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Pahuja S, Bheri M, Bisht D, Pandey GK. Calcium signalling components underlying NPK homeostasis: potential avenues for exploration. Biochem J 2023; 480:1015-1034. [PMID: 37418287 DOI: 10.1042/bcj20230156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Plants require the major macronutrients, nitrogen (N), phosphorus (P) and potassium (K) for normal growth and development. Their deficiency in soil directly affects vital cellular processes, particularly root growth and architecture. Their perception, uptake and assimilation are regulated by complex signalling pathways. To overcome nutrient deficiencies, plants have developed certain response mechanisms that determine developmental and physiological adaptations. The signal transduction pathways underlying these responses involve a complex interplay of components such as nutrient transporters, transcription factors and others. In addition to their involvement in cross-talk with intracellular calcium signalling pathways, these components are also engaged in NPK sensing and homeostasis. The NPK sensing and homeostatic mechanisms hold the key to identify and understand the crucial players in nutrient regulatory networks in plants under both abiotic and biotic stresses. In this review, we discuss calcium signalling components/pathways underlying plant responses to NPK sensing, with a focus on the sensors, transporters and transcription factors involved in their respective signalling and homeostasis.
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Affiliation(s)
- Sonam Pahuja
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Diksha Bisht
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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Asim M, Ullah Z, Xu F, An L, Aluko OO, Wang Q, Liu H. Nitrate Signaling, Functions, and Regulation of Root System Architecture: Insights from Arabidopsis thaliana. Genes (Basel) 2020; 11:E633. [PMID: 32526869 PMCID: PMC7348705 DOI: 10.3390/genes11060633] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 01/07/2023] Open
Abstract
Root system architecture (RSA) is required for the acquisition of water and mineral nutrients from the soil. One of the essential nutrients, nitrate (NO3-), is sensed and transported by nitrate transporters NRT1.1 and NRT2.1 in the plants. Nitrate transporter 1.1 (NRT1.1) is a dual-affinity nitrate transporter phosphorylated at the T101 residue by calcineurin B-like interacting protein kinase (CIPKs); it also regulates the expression of other key nitrate assimilatory genes. The differential phosphorylation (phosphorylation and dephosphorylation) strategies and underlying Ca2+ signaling mechanism of NRT1.1 stimulate lateral root growth by activating the auxin transport activity and Ca2+-ANR1 signaling at the plasma membrane and the endosomes, respectively. NO3- additionally functions as a signal molecule that forms a signaling system, which consists of a vast array of transcription factors that control root system architecture that either stimulate or inhibit lateral and primary root development in response to localized and high nitrate (NO3-), respectively. This review elucidates the so-far identified nitrate transporters, nitrate sensing, signal transduction, and the key roles of nitrate transporters and its downstream transcriptional regulatory network in the primary and lateral root development in Arabidopsis thaliana under stress conditions.
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Affiliation(s)
- Muhammad Asim
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zia Ullah
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Fangzheng Xu
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Lulu An
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Oluwaseun Olayemi Aluko
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Qian Wang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Haobao Liu
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (M.A.); (Z.U.); (L.A.); (O.O.A.)
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Vissenberg K, Claeijs N, Balcerowicz D, Schoenaers S. Hormonal regulation of root hair growth and responses to the environment in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2412-2427. [PMID: 31993645 PMCID: PMC7178432 DOI: 10.1093/jxb/eraa048] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/23/2020] [Indexed: 05/04/2023]
Abstract
The main functions of plant roots are water and nutrient uptake, soil anchorage, and interaction with soil-living biota. Root hairs, single cell tubular extensions of root epidermal cells, facilitate or enhance these functions by drastically enlarging the absorptive surface. Root hair development is constantly adapted to changes in the root's surroundings, allowing for optimization of root functionality in heterogeneous soil environments. The underlying molecular pathway is the result of a complex interplay between position-dependent signalling and feedback loops. Phytohormone signalling interconnects this root hair signalling cascade with biotic and abiotic changes in the rhizosphere, enabling dynamic hormone-driven changes in root hair growth, density, length, and morphology. This review critically discusses the influence of the major plant hormones on root hair development, and how changes in rhizosphere properties impact on the latter.
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Affiliation(s)
- Kris Vissenberg
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
- Plant Biochemistry and Biotechnology Lab, Department of Agriculture, Hellenic Mediterranean University, Stavromenos PC, Heraklion, Crete, Greece
| | - Naomi Claeijs
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Daria Balcerowicz
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Sébastjen Schoenaers
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
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Rashid M, Bera S, Medvinsky AB, Sun GQ, Li BL, Chakraborty A. Adaptive Regulation of Nitrate Transceptor NRT1.1 in Fluctuating Soil Nitrate Conditions. iScience 2018; 2:41-50. [PMID: 30428377 PMCID: PMC6135930 DOI: 10.1016/j.isci.2018.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/12/2018] [Accepted: 02/22/2018] [Indexed: 12/23/2022] Open
Abstract
Plant adaptation in variable soil nitrate concentrations involves sophisticated signaling and transport systems that modulate a variety of physiological and developmental responses. However, we know very little about their molecular mechanisms. It has recently been reported that many of these responses are regulated by a transceptor NRT1.1, a transporter cum receptor of nitrate signaling. NRT1.1 displays dual-affinity modes of nitrate binding and establishes phosphorylated/non-phosphorylated states at the amino acid residue threonine 101 in response to fluctuating nitrate concentrations. Here we report that intrinsic structural asymmetries between the protomers of the homodimer NRT1.1 provide a functional basis for having dual-affinity modes of nitrate binding and play a pivotal role for the phosphorylation switch. Nitrate-triggered local conformational changes facilitate allosteric communications between the nitrate binding and the phosphorylation site in one protomer, but such communications are impeded in the other. Structural analysis therefore suggests the functional relevance of NRT1.1 interprotomer asymmetries. NRT1.1 interprotomer asymmetry provides a functional basis for dual affinity Nitrate-triggered conformational changes facilitate intraprotomer allostery NRT1.1 interprotomer asymmetry is correlated with the phosphorylation switch Allostery plays a critical role in regulating the phosphorylation
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Affiliation(s)
- Mubasher Rashid
- School of Mathematics, Statistics and Computational Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, India
| | - Soumen Bera
- School of Mathematics, Statistics and Computational Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, India
| | | | - Gui-Quan Sun
- Department of Mathematics, Shanxi University, Taiyuan, People's Republic of China
| | - Bai-Lian Li
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Amit Chakraborty
- School of Mathematics, Statistics and Computational Sciences, Central University of Rajasthan, Bandarsindri, Ajmer, India; Department of Botany and Plant Sciences, University of California, Riverside, USA.
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Steyfkens F, Zhang Z, Van Zeebroeck G, Thevelein JM. Multiple Transceptors for Macro- and Micro-Nutrients Control Diverse Cellular Properties Through the PKA Pathway in Yeast: A Paradigm for the Rapidly Expanding World of Eukaryotic Nutrient Transceptors Up to Those in Human Cells. Front Pharmacol 2018; 9:191. [PMID: 29662449 PMCID: PMC5890159 DOI: 10.3389/fphar.2018.00191] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/20/2018] [Indexed: 12/17/2022] Open
Abstract
The nutrient composition of the medium has dramatic effects on many cellular properties in the yeast Saccharomyces cerevisiae. In addition to the well-known specific responses to starvation for an essential nutrient, like nitrogen or phosphate, the presence of fermentable sugar or a respirative carbon source leads to predominance of fermentation or respiration, respectively. Fermenting and respiring cells also show strong differences in other properties, like storage carbohydrate levels, general stress tolerance and cellular growth rate. However, the main glucose repression pathway, which controls the switch between respiration and fermentation, is not involved in control of these properties. They are controlled by the protein kinase A (PKA) pathway. Addition of glucose to respiring yeast cells triggers cAMP synthesis, activation of PKA and rapid modification of its targets, like storage carbohydrate levels, general stress tolerance and growth rate. However, starvation of fermenting cells in a glucose medium for any essential macro- or micro-nutrient counteracts this effect, leading to downregulation of PKA and its targets concomitant with growth arrest and entrance into G0. Re-addition of the lacking nutrient triggers rapid activation of the PKA pathway, without involvement of cAMP as second messenger. Investigation of the sensing mechanism has revealed that the specific high-affinity nutrient transporter(s) induced during starvation function as transporter-receptors or transceptors for rapid activation of PKA upon re-addition of the missing substrate. In this way, transceptors have been identified for amino acids, ammonium, phosphate, sulfate, iron, and zinc. We propose a hypothesis for regulation of PKA activity by nutrient transceptors to serve as a conceptual framework for future experimentation. Many properties of transceptors appear to be similar to those of classical receptors and nutrient transceptors may constitute intermediate forms in the development of receptors from nutrient transporters during evolution. The nutrient-sensing transceptor system in yeast for activation of the PKA pathway has served as a paradigm for similar studies on candidate nutrient transceptors in other eukaryotes and we succinctly discuss the many examples of transceptors that have already been documented in other yeast species, filamentous fungi, plants, and animals, including the examples in human cells.
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Affiliation(s)
- Fenella Steyfkens
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Zhiqiang Zhang
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Flanders, Belgium
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Fan X, Naz M, Fan X, Xuan W, Miller AJ, Xu G. Plant nitrate transporters: from gene function to application. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2463-2475. [PMID: 28158856 DOI: 10.1093/jxb/erx011] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We summarize nitrate transporters and discuss their potential in breeding for improved nitrogen use efficiency and yield.
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Affiliation(s)
- Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Misbah Naz
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoru Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Anthony J Miller
- Metabolic Biology Department, John Innes Centre, Norwich Research Park , Norwich NR4 7UH, UK
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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O'Brien JA, Vega A, Bouguyon E, Krouk G, Gojon A, Coruzzi G, Gutiérrez RA. Nitrate Transport, Sensing, and Responses in Plants. MOLECULAR PLANT 2016; 9:837-56. [PMID: 27212387 DOI: 10.1016/j.molp.2016.05.004] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) is an essential macronutrient that affects plant growth and development. N is an important component of chlorophyll, amino acids, nucleic acids, and secondary metabolites. Nitrate is one of the most abundant N sources in the soil. Because nitrate and other N nutrients are often limiting, plants have developed sophisticated mechanisms to ensure adequate supply of nutrients in a variable environment. Nitrate is absorbed in the root and mobilized to other organs by nitrate transporters. Nitrate sensing activates signaling pathways that impinge upon molecular, metabolic, physiological, and developmental responses locally and at the whole plant level. With the advent of genomics technologies and genetic tools, important advances in our understanding of nitrate and other N nutrient responses have been achieved in the past decade. Furthermore, techniques that take advantage of natural polymorphisms present in divergent individuals from a single species have been essential in uncovering new components. However, there are still gaps in our understanding of how nitrate signaling affects biological processes in plants. Moreover, we still lack an integrated view of how all the regulatory factors identified interact or crosstalk to orchestrate the myriad N responses plants typically exhibit. In this review, we provide an updated overview of mechanisms by which nitrate is sensed and transported throughout the plant. We discuss signaling components and how nitrate sensing crosstalks with hormonal pathways for developmental responses locally and globally in the plant. Understanding how nitrate impacts on plant metabolism, physiology, and growth and development in plants is key to improving crops for sustainable agriculture.
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Affiliation(s)
- José A O'Brien
- Departamento de Genética Molecular y Microbiología, FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 8331150, Chile; Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
| | - Andrea Vega
- Departamento de Ciencias Vegetales, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile
| | - Eléonore Bouguyon
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS, INRA, SupAgro, UM, 2 Place Viala, 34060 Montpellier Cedex, France
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS, INRA, SupAgro, UM, 2 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, UM, 2 Place Viala, 34060 Montpellier Cedex, France
| | - Gloria Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Pontificia Universidad Católica de Chile, 8331150, Chile.
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Araya T, Kubo T, von Wirén N, Takahashi H. Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:254-265. [PMID: 26425993 DOI: 10.1111/jipb.12433] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained as widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with: (i) inhibition of primary root growth under nitrogen limitation or on ammonium; (ii) rapid progression of lateral root emergence in response to ammonium; and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta-analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies.
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Affiliation(s)
- Takao Araya
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Takuya Kubo
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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