1
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Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: it's about time and space. Plant Cell 2024; 36:1482-1503. [PMID: 38366121 PMCID: PMC11062454 DOI: 10.1093/plcell/koae038] [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] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
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Affiliation(s)
- Carly M Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Rothkegel
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - Chia-Yi Cheng
- Department of Life Science, National Taiwan University, Taipei 10663, Taiwan
| | - José M Alvarez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés Bello, 8370035 Santiago, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Rodrigo A Gutiérrez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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2
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Crabos A, Huang Y, Boursat T, Maurel C, Ruffel S, Krouk G, Boursiac Y. Distinct early transcriptional regulations by turgor and osmotic potential in the roots of Arabidopsis. J Exp Bot 2023; 74:5917-5930. [PMID: 37603421 DOI: 10.1093/jxb/erad307] [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] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/28/2023] [Indexed: 08/23/2023]
Abstract
In a context of climate change, deciphering signaling pathways driving plant adaptation to drought, changes in water availability, and salt is key. A crossing point of these plant stresses is their impact on plant water potential (Ψ), a composite physico-chemical variable reflecting the availability of water for biological processes such as plant growth and stomatal aperture. The Ψ of plant cells is mainly driven by their turgor and osmotic pressures. Here we investigated the effect of a variety of osmotic treatments on the roots of Arabidopsis plants grown in hydroponics. We used, among others, a permeating solute as a way to differentiate variations on turgor from variations in osmotic pressure. Measurement of cortical cell turgor pressure with a cell pressure probe allowed us to monitor the intensity of the treatments and thereby preserve the cortex from plasmolysis. Transcriptome analyses at an early time point (15 min) showed specific and quantitative transcriptomic responses to both osmotic and turgor pressure variations. Our results highlight how water-related biophysical parameters can shape the transcriptome of roots under stress and provide putative candidates to explore further the early perception of water stress in plants.
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Affiliation(s)
- Amandine Crabos
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Yunji Huang
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Thomas Boursat
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
- Laboratoire de Mécanique et Génie Civil (LMGC), Univ Montpellier, CNRS, Montpellier, France
| | - Christophe Maurel
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Yann Boursiac
- Institute for Plant Sciences of Montpellier (IPSiM), Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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3
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Nguyen NN, Lamotte O, Alsulaiman M, Ruffel S, Krouk G, Berger N, Demolombe V, Nespoulous C, Dang TMN, Aimé S, Berthomieu P, Dubos C, Wendehenne D, Vile D, Gosti F. Reduction in PLANT DEFENSIN 1 expression in Arabidopsis thaliana results in increased resistance to pathogens and zinc toxicity. J Exp Bot 2023; 74:5374-5393. [PMID: 37326591 DOI: 10.1093/jxb/erad228] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 06/14/2023] [Indexed: 06/17/2023]
Abstract
Ectopic expression of defensins in plants correlates with their increased capacity to withstand abiotic and biotic stresses. This applies to Arabidopsis thaliana, where some of the seven members of the PLANT DEFENSIN 1 family (AtPDF1) are recognised to improve plant responses to necrotrophic pathogens and increase seedling tolerance to excess zinc (Zn). However, few studies have explored the effects of decreased endogenous defensin expression on these stress responses. Here, we carried out an extensive physiological and biochemical comparative characterization of (i) novel artificial microRNA (amiRNA) lines silenced for the five most similar AtPDF1s, and (ii) a double null mutant for the two most distant AtPDF1s. Silencing of five AtPDF1 genes was specifically associated with increased aboveground dry mass production in mature plants under excess Zn conditions, and with increased plant tolerance to different pathogens - a fungus, an oomycete and a bacterium, while the double mutant behaved similarly to the wild type. These unexpected results challenge the current paradigm describing the role of PDFs in plant stress responses. Additional roles of endogenous plant defensins are discussed, opening new perspectives for their functions.
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Affiliation(s)
- Ngoc Nga Nguyen
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Olivier Lamotte
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne-Franche Comté, F-21 000 Dijon, France
| | - Mohanad Alsulaiman
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Sandrine Ruffel
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Gabriel Krouk
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Nathalie Berger
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Vincent Demolombe
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Claude Nespoulous
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Thi Minh Nguyet Dang
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Sébastien Aimé
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne-Franche Comté, F-21 000 Dijon, France
| | - Pierre Berthomieu
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Christian Dubos
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - David Wendehenne
- Agroécologie, CNRS, INRAE, Institut Agro, Université de Bourgogne, Université Bourgogne-Franche Comté, F-21 000 Dijon, France
| | - Denis Vile
- LEPSE, INRAE, Institut Agro, Université de Montpellier, 2 Place P. Viala, F-34 060 Montpellier Cedex 2, France
| | - Françoise Gosti
- IPSiM, CNRS, INRAE, Institut Agro, Université de Montpellier, 2, Place P. Viala, F-34 060 Montpellier Cedex 2, France
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4
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Krouk G, Szponarski W, Ruffel S. Unleashing the potential of peptides in agriculture and beyond. Trends Plant Sci 2023; 28:734-736. [PMID: 37069001 DOI: 10.1016/j.tplants.2023.03.025] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 06/17/2023]
Abstract
Peptides display a broad range of regulatory functions. Ormancey et al. recently identified an important new mechanism - complementary peptides (cPEPs) - that provide a versatile means to control cell functions. We draw a parallel between RNA and peptide biology, and discuss new routes of investigation and industrial applications opened by this work.
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Affiliation(s)
- Gabriel Krouk
- Institut des Sciences des Plantes de Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier, France.
| | - Wojciech Szponarski
- Institut des Sciences des Plantes de Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier, France
| | - Sandrine Ruffel
- Institut des Sciences des Plantes de Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier, France.
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5
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Cho H, Banf M, Shahzad Z, Van Leene J, Bossi F, Ruffel S, Bouain N, Cao P, Krouk G, De Jaeger G, Lacombe B, Brandizzi F, Rhee SY, Rouached H. ARSK1 activates TORC1 signaling to adjust growth to phosphate availability in Arabidopsis. Curr Biol 2023; 33:1778-1786.e5. [PMID: 36963384 PMCID: PMC10175222 DOI: 10.1016/j.cub.2023.03.005] [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: 10/15/2022] [Revised: 02/12/2023] [Accepted: 03/02/2023] [Indexed: 03/26/2023]
Abstract
Nutrient sensing and signaling are essential for adjusting growth and development to available resources. Deprivation of the essential mineral phosphorus (P) inhibits root growth.1 The molecular processes that sense P limitation to trigger early root growth inhibition are not known yet. Target of rapamycin (TOR) kinase is a central regulatory hub in eukaryotes to adapt growth to internal and external nutritional cues.2,3 How nutritional signals are transduced to TOR to control plant growth remains unclear. Here, we identify Arabidopsis-root-specific kinase 1 (ARSK1), which attenuates initial root growth inhibition in response to P limitation. We demonstrate that ARSK1 phosphorylates and stabilizes the regulatory-associated protein of TOR 1B (RAPTOR1B), a component of the TOR complex 1, to adjust root growth to P availability. These findings uncover signaling components acting upstream of TOR to balance growth to P availability.
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Affiliation(s)
- Huikyong Cho
- The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Zaigham Shahzad
- Department of Life Sciences, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Jelle Van Leene
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Flavia Bossi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Nadia Bouain
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Pengfei Cao
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Gabiel Krouk
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Benoit Lacombe
- Institute for Plant Sciences of Montpellier, University Montpellier, CNRS, INRAE, Montpellier 34060, France
| | - Federica Brandizzi
- MSU DOE-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Hatem Rouached
- The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.
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6
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Camut L, Gallova B, Jilli L, Sirlin-Josserand M, Carrera E, Sakvarelidze-Achard L, Ruffel S, Krouk G, Thomas SG, Hedden P, Phillips AL, Davière JM, Achard P. Nitrate signaling promotes plant growth by upregulating gibberellin biosynthesis and destabilization of DELLA proteins. Curr Biol 2021; 31:4971-4982.e4. [PMID: 34614391 DOI: 10.1016/j.cub.2021.09.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Nitrate, one of the main nitrogen (N) sources for crops, acts as a nutrient and key signaling molecule coordinating gene expression, metabolism, and various growth processes throughout the plant life cycle. It is widely accepted that nitrate-triggered developmental programs cooperate with hormone synthesis and transport to finely adapt plant architecture to N availability. Here, we report that nitrate, acting through its signaling pathway, promotes growth in Arabidopsis and wheat, in part by modulating the accumulation of gibberellin (GA)-regulated DELLA growth repressors. We show that nitrate reduces the abundance of DELLAs by increasing GA contents through activation of GA metabolism gene expression. Consistently, the growth restraint conferred by nitrate deficiency is partially rescued in global-DELLA mutant that lacks all DELLAs. At the cellular level, we show that nitrate enhances both cell proliferation and elongation in a DELLA-dependent and -independent manner, respectively. Our findings establish a connection between nitrate and GA signaling pathways that allow plants to adapt their growth to nitrate availability.
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Affiliation(s)
- Lucie Camut
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Barbora Gallova
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Lucas Jilli
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Mathilde Sirlin-Josserand
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 Valencia, Spain
| | - Lali Sakvarelidze-Achard
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stephen G Thomas
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Peter Hedden
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK; Laboratory of Growth Regulators, Institute of Experimental Botany and Palacky University, 78371 Olomouc, Czech Republic
| | - Andrew L Phillips
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Jean-Michel Davière
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Patrick Achard
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France.
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Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O’Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. Plant Physiol 2021; 186:696-714. [PMID: 33582801 PMCID: PMC8154064 DOI: 10.1093/plphys/kiab047] [Citation(s) in RCA: 6] [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: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/14/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O’Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
- Author for communication:
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8
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Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O'Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. Plant Physiol 2021; 186:696-714. [PMID: 33582801 DOI: 10.1101/822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O'Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
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9
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Safi A, Medici A, Szponarski W, Martin F, Clément-Vidal A, Marshall-Colon A, Ruffel S, Gaymard F, Rouached H, Leclercq J, Coruzzi G, Lacombe B, Krouk G. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways. J Exp Bot 2021; 72:3881-3901. [PMID: 33758916 PMCID: PMC8096604 DOI: 10.1093/jxb/erab114] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 12/07/2020] [Accepted: 03/22/2021] [Indexed: 05/04/2023]
Abstract
Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.
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Affiliation(s)
- Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Correspondence: or
| | - Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | - Florence Martin
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Anne Clément-Vidal
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Amy Marshall-Colon
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
- Present address: Department of Plant Biology, University of Illinois at Urbana -Champaign, Urbana, IL, USA
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Frédéric Gaymard
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, and Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - Julie Leclercq
- CIRAD, AGAP Institut, Montpellier, France
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gloria Coruzzi
- New York University, Department of Biology, Center for Genomics & Systems Biology, New York, NY, USA
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Correspondence: or
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10
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Gautrat P, Laffont C, Frugier F, Ruffel S. Nitrogen Systemic Signaling: From Symbiotic Nodulation to Root Acquisition. Trends Plant Sci 2021; 26:392-406. [PMID: 33358560 DOI: 10.1016/j.tplants.2020.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 07/20/2020] [Revised: 10/30/2020] [Accepted: 11/16/2020] [Indexed: 05/27/2023]
Abstract
Plant nutrient acquisition is tightly regulated by resource availability and metabolic needs, implying the existence of communication between roots and shoots to ensure their integration at the whole-plant level. Here, we focus on systemic signaling pathways controlling nitrogen (N) nutrition, achieved both by the root import of mineral N and, in legume plants, through atmospheric N fixation by symbiotic bacteria inside dedicated root nodules. We explore features conserved between systemic pathways repressing or enhancing symbiotic N fixation and the regulation of mineral N acquisition by roots, as well as their integration with other environmental factors, such as phosphate, light, and CO2 availability.
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Affiliation(s)
- Pierre Gautrat
- IPS2 (Institute of Plant Sciences - Paris Saclay), CNRS, INRAe, Université Paris-Diderot, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Gif-sur-Yvette, France
| | - Carole Laffont
- IPS2 (Institute of Plant Sciences - Paris Saclay), CNRS, INRAe, Université Paris-Diderot, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Gif-sur-Yvette, France
| | - Florian Frugier
- IPS2 (Institute of Plant Sciences - Paris Saclay), CNRS, INRAe, Université Paris-Diderot, Université d'Evry, Université Paris-Saclay, Bâtiment 630, Gif-sur-Yvette, France.
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRAe, Montpellier SupAgro, Montpellier, France.
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11
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Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks MD, Krouk G, Ruffel S, Lejay L, Crawford NM, Coruzzi GM, Gutiérrez RA. Nitrate in 2020: Thirty Years from Transport to Signaling Networks. Plant Cell 2020; 32:2094-2119. [PMID: 32169959 PMCID: PMC7346567 DOI: 10.1105/tpc.19.00748] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/05/2020] [Accepted: 03/10/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.
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Affiliation(s)
- Elena A Vidal
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
| | - José M Alvarez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
| | - Matthew D Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Gabriel Krouk
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Sandrine Ruffel
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Laurence Lejay
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, 92093
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
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12
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Li Y, Brooks M, Yeoh-Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM. SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling. Plant Physiol 2020; 182:215-227. [PMID: 31641075 PMCID: PMC6945839 DOI: 10.1104/pp.19.00682] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 05/04/2023]
Abstract
Chromatin modification has gained increased attention for its role in the regulation of plant responses to environmental changes, but the specific mechanisms and molecular players remain elusive. Here, we show that the Arabidopsis (Arabidopsis thaliana) histone methyltransferase SET DOMAIN GROUP8 (SDG8) mediates genome-wide changes in H3K36 methylation at specific genomic loci functionally relevant to nitrate treatments. Moreover, we show that the specific H3K36 methyltransferase encoded by SDG8 is required for canonical RNA processing, and that RNA isoform switching is more prominent in the sdg8-5 deletion mutant than in the wild type. To demonstrate that SDG8-mediated regulation of RNA isoform expression is functionally relevant, we examined a putative regulatory gene, CONSTANS, CO-like, and TOC1 101 (CCT101), whose nitrogen-responsive isoform-specific RNA expression is mediated by SDG8. We show by functional expression in shoot cells that the different RNA isoforms of CCT101 encode distinct regulatory proteins with different effects on genome-wide transcription. We conclude that SDG8 is involved in plant responses to environmental nitrogen supply, affecting multiple gene regulatory processes including genome-wide histone modification, transcriptional regulation, and RNA processing, and thereby mediating developmental and metabolic processes related to nitrogen use.
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Affiliation(s)
- Ying Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Matthew Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Jenny Yeoh-Wang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rachel M McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Tara M Rock
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Chang In Moon
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, French National Institute for Agricultural Research, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | | | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
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13
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Medici A, Szponarski W, Dangeville P, Safi A, Dissanayake IM, Saenchai C, Emanuel A, Rubio V, Lacombe B, Ruffel S, Tanurdzic M, Rouached H, Krouk G. Identification of Molecular Integrators Shows that Nitrogen Actively Controls the Phosphate Starvation Response in Plants. Plant Cell 2019; 31:1171-1184. [PMID: 30872321 PMCID: PMC6533016 DOI: 10.1105/tpc.18.00656] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) and phosphorus (P) are key macronutrients sustaining plant growth and crop yield and ensuring food security worldwide. Understanding how plants perceive and interpret the combinatorial nature of these signals thus has important agricultural implications within the context of (1) increased food demand, (2) limited P supply, and (3) environmental pollution due to N fertilizer usage. Here, we report the discovery of an active control of P starvation response (PSR) by a combination of local and long-distance N signaling pathways in plants. We show that, in Arabidopsis (Arabidopsis thaliana), the nitrate transceptor CHLORINA1/NITRATE TRANSPORTER1.1 (CHL1/NRT1.1) is a component of this signaling crosstalk. We also demonstrate that this crosstalk is dependent on the control of the accumulation and turnover by N of the transcription factor PHOSPHATE STARVATION RESPONSE1 (PHR1), a master regulator of P sensing and signaling. We further show an important role of PHOSPHATE2 (PHO2) as an integrator of the N availability into the PSR since the effect of N on PSR is strongly affected in pho2 mutants. We finally show that PHO2 and NRT1.1 influence each other's transcript levels. These observations are summarized in a model representing a framework with several entry points where N signal influence PSR. Finally, we demonstrate that this phenomenon is conserved in rice (Oryza sativa) and wheat (Triticum aestivum), opening biotechnological perspectives in crop plants.
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Affiliation(s)
- Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | | | - Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | - Chorpet Saenchai
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Amélie Emanuel
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Darwin 3, Campus de la Universidad Autónoma Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Institut Claude Grignon, Biochime et Physiologie Moleculaire des Plantes, Centre National de la Recherche Scientifique, 34060 Montpellier, France
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Milos Tanurdzic
- School of Biological Sciences, University of Queensland, Brisbane 4072, Queensland, Australia
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
- Institut Claude Grignon, Biochime et Physiologie Moleculaire des Plantes, Centre National de la Recherche Scientifique, 34060 Montpellier, France
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14
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Coruzzi G, Varala K, Marshall‐Colon A, Brooks M, Ruffel S, Alvarez J, Pasquino A, Cirrone J, Shasha D. The 4th Dimension of Transcriptional Networks: TIME. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.343.1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kranthi Varala
- New York UniveristyNew YorkNY
- Purdue UniversityWest LafayetteIN
| | | | | | - Sandrine Ruffel
- Biochemistry and Plant Molecular Physiology Research UnitCNRS/INRA/MontpellierMontpellierFrance
| | | | | | - Jacopo Cirrone
- New York UniveristyNew YorkNY
- NYU Courant Institute of Mathematical SciencesNew YorkNY
| | - Dennis Shasha
- NYU Courant Institute of Mathematical SciencesNew YorkNY
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15
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Ruffel S. Nutrient-Related Long-Distance Signals: Common Players and Possible Cross-Talk. Plant Cell Physiol 2018; 59:1723-1732. [PMID: 30085239 DOI: 10.1093/pcp/pcy152] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 05/01/2018] [Accepted: 07/19/2018] [Indexed: 05/20/2023]
Abstract
Nutrient fluctuations are more a rule rather than an exception in the life of sessile organisms such as plants. Despite this constraint that adds up to abiotic and biotic stresses, plants are able to accomplish their life cycle thanks to an efficient signaling network that reciprocally controls nutrient acquisition and use with growth and development. The majority of nutrients are acquired by the root system where multiple local signaling pathways that rely on nutrient-sensing systems are implemented to direct root growth toward soil resources. Moreover, long-distance signaling plays an essential role in integrating nutrient availability at the whole-plant level and adjusting nutrient acquisition to plant growth requirements. By studying the signaling network for single mineral nutrients, several long-distance signals traveling between roots and shoots and taking a diversity of forms have been identified and are summarized here. However, the nutritional environment is multifactorial, adding a tremendous complexity for our understanding of the nutrient signaling network as a unique system. For instance, long-distance signals are expected to support this nutrient cross-talk in part, but the mechanisms are still largely unknown. Therefore, the involvement of possible long-distance signals as conveyers of nutrient cross-talk is discussed here together with approaches and strategies that are now considered to build a picture from the nutrient signaling puzzle.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, INRA, CNRS, Universit� de Montpellier, Montpellier SupAgro, Montpellier, France
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16
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Poitout A, Crabos A, Petřík I, Novák O, Krouk G, Lacombe B, Ruffel S. Responses to Systemic Nitrogen Signaling in Arabidopsis Roots Involve trans-Zeatin in Shoots. Plant Cell 2018; 30:1243-1257. [PMID: 29764985 PMCID: PMC6048791 DOI: 10.1105/tpc.18.00011] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/19/2018] [Accepted: 05/14/2018] [Indexed: 05/18/2023]
Abstract
Plants face temporal and spatial variation in nitrogen (N) availability. This includes heterogeneity in soil nitrate (NO3-) content. To overcome these constraints, plants modify their gene expression and physiological processes to optimize N acquisition. This plasticity relies on a complex long-distance root-shoot-root signaling network that remains poorly understood. We previously showed that cytokinin (CK) biosynthesis is required to trigger systemic N signaling. Here, we performed split-root experiments and used a combination of CK-related mutant analyses, hormone profiling, transcriptomic analysis, NO3- uptake assays, and root growth measurements to gain insight into systemic N signaling in Arabidopsis thaliana By comparing wild-type plants and mutants affected in CK biosynthesis and ABCG14-dependent root-to-shoot translocation of CK, we revealed an important role for active trans-zeatin (tZ) in systemic N signaling. Both rapid sentinel gene regulation and long-term functional acclimation to heterogeneous NO3- supply, including NO3- transport and root growth regulation, are likely mediated by the integration of tZ content in shoots. Furthermore, shoot transcriptome profiling revealed that glutamate/glutamine metabolism is likely a target of tZ root-to-shoot translocation, prompting an interesting hypothesis regarding shoot-to-root communication. Finally, this study highlights tZ-independent pathways regulating gene expression in shoots as well as NO3- uptake activity in response to total N deprivation.
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Affiliation(s)
- Arthur Poitout
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Amandine Crabos
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Ivan Petřík
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Ondrej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Gabriel Krouk
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Benoît Lacombe
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Sandrine Ruffel
- BPMP, INRA, CNRS, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
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17
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Safi A, Medici A, Szponarski W, Ruffel S, Lacombe B, Krouk G. The world according to GARP transcription factors. Curr Opin Plant Biol 2017; 39:159-167. [PMID: 28802165 DOI: 10.1016/j.pbi.2017.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/10/2017] [Accepted: 07/15/2017] [Indexed: 05/26/2023]
Abstract
Plant specific GARP transcription factor family (made of ARR-B and G2-like) contains genes with very diverse in planta functions: nutrient sensing, root and shoot development, floral transition, chloroplast development, circadian clock oscillation maintenance, hormonal transport and signaling. In this work we review: first, their structural but distant relationships with MYB transcription factors, second, their role in planta, third, the diversity of their Cis-regulatory elements, fourth, their potential protein partners. We conclude that the GARP family may hold keys to understand the interactions between nutritional signaling pathways (nitrogen and phosphate at least) and development. Understanding how plant nutrition and development are coordinated is central to understand how to adapt plants to an ever-changing environment. Consequently GARPs are likely to attract increasing research attentions, as they are likely at the crossroads of these fundamental processes.
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Affiliation(s)
- Alaeddine Safi
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR5004 CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Pierre Viala, 34060 Montpellier, France
| | - Anna Medici
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR5004 CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Pierre Viala, 34060 Montpellier, France
| | - Wojciech Szponarski
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR5004 CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Pierre Viala, 34060 Montpellier, France
| | - Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR5004 CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Pierre Viala, 34060 Montpellier, France
| | - Benoît Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR5004 CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Pierre Viala, 34060 Montpellier, France
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR5004 CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Pierre Viala, 34060 Montpellier, France.
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18
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Abstract
This article comments on: Cochetel N, Escudié F, Cookson SJ, Dai Z, Vivin P, Bert P-F, Muñoz MS, Delrot S, Klopp C, Ollat N, Lauvergeat V. 2017. Root transcriptomic responses of grafted grapevine to heterogeneous N availability depend on rootstock genotype. Journal of Experimental Botany 68, 4339–4355.
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Affiliation(s)
- Anna Medici
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes ‘Claude Grignon’, Place Pierre Viala, Montpellier, France
| | - Benoit Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes ‘Claude Grignon’, Place Pierre Viala, Montpellier, France
| | - Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes ‘Claude Grignon’, Place Pierre Viala, Montpellier, France
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19
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Affiliation(s)
- Sandrine Ruffel
- Biochemistry and Plant Molecular Physiology Research Unit, CNRS/INRA/Montpellier SupAgro/Université de Montpellier, 2 Place Viala, 34060 Montpellier, France
| | - Alain Gojon
- Biochemistry and Plant Molecular Physiology Research Unit, CNRS/INRA/Montpellier SupAgro/Université de Montpellier, 2 Place Viala, 34060 Montpellier, France
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20
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Ristova D, Carré C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G. Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root. Sci Signal 2016; 9:rs13. [PMID: 27811143 DOI: 10.1126/scisignal.aaf2768] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Plants form the basis of the food webs that sustain animal life. Exogenous factors, such as nutrients and sunlight, and endogenous factors, such as hormones, cooperate to control both the growth and the development of plants. We assessed how Arabidopsis thaliana integrated nutrient and hormone signaling pathways to control root growth and development by investigating the effects of combinatorial treatment with the nutrients nitrate and ammonium; the hormones auxin, cytokinin, and abscisic acid; and all binary combinations of these factors. We monitored and integrated short-term genome-wide changes in gene expression over hours and long-term effects on root development and architecture over several days. Our analysis revealed trends in nutrient and hormonal signal crosstalk and feedback, including responses that exhibited logic gate behavior, which means that they were triggered only when specific combinations of signals were present. From the data, we developed a multivariate network model comprising the signaling molecules, the early gene expression modulation, and the subsequent changes in root phenotypes. This multivariate network model pinpoints several genes that play key roles in the control of root development and may help understand how eukaryotes manage multifactorial signaling inputs.
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Affiliation(s)
- Daniela Ristova
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.,Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Clément Carré
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.,Institut Montpelliérain Alexander Grothendieck, Place Eugene Bataillon, 34090 Montpellier, France
| | - Marjorie Pervent
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France
| | - Anna Medici
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France
| | - Grace Jaeyoon Kim
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Domenica Scalia
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Benoît Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/SupAgro/UM, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier Cedex, France.
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21
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Ruffel S, Poitout A, Krouk G, Coruzzi GM, Lacombe B. Long-distance nitrate signaling displays cytokinin dependent and independent branches. J Integr Plant Biol 2016; 58:226-229. [PMID: 26619818 DOI: 10.1111/jipb.12453] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/27/2015] [Indexed: 05/29/2023]
Abstract
The long-distance signaling network allowing a plant to properly develop its root system is crucial to optimize root foraging in areas where nutrients are available. Cytokinin is an essential element of the systemic signaling network leading to the enhancement of lateral root proliferation in areas where nitrate is available. Here, we explore more precisely: (i) which particular traits of lateral root growth (density and length of emerged lateral roots) are the targets of systemic signaling in a context of heterogeneous nitrate supply; and (ii) if the systemic signaling depends only on cytokinin or on a combination of several signalings.
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Affiliation(s)
- Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM, Place Pierre Viala, 34060 Montpellier cedex, France
| | - Arthur Poitout
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM, Place Pierre Viala, 34060 Montpellier cedex, France
| | - Gabriel Krouk
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM, Place Pierre Viala, 34060 Montpellier cedex, France
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Benoit Lacombe
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM, Place Pierre Viala, 34060 Montpellier cedex, France
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22
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Krouk G, Carré C, Fizames C, Gojon A, Ruffel S, Lacombe B. GeneCloud Reveals Semantic Enrichment in Lists of Gene Descriptions. Mol Plant 2015; 8:971-973. [PMID: 25707756 DOI: 10.1016/j.molp.2015.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France.
| | - Clément Carré
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France; Institut de Modélisation Mathématique de Montpellier, CNRS UMR 5149, Université de Montpellier, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France
| | - Cecile Fizames
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France
| | - Alain Gojon
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France
| | - Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France
| | - Benoit Lacombe
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/ SupAgro/UM, Place Pierre Viala, 34060 Montpellier Cedex, France.
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23
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Medici A, Marshall-Colon A, Ronzier E, Szponarski W, Wang R, Gojon A, Crawford NM, Ruffel S, Coruzzi GM, Krouk G. AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun 2015. [PMID: 25723764 DOI: 10.1038/ncomms72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO3(-)) and phosphate (PO4(3-)) are also signalling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signalling pathways are integrated. Here we report the identification of a highly NO3(-)-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory elements. We demonstrate that this transcription factor and a close homologue repress the primary root growth in response to P deficiency conditions, but only when NO3(-) is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO3(-) and P signalling converge via double transcriptional and post-transcriptional control of the same protein, HRS1.
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Affiliation(s)
- Anna Medici
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Amy Marshall-Colon
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Elsa Ronzier
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Wojciech Szponarski
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Rongchen Wang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Alain Gojon
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
| | - Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, USA
| | - Gabriel Krouk
- Biochimie et Physiologie Moléculaire des Plantes, Institut Claude Grignon, UMR5004 CNRS/INRA/Supagro-M/UM2, Place Viala, F-34060 Montpellier cedex 2, France
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24
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Alvarez JM, Riveras E, Vidal EA, Gras DE, Contreras-López O, Tamayo KP, Aceituno F, Gómez I, Ruffel S, Lejay L, Jordana X, Gutiérrez RA. Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. Plant J 2014; 80:1-13. [PMID: 25039575 DOI: 10.1111/tpj.12618] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [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: 11/27/2013] [Revised: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 05/19/2023]
Abstract
Nitrate acts as a potent signal to control global gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly after nitrate treatments in roots. Global gene expression analysis revealed 97% of the genes with altered expression in tga1 tga4 double mutant plants respond to nitrate treatments, indicating that these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. We found TGA1 and TGA4 regulate the expression of nitrate transporter genes NRT2.1 and NRT2.2. Specific binding of TGA1 to its cognate DNA sequence on NRT2.1 and NRT2.2 promoters was confirmed by chromatin immunoprecipitation assays. The tga1 tga4 double mutant plants exhibit nitrate-dependent lateral and primary root phenotypes. Lateral root initiation is affected in both tga1 tga4 and nrt1.2 nrt2.2 double mutants, suggesting TGA1 and TGA4 regulate lateral root development at least partly via NRT2.1 and NRT2.2. Additional root phenotypes of tga1 tga4 double mutants indicate that these transcription factors play an important role in root developmental responses to nitrate. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots.
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Affiliation(s)
- José M Alvarez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Nucleus Center for Plant Functional Genomics, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
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25
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Li Y, Krouk G, Coruzzi GM, Ruffel S. Finding a nitrogen niche: a systems integration of local and systemic nitrogen signalling in plants. J Exp Bot 2014; 65:5601-10. [PMID: 24963003 DOI: 10.1093/jxb/eru263] [Citation(s) in RCA: 24] [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] [Indexed: 05/22/2023]
Abstract
The ability of plants to sense their nitrogen (N) microenvironment in the soil and deploy strategic root growth in N-rich patches requires exquisite systems integration. Remarkably, this new paradigm for systems biology research has intrigued plant biologists for more than a century, when a split-root framework was first used to study how plants sense and respond to heterogeneous soil nutrient environments. This systemic N-signalling mechanism, allowing plants to sense and forage for mineral nutrients in resource-rich patches, has important implications for agriculture. In this review, we will focus on how advances in the post-genomic era have uncovered the gene regulatory networks underlying systemic N-signalling. After defining how local and systemic N-signalling can be experimentally distinguished for molecular study using a split-root system, the genetic factors that have been shown to mediate local and/or systemic N-signalling are reviewed. Second, the genetic mechanism of this regulatory system is broadened to the whole genome level. To do this, publicly available N-related transcriptomic datasets are compared with genes that have previously been identified as local and systemic N responders in a split-root transcriptome dataset. Specifically, (i) it was found that transcriptional reprogramming triggered by homogeneous N-treatments is composed of both local and systemic responses, (ii) the spatio-temporal signature of local versus systemic responsive genes is defined, and (iii) the conservation of systemic N-signalling between Arabidopsis and Medicago is assessed. Finally, the potential mediators, i.e. metabolites and phytohormones, of the N-related long-distance signals, are discussed.
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Affiliation(s)
- Ying Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Gabriel Krouk
- Institut de Biologie Intégrative des Plantes-Claude Grignon, Unité Mixte de Recherche 5004, Biochimie et Physiologie Moléculaire des Plantes, Agro-M/Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro/Université Montpellier 2, F-34060 Montpellier, France
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sandrine Ruffel
- Institut de Biologie Intégrative des Plantes-Claude Grignon, Unité Mixte de Recherche 5004, Biochimie et Physiologie Moléculaire des Plantes, Agro-M/Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique/SupAgro/Université Montpellier 2, F-34060 Montpellier, France
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26
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Abstract
In most aerobic soils, nitrate (NO3(-)) is the main nitrogen source for plants and is often limiting for plant growth and development. To adapt to a changing environment, plants have developed complex regulatory mechanisms that involve short and long-range signalling pathways in response to both NO3(-) availability in the soil and other physiological processes like growth or nitrogen (N) and carbon (C) metabolisms. Over the past decade, transcriptomic approaches largely contributed to the identification of molecular elements involved in these regulatory mechanisms, especially at the level of root NO3(-)uptake. Most strikingly, the data obtained revealed the high level of interaction between N and both hormone and C signalling pathways, suggesting a strong dependence on growth, development, and C metabolism to adapt root NO3(-) uptake to both external NO3(-) availability and the N status of the plant. However, the signalling mechanisms involved in the cross-talk between N, C, and hormones for the regulation of root NO3(-) uptake remain largely obscure. The aim of this review is to discuss the recent advances concerning the regulatory pathways controlling NO3(-) uptake in response to N signalling, hormones, and C in the model plant Arabidopsis thaliana. Then, to further characterize the level of interaction between these signalling pathways we built on publicly available transcriptome data to determine how hormones and C treatments modify the gene network connecting root NO3(-) transporters and their regulators.
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Affiliation(s)
- Sandrine Ruffel
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
| | - Alain Gojon
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
| | - Laurence Lejay
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060 Montpellier cedex, France
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27
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Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G. TARGET: a transient transformation system for genome-wide transcription factor target discovery. Mol Plant 2013; 6:978-80. [PMID: 23335732 PMCID: PMC3660954 DOI: 10.1093/mp/sst010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Bastiaan O.R. Bargmann
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Amy Marshall-Colon
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Idan Efroni
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Sandrine Ruffel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France
| | - Kenneth D. Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Gloria M. Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- To whom correspondence should be addressed. G.K. E-mail , , tel. +0(33)499612518. G.M.C. E-mail
| | - Gabriel Krouk
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- Biochimie et Physiologie Moléculaire des Plantes, UMR 5004 CNRS/INRA/SupAgro-M/UM2, Institut de Biologie Intégrative des Plantes-Claude Grignon, Montpellier, France
- To whom correspondence should be addressed. G.K. E-mail , , tel. +0(33)499612518. G.M.C. E-mail
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28
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Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM. RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. Plant Physiol 2013; 161:1086-96. [PMID: 23335624 PMCID: PMC3585581 DOI: 10.1104/pp.112.210872] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/15/2013] [Indexed: 05/21/2023]
Abstract
The architecture of plant roots affects essential functions including nutrient and water uptake, soil anchorage, and symbiotic interactions. Root architecture comprises many features that arise from the growth of the primary and lateral roots. These root features are dictated by the genetic background but are also highly responsive to the environment. Thus, root system architecture (RSA) represents an important and complex trait that is highly variable, affected by genotype × environment interactions, and relevant to survival/performance. Quantification of RSA in Arabidopsis (Arabidopsis thaliana) using plate-based tissue culture is a very common and relatively rapid assay, but quantifying RSA represents an experimental bottleneck when it comes to medium- or high-throughput approaches used in mutant or genotype screens. Here, we present RootScape, a landmark-based allometric method for rapid phenotyping of RSA using Arabidopsis as a case study. Using the software AAMToolbox, we created a 20-point landmark model that captures RSA as one integrated trait and used this model to quantify changes in the RSA of Arabidopsis (Columbia) wild-type plants grown under different hormone treatments. Principal component analysis was used to compare RootScape with conventional methods designed to measure root architecture. This analysis showed that RootScape efficiently captured nearly all the variation in root architecture detected by measuring individual root traits and is 5 to 10 times faster than conventional scoring. We validated RootScape by quantifying the plasticity of RSA in several mutant lines affected in hormone signaling. The RootScape analysis recapitulated previous results that described complex phenotypes in the mutants and identified novel gene × environment interactions.
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29
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Krouk G, Ruffel S, Gutiérrez RA, Gojon A, Crawford NM, Coruzzi GM, Lacombe B. A framework integrating plant growth with hormones and nutrients. Trends Plant Sci 2011; 16:178-82. [PMID: 21393048 DOI: 10.1016/j.tplants.2011.02.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/02/2011] [Accepted: 02/07/2011] [Indexed: 05/03/2023]
Abstract
It is well known that nutrient availability controls plant development. Moreover, plant development is finely tuned by a myriad of hormonal signals. Thus, it is not surprising to see increasing evidence of coordination between nutritional and hormonal signaling. In this opinion article, we discuss how nitrogen signals control the hormonal status of plants and how hormonal signals interplay with nitrogen nutrition. We further expand the discussion to include other nutrient-hormone pairs. We propose that nutrition and growth are linked by a multi-level, feed-forward cycle that regulates plant growth, development and metabolism via dedicated signaling pathways that mediate nutrient and hormonal regulation. We believe this model will provide a useful concept for past and future research in this field.
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Affiliation(s)
- Gabriel Krouk
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
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30
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Ruffel S, Krouk G, Coruzzi GM. A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol 2010; 152:445-52. [PMID: 19939945 PMCID: PMC2815908 DOI: 10.1104/pp.109.148502] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 11/20/2009] [Indexed: 05/19/2023]
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31
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Jeudy C, Ruffel S, Freixes S, Tillard P, Santoni AL, Morel S, Journet EP, Duc G, Gojon A, Lepetit M, Salon C. Adaptation of Medicago truncatula to nitrogen limitation is modulated via local and systemic nodule developmental responses. New Phytol 2010; 185:817-28. [PMID: 20015066 DOI: 10.1111/j.1469-8137.2009.03103.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Adaptation of Medicago truncatula to local nitrogen (N) limitation was investigated to provide new insights into local and systemic N signaling. The split-root technique allowed a characterization of the local and systemic responses of NO(3)(-) or N(2)-fed plants to localized N limitation. (15)N and (13)C labeling were used to monitor plant nutrition. Plants expressing pMtENOD11-GUS and the sunn-2 hypernodulating mutant were used to unravel mechanisms involved in these responses. Unlike NO(3)(-)-fed plants, N(2)-fixing plants lacked the ability to compensate rapidly for a localized N limitation by up-regulating the N(2)-fixation activity of roots supplied elsewhere with N. However they displayed a long-term response via a growth stimulation of pre-existing nodules, and the generation of new nodules, likely through a decreased abortion rate of early nodulation events. Both these responses involve systemic signaling. The latter response is abolished in the sunn mutant, but the mutation does not prevent the first response. Local but also systemic regulatory mechanisms related to plant N status regulate de novo nodule development in Mt, and SUNN is required for this systemic regulation. By contrast, the stimulation of nodule growth triggered by systemic N signaling does not involve SUNN, indicating SUNN-independent signaling.
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Affiliation(s)
- Christian Jeudy
- Unité Mixte de Recherche en Génétique et Ecophysiologie des Légumineuses, UMR INRA 102, BP 86510, F-21065 Dijon, France
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Ruffel S, Freixes S, Balzergue S, Tillard P, Jeudy C, Martin-Magniette ML, van der Merwe MJ, Kakar K, Gouzy J, Fernie AR, Udvardi M, Salon C, Gojon A, Lepetit M. Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol 2008; 146:2020-35. [PMID: 18287487 PMCID: PMC2287368 DOI: 10.1104/pp.107.115667] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Accepted: 02/13/2008] [Indexed: 05/18/2023]
Abstract
Legumes can acquire nitrogen (N) from NO(3)(-), NH(4)(+), and N(2) (through symbiosis with Rhizobium bacteria); however, the mechanisms by which uptake and assimilation of these N forms are coordinately regulated to match the N demand of the plant are currently unknown. Here, we find by use of the split-root approach in Medicago truncatula plants that NO(3)(-) uptake, NH(4)(+) uptake, and N(2) fixation are under general control by systemic signaling of plant N status. Indeed, irrespective of the nature of the N source, N acquisition by one side of the root system is repressed by high N supply to the other side. Transcriptome analysis facilitated the identification of over 3,000 genes that were regulated by systemic signaling of the plant N status. However, detailed scrutiny of the data revealed that the observation of differential gene expression was highly dependent on the N source. Localized N starvation results, in the unstarved roots of the same plant, in a strong compensatory up-regulation of NO(3)(-) uptake but not of either NH(4)(+) uptake or N(2) fixation. This indicates that the three N acquisition pathways do not always respond similarly to a change in plant N status. When taken together, these data indicate that although systemic signals of N status control root N acquisition, the regulatory gene networks targeted by these signals, as well as the functional response of the N acquisition systems, are predominantly determined by the nature of the N source.
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Affiliation(s)
- Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, UMR 5004, INRA-CNRS-Sup Agro-UM2, Institut de Biologie Intégrative des Plantes, F-34060 Montpellier, France
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Ruffel S, Gallois JL, Moury B, Robaglia C, Palloix A, Caranta C. Simultaneous mutations in translation initiation factors eIF4E and eIF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper. J Gen Virol 2006; 87:2089-2098. [PMID: 16760413 DOI: 10.1099/vir.0.81817-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Capsicum resistance to Pepper veinal mottle virus (PVMV) results from complementation between the pvr2 and pvr6 resistance genes: recessive alleles at these two loci are necessary for resistance, whereas any dominant allele confers susceptibility. In line with previous results showing that pvr2 resistance alleles encode mutated versions of the eukaryotic translation initiation factor 4E (eIF4E), the involvement of other members of the eIF4E multigenic family in PVMV resistance was investigated. It was demonstrated that pvr6 corresponds to an eIF(iso)4E gene, predicted to encode the second cap-binding isoform identified in plants. Comparative genetic mapping in pepper and tomato indicated that eIF(iso)4E maps in the same genomic region as pvr6. Sequence analysis revealed an 82 nt deletion in eIF(iso)4E cDNAs from genotypes with the pvr6 resistance allele, leading to a truncated protein. This deletion was shown to co-segregate with pvr6 in doubled haploid and F(2) progeny. Transient expression in a PVMV-resistant genotype of eIF(iso)4E derived from a genotype with the pvr6(+) susceptibility allele resulted in loss of resistance to subsequent PVMV inoculation, confirming that pvr6 encodes the translation factor eIF(iso)4E. Similarly, transient expression of eIF4E from a genotype with the pvr2(+)-eIF4E susceptibility allele also resulted in loss of resistance, demonstrating that wild-type eIF4E and eIF(iso)4E are susceptibility factors for PVMV and that resistance results from the combined effect of mutations in the two cap-binding isoforms. Thus, whilst most potyviruses specifically require one eIF4E isoform to perform their replication cycle, PVMV uses either eIF4E or eIF(iso)4E for infection of pepper.
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Affiliation(s)
- Sandrine Ruffel
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Jean-Luc Gallois
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Benoît Moury
- Plant Pathology, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, CEA-CNRS-Université Aix-Marseille II, Faculté des Sciences de Luminy, F-13009 Marseille, France
| | - Alain Palloix
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Carole Caranta
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
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Ruffel S, Gallois JL, Lesage ML, Caranta C. The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol Genet Genomics 2005; 274:346-53. [PMID: 15971038 DOI: 10.1007/s00438-005-0003-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/27/2005] [Indexed: 10/25/2022]
Abstract
The translation initiation factor 4E (eIF4E) has been implicated in naturally occurring resistance to Potato virus Y (PVY) determined by the pvr2 locus in pepper (Capsicum annuum). Here, the molecular basis of the recessive resistance to PVY and Tobacco etch virus (TEV) controlled by the pot-1 locus in tomato (Lycopersicon esculentum; now Solanum lycopersicum) was investigated. On the basis of genetic mapping data that indicated that pot-1 and pvr2 are located in syntenic regions of the tomato and pepper genomes, the possible involvement of eIF4E in pot-1-mediated resistance was assessed. Genetic mapping of members of the eIF4E multigenic family in tomato introgression lines revealed that an eIF4E locus indeed maps in the same genomic region as pot-1. By comparing eIF4E coding sequences between resistant and susceptible Lycopersicon genotypes, a small number of polymorphisms that co-segregate with the pot-1 locus were identified, suggesting that this gene could be involved in resistance to potyviruses. Functional complementation experiments using Potato virus X-mediated transient expression of eIF4E from a susceptible genotype in a resistant pepper genotype confirmed that a small number of amino acid substitutions in the eIF4E protein indeed account for resistance/susceptibility to both the PVY and TEV, and consequently that pot-1 and pvr2 are orthologues. Taken together, these results support the role of this eIF4E gene as a key component of recessive resistance to potyviruses, and validate the comparative genomic approach for the molecular characterization of recessive resistance genes.
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Affiliation(s)
- S Ruffel
- Institut National de la Recherche Agronomique, Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, BP94, 84143, Montfavet Cedex, France
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Ruffel S, Caranta C, Palloix A, Lefebvre V, Caboche M, Bendahmane A. Structural analysis of the eukaryotic initiation factor 4E gene controlling potyvirus resistance in pepper: exploitation of a BAC library. Gene 2004; 338:209-16. [PMID: 15315824 DOI: 10.1016/j.gene.2004.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2003] [Revised: 04/21/2004] [Accepted: 05/17/2004] [Indexed: 11/28/2022]
Abstract
The pvr2 locus in pepper codes for a eukaryotic translation initiation factor 4E (eIF4E) gene that confers resistance to viruses belonging to the potyvirus genus. In this work, we describe the isolation and characterisation of the genomic sequence carrying the pvr2 locus. A Bacterial Artificial Chromosome (BAC) library that consisted of 239,232 clones with an average insert size of 123 kilobases (kb) was constructed from a Capsicum annuum line with the pvr2(+) allele for susceptibility to potato virus Y (PVY) and tobacco etch virus (TEV). Based on a polymerase chain reaction (PCR) screen with single-copy markers, three to seven positive BAC clones per markers were identified, indicating that the BAC library is suitable for pepper genome analysis. To determine the genomic organization of the pepper eIF4E gene, the library was screened with primers designed from the cDNA sequence and four positive BAC clones carrying the pvr2 locus were identified. A 7-kb DNA fragment containing the complete eIF4E gene was sub-cloned from the positive BAC clones and analysed. The eIF4E gene is organised into five exons and four introns and showed a strictly conserved exon/intron structure with eIF4E genes from Arabidopsis thaliana and rice. Moreover, the splice sites between plant exons 1/2 and 2/3 are conserved among eukaryotes including human, Drosophila and yeast. Several potential binding sites for MADS box transcription factors within the 5' flanking region of eIF4E genes from the three plant species were also predicted.
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Affiliation(s)
- Sandrine Ruffel
- INRA, Plant Genomics Research Unit, 2 rue G. Cremieux, CP 5708, F-91057 Evry Cedex, France
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Asnaghi C, Roques D, Ruffel S, Kaye C, Hoarau JY, Télismart H, Girard JC, Raboin LM, Risterucci AM, Grivet L, D'Hont A. Targeted mapping of a sugarcane rust resistance gene (Bru1) using bulked segregant analysis and AFLP markers. Theor Appl Genet 2004; 108:759-64. [PMID: 14586507 DOI: 10.1007/s00122-003-1487-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 08/28/2003] [Indexed: 05/07/2023]
Abstract
The presence of a major resistance gene (Bru1) for brown rust in the sugarcane cultivar R570 (2n about 115) was confirmed by analyzing segregation of rust resistance in a large population of 658 individuals, derived from selfing of clone R570. A subset of this population was analyzed with AFLP and bulked segregant analysis (BSA) to develop a detailed genetic map around the resistance gene. Four hundred and forty three primer pairs were used resulting in the identification of eight AFLP markers surrounding the resistance gene in an interval of 10 cM, with the closest markers located at 1.9 and 2.2 cM on each side of the gene. Efficiency of the AFLP/BSA applied to the complex polyploid genome of sugarcane is discussed, as well as the potential of the newly identified AFLP markers for developing a map-based cloning approach exploiting, synteny conservation with sorghum.
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Affiliation(s)
- C Asnaghi
- CIRAD, UMR 1096, TA40/03, avenue Agropolis, 34398, Montpellier Cedex 5, France
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Ruffel S, Dussault MH, Palloix A, Moury B, Bendahmane A, Robaglia C, Caranta C. A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukaryotic initiation factor 4E (eIF4E). Plant J 2002; 32:1067-75. [PMID: 12492847 DOI: 10.1046/j.1365-313x.2002.01499.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We show here that the pvr2 locus in pepper, conferring recessive resistance against strains of potato virus Y (PVY), corresponds to a eukaryotic initiation factor 4E (eIF4E) gene. RFLP analysis on the PVY-susceptible and resistant pepper cultivars, using an eIF4E cDNA from tobacco as probe, revealed perfect map co-segregation between a polymorphism in the eIF4E gene and the pvr2 alleles, pvr2(1) (resistant to PVY-0) and pvr2(2) (resistant to PVY-0 and 1). The cloned pepper eIF4E cDNA encoded a 228 amino acid polypeptide with 70-86% nucleotide sequence identity with other plant eIF4Es. The sequences of eIF4E protein from two PVY-susceptible cultivars were identical and differed from the eIF4E sequences of the two PVY-resistant cultivars Yolo Y (YY) (pvr2(1)) and FloridaVR2 (F) (pvr2(2)) at two amino acids, a mutation common to both resistant genotypes and a second mutation specific to each. Complementation experiments were used to show that the eIF4E gene corresponds to pvr2. Thus, potato virus X-mediated transient expression of eIF4E from susceptible cultivar Yolo Wonder (YW) in the resistant genotype YY resulted in loss of resistance to subsequent PVY-0 inoculation and transient expression of eIF4E from YY (resistant to PVY-0; susceptible to PVY-1) rendered genotype F susceptible to PVY-1. Several lines of evidence indicate that interaction between the potyvirus genome-linked protein (VPg) and eIF4E are important for virus infectivity, suggesting that the recessive resistance could be due to incompatibility between the VPg and eIF4E in the resistant genotype.
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Affiliation(s)
- Sandrine Ruffel
- Genetics and Breeding of Fruits and Vegetable, Dom St Maurice, BP94, F-84143 Montfavet
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Parrella G, Ruffel S, Moretti A, Morel C, Palloix A, Caranta C. Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato ( Lycopersicon spp.) and pepper ( Capsicum spp.) genomes. Theor Appl Genet 2002; 105:855-861. [PMID: 12582910 DOI: 10.1007/s00122-002-1005-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2002] [Accepted: 03/15/2002] [Indexed: 05/24/2023]
Abstract
Resistance against both Potato virus Y (PVY) and Tobacco etch virus (TEV) was identified in the wild tomato relative Lycopersicon hirsutum PI247087. Analysis of the segregation ratio in F(2)/F(3) and BC(1) interspecific progenies indicated that a single recessive gene, or two very tightly linked recessive loci, are involved in resistance to both potyviruses. This locus was named pot-1. Using amplified fragment length polymorphism markers and a set of L. hirsutum introgression lines, pot-1 was mapped to the short arm of tomato chromosome 3, in the vicinity of the recessive py-1 locus for resistance to corky root rot. Because of the occurrence of phenotypically similar genes in pepper ( Capsicum spp.), the comparative genetics of resistance to potyviruses between tomato and pepper was investigated. Unlike most of the comparative genetic studies on resistance genes, pot-1 was tightly flanked by the same restriction fragment length polymorphism (RFLP) markers than the pvr2/pvr5 locus for resistance to PVY and TEV from pepper. These results may indicate that recessive resistance genes against potyviruses evolve less rapidly than the majority of the dominant genes cloned so far, and consequently may belong to a different family of resistance genes.
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Affiliation(s)
- G. Parrella
- Institut National de la Recherche Agronomique (INRA), Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, BP94, 84143 Montfavet cedex, France
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