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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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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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3
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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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Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Correction to: Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell 2022; 34:2806. [PMID: 35357494 PMCID: PMC9252476 DOI: 10.1093/plcell/koac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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5
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Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell 2020; 32:3388-3407. [PMID: 32843435 PMCID: PMC7610282 DOI: 10.1105/tpc.20.00235] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/22/2020] [Accepted: 08/21/2020] [Indexed: 05/19/2023]
Abstract
Proximity labeling is a powerful approach for detecting protein-protein interactions. Most proximity labeling techniques use a promiscuous biotin ligase or a peroxidase fused to a protein of interest, enabling the covalent biotin labeling of proteins and subsequent capture and identification of interacting and neighboring proteins without the need for the protein complex to remain intact. To date, only a few studies have reported on the use of proximity labeling in plants. Here, we present the results of a systematic study applying a variety of biotin-based proximity labeling approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols that combine mass spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as a test case. We further benchmark the efficiency of various promiscuous biotin ligases in comparison with one-step affinity purification approaches. We identified both known and novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both nonbiotinylated and biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to suggest structural information of protein complexes.
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Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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6
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Ochoa-Fernandez R, Abel NB, Wieland FG, Schlegel J, Koch LA, Miller JB, Engesser R, Giuriani G, Brandl SM, Timmer J, Weber W, Ott T, Simon R, Zurbriggen MD. Optogenetic control of gene expression in plants in the presence of ambient white light. Nat Methods 2020; 17:717-725. [PMID: 32601426 DOI: 10.1038/s41592-020-0868-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/24/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
Optogenetics is the genetic approach for controlling cellular processes with light. It provides spatiotemporal, quantitative and reversible control over biological signaling and metabolic processes, overcoming limitations of chemically inducible systems. However, optogenetics lags in plant research because ambient light required for growth leads to undesired system activation. We solved this issue by developing plant usable light-switch elements (PULSE), an optogenetic tool for reversibly controlling gene expression in plants under ambient light. PULSE combines a blue-light-regulated repressor with a red-light-inducible switch. Gene expression is only activated under red light and remains inactive under white light or in darkness. Supported by a quantitative mathematical model, we characterized PULSE in protoplasts and achieved high induction rates, and we combined it with CRISPR-Cas9-based technologies to target synthetic signaling and developmental pathways. We applied PULSE to control immune responses in plant leaves and generated Arabidopsis transgenic plants. PULSE opens broad experimental avenues in plant research and biotechnology.
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Affiliation(s)
- Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany.,iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany
| | - Nikolaj B Abel
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | | | - Jenia Schlegel
- iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany.,Institute of Developmental Genetics, University of Düsseldorf, Düsseldorf, Germany
| | - Leonie-Alexa Koch
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany
| | - J Benjamin Miller
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Raphael Engesser
- Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany
| | - Giovanni Giuriani
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany.,Univeersity of Glasgow, Glasgow, Scotland, UK
| | - Simon M Brandl
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jens Timmer
- Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Thomas Ott
- Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Rüdiger Simon
- iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany.,Institute of Developmental Genetics, University of Düsseldorf, Düsseldorf, Germany.,CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany. .,iGRAD Plant Graduate School, University of Düsseldorf, Düsseldorf, Germany. .,CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
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7
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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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8
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Holt DB, Gupta V, Meyer D, Abel NB, Andersen SU, Stougaard J, Markmann K. micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules. New Phytol 2015; 208:241-56. [PMID: 25967282 DOI: 10.1111/nph.13445] [Citation(s) in RCA: 34] [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] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/26/2015] [Indexed: 05/13/2023]
Abstract
Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization. Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves. The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis.
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Affiliation(s)
- Dennis B Holt
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Vikas Gupta
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Dörte Meyer
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Nikolaj B Abel
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
| | - Katharina Markmann
- Department of Molecular Biology and Genetics, Centre for Carbohydrate Recognition and Signalling (CARB), Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
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