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1. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

Author

José M. Alvarez, Anna-Lena Schinke, Matthew D. Brooks, Angelo Pasquino, Lauriebeth Leonelli, Kranthi Varala, Alaeddine Safi, Gabriel Krouk, Anne Krapp, and Gloria M. Coruzzi

Subjects
Science
Abstract

Conventional methods cannot reveal transient transcription factors (TFs) and targets interactions. Here, Alvarez et al. capture both stable and transient TF-target interactions by time-series ChIP-seq and/or DamID-seq in a cell-based TF perturbation system and show NLP7 as a master TF to initiate a rapid nitrogen-response cascade.

Published
2020
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2. LPCAT1 controls phosphate homeostasis in a zinc-dependent manner

Author

Mushtak Kisko, Nadia Bouain, Alaeddine Safi, Anna Medici, Robert C Akkers, David Secco, Gilles Fouret, Gabriel Krouk, Mark GM Aarts, Wolfgang Busch, and Hatem Rouached

Subjects
natural variation, phosphate homeostasis, zinc deficiency, Medicine, Science, Biology (General), QH301-705.5
Abstract

All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation.

Published
2018
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5. Phase separation to visualize protein-protein interactions and kinase activities in planta

Author

Alaeddine Safi, Wouter Smagghe, Amanda Goncalves, Benjamin Cappe, Franck Riquet, Evelyn Mylle, Daniël Van Damme, Danny Geelen, Geert De Jaeger, Tom Beeckman, Jelle Van Leene, and Steffen Vanneste

Abstract

Protein complex formation and dynamic post-translational modifications are notoriously difficult to monitor at cellular resolution. Here, we developed a versatile modular toolbox of fluorescently labelled, artificial homo-oligomerizing peptide-tags (HOTag) that install interaction-dependent liquid-liquid phase-separation upon interaction between two proteins of interest. We deployed our novel toolbox for the in planta visualization of inducible, binary and ternary protein-protein interactions (PPIs), as well as specific phosphorylation, showing its great potential to become a robust standard technique to study PPIs and phosphorylation in plants.

Published
2022

6. Phase separation-based visualization of protein-protein interactions and kinase activities in plants

Author

Alaeddine Safi, Wouter Smagghe, Amanda Gonçalves, Ke Xu, Ana Ibis Fernandez, Benjamin Cappe, Franck B. Riquet, Evelien Mylle, Daniël Van Damme, Danny Geelen, Geert De Jaeger, Tom Beeckman, Jelle Van Leene, and Steffen Vanneste

Abstract

Protein activities depend heavily on protein complex formation and dynamic post-translational modifications, such as phosphorylation. Their dynamic nature is notoriously difficult to monitor in planta at cellular resolution, often requiring extensive optimization and high-end microscopy. Here, we generated and exploited the SYnthetic Multivalency in PLants (SYMPL)-vector set to study protein-protein interactions (PPIs) and kinase activities in planta based on phase separation. This technology enabled easy detection of inducible, binary and ternary protein-protein interactions among cytoplasmic, nuclear and plasma membrane proteins in plant cells via a robust image-based readout. Moreover, we applied the SYMPL toolbox to develop an in vivo reporter for SnRK1 kinase activity, allowing us to visualize tissue-specific, dynamic SnRK1 activation upon energy deprivation in stable transgenic Arabidopsis plants. The applications of the SYMPL cloning toolbox lay the foundation for the exploration of PPIs, phosphorylation and other post-translational modifications with unprecedented ease and sensitivity.

Published
2022

8. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways

Author

Florence Martin, Wojciech Szponarski, Alaeddine Safi, Anne Clément-Vidal, Anna Medici, Gloria M. Coruzzi, Sandrine Ruffel, Amy Marshall-Colon, Hatem Rouached, Frédéric Gaymard, Julie Leclercq, Gabriel Krouk, Benoît Lacombe, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), and ANR-14-CE19-0008,IMANA,Identification de régulations moléculaires majeures impliquées dans l'adaptation des plantes à la disponibilité en azote(2014)

Subjects
0106 biological sciences, 0301 basic medicine, GARP transcription factors, Physiology, [SDV]Life Sciences [q-bio], Plant Science, METABOLISM, 01 natural sciences, 03 medical and health sciences, HYDROGEN-PEROXIDE, TGA FACTORS, Glutaredoxin, Arabidopsis, root protoplasts, NITRATE TRANSPORTER, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, Gene, LONG-DISTANCE, 2. Zero hunger, THALIANA, biology, Chemistry, Biology and Life Sciences, ROS, plant growth, biology.organism_classification, GENE, NO3-UPTAKE, Cell biology, Cell sorting, PLANT-RESPONSES, 030104 developmental biology, TARGET, Nitrate transport, root nitrate uptake, Signal transduction, Starvation response, nitrogen starvation response, GLUTAREDOXINS, Functional genomics, 010606 plant biology & botany
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.

Published
2021

9. The mechanism of auxin transport in lateral root spacing

Author

Jian Chen, Alaeddine Safi, Hugues De Gernier, Steffen Vanneste, and Tom Beeckman

Subjects
chemistry.chemical_classification, Indoleacetic Acids, Mechanism (biology), Lateral root, Arabidopsis, Biological Transport, Plant Science, Biology, Plant Roots, Plant science, chemistry, Plant Growth Regulators, Auxin, Mutation, Biophysics, Molecular Biology
Published
2021

10. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade

Author

Angelo Pasquino, Matthew D. Brooks, Gabriel Krouk, Anne Krapp, Lauriebeth Leonelli, Gloria M. Coruzzi, Alaeddine Safi, Anna Lena Schinke, José M. Alvarez, Kranthi Varala, Center for Genomics and Systems Biology, Centro de Genómica y Bioinformática, Department of Horticulture and Landscape Architecture, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-14-CE19-0008,IMANA,Identification de régulations moléculaires majeures impliquées dans l'adaptation des plantes à la disponibilité en azote(2014)

Subjects
0106 biological sciences, 0301 basic medicine, Transcription, Genetic, Dynamic networks, [SDV]Life Sciences [q-bio], genetic processes, Arabidopsis, Gene regulatory network, PROTEIN, General Physics and Astronomy, Plant Roots, 01 natural sciences, Gene Expression Regulation, Plant, Transcription (biology), perturbateur environnemental, lcsh:Science, Regulation of gene expression, Multidisciplinary, Chemistry, Cell biology, Signal transduction, Reprogramming, Genome, Plant, NITRATE RESPONSE, Plant molecular biology, Nitrogen, Science, Active Transport, Cell Nucleus, Genetics and Molecular Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Gene expression analysis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, natural sciences, Gene, Transcription factor, Binding Sites, IDENTIFICATION, Arabidopsis Proteins, Biology and Life Sciences, General Chemistry, 030104 developmental biology, Plant signalling, General Biochemistry, lcsh:Q, Chromatin immunoprecipitation, Transcription Factors, 010606 plant biology & botany
Abstract

Dynamic reprogramming of gene regulatory networks (GRNs) enables organisms to rapidly respond to environmental perturbation. However, the underlying transient interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical detection. Here, we capture both stable and transient TF-target interactions genome-wide within minutes after controlled TF nuclear import using time-series chromatin immunoprecipitation (ChIP-seq) and/or DNA adenine methyltransferase identification (DamID-seq). The transient TF-target interactions captured uncover the early mode-of-action of NIN-LIKE PROTEIN 7 (NLP7), a master regulator of the nitrogen signaling pathway in plants. These transient NLP7 targets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes not detectably bound by NLP7 in planta. Rapid and transient NLP7 binding activates early nitrogen response TFs, which we validate to amplify the NLP7-initiated transcriptional cascade. Our approaches to capture transient TF-target interactions genome-wide can be applied to validate dynamic GRN models for any pathway or organism of interest., Conventional methods cannot reveal transient transcription factors (TFs) and targets interactions. Here, Alvarez et al. capture both stable and transient TF-target interactions by time-series ChIP-seq and/or DamID-seq in a cell-based TF perturbation system and show NLP7 as a master TF to initiate a rapid nitrogen-response cascade.

Published
2020

11. The world according to GARP transcription factors

Author

Wojciech Szponarski, Anna Medici, Sandrine Ruffel, Benoît Lacombe, Alaeddine Safi, Gabriel Krouk, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Circadian clock, Plant Science, Nutrient sensing, 01 natural sciences, 03 medical and health sciences, transcription factors, Arabidopsis, Oscillation (cell signaling), MYB, Transcription factor, Gene, phosphate, 2. Zero hunger, biology, Arabidopsis Proteins, Ecology, nitrogène, fungi, food and beverages, DNA, Plants, 15. Life on land, biology.organism_classification, Protein Structure, Tertiary, DNA metabolism, arabidopsis, 030104 developmental biology, Evolutionary biology, inorganic phosphates, facteur de transcription, 010606 plant biology & botany
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.

Published
2017

12. Identification of molecular integrators shows that nitrogen actively controls the phosphate starvation response in plants

Author

Amélie Emanuel, Milos Tanurdzic, Pierre Dangeville, Wojciech Szponarski, Hatem Rouached, Vicente Rubio, Benoît Lacombe, Sandrine Ruffel, Anna Medici, Gabriel Krouk, Indeewari Madhubhashini Dissanayake, Alaeddine Safi, Chorpet Saenchai, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), School of Biological Sciences, Centre for Marine Science, School of Biological Sciences, University of Queensland, University of Queensland [Brisbane], Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche (France), Centre National de la Recherche Scientifique (France), National Science Foundation (US), and Ministerio de Economía y Competitividad (España)

Subjects
0106 biological sciences, 0301 basic medicine, Nitrogen, phosphorus (P), [SDV]Life Sciences [q-bio], Mutant, Anion Transport Proteins, Arabidopsis, Triticum aestivum, Environmental pollution, Oryza sativa, Plant Science, 01 natural sciences, Phosphates, 03 medical and health sciences, chemistry.chemical_compound, PHOSPHATE STARVATION RESPONSE, Nitrate, Gene Expression Regulation, Plant, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Research Articles, Triticum, Plant Proteins, 2. Zero hunger, Nitrates, biology, Arabidopsis Proteins, Crop yield, food and beverages, Oryza, Phosphorus, Cell Biology, biology.organism_classification, Crosstalk (biology), 030104 developmental biology, chemistry, environmental pollution, Starvation response, Nitrogen (N), 010606 plant biology & botany, Signal Transduction, Transcription Factors
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., This work was supported in the Honude group (Biochemistry & Plant Molecular Physiology) by Agence Nationale de la Recherche (IMANA ANR-14-CE19-0008 with a doctoral fellowship to A.S.), by the Centre National de la Recherche Scientifique (CNRS LIA-CoopNet to G.K.), and by the National Science Foundation (NSF IOS 1339362-NutriNet). Research in V.R.’s laboratory was funded by the Ministry of Economy and Competitiveness and AEI/FEDER/European (grants BIO2013-46539-R and BIO2016-80551-R).

Published
2019

13. HRS1/HHOs GARP transcription factors and reactive oxygen species are regulators of Arabidopsis nitrogen starvation response

Author

Wojciech Szponarski, Sandrine Ruffel, Gloria M. Coruzzi, Frédéric Gaymard, Amy Marshall-Colon, Anna Medici, Alaeddine Safi, Gabriel Krouk, Benoît Lacombe, Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Equipe Hormones, Nutriments et Développement (HoNuDe) ( HONUDE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Department of Biology, University of Minho, New York University, Equipe Nutrition Minérale et Stress Oxydatif ( FEROS ), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), New York University [New York] (NYU), NYU System (NYU), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and Equipe Nutrition Minérale et Stress Oxydatif (FEROS)

Subjects
0106 biological sciences, 2. Zero hunger, Molecular breeding, transport de nitrate, 0303 health sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, biology, Wild type, biology.organism_classification, 01 natural sciences, Cell biology, 03 medical and health sciences, arabidopsis, Nitrate transport, absorption azotée, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, espèce reactive de l'oxygène, Starvation response, Transcription factor, Gene, Functional genomics, azote du sol, 030304 developmental biology, 010606 plant biology & botany
Abstract

Plants need to cope with strong variations in the nitrogen content of the soil solution. Although many molecular actors are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of Nitrogen. Indeed, following N removal plants activate their Nitrogen Starvation Response (NSR) being characterized in particular by the activation of very high affinity nitrate transport systems (NRT2.4, NRT2.5) and other sentinel genes such as GDH3. Here we show using a combination of functional genomics (via TF perturbation) and molecular physiology studies, that the GARP Transcription Factors (TFs) belonging the HHO sub-family are important regulators of the NSR through two potential mechanisms. First, HHOs directly repress NRT2.4 and NRT2.5 high-affinity nitrate transporters. Genotypes affected in HHO genes (mutants and overexpressors) display modified high-affinity nitrate transport activities opening interesting perspectives in biotechnology applications. Second, we show that Reactive Oxygen Species (ROS) are important to control NSR in wild type plants and that HRS1 and HHO1 overexpressors are affected in their ROS content, defining a potential feedforward branch of the signaling pathway. Taken together our results define two new classes of molecular actors in the control of NSR including ROS and the first transcription factors to date. This work (i) opens perspectives on a poorly understood nutrient related signaling pathway, and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.

Published
2018

15. LPCAT1 controls phosphate homeostasis in a zinc-dependent manner

Author

Robert C. Akkers, Gabriel Krouk, David Secco, Alaeddine Safi, Gilles Fouret, Hatem Rouached, Anna Medici, Wolfgang Busch, Mushtak Kisko, Mark G. M. Aarts, Nadia Bouain, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratory of Genetics, Wageningen University, Dynamique Musculaire et Métabolisme (DMEM), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM), Institut des sciences biologiques (INSB), Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Wageningen University and Research [Wageningen] (WUR), Institut des sciences biologiques (INSB-CNRS), and Rouached, Hatem

Subjects
0301 basic medicine, chemistry.chemical_compound, phosphate homeostasis, Arabidopsis, Gene expression, zinc deficiency, natural variation, NETWORK, Biology (General), ADAPTATION, GENE-EXPRESSION, Regulation of gene expression, plant biology, Vegetal Biology, biology, General Neuroscience, zinc, food and beverages, General Medicine, respiratory system, ARABIDOPSIS, LYSOPHOSPHATIDYLCHOLINE, Cell biology, DEFICIENCY, PHOSPHORUS, Acyltransferase, buildup, Medicine, Laboratory of Genetics, lipids (amino acids, peptides, and proteins), inorganic phosphates, QH301-705.5, Science, Phospholipid, Laboratorium voor Erfelijkheidsleer, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Life Science, Groep Koornneef, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, PLANTS, GENOME-WIDE ASSOCIATION, Gene, phosphate, General Immunology and Microbiology, Biology and Life Sciences, Transporter, biology.organism_classification, 030104 developmental biology, chemistry, MICRORNA399, A. thaliana, EPS, accumulation, Homeostasis, Biologie végétale
Abstract

All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation.

Published
2018

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