5, belong to a large family of proteins, which suggests that other similar receptors may be involved in Nod factor signaling as well. Now, Murakami et al. identified the role of another receptor called NRFe by studying the legume species Lotus japonicus. The results showed that NFRe and NFR1 share distinct biochemical and molecular properties. NRFe is primarily active in the cells located in a specific area on the surface of the roots. Unlike NFR1, however, NFRe has a restricted signaling capacity limited to the outer root cell layer. Murakami et al. found that when NRFe was mutated, the Nod factor signaling inside the root was less activated and fewer nodules formed, suggesting NRFe plays an important role in this symbiosis. NFR1-type receptors have also been found in plants outside legumes, which do not form a symbiotic relationship with rhizobia. Identifying more receptors important for Nod-factor signaling could provide a basis for new biotechnological targets in non-symbiotic crops, to improve their growth in nutrient-poor conditions.
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Affiliation(s)
- Eiichi Murakami
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jeryl Cheng
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Zoltan Bozsoki
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Ke Tao
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Francesco Venice
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | - Noor de Jong
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Maria Vinther
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dorthe Bødker Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Knud Jørgen Jensen
- Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Michael Blaise
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lene Heegaard Madsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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Muszyński A, Heiss C, Hjuler CT, Sullivan JT, Kelly SJ, Thygesen MB, Stougaard J, Azadi P, Carlson RW, Ronson CW. Structures of exopolysaccharides involved in receptor-mediated perception of Mesorhizobium loti by Lotus japonicus. J Biol Chem 2018; 293:5376. [DOI: 10.1074/jbc.aac118.002877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Reid D, Liu H, Kelly S, Kawaharada Y, Mun T, Andersen SU, Desbrosses G, Stougaard J. Dynamics of Ethylene Production in Response to Compatible Nod Factor. Plant Physiol 2018; 176:1764-1772. [PMID: 29187569 PMCID: PMC5813561 DOI: 10.1104/pp.17.01371] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/28/2017] [Indexed: 05/22/2023]
Abstract
Establishment of symbiotic nitrogen-fixation in legumes is regulated by the plant hormone ethylene, but it has remained unclear whether and how its biosynthesis is regulated by the symbiotic pathway. We established a sensitive ethylene detection system for Lotus japonicus and found that ethylene production increased as early as 6 hours after inoculation with Mesorhizobium loti This ethylene response was dependent on Nod factor production by compatible rhizobia. Analyses of nodulation mutants showed that perception of Nod factor was required for ethylene emission, while downstream transcription factors including CYCLOPS, NIN, and ERN1 were not required for this response. Activation of the nodulation signaling pathway in spontaneously nodulating mutants was also sufficient to elevate ethylene production. Ethylene signaling is controlled by EIN2, which is duplicated in L. japonicus We obtained a L. japonicus Ljein2a Ljein2b double mutant that exhibits complete ethylene insensitivity and confirms that these two genes act redundantly in ethylene signaling. Consistent with this redundancy, both LjEin2a and LjEin2b are required for negative regulation of nodulation and Ljein2a Ljein2b double mutants are hypernodulating and hyperinfected. We also identified an unexpected role for ethylene in the onset of nitrogen fixation, with the Ljein2a Ljein2b double mutant showing severely reduced nitrogen fixation. These results demonstrate that ethylene production is an early and sustained nodulation response that acts at multiple stages to regulate infection, nodule organogenesis, and nitrogen fixation in L. japonicus.
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Affiliation(s)
- Dugald Reid
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Huijun Liu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Simon Kelly
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Yasuyuki Kawaharada
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Terry Mun
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Stig U Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Guilhem Desbrosses
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Université Montpellier 2, IRD, CIRAD, SupAgro, INRA Montpellier Cedex 05 France
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
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Kelly S, Sullivan JT, Kawaharada Y, Radutoiu S, Ronson CW, Stougaard J. Regulation of Nod factor biosynthesis by alternative NodD proteins at distinct stages of symbiosis provides additional compatibility scrutiny. Environ Microbiol 2018; 20:97-110. [PMID: 29194913 DOI: 10.1111/1462-2920.14006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/07/2017] [Accepted: 11/14/2017] [Indexed: 01/18/2023]
Abstract
The Lotus japonicus symbiont Mesorhizobium loti R7A encodes two copies of nodD and here we identify striking differences in Nod factor biosynthesis gene induction by NodD1 and NodD2 both in vitro and in planta. We demonstrate that induction of Nod factor biosynthesis genes is preferentially controlled by NodD1 and NodD2 at specific stages of symbiotic infection. NodD2 is primarily responsible for induction in the rhizosphere and within nodules, while NodD1 is primarily responsible for induction within root hair infection threads. nodD1 and nodD2 mutants showed significant symbiotic phenotypes and competition studies establish that nodD1 and nodD2 mutants were severely outcompeted by wild-type R7A, indicating that both proteins are required for proficient symbiotic infection. These results suggest preferential activation of NodD1 and NodD2 by different inducing compounds produced at defined stages of symbiotic infection. We identified Lotus chalcone isomerase CHI4 as a root hair induced candidate involved in the biosynthesis of an inducer compound that may be preferentially recognized by NodD1 within root hair infection threads. We propose an alternative explanation for the function of multiple copies of nodD that provides the host plant with another level of compatibility scrutiny at the stage of infection thread development.
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Affiliation(s)
- Simon Kelly
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Aarhus 8000 C, Denmark
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Kelly S, Mun T, Stougaard J, Ben C, Andersen SU. Distinct Lotus japonicus Transcriptomic Responses to a Spectrum of Bacteria Ranging From Symbiotic to Pathogenic. Front Plant Sci 2018; 9:1218. [PMID: 30177945 PMCID: PMC6110179 DOI: 10.3389/fpls.2018.01218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/30/2018] [Indexed: 05/12/2023]
Abstract
Lotus japonicus is a well-studied nodulating legume and a model organism for the investigation of plant-microbe interactions. The majority of legume transcriptome studies have focused on interactions with compatible symbionts, whereas responses to non-adapted rhizobia and pathogenic bacteria have not been well-characterized. In this study, we first characterized the transcriptomic response of L. japonicus to its compatible symbiont, Mesorhizobium loti R7A, through RNA-seq analysis of various plant tissues. Early symbiotic signaling was largely Nod factor-dependent and enhanced within root hairs, and we observed large-scale transcriptional reprogramming in nodule primordia and mature nitrogen-fixing nodules. We then characterized root transcriptional responses to a spectrum of L. japonicus interacting bacteria ranging from semi-compatible symbionts to pathogens. M. loti R7A and the semi-compatible strain Sinorhizobium fredii HH103 showed remarkably similar responses, allowing us to identify a small number of genes potentially involved in differentiating between fully and semi-compatible symbionts. The incompatible symbiont Bradyrhizobium elkanii USDA61 induced a more attenuated response, but the weakest response was observed for the foliar pathogen Pseudomonas syringae pv. tomato DC3000, where the affected genes also responded to other tested bacteria, pointing to a small set of common bacterial response genes. In contrast, the root pathogen Ralstonia solanacearum JS763 induced a pronounced and distinct transcriptomic pathogen response, which we compared to the results of the other treatments. This comparative analysis did not support the concept that an early defense-like response is generally evoked by compatible rhizobia during establishment of symbiosis.
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Affiliation(s)
- Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Terry Mun
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cécile Ben
- ECOLAB, Université de Toulouse, CNRS, INP, UPS, Toulouse, France
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- *Correspondence: Stig U. Andersen,
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Fuechtbauer W, Yunusov T, Bozsóki Z, Gavrin A, James EK, Stougaard J, Schornack S, Radutoiu S. LYS12 LysM receptor decelerates Phytophthora palmivora disease progression in Lotus japonicus. Plant J 2018; 93:297-310. [PMID: 29171909 DOI: 10.1111/tpj.13785] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/31/2017] [Accepted: 11/03/2017] [Indexed: 05/19/2023]
Abstract
Phytophthora palmivora is a devastating oomycete plant pathogen. We found that P. palmivora induces disease in Lotus japonicus and used this interaction to identify cellular and molecular events in response to this oomycete, which has a broad host range. Transcript quantification revealed that Lys12 was highly and rapidly induced during P. palmivora infection. Mutants of Lys12 displayed accelerated disease progression, earlier plant death and a lower level of defence gene expression than the wild type, while the defence program after chitin, laminarin, oligogalacturonide or flg22 treatment and the root symbioses with nitrogen-fixing rhizobia and arbuscular mycorrhiza were similar to the wild type. On the microbial side, we found that P. palmivora encodes an active chitin synthase-like protein, and mycelial growth is impaired after treatment with a chitin-synthase inhibitor. However, wheat germ agglutinin-detectable N-acetyl-glucosamine (GlcNAc) epitopes were not identified when the oomycete was grown in vitro or while infecting the roots. This indicates that conventional GlcNAc-mers are unlikely to be produced and/or accumulate in P. palmivora cell walls and that LYS12 might perceive an unknown carbohydrate. The impact of Lys12 on progression of root rot disease, together with the finding that similar genes are present in other P. palmivora hosts, suggests that LYS12 might mediate a common early response to this pathogen.
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Affiliation(s)
- Winnie Fuechtbauer
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Temur Yunusov
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Zoltán Bozsóki
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Aleksandr Gavrin
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge, CB2 1LR, UK
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus, Denmark
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Hjuler CT, Maolanon NN, Sauer J, Stougaard J, Thygesen MB, Jensen KJ. Preparation of glycoconjugates from unprotected carbohydrates for protein-binding studies. Nat Protoc 2017; 12:2411-2422. [PMID: 29072708 DOI: 10.1038/nprot.2017.109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Glycobiology, in particular the study of carbohydrate-protein interactions and the events that follow, has become an important research focus in recent decades. To study these interactions, many assays require homogeneous glycoconjugates in suitable amounts. Their synthesis is one of the methodological challenges of glycobiology. Here, we describe a versatile, three-stage protocol for the formation of glycoconjugates from unprotected carbohydrates, including those purified from natural sources, as exemplified here by rhizobial Nod factors and exopolysaccharide fragments. The first stage is to add an oligo(ethylene glycol) linker (OEG-linker) that has a terminal triphenylmethanethiol group to the reducing end of the oligosaccharide by oxime formation catalyzed by aniline. The triphenylmethyl (trityl) tag is then removed from the linker to expose a thiol (stage 2) to allow a conjugation reaction at the thiol group (stage 3). There are many possible conjugation reactions, depending on the desired application. Examples shown in this protocol are as follows: (i) coupling of the oligosaccharide to a support for surface plasmon resonance (SPR) studies, (ii) fluorescence labeling for microscale thermophoresis (MST) or bioimaging, and (iii) biotinylation for biolayer interferometry (BLI) studies. This protocol starts from unprotected carbohydrates and provides glycoconjugates in milligram amounts in just 2 d.
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Affiliation(s)
- Christian T Hjuler
- Centre for Carbohydrate Recognition and Signaling, Copenhagen University, Frederiksberg, Denmark.,Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Nicolai N Maolanon
- Centre for Carbohydrate Recognition and Signaling, Copenhagen University, Frederiksberg, Denmark.,Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Jørgen Sauer
- Centre for Carbohydrate Recognition and Signaling, Copenhagen University, Frederiksberg, Denmark.,Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signaling, Aarhus University, Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mikkel B Thygesen
- Centre for Carbohydrate Recognition and Signaling, Copenhagen University, Frederiksberg, Denmark.,Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
| | - Knud J Jensen
- Centre for Carbohydrate Recognition and Signaling, Copenhagen University, Frederiksberg, Denmark.,Department of Chemistry, University of Copenhagen, Frederiksberg, Denmark
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Kelly S, Radutoiu S, Stougaard J. Legume LysM receptors mediate symbiotic and pathogenic signalling. Curr Opin Plant Biol 2017; 39:152-158. [PMID: 28787662 DOI: 10.1016/j.pbi.2017.06.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/14/2017] [Accepted: 06/16/2017] [Indexed: 05/13/2023]
Abstract
Legume-rhizobia symbiosis is coordinated through the production and perception of signal molecules by both partners with legume LysM receptor kinases performing a central role in this process. Receptor complex formation and signalling outputs derived from these are regulated through ligand binding and further modulated by a diverse variety of interactors. The challenge now is to understand the molecular mechanisms of these reported interactors. Recently attributed roles of LysM receptors in the perception of rhizobial exopolysaccharide, distinguishing between pathogens and symbionts, and assembly of root and rhizosphere communities expand on the importance of these receptors. These studies also highlight challenges, such as identification of cognate ligands, formation of responsive receptor complexes and separation of downstream signal transduction pathways.
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Affiliation(s)
- Simon Kelly
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK - 8000 Aarhus, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK - 8000 Aarhus, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK - 8000 Aarhus, Denmark.
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Bozsoki Z, Cheng J, Feng F, Gysel K, Vinther M, Andersen KR, Oldroyd G, Blaise M, Radutoiu S, Stougaard J. Receptor-mediated chitin perception in legume roots is functionally separable from Nod factor perception. Proc Natl Acad Sci U S A 2017; 114:E8118-E8127. [PMID: 28874587 PMCID: PMC5617283 DOI: 10.1073/pnas.1706795114] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The ability of root cells to distinguish mutualistic microbes from pathogens is crucial for plants that allow symbiotic microorganisms to infect and colonize their internal root tissues. Here we show that Lotus japonicus and Medicago truncatula possess very similar LysM pattern-recognition receptors, LjLYS6/MtLYK9 and MtLYR4, enabling root cells to separate the perception of chitin oligomeric microbe-associated molecular patterns from the perception of lipochitin oligosaccharide by the LjNFR1/MtLYK3 and LjNFR5/MtNFP receptors triggering symbiosis. Inactivation of chitin-receptor genes in Ljlys6, Mtlyk9, and Mtlyr4 mutants eliminates early reactive oxygen species responses and induction of defense-response genes in roots. Ljlys6, Mtlyk9, and Mtlyr4 mutants were also more susceptible to fungal and bacterial pathogens, while infection and colonization by rhizobia and arbuscular mycorrhizal fungi was maintained. Biochemical binding studies with purified LjLYS6 ectodomains further showed that at least six GlcNAc moieties (CO6) are required for optimal binding efficiency. The 2.3-Å crystal structure of the LjLYS6 ectodomain reveals three LysM βααβ motifs similar to other LysM proteins and a conserved chitin-binding site. These results show that distinct receptor sets in legume roots respond to chitin and lipochitin oligosaccharides found in the heterogeneous mixture of chitinaceous compounds originating from soil microbes. This establishes a foundation for genetic and biochemical dissection of the perception and the downstream responses separating defense from symbiosis in the roots of the 80-90% of land plants able to develop rhizobial and/or mycorrhizal endosymbiosis.
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Affiliation(s)
- Zoltan Bozsoki
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Jeryl Cheng
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Feng Feng
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Kira Gysel
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Maria Vinther
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Kasper R Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | | | - Mickael Blaise
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, University of Aarhus, DK-8000 Aarhus, Denmark;
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Reid D, Nadzieja M, Novák O, Heckmann AB, Sandal N, Stougaard J. Cytokinin Biosynthesis Promotes Cortical Cell Responses during Nodule Development. Plant Physiol 2017; 175:361-375. [PMID: 28733389 PMCID: PMC5580777 DOI: 10.1104/pp.17.00832] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/18/2017] [Indexed: 05/22/2023]
Abstract
Legume mutants have shown the requirement for receptor-mediated cytokinin signaling in symbiotic nodule organogenesis. While the receptors are central regulators, cytokinin also is accumulated during early phases of symbiotic interaction, but the pathways involved have not yet been fully resolved. To identify the source, timing, and effect of this accumulation, we followed transcript levels of the cytokinin biosynthetic pathway genes in a sliding developmental zone of Lotus japonicus roots. LjIpt2 and LjLog4 were identified as the major contributors to the first cytokinin burst. The genetic dependence and Nod factor responsiveness of these genes confirm that cytokinin biosynthesis is a key target of the common symbiosis pathway. The accumulation of LjIpt2 and LjLog4 transcripts occurs independent of the LjLhk1 receptor during nodulation. Together with the rapid repression of both genes by cytokinin, this indicates that LjIpt2 and LjLog4 contribute to, rather than respond to, the initial cytokinin buildup. Analysis of the cytokinin response using the synthetic cytokinin sensor, TCSn, showed that this response occurs in cortical cells before spreading to the epidermis in L. japonicus While mutant analysis identified redundancy in several biosynthesis families, we found that mutation of LjIpt4 limits nodule numbers. Overexpression of LjIpt3 or LjLog4 alone was insufficient to produce the robust formation of spontaneous nodules. In contrast, overexpressing a complete cytokinin biosynthesis pathway leads to large, often fused spontaneous nodules. These results show the importance of cytokinin biosynthesis in initiating and balancing the requirement for cortical cell activation without uncontrolled cell proliferation.
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Affiliation(s)
- Dugald Reid
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Marcin Nadzieja
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, CZ-78371 Olomouc, Czech Republic
| | - Anne B Heckmann
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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Pedersen CT, Loke I, Lorentzen A, Wolf S, Kamble M, Kristensen SK, Munch D, Radutoiu S, Spillner E, Roepstorff P, Thaysen-Andersen M, Stougaard J, Dam S. N-glycan maturation mutants in Lotus japonicus for basic and applied glycoprotein research. Plant J 2017; 91:394-407. [PMID: 28407380 DOI: 10.1111/tpj.13570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/27/2017] [Accepted: 04/03/2017] [Indexed: 05/11/2023]
Abstract
Studies of protein N-glycosylation are important for answering fundamental questions on the diverse functions of glycoproteins in plant growth and development. Here we generated and characterised a comprehensive collection of Lotus japonicusLORE1 insertion mutants, each lacking the activity of one of the 12 enzymes required for normal N-glycan maturation in the glycosylation machinery. The inactivation of the individual genes resulted in altered N-glycan patterns as documented using mass spectrometry and glycan-recognising antibodies, indicating successful identification of null mutations in the target glyco-genes. For example, both mass spectrometry and immunoblotting experiments suggest that proteins derived from the α1,3-fucosyltransferase (Lj3fuct) mutant completely lacked α1,3-core fucosylation. Mass spectrometry also suggested that the Lotus japonicus convicilin 2 was one of the main glycoproteins undergoing differential expression/N-glycosylation in the mutants. Demonstrating the functional importance of glycosylation, reduced growth and seed production phenotypes were observed for the mutant plants lacking functional mannosidase I, N-acetylglucosaminyltransferase I, and α1,3-fucosyltransferase, even though the relative protein composition and abundance appeared unaffected. The strength of our N-glycosylation mutant platform is the broad spectrum of resulting glycoprotein profiles and altered physiological phenotypes that can be produced from single, double, triple and quadruple mutants. This platform will serve as a valuable tool for elucidating the functional role of protein N-glycosylation in plants. Furthermore, this technology can be used to generate stable plant mutant lines for biopharmaceutical production of glycoproteins displaying relative homogeneous and mammalian-like N-glycosylation features.
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Affiliation(s)
- Carina T Pedersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Ian Loke
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Andrea Lorentzen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Sara Wolf
- Department of Engineering, Aarhus University, DK-8000, Aarhus, Denmark
| | - Manoj Kamble
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Sebastian K Kristensen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - David Munch
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Simona Radutoiu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Edzard Spillner
- Department of Engineering, Aarhus University, DK-8000, Aarhus, Denmark
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Morten Thaysen-Andersen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Svend Dam
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
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Zagari N, Sandoval-Ibañez O, Sandal N, Su J, Rodriguez-Concepcion M, Stougaard J, Pribil M, Leister D, Pulido P. SNOWY COTYLEDON 2 Promotes Chloroplast Development and Has a Role in Leaf Variegation in Both Lotus japonicus and Arabidopsis thaliana. Mol Plant 2017; 10:721-734. [PMID: 28286296 DOI: 10.1016/j.molp.2017.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/17/2017] [Accepted: 02/26/2017] [Indexed: 05/20/2023]
Abstract
Plants contain various factors that transiently interact with subunits or intermediates of the thylakoid multiprotein complexes, promoting their stable association and integration. Hence, assembly factors are essential for chloroplast development and the transition from heterotrophic to phototrophic growth. Snowy cotyledon 2 (SCO2) is a DNAJ-like protein involved in thylakoid membrane biogenesis and interacts with the light-harvesting chlorophyll-binding protein LHCB1. In Arabidopsis thaliana, SCO2 function was previously reported to be restricted to cotyledons. Here we show that disruption of SCO2 in Lotus japonicus results not only in paler cotyledons but also in variegated true leaves. Furthermore, smaller and pale-green true leaves can also be observed in A. thaliana sco2 (atsco2) mutants under short-day conditions. In both species, SCO2 is required for proper accumulation of PSII-LHCII complexes. In contrast to other variegated mutants, inhibition of chloroplastic translation strongly affects L. japonicus sco2 mutant development and fails to suppress their variegated phenotype. Moreover, inactivation of the suppressor of variegation AtClpR1 in the atsco2 background results in an additive double-mutant phenotype with variegated true leaves. Taken together, our results indicate that SCO2 plays a distinct role in PSII assembly or repair and constitutes a novel factor involved in leaf variegation.
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Affiliation(s)
- Nicola Zagari
- Plant Molecular Biology, Department of Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark; Research and Innovation Center, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Omar Sandoval-Ibañez
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Junyi Su
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Mathias Pribil
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Dario Leister
- Plant Molecular Biology, Department of Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark.
| | - Pablo Pulido
- Plant Molecular Biology, Department of Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
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Kawaharada Y, James EK, Kelly S, Sandal N, Stougaard J. The Ethylene Responsive Factor Required for Nodulation 1 (ERN1) Transcription Factor Is Required for Infection-Thread Formation in Lotus japonicus. Mol Plant Microbe Interact 2017; 30:194-204. [PMID: 28068194 DOI: 10.1094/mpmi-11-16-0237-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Several hundred genes are transcriptionally regulated during infection-thread formation and development of nitrogen-fixing root nodules. We have characterized a set of Lotus japonicus mutants impaired in root-nodule formation and found that the causative gene, Ern1, encodes a protein with a characteristic APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription-factor domain. Phenotypic characterization of four ern1 alleles shows that infection pockets are formed but root-hair infection threads are absent. Formation of root-nodule primordia is delayed and no normal transcellular infection threads are found in the infected nodules. Corroborating the role of ERN1 (ERF Required for Nodulation1) in nodule organogenesis, spontaneous nodulation induced by an autoactive CCaMK and cytokinin-induced nodule primordia were not observed in ern1 mutants. Expression of Ern1 is induced in the susceptible zone by Nod factor treatment or rhizobial inoculation. At the cellular level, the pErn1:GUS reporter is highly expressed in root epidermal cells of the susceptible zone and in the cortical cells that form nodule primordia. The genetic regulation of this cellular expression pattern was further investigated in symbiotic mutants. Nod factor induction of Ern1 in epidermal cells was found to depend on Nfr1, Cyclops, and Nsp2 but was independent of Nin and Nf-ya1. These results suggest that ERN1 functions as a transcriptional regulator involved in the formation of infection threads and development of nodule primordia and may coordinate these two processes.
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Affiliation(s)
- Yasuyuki Kawaharada
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Euan K James
- 2 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Simon Kelly
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Niels Sandal
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
| | - Jens Stougaard
- 1 Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark; and
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Abstract
Lotus japonicus is a model legume used in the study of plant-microbe interactions, especially in the field of biological nitrogen fixation due to its ability to enter into a symbiotic relationship with a soil bacterium, Mesorhizobium loti. The LORE1 mutant population is a valuable resource for reverse genetics in L. japonicus due to its non-transgenic nature, high tagging efficiency, and low copy count. Here, we outline a workflow for identifying, ordering, and establishing homozygous LORE1 mutant lines for a gene of interest, LjFls2, including protocols for growth and genotyping of a segregating LORE1 population.
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Affiliation(s)
- Terry Mun
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Anna Małolepszy
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark.
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Mun T, Bachmann A, Gupta V, Stougaard J, Andersen SU. Lotus Base: An integrated information portal for the model legume Lotus japonicus. Sci Rep 2016; 6:39447. [PMID: 28008948 PMCID: PMC5180183 DOI: 10.1038/srep39447] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/22/2016] [Indexed: 12/04/2022] Open
Abstract
Lotus japonicus is a well-characterized model legume widely used in the study of plant-microbe interactions. However, datasets from various Lotus studies are poorly integrated and lack interoperability. We recognize the need for a comprehensive repository that allows comprehensive and dynamic exploration of Lotus genomic and transcriptomic data. Equally important are user-friendly in-browser tools designed for data visualization and interpretation. Here, we present Lotus Base, which opens to the research community a large, established LORE1 insertion mutant population containing an excess of 120,000 lines, and serves the end-user tightly integrated data from Lotus, such as the reference genome, annotated proteins, and expression profiling data. We report the integration of expression data from the L. japonicus gene expression atlas project, and the development of tools to cluster and export such data, allowing users to construct, visualize, and annotate co-expression gene networks. Lotus Base takes advantage of modern advances in browser technology to deliver powerful data interpretation for biologists. Its modular construction and publicly available application programming interface enable developers to tap into the wealth of integrated Lotus data. Lotus Base is freely accessible at: https://lotus.au.dk.
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Affiliation(s)
- Terry Mun
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Asger Bachmann
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
- Bioinformatics Research Centre, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
- Bioinformatics Research Centre, Aarhus University, C. F. Møllers Allé 8, DK-8000 Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
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Acosta-Jurado S, Rodríguez-Navarro DN, Kawaharada Y, Perea JF, Gil-Serrano A, Jin H, An Q, Rodríguez-Carvajal MA, Andersen SU, Sandal N, Stougaard J, Vinardell JM, Ruiz-Sainz JE. Sinorhizobium fredii HH103 Invades Lotus burttii by Crack Entry in a Nod Factor-and Surface Polysaccharide-Dependent Manner. Mol Plant Microbe Interact 2016; 29:925-937. [PMID: 27827003 DOI: 10.1094/mpmi-09-16-0195-r] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sinorhizobium fredii HH103-Rifr, a broad host range rhizobial strain, induces nitrogen-fixing nodules in Lotus burttii but ineffective nodules in L. japonicus. Confocal microscopy studies showed that Mesorhizobium loti MAFF303099 and S. fredii HH103-Rifr invade L. burttii roots through infection threads or epidermal cracks, respectively. Infection threads in root hairs were not observed in L. burttii plants inoculated with S. fredii HH103-Rifr. A S. fredii HH103-Rifr nodA mutant failed to nodulate L. burttii, demonstrating that Nod factors are strictly necessary for this crack-entry mode, and a noeL mutant was also severely impaired in L. burttii nodulation, indicating that the presence of fucosyl residues in the Nod factor is symbiotically relevant. However, significant symbiotic impacts due to the absence of methylation or to acetylation of the fucosyl residue were not detected. In contrast S. fredii HH103-Rifr mutants showing lipopolysaccharide alterations had reduced symbiotic capacity, while mutants affected in production of either exopolysaccharides, capsular polysaccharides, or both were not impaired in nodulation. Mutants unable to produce cyclic glucans and purine or pyrimidine auxotrophic mutants formed ineffective nodules with L. burttii. Flagellin-dependent bacterial mobility was not required for crack infection, since HH103-Rifr fla mutants nodulated L. burttii. None of the S. fredii HH103-Rifr surface-polysaccharide mutants gained effective nodulation with L. japonicus.
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Affiliation(s)
- Sebastián Acosta-Jurado
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | | | - Yasuyuki Kawaharada
- 3 Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus C DK-8000, Denmark; and
| | - Juan Fernández Perea
- 2 IFAPA, Centro Las Torres-Tomejil, Apartado Oficial 41200, Alcalá del Río, Sevilla, Spain
| | - Antonio Gil-Serrano
- 4 Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P. 41012, Sevilla, Spain
| | - Haojie Jin
- 3 Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus C DK-8000, Denmark; and
| | - Qi An
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Miguel A Rodríguez-Carvajal
- 4 Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P. 41012, Sevilla, Spain
| | - Stig U Andersen
- 3 Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus C DK-8000, Denmark; and
| | - Niels Sandal
- 3 Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus C DK-8000, Denmark; and
| | - Jens Stougaard
- 3 Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling, Aarhus University, Gustav Wieds Vej 10, Aarhus C DK-8000, Denmark; and
| | - José-María Vinardell
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - José E Ruiz-Sainz
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
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Małolepszy A, Mun T, Sandal N, Gupta V, Dubin M, Urbański D, Shah N, Bachmann A, Fukai E, Hirakawa H, Tabata S, Nadzieja M, Markmann K, Su J, Umehara Y, Soyano T, Miyahara A, Sato S, Hayashi M, Stougaard J, Andersen SU. The LORE1 insertion mutant resource. Plant J 2016; 88:306-317. [PMID: 27322352 DOI: 10.1111/tpj.13243] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 05/08/2023]
Abstract
Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.
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Affiliation(s)
- Anna Małolepszy
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Terry Mun
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Vikas Gupta
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Manu Dubin
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Dorian Urbański
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Niraj Shah
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Asger Bachmann
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Eigo Fukai
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Marcin Nadzieja
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Katharina Markmann
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Junyi Su
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Yosuke Umehara
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Takashi Soyano
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Akira Miyahara
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Makoto Hayashi
- Division of Plant Sciences, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannon-dai, Tsukuba, 305-8602, Japan
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
| | - Stig U Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000, Aarhus C, Denmark
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Shah N, Hirakawa H, Kusakabe S, Sandal N, Stougaard J, Schierup MH, Sato S, Andersen SU. High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. DNA Res 2016; 23:487-494. [PMID: 27374610 PMCID: PMC5066174 DOI: 10.1093/dnares/dsw033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 11/13/2022] Open
Abstract
Recombinant inbred lines (RILs) derived from bi-parental populations are stable genetic resources, which are widely used for constructing genetic linkage maps. These genetic maps are essential for QTL mapping and can aid contig and scaffold anchoring in the final stages of genome assembly. In this study, two Lotus sp. RIL populations, Lotus japonicus MG-20 × Gifu and Gifu × L. burttii, were characterized by Illumina re-sequencing. Genotyping of 187 MG-20 × Gifu RILs at 87,140 marker positions and 96 Gifu × L. burttii RILs at 357,973 marker positions allowed us to accurately identify 1,929 recombination breakpoints in the MG-20 × Gifu RILs and 1,044 breakpoints in the Gifu × L. burttii population. The resulting high-density genetic maps now facilitate high-accuracy QTL mapping, identification of reference genome mis-assemblies, and characterization of structural variants.
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Affiliation(s)
- Niraj Shah
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Shohei Kusakabe
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Niels Sandal
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jens Stougaard
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Shusei Sato
- Kazusa DNA Research Institute, Chiba 292-0818, Japan.,Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Stig Uggerhøj Andersen
- Center for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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Fukudome M, Calvo-Begueria L, Kado T, Osuki KI, Rubio MC, Murakami EI, Nagata M, Kucho KI, Sandal N, Stougaard J, Becana M, Uchiumi T. Hemoglobin LjGlb1-1 is involved in nodulation and regulates the level of nitric oxide in the Lotus japonicus-Mesorhizobium loti symbiosis. J Exp Bot 2016; 67:5275-83. [PMID: 27443280 PMCID: PMC5014168 DOI: 10.1093/jxb/erw290] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Leghemoglobins transport and deliver O2 to the symbiosomes inside legume nodules and are essential for nitrogen fixation. However, the roles of other hemoglobins (Hbs) in the rhizobia-legume symbiosis are unclear. Several Lotus japonicus mutants affecting LjGlb1-1, a non-symbiotic class 1 Hb, have been used to study the function of this protein in symbiosis. Two TILLING alleles with single amino acid substitutions (A102V and E127K) and a LORE1 null allele with a retrotransposon insertion in the 5'-untranslated region (96642) were selected for phenotyping nodulation. Plants of all three mutant lines showed a decrease in long infection threads and nodules, and an increase in incipient infection threads. About 4h after inoculation, the roots of mutant plants exhibited a greater transient accumulation of nitric oxide (NO) than did the wild-type roots; nevertheless, in vitro NO dioxygenase activities of the wild-type, A102V, and E127K proteins were similar, suggesting that the mutated proteins are not fully functional in vivo The expression of LjGlb1-1, but not of the other class 1 Hb of L. japonicus (LjGlb1-2), was affected during infection of wild-type roots, further supporting a specific role for LjGlb1-1. In conclusion, the LjGlb1-1 mutants reveal that this protein is required during rhizobial infection and regulates NO levels.
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Affiliation(s)
- Mitsutaka Fukudome
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Laura Calvo-Begueria
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Tomohiro Kado
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Ken-Ichi Osuki
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Maria Carmen Rubio
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Ei-Ichi Murakami
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Maki Nagata
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Ken-Ichi Kucho
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080 Zaragoza, Spain
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065, Japan
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