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Flores-Sánchez ID, Sandoval-Villa M, Uscanga-Mortera E. Nutrient Uptake of Two Semidomesticated Jaltomata Schltdl. Species for Their Cultivation. PLANTS (BASEL, SWITZERLAND) 2025; 14:1124. [PMID: 40219191 PMCID: PMC11991384 DOI: 10.3390/plants14071124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2025] [Revised: 02/22/2025] [Accepted: 02/22/2025] [Indexed: 04/14/2025]
Abstract
The nutrient uptake of a species under cultivated conditions is important for program fertilization. The Jaltomata genus has two semidomesticated species, J. procumbens and J. tlaxcala, used as food and considered with potential for their study in controlled environments. The objective of this research was to determine nutrient uptake curves of these species in a greenhouse and using hydroponics. The research was carried out at the Colegio de Postgraduados, Campus Montecillo, Texcoco, State of Mexico, from August to November 2020. The treatments included the following: two species and three electrical conductivity levels: 1, 2, and 3 dS m-1. Nutrients in leaf and total dry matter (TDM) were determined. Variability between species and phenological stages on the nutrient concentration and accumulation of TDM was observed. For macronutrients, J. procumbens concentrated in descending order more P from the vegetative stage (4.21-2.43 g kg-1 dry matter), and Mg until fructification (4.92-3.26 g kg-1 dry matter), for K it was higher at vegetative (52.29 g kg-1 dry matter) and harvesting stages (26.05 g kg-1 dry matter), and N (23.92 g kg-1 dry matter) at flowering; J. tlaxcala concentrated more Ca from fructification (10.10-13.85 g kg-1 dry matter). For micronutrients, J. tlaxcala concentrated more Fe from the vegetative stage (157.7-207.5 mg kg-1 dry matter), B and Zn at 23.3-38.4 and 26.04-28.45 mg kg-1 dry matter, respectively, from flowering, and Mn (108.4-232.28 mg kg-1 dry matter) from fructification. The main structures of TDM accumulation by vegetative stage in J. procumbens were the leaf and root (vegetative and flowering), root and stem (fructification), and reproductive structures and root (harvesting); in J. tlaxcala, the main structures were the leaf and root (vegetative), root and leaf (flowering and fructification), and root and reproductive structures (harvesting). Due to this variability, specific fertilization programs are required for each species.
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Affiliation(s)
- Ignacio Darío Flores-Sánchez
- Postgraduate in Edaphology, Colegio de Postgraduados, Mexico-Texcoco Highway, km 36.5, Montecillo, Texcoco 56264, Mexico;
| | - Manuel Sandoval-Villa
- Postgraduate in Edaphology, Colegio de Postgraduados, Mexico-Texcoco Highway, km 36.5, Montecillo, Texcoco 56264, Mexico;
| | - Ebandro Uscanga-Mortera
- Postgraduate in Botany, Colegio de Postgraduados, Mexico-Texcoco Highway, km 36.5, Montecillo, Texcoco 56264, Mexico;
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2
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Samant SB, Swain J, Yadav N, Yadav R, Singh P, Rai P, Sheri V, Sreeman S, Subramanyam R, Pareek A, Gupta KJ. Overexpression of Phytoglobin1 in Rice Leads to Enhanced Nitrogen Use Efficiency via Modulation of Nitric Oxide. PLANT, CELL & ENVIRONMENT 2025; 48:2755-2768. [PMID: 39569580 DOI: 10.1111/pce.15289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 10/23/2024] [Accepted: 11/04/2024] [Indexed: 11/22/2024]
Abstract
Nitric oxide (NO) is one of the byproducts of nitrogen metabolism. Excess amount of NO is scavenged by phytoglobins. The role of phytoglobin mediated NO homoeostasis in modulation of nitrate transporters was investigated using NO scavenger cPTIO, phytoglobin overexpressing rice and Arabidopsis. Growing plants under low nitrate leads to generation of reduced levels of NO accompanied by elevated expression of high affinity transporters (HATs) such as NRT2.1, NRT2.3 and NRT2.4. Scavenging of NO by cPTIO under optimal nitrate caused enhanced HATs expression. Phytoglobin overexpressing Arabidopsis showed improved growth and enhanced expression of HATs under low nitrogen in comparison to WT. Pretreatment of optimal nitrate grown plants with NO scavenger cPTIO enhanced HATs expression and shifting of these primed plants from optimal to low nitrate leads to further elevation of HATs expression accompanied by enhanced nitrogen uptake and its accumulation with positive effect on growth. Phytoglobin overexpression in rice leads to enhanced HATs expression, improved growth, nitrogen accumulation under low nitrate. Pgb OE lines showed enhanced accumulation of amino acids. Taken together our results suggest an important role of phytoglobins in nitrogen uptake and assimilation.
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Affiliation(s)
- Sanjib Bal Samant
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Jagannath Swain
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Nidhi Yadav
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Reena Yadav
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Pooja Singh
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Preeti Rai
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Vijay Sheri
- National Institute of Plant Genome Research, New Delhi, Delhi, India
| | - Sheshshayee Sreeman
- Department of Physiology, University of Agricultural Sciences, Bangalore, Karnataka, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Ashwani Pareek
- National Agri-Food and Bio Manufacturing Institute, Mohali, Punjab, India
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3
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Wang Q, Wang M, Xia A, Wang J, Wang Z, Xu T, Jia D, Lu M, Tan W, Luo J, He Y. Natural variation in ZmNRT2.5 modulates husk leaf width and promotes seed protein content in maize. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:1039-1052. [PMID: 39757743 PMCID: PMC11933875 DOI: 10.1111/pbi.14559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 12/08/2024] [Accepted: 12/11/2024] [Indexed: 01/07/2025]
Abstract
The husk leaf of maize (Zea mays) encases the ear as a modified leaf and plays pivotal roles in protecting the ear from pathogen infection, translocating nutrition for grains and warranting grain yield. However, the natural genetic basis for variation in husk leaf width remains largely unexplored. Here, we performed a genome-wide association study for maize husk leaf width and identified a 3-bp InDel (insertion/deletion) in the coding region of the nitrate transporter gene ZmNRT2.5. This polymorphism altered the interaction strength of ZmNRT2.5 with another transporter, ZmNPF5, thereby contributing to variation in husk leaf width. We also isolated loss-of-function mutants in ZmNRT2.5, which exhibited a substantial decrease in husk leaf width relative to their controls. We demonstrate that ZmNRT2.5 facilitates the transport of nitrate from husk leaves to maize kernels in plants grown under low-nitrogen conditions, contributing to the accumulation of proteins in maize seeds. Together, our findings uncovered a key gene controlling maize husk leaf width and nitrate transport from husk leaves to kernels. Identification of the ZmNRT2.5 loci offers direct targets for improving the protein content of maize seeds via molecular-assisted maize breeding.
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Affiliation(s)
- Qi Wang
- College of Agronomy and BiotechnologyChina Agricultural UniversityChina
| | - Min Wang
- College of Agronomy and BiotechnologyChina Agricultural UniversityChina
| | - Ai‐Ai Xia
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS)Chinese Academy of SciencesShanghaiChina
| | - Jin‐Yu Wang
- College of Agronomy and BiotechnologyChina Agricultural UniversityChina
| | - Zi Wang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Tao Xu
- Tieling Academy of Agricultural SciencesTielingChina
| | - De‐Tao Jia
- Tieling Academy of Agricultural SciencesTielingChina
| | - Ming Lu
- Maize Research InstituteJilin Academy of Agricultural SciencesGongzhulingChina
| | - Wei‐Ming Tan
- College of Agronomy and BiotechnologyChina Agricultural UniversityChina
| | - Jin‐Hong Luo
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yan He
- College of Agronomy and BiotechnologyChina Agricultural UniversityChina
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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4
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Schley TR, Zhu T, Geist B, Crabos A, Dietrich D, Alandes RA, Bennett M, Nacry P, Schäffner AR. The Arabidopsis PIP1;1 Aquaporin Represses Lateral Root Development and Nitrate Uptake Under Low Nitrate Availability. PLANT, CELL & ENVIRONMENT 2025; 48:1500-1513. [PMID: 39462913 PMCID: PMC11695785 DOI: 10.1111/pce.15222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 08/23/2024] [Accepted: 10/02/2024] [Indexed: 10/29/2024]
Abstract
Nitrate (NO3 -) deficiency decreases root water uptake and root hydraulic conductance. This adaptive response is correlated with reduced abundance and activity of plasma membrane intrinsic protein (PIP) aquaporins. We therefore screened changes in the root architecture of a complete set of Arabidopsis pip loss-of-function mutants grown under NO3 - deficiency to systematically approach the impact of PIPs under these conditions. NO3 - deprivation led to attenuated responses of specific pip single mutants compared to the strongly altered LR parameters of wild-type plants. In particular, pip1;1 exhibited a lower relative reduction in LR length and LR density, revealing that PIP1;1 represses LR development when NO3 - is scarce. Indeed, PIP1;1 compromises root and shoot NO3 - accumulation during early developmental stages. A fluorescent VENUS-PIP1;1 fusion revealed that PIP1;1 is specifically repressed in the pericycle, endodermis and at the flanks of emerging LRs upon NO3 - deficiency. Thus, LR plasticity and NO3 - uptake are affected by an interactive mechanism involving aquaporins (PIP1;1) and nitrate accumulation during seedling development under NO3 --deficient conditions.
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Affiliation(s)
- Thayssa Rabelo Schley
- Department of Environmental SciencesInstitute of Biochemical Plant PathologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Ting Zhu
- Department of Environmental SciencesInstitute of Biochemical Plant PathologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Birgit Geist
- Department of Environmental SciencesInstitute of Biochemical Plant PathologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Amandine Crabos
- IPSiM, CNRS, INRAE, Institut AgroUniversity of MontpellierMontpellierFrance
| | - Daniela Dietrich
- Plant & Crop Sciences, School of BiosciencesUniversity of NottinghamNottinghamUK
| | - Regina A. Alandes
- Plant & Crop Sciences, School of BiosciencesUniversity of NottinghamNottinghamUK
| | - Malcolm Bennett
- Plant & Crop Sciences, School of BiosciencesUniversity of NottinghamNottinghamUK
| | - Philippe Nacry
- IPSiM, CNRS, INRAE, Institut AgroUniversity of MontpellierMontpellierFrance
| | - Anton R. Schäffner
- Department of Environmental SciencesInstitute of Biochemical Plant PathologyHelmholtz Zentrum MünchenNeuherbergGermany
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5
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Yue L, Liu M, Liao J, Zhang K, Wu WH, Wang Y. CPK28-mediated phosphorylation enhances nitrate transport activity of NRT2.1 during nitrogen deprivation. THE NEW PHYTOLOGIST 2025; 245:249-262. [PMID: 39487627 DOI: 10.1111/nph.20236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 10/09/2024] [Indexed: 11/04/2024]
Abstract
Nitrate (NO3 -) serves as the primary inorganic nitrogen source assimilated by most terrestrial plants. The acquisition of nitrate from the soil is facilitated by NITRATE TRANSPORTERS (NRTs), with NRT2.1 being the key high-affinity nitrate transporter. The activity of NRT2.1, which has multiple potential phosphorylation sites, is intricately regulated under various physiological conditions. Here, we discovered that CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28) positively regulates nitrate uptake under nitrogen deprivation conditions. We found CPK28 as the kinase targeted by immunoprecipitation followed by mass spectrometry and examined the in-planta phosphorylation status of NRT2.1 in cpk28 mutant plants by employing quantitative MS-based phosphoproteomics. Through a combination of in vitro phosphorylation experiment and immunoblotting using phospho-specific antibody, we successfully demonstrated that CPK28 specifically phosphorylates NRT2.1 at Ser21. Functional analysis conducted in Xenopus oocytes revealed that co-expression of CPK28 significantly enhanced high-affinity nitrate uptake of NRT2.1. Further investigation using transgenic plants showed that the phosphomimic variant NRT2.1S21E, but not the nonphosphorylatable variant NRT2.1S21A, fully restored high-affinity 15NO3 - uptake ability in both nrt2.1 and cpk28 mutant backgrounds. This study clarifies that the kinase activity of CPK28 is promoted during nitrogen deprivation conditions. These significant findings provide valuable insights into the intricate regulatory mechanisms that govern nitrate-demand adaptation.
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Affiliation(s)
- Lindi Yue
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Mengyuan Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, 100097, China
| | - Jiahui Liao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kaina Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei-Hua Wu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yang Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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6
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Luo Y, Nan L. Genome-wide identification of high-affinity nitrate transporter 2 (NRT2) gene family under phytohormones and abiotic stresses in alfalfa (Medicago sativa). Sci Rep 2024; 14:31920. [PMID: 39738449 PMCID: PMC11685795 DOI: 10.1038/s41598-024-83438-9] [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: 04/13/2024] [Accepted: 12/16/2024] [Indexed: 01/02/2025] Open
Abstract
The high-affinity nitrate transporter 2 (NRT2) protein plays an important role in nitrate uptake and transport in plants. In this study, the NRT2s gene family were systematically analyzed in alfalfa. We identified three MsNRT2 genes from the genomic database. They were named MsNRT2.1-2.3 based on their chromosomal location. The phylogenetic tree revealed that NRT2 proteins were categorized into two main subgroups, which were further confirmed by their gene structure and conserved motifs. Three MsNRT2 genes distributed on 2 chromosomes. Furthermore, we studied the expression patterns of MsNRT2 genes in six tissues based on RNA-sequencing data from the Short Read Archive (SRA) database of NCBI, and the results showed that MsNRT2 genes were widely expressed in six tissues. After leaves and roots were treated with drought, salt, abscisic acid (ABA) and salicylic acid (SA) for 0-48 h, and we used quantitative RT-PCR to analyze the expression levels of MsNRT2 genes and the results showed that most of the MsNRT2 genes responded to these stresses. However, there are specific genes that play a role under specific treatment conditions. This result provides a basis for further research on the target genes. In summary, MsNRT2s play an irreplaceable role in the growth, development and stress response of alfalfa, and this study provides valuable information and theoretical basis for future research on MsNRT2 function.
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Affiliation(s)
- Yanyan Luo
- Pratacultural College, Key Laboratory of Grassland Ecosystem (Ministry of Education), Key Laboratory of Forage Gerplasm Innovation and New Variety Breeding of Ministry of Agriculture and Rural Affairs (Co-sponsored by Ministry and Province), Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Lili Nan
- Pratacultural College, Key Laboratory of Grassland Ecosystem (Ministry of Education), Key Laboratory of Forage Gerplasm Innovation and New Variety Breeding of Ministry of Agriculture and Rural Affairs (Co-sponsored by Ministry and Province), Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
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7
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Hasegawa Y, Luo Y, Sato T. Recent Advances in Ubiquitin Signals Regulating Plant Membrane Trafficking. PLANT & CELL PHYSIOLOGY 2024; 65:1907-1924. [PMID: 39446594 DOI: 10.1093/pcp/pcae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 09/11/2024] [Accepted: 10/23/2024] [Indexed: 10/26/2024]
Abstract
Ubiquitination is a reversible post-translational modification involving the attachment of ubiquitin, a 76-amino acid protein conserved among eukaryotes. The protein 'ubiquitin' was named after it was found to be ubiquitously expressed in cells. Ubiquitination was first identified as a post-translational modification that mediates energy-consuming protein degradation by the proteasome. After half a century, the manifold functions of ubiquitin are widely recognized to play key roles in diverse molecular pathways and physiological processes. Compared to humans, the number of enzymes related to ubiquitination is almost twice as high in plant species, such as Arabidopsis and rice, suggesting that this modification plays a critical role in many aspects of plant physiology including development and environmental stress responses. Here, we summarize and discuss recent knowledge of ubiquitination focusing on the regulation of membrane trafficking in plants. Ubiquitination of plasma membrane-localized proteins often leads to endocytosis and vacuolar targeting. In addition to cargo proteins, ubiquitination of membrane trafficking regulators regulates the morphodynamics of the endomembrane system. Thus, throughout this review, we focus on the physiological responses regulated by ubiquitination and their underlying mechanisms to clarify what is already known and what would be interesting to investigate in the future.
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Affiliation(s)
- Yoko Hasegawa
- Laboratoire Reproduction et Développement des Plantes (RDP), Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon 69342, France
| | - Yongming Luo
- Faculty of Science, Hokkaido University, Kita-ku N10-W8, Sapporo, 060-0810 Japan
| | - Takeo Sato
- Faculty of Science, Hokkaido University, Kita-ku N10-W8, Sapporo, 060-0810 Japan
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8
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Rzemieniewski J, Leicher H, Lee HK, Broyart C, Nayem S, Wiese C, Maroschek J, Camgöz Z, Olsson Lalun V, Djordjevic MA, Vlot AC, Hückelhoven R, Santiago J, Stegmann M. CEP signaling coordinates plant immunity with nitrogen status. Nat Commun 2024; 15:10686. [PMID: 39681561 PMCID: PMC11649690 DOI: 10.1038/s41467-024-55194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/04/2024] [Indexed: 12/18/2024] Open
Abstract
Plant endogenous signaling peptides shape growth, development and adaptations to biotic and abiotic stress. Here, we identify C-TERMINALLY ENCODED PEPTIDEs (CEPs) as immune-modulatory phytocytokines in Arabidopsis thaliana. Our data reveals that CEPs induce immune outputs and are required to mount resistance against the leaf-infecting bacterial pathogen Pseudomonas syringae pv. tomato. We show that effective immunity requires CEP perception by tissue-specific CEP RECEPTOR 1 (CEPR1) and CEPR2. Moreover, we identify the related RECEPTOR-LIKE KINASE 7 (RLK7) as a CEP4-specific CEP receptor contributing to CEP-mediated immunity, suggesting a complex interplay of multiple CEP ligands and receptors in different tissues during biotic stress. CEPs have a known role in the regulation of root growth and systemic nitrogen (N)-demand signaling. We provide evidence that CEPs and their receptors promote immunity in an N status-dependent manner, suggesting a previously unknown molecular crosstalk between plant nutrition and cell surface immunity. We propose that CEPs and their receptors are central regulators for the adaptation of biotic stress responses to plant-available resources.
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Affiliation(s)
- Jakub Rzemieniewski
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Henriette Leicher
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hyun Kyung Lee
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Caroline Broyart
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Shahran Nayem
- Helmholtz Zentrum Munich, Institute of Biochemical Plant Pathology, Neuherberg, Germany
- Chair of Crop Plant Genetics, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Kulmbach, Germany
| | - Christian Wiese
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julian Maroschek
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Zeynep Camgöz
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Vilde Olsson Lalun
- Department of Biosciences Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - A Corina Vlot
- Helmholtz Zentrum Munich, Institute of Biochemical Plant Pathology, Neuherberg, Germany
- Chair of Crop Plant Genetics, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Kulmbach, Germany
| | - Ralph Hückelhoven
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julia Santiago
- The Plant Signaling Mechanisms Laboratory, Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Martin Stegmann
- Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
- Institute of Botany, Molecular Botany, Ulm University, Ulm, Germany.
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9
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Delgado LD, Nunez-Pascual V, Riveras E, Ruffel S, Gutiérrez RA. Recent advances in local and systemic nitrate signaling in Arabidopsisthaliana. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102605. [PMID: 39033715 DOI: 10.1016/j.pbi.2024.102605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024]
Abstract
Nitrate is the most abundant form of inorganic nitrogen in aerobic soils, serving both as a nutrient and a signaling molecule. Central to nitrate signaling in higher plants is the intricate balance between local and systemic signaling and response pathways. The interplay between local and systemic responses allows plants to regulate their global gene expression, metabolism, physiology, growth, and development under fluctuating nitrate availability. This review offers an overview of recent discoveries regarding new players on nitrate sensing and signaling, in local and systemic contexts in Arabidopsis thaliana. Additionally, it addresses unanswered questions that warrant further investigation for a better understanding of nitrate signaling and responses in plants.
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Affiliation(s)
- Laura D Delgado
- Millennium Institute for Integrative Biology, Millennium Institute Center for Genome Regulation, Institute of Ecology and Biodiversity, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Valentina Nunez-Pascual
- Millennium Institute for Integrative Biology, Millennium Institute Center for Genome Regulation, Institute of Ecology and Biodiversity, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology, Millennium Institute Center for Genome Regulation, Institute of Ecology and Biodiversity, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, 34060, France
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology, Millennium Institute Center for Genome Regulation, Institute of Ecology and Biodiversity, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile.
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10
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Hajibarat Z, Saidi A, Ghazvini H, Hajibarat Z. Investigation of morpho-physiolgical traits and gene expression in barley under nitrogen deficiency. Sci Rep 2024; 14:8875. [PMID: 38632431 PMCID: PMC11024206 DOI: 10.1038/s41598-024-59714-z] [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: 11/07/2023] [Accepted: 04/15/2024] [Indexed: 04/19/2024] Open
Abstract
Nitrogen (N) is an essential element for plant growth, and its deficiency influences plants at several physiological and gene expression levels. Barley (Hordeum vulgare) is one of the most important food grains from the Poaceae family and one of the most important staple food crops. However, the seed yield is limited by a number of stresses, the most important of which is the insufficient use of N. Thus, there is a need to develop N-use effective cultivars. In this study, comparative physiological and molecular analyses were performed using leaf and root tissues from 10 locally grown barley cultivars. The expression levels of nitrate transporters, HvNRT2 genes, were analyzed in the leaf and root tissues of N-deficient (ND) treatments of barley cultivars after 7 and 14 days following ND treatment as compared to the normal condition. Based on the correlation between the traits, root length (RL) had a positive and highly significant correlation with fresh leaf weight (FLW) and ascorbate peroxidase (APX) concentration in roots, indicating a direct root and leaf relationship with the plant development under ND. From the physiological aspects, ND enhanced carotenoids, chlorophylls a/b (Chla/b), total chlorophyll (TCH), leaf antioxidant enzymes such as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT), and root antioxidant enzymes (APX and POD) in the Sahra cultivar. The expression levels of HvNRT2.1, HvNRT2.2, and HvNRT2.4 genes were up-regulated under ND conditions. For the morphological traits, ND maintained root dry weight among the cultivars, except for Sahra. Among the studied cultivars, Sahra responded well to ND stress, making it a suitable candidate for barely improvement programs. These findings may help to better understand the mechanism of ND tolerance and thus lead to the development of cultivars with improved nitrogen use efficiency (NUE) in barley.
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Affiliation(s)
- Zohreh Hajibarat
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Habibollah Ghazvini
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31587-77871, Karaj, Iran
| | - Zahra Hajibarat
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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11
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Li Z, Na Wu X, Jacquot A, Chaput V, Adamo M, Neuhäuser B, Straub T, Lejay L, Schulze WX. Phosphoregulation in the N-terminus of NRT2.1 affects nitrate uptake by controlling the interaction of NRT2.1 with NAR2.1 and kinase HPCAL1 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2127-2142. [PMID: 38066636 PMCID: PMC10967239 DOI: 10.1093/jxb/erad490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 03/28/2024]
Abstract
NRT2.1, the major high affinity nitrate transporter in roots, can be phosphorylated at five different sites within the N- and the C-terminus. Here, we characterized the functional relationship of two N-terminal phosphorylation sites, S21 and S28, in Arabidopsis. Based on a site-specific correlation network, we identified a receptor kinase (HPCAL1, AT5G49770), phosphorylating NRT2.1 at S21 and resulting in active nitrate uptake. HPCAL1 itself was regulated by phosphorylation at S839 and S870 within its kinase domain. In the active state, when S839 was dephosphorylated and S870 was phosphorylated, HPCAL1 was found to interact with the N-terminus of NRT2.1, mainly when S28 was dephosphorylated. Phosphorylation of NRT2.1 at S21 resulted in a reduced interaction of NRT2.1 with its activator NAR2.1, but nitrate transport activity remained. By contrast, phosphorylated NRT2.1 at S28 enhanced the interaction with NAR2.1, but reduced the interaction with HPCAL1. Here we identified HPCAL1 as the kinase affecting this phospho-switch through phosphorylation of NRT2.1 at S21.
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Affiliation(s)
- Zhi Li
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Aurore Jacquot
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Valentin Chaput
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Mattia Adamo
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Benjamin Neuhäuser
- Department of Crop Physiology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Tatsiana Straub
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
| | - Laurence Lejay
- BPMP, University Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, D-70593, Stuttgart, Germany
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12
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Xu N, Cheng L, Kong Y, Chen G, Zhao L, Liu F. Functional analyses of the NRT2 family of nitrate transporters in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1351998. [PMID: 38501135 PMCID: PMC10944928 DOI: 10.3389/fpls.2024.1351998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Nitrogen is an essential macronutrient for plant growth and development. Nitrate is the major form of nitrogen acquired by most crops and also serves as a vital signaling molecule. Nitrate is absorbed from the soil into root cells usually by the low-affinity NRT1 NO3 - transporters and high-affinity NRT2 NO3 - transporters, with NRT2s serving to absorb NO3 - under NO3 -limiting conditions. Seven NRT2 members have been identified in Arabidopsis, and they have been shown to be involved in various biological processes. In this review, we summarize the spatiotemporal expression patterns, localization, and biotic and abiotic responses of these transporters with a focus on recent advances in the current understanding of the functions of the seven AtNRT2 genes. This review offers beneficial insight into the mechanisms by which plants adapt to changing environmental conditions and provides a theoretical basis for crop research in the near future.
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Affiliation(s)
- Na Xu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Li Cheng
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Yuan Kong
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Guiling Chen
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | - Lufei Zhao
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, Shandong, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, China
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13
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Taleski M, Jin M, Chapman K, Taylor K, Winning C, Frank M, Imin N, Djordjevic MA. CEP hormones at the nexus of nutrient acquisition and allocation, root development, and plant-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:538-552. [PMID: 37946363 PMCID: PMC10773996 DOI: 10.1093/jxb/erad444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
A growing understanding is emerging of the roles of peptide hormones in local and long-distance signalling that coordinates plant growth and development as well as responses to the environment. C-TERMINALLY ENCODED PEPTIDE (CEP) signalling triggered by its interaction with CEP RECEPTOR 1 (CEPR1) is known to play roles in systemic nitrogen (N) demand signalling, legume nodulation, and root system architecture. Recent research provides further insight into how CEP signalling operates, which involves diverse downstream targets and interactions with other hormone pathways. Additionally, there is emerging evidence of CEP signalling playing roles in N allocation, root responses to carbon levels, the uptake of other soil nutrients such as phosphorus and sulfur, root responses to arbuscular mycorrhizal fungi, plant immunity, and reproductive development. These findings suggest that CEP signalling more broadly coordinates growth across the whole plant in response to diverse environmental cues. Moreover, CEP signalling and function appear to be conserved in angiosperms. We review recent advances in CEP biology with a focus on soil nutrient uptake, root system architecture and organogenesis, and roles in plant-microbe interactions. Furthermore, we address knowledge gaps and future directions in this research field.
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Affiliation(s)
- Michael Taleski
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Marvin Jin
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Kelly Chapman
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Katia Taylor
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Courtney Winning
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
| | - Manuel Frank
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Nijat Imin
- School of Science, Western Sydney University, Penrith, New South Wales 2751, Australia
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT, 2601Australia
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14
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Deng QY, Luo JT, Zheng JM, Tan WF, Pu ZJ, Wang F. Genome-wide systematic characterization of the NRT2 gene family and its expression profile in wheat (Triticum aestivum L.) during plant growth and in response to nitrate deficiency. BMC PLANT BIOLOGY 2023; 23:353. [PMID: 37420192 DOI: 10.1186/s12870-023-04333-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/06/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is a major cereal crop that is grown worldwide, and it is highly dependent on sufficient N supply. The molecular mechanisms associated with nitrate uptake and assimilation are still poorly understood in wheat. In plants, NRT2 family proteins play a crucial role in NO3- acquisition and translocation under nitrate limited conditions. However, the biological functions of these genes in wheat are still unclear, especially their roles in NO3- uptake and assimilation. RESULTS In this study, a comprehensive analysis of wheat TaNRT2 genes was conducted using bioinformatics and molecular biology methods, and 49 TaNRT2 genes were identified. A phylogenetic analysis clustered the TaNRT2 genes into three clades. The genes that clustered on the same phylogenetic branch had similar gene structures and nitrate assimilation functions. The identified genes were further mapped onto the 13 wheat chromosomes, and the results showed that a large duplication event had occurred on chromosome 6. To explore the TaNRT2 gene expression profiles in wheat, we performed transcriptome sequencing after low nitrate treatment for three days. Transcriptome analysis revealed the expression levels of all TaNRT2 genes in shoots and roots, and based on the expression profiles, three highly expressed genes (TaNRT2-6A.2, TaNRT2-6A.6, and TaNRT2-6B.4) were selected for qPCR analysis in two different wheat cultivars ('Mianmai367' and 'Nanmai660') under nitrate-limited and normal conditions. All three genes were upregulated under nitrate-limited conditions and highly expressed in the high nitrogen use efficiency (NUE) wheat 'Mianmai367' under low nitrate conditions. CONCLUSION We systematically identified 49 NRT2 genes in wheat and analysed the transcript levels of all TaNRT2s under nitrate deficient conditions and over the whole growth period. The results suggest that these genes play important roles in nitrate absorption, distribution, and accumulation. This study provides valuable information and key candidate genes for further studies on the function of TaNRT2s in wheat.
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Affiliation(s)
- Qing-Yan Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Jiang-Tao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Jian-Min Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China
| | - Wen-Fang Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
| | - Zong-Jun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Chengdu, Sichuan, 610066, China.
| | - Fang Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, Sichuan, China.
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15
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Choi SJ, Lee Z, Jeong E, Kim S, Seo JS, Um T, Shim JS. Signaling pathways underlying nitrogen transport and metabolism in plants. BMB Rep 2023; 56:56-64. [PMID: 36658636 PMCID: PMC9978367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 01/21/2023] Open
Abstract
Nitrogen (N) is an essential macronutrient required for plant growth and crop production. However, N in soil is usually insufficient for plant growth. Thus, chemical N fertilizer has been extensively used to increase crop production. Due to negative effects of N rich fertilizer on the environment, improving N usage has been a major issue in the field of plant science to achieve sustainable production of crops. For that reason, many efforts have been made to elucidate how plants regulate N uptake and utilization according to their surrounding habitat over the last 30 years. Here, we provide recent advances focusing on regulation of N uptake, allocation of N by N transporting system, and signaling pathway controlling N responses in plants. [BMB Reports 2023; 56(2): 56-64].
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Affiliation(s)
- Su Jeong Choi
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Zion Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Eui Jeong
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Sohyun Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Jun Sung Seo
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea,Corresponding author. Tel: +82-62-530-0507; Fax: +82-62-530-2199; E-mail:
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16
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Cassan O, Pimparé LL, Dubos C, Gojon A, Bach L, Lèbre S, Martin A. A gene regulatory network in Arabidopsis roots reveals features and regulators of the plant response to elevated CO 2. THE NEW PHYTOLOGIST 2023. [PMID: 36727308 DOI: 10.1111/nph.18788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
The elevation of CO2 in the atmosphere increases plant biomass but decreases their mineral content. The genetic and molecular bases of these effects remain mostly unknown, in particular in the root system, which is responsible for plant nutrient uptake. To gain knowledge about the effect of elevated CO2 on plant growth and physiology, and to identify its regulatory in the roots, we analyzed genome expression in Arabidopsis roots through a combinatorial design with contrasted levels of CO2 , nitrate, and iron. We demonstrated that elevated CO2 has a modest effect on root genome expression under nutrient sufficiency, but by contrast leads to massive expression changes under nitrate or iron deficiencies. We demonstrated that elevated CO2 negatively targets nitrate and iron starvation modules at the transcriptional level, associated with a reduction in high-affinity nitrate uptake. Finally, we inferred a gene regulatory network governing the root response to elevated CO2 . This network allowed us to identify candidate transcription factors including MYB15, WOX11, and EDF3 which we experimentally validated for their role in the stimulation of growth by elevated CO2 . Our approach identified key features and regulators of the plant response to elevated CO2 , with the objective of developing crops resilient to climate change.
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Affiliation(s)
- Océane Cassan
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France
| | - Léa-Lou Pimparé
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France
| | - Christian Dubos
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France
| | - Alain Gojon
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France
| | - Liên Bach
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France
| | - Sophie Lèbre
- IMAG, Univ. Montpellier, CNRS, 34000, Montpellier, France
- Université Paul-Valéry-Montpellier 3, 34000, Montpellier, France
| | - Antoine Martin
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, 34000, Montpellier, France
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17
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Séré D, Cassan O, Bellegarde F, Fizames C, Boucherez J, Schivre G, Azevedo J, Lagrange T, Gojon A, Martin A. Loss of Polycomb proteins CLF and LHP1 leads to excessive RNA degradation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5400-5413. [PMID: 35595271 DOI: 10.1093/jxb/erac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Polycomb-group (PcG) proteins are major chromatin complexes that regulate gene expression, mainly described as repressors keeping genes in a transcriptionally silent state during development. Recent studies have nonetheless suggested that PcG proteins might have additional functions, including targeting active genes or acting independently of gene expression regulation. However, the reasons for the implication of PcG proteins and their associated chromatin marks on active genes are still largely unknown. Here, we report that combining mutations for CURLY LEAF (CLF) and LIKE HETEROCHROMATIN PROTEIN1 (LHP1), two Arabidopsis PcG proteins, results in deregulation of expression of active genes that are targeted by PcG proteins or enriched in associated chromatin marks. We show that this deregulation is associated with accumulation of small RNAs corresponding to massive degradation of active gene transcripts. We demonstrate that transcriptionally active genes and especially those targeted by PcG proteins are prone to RNA degradation, even though deregulation of RNA degradation following the loss of function of PcG proteins is not likely to be mediated by a PcG protein-mediated chromatin environment. Therefore, we conclude that PcG protein function is essential to maintain an accurate level of RNA degradation to ensure accurate gene expression.
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Affiliation(s)
- David Séré
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Océane Cassan
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Fanny Bellegarde
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Cécile Fizames
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Jossia Boucherez
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Geoffrey Schivre
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Jacinthe Azevedo
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Thierry Lagrange
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Alain Gojon
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Antoine Martin
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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18
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Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system. Mol Genet Genomics 2022; 297:1403-1421. [PMID: 35879567 DOI: 10.1007/s00438-022-01929-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
KEY MESSAGE Nitrate uptake in sugarcane roots is regulated at the transcriptional and posttranscriptional levels based on the physiological status of the plant and is likely a determinant mechanism for discrimination against nitrate. Sugarcane (Saccharum spp.) is one of the most suitable energy crops for biofuel feedstock, but the reduced recovery of nitrogen (N) fertilizer by sugarcane roots increases the crop carbon footprint. The low nitrogen use efficiency (NUE) of sugarcane has been associated with the significantly low nitrate uptake, which limits the utilization of the large amount of nitrate available in agricultural soils. To understand the regulation of nitrate uptake in sugarcane roots, we identified the major canonical nitrate transporter genes (NRTs-NITRATE TRANSPORTERS) and then determined their expression profiles in roots under contrasting N conditions. Correlation of gene expression with 15N-nitrate uptake revealed that under N deprivation or inorganic N (ammonium or nitrate) supply in N-sufficient roots, the regulation of ScNRT2.1 and ScNRT3.1 expression is the predominant mechanism for the modulation of the activity of the nitrate high-affinity transport system. Conversely, in N-deficient roots, the induction of ScNRT2.1 and ScNRT3.1 transcription is not correlated with the marked repression of nitrate uptake in response to nitrate resupply or high N provision, which suggested the existence of a posttranscriptional regulatory mechanism. Our findings suggested that high-affinity nitrate uptake is regulated at the transcriptional and presumably at the posttranscriptional levels based on the physiological N status and that the regulation of NRT2.1 and NRT3.1 activity is likely a determinant mechanism for the discrimination against nitrate uptake observed in sugarcane roots, which contributes to the low NUE in this crop species.
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19
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Yuan T, Zhu C, Li G, Liu Y, Yang K, Li Z, Song X, Gao Z. An Integrated Regulatory Network of mRNAs, microRNAs, and lncRNAs Involved in Nitrogen Metabolism of Moso Bamboo. Front Genet 2022; 13:854346. [PMID: 35651936 PMCID: PMC9149284 DOI: 10.3389/fgene.2022.854346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is a key macronutrient essential for plant growth and development, and its availability has a strong influence on biological processes. Nitrogen fertilizer has been widely applied in bamboo forests in recent decades; however, the mechanism of nitrogen metabolism in bamboo is not fully elucidated. Here, we characterized the morphological, physiological, and transcriptome changes of moso bamboo in response to different schemes for nitrogen addition to illuminate the regulation mechanism of nitrogen metabolism. The appropriate addition of nitrogen improved the chlorophyll content and Pn (net photosynthetic rate) of leaves, the nitrogen and ammonium contents of the seedling roots, the biomass of the whole seedling, the number of lateral roots, and the activity of enzymes involved in nitrogen metabolism in the roots. Based on the whole transcriptome data of the roots, a total of 8,632 differentially expressed mRNAs (DEGs) were identified under different nitrogen additions, such as 52 nitrate transporter genes, 6 nitrate reductase genes, 2 nitrite reductase genes, 2 glutamine synthase genes, 2 glutamate synthase genes (GOGAT), 3 glutamate dehydrogenase genes, and 431 TFs belonging to 23 families. Meanwhile, 123 differentially expressed miRNAs (DEMs) and 396 differentially expressed lncRNAs (DELs) were characterized as nitrogen responsive, respectively. Furthermore, 94 DEM-DEG pairs and 23 DEL-DEG pairs involved in nitrogen metabolism were identified. Finally, a predicted regulatory network of nitrogen metabolism was initially constructed, which included 17 nitrogen metabolic pathway genes, 15 TFs, 4 miRNAs, and 10 lncRNAs by conjoint analysis of DEGs, DEMs, and DELs and their regulatory relationships, which was supported by RNA-seq data and qPCR results. The lncRNA-miRNA-mRNA network provides new insights into the regulation mechanism of nitrogen metabolism in bamboo, which facilitates further genetic improvement for bamboo to adapt to the fluctuating nitrogen environment.
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Affiliation(s)
- Tingting Yuan
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Guangzhu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Yan Liu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Zhen Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Hangzhou, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
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20
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Molecular mechanisms underlying nitrate responses in plants. Curr Biol 2022; 32:R433-R439. [DOI: 10.1016/j.cub.2022.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Lu Y, Deng S, Li Z, Wu J, Zhu D, Shi W, Zhou J, Fayyaz P, Luo ZB. Physiological Characteristics and Transcriptomic Dissection in Two Root Segments with Contrasting Net Fluxes of Ammonium and Nitrate of Poplar Under Low Nitrogen Availability. PLANT & CELL PHYSIOLOGY 2022; 63:30-44. [PMID: 34508646 DOI: 10.1093/pcp/pcab137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/20/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
To investigate physiological and transcriptomic regulation mechanisms underlying the distinct net fluxes of NH4+ and NO3- in different root segments of Populus species under low nitrogen (N) conditions, we used saplings of Populus × canescens supplied with either 500 (normal N) or 50 (low N) μM NH4NO3. The net fluxes of NH4+ and NO3-, the concentrations of NH4+, amino acids and organic acids and the enzymatic activities of nitrite reductase (NiR) and glutamine synthetase (GS) in root segment II (SII, 35-70 mm to the apex) were lower than those in root segment I (SI, 0-35 mm to the apex). The net NH4+ influxes and the concentrations of organic acids were elevated, whereas the concentrations of NH4+ and NO3- and the activities of NiR and GS were reduced in SI and SII in response to low N. A number of genes were significantly differentially expressed in SII vs SI and in both segments grown under low vs normal N conditions, and these genes were mainly involved in the transport of NH4+ and NO3-, N metabolism and adenosine triphosphate synthesis. Moreover, the hub gene coexpression networks were dissected and correlated with N physiological processes in SI and SII under normal and low N conditions. These results suggest that the hub gene coexpression networks play pivotal roles in regulating N uptake and assimilation, amino acid metabolism and the levels of organic acids from the tricarboxylic acid cycle in the two root segments of poplars in acclimation to low N availability.
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Affiliation(s)
- Yan Lu
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Shurong Deng
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Zhuorong Li
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Jiangting Wu
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Dongyue Zhu
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Wenguang Shi
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Jing Zhou
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Payam Fayyaz
- Forest, Range and Watershed Management Department, Agriculture and Natural Resources Faculty, Chinese Academy of Forestry, Beijing 100091, P. R. China
| | - Zhi-Bin Luo
- State key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, P. R. China
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22
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Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. Proc Natl Acad Sci U S A 2022; 119:2107879119. [PMID: 35046022 PMCID: PMC8794810 DOI: 10.1073/pnas.2107879119] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.
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New insights into the role of chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23 in nitrate signaling in Arabidopsis roots. Sci Rep 2022; 12:1018. [PMID: 35046428 PMCID: PMC8770472 DOI: 10.1038/s41598-021-04758-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
Nitrate is an important source of nitrogen and also acts as a signaling molecule to trigger numerous physiological, growth, and developmental processes throughout the life of the plant. Many nitrate transporters, transcription factors, and protein kinases participate in the regulation of nitrate signaling. Here, we identified a gene encoding the chrysanthemum calcineurin B-like interacting protein kinase CmCIPK23, which participates in nitrate signaling pathways. In Arabidopsis, overexpression of CmCIPK23 significantly decreased lateral root number and length and primary root length compared to the WT when grown on modified Murashige and Skoog medium with KNO3 as the sole nitrogen source (modified MS). The expression of nitrate-responsive genes differed significantly between CmCIPK23-overexpressing Arabidopsis (CmCIPK23-OE) and the WT after nitrate treatment. Nitrate content was significantly lower in CmCIPK23-OE roots, which may have resulted from reduced nitrate uptake at high external nitrate concentrations (≥ 1 mM). Nitrate reductase activity and the expression of nitrate reductase and glutamine synthase genes were lower in CmCIPK23-OE roots. We also found that CmCIPK23 interacted with the transcription factor CmTGA1, whose Arabidopsis homolog regulates the nitrate response. We inferred that CmCIPK23 overexpression influences root development on modified MS medium, as well as root nitrate uptake and assimilation at high external nitrate supply. These findings offer new perspectives on the mechanisms by which the chrysanthemum CBL interacting protein kinase CmCIPK23 influences nitrate signaling.
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24
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Sathee L, Krishna GK, Adavi SB, Jha SK, Jain V. Role of protein phosphatases in the regulation of nitrogen nutrition in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2911-2922. [PMID: 35035144 PMCID: PMC8720119 DOI: 10.1007/s12298-021-01115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 05/20/2023]
Abstract
The reversible protein phosphorylation and dephosphorylation mediated by protein kinases and phosphatases regulate different biological processes and their response to environmental cues, including nitrogen (N) availability. Nitrate assimilation is under the strict control of phosphorylation-dephosphorylation mediated post-translational regulation. The protein phosphatase family with approximately 150 members in Arabidopsis and around 130 members in rice is a promising player in N uptake and assimilation pathways. Protein phosphatase 2A (PP2A) enhances the activation of nitrate reductase (NR) by deactivating SnRK1 and reduces the binding of inhibitory 14-3-3 proteins on NR. The functioning of nitrate transporter NPF6.3 is regulated by phosphorylation of CBL9 (Calcineurin B like protein 9) and CIPK23 (CBL interacting protein kinase 23) module. Phosphorylation by CIPK23 inhibits the activity of NPF6.3, whereas protein phosphatases (PP2C) enhance the NPF6.3-dependent nitrate sensing. PP2Cs and CIPK23 also regulate ammonium transporters (AMTs). Under either moderate ammonium supply or high N demand, CIPK23 is bound and inactivated by PP2Cs. Ammonium uptake is mediated by nonphosphorylated and active AMT1s. Whereas, under high ammonium availability, CIPK23 gets activated and phosphorylate AMT1;1 and AMT1;2 rendering them inactive. Recent reports suggest the critical role of protein phosphatases in regulating N use efficiency (NUE). In rice, PP2C9 regulates NUE by improving N uptake and assimilation. Comparative leaf proteome of wild type and PP2C9 over-expressing transgenic rice lines showed 30 differentially expressed proteins under low N level. These proteins are involved in photosynthesis, N metabolism, signalling, and defence.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - G. K. Krishna
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Thrissur, 680 656 India
| | - Sandeep B. Adavi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Vanita Jain
- Agricultural Education Division, ICAR, KAB-II, New Delhi, 110 012 India
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25
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Diao J, Li S, Ma L, Zhang P, Bai J, Wang J, Ma X, Ma W. Genome-Wide Analysis of Major Facilitator Superfamily and Its Expression in Response of Poplar to Fusarium oxysporum. Front Genet 2021; 12:769888. [PMID: 34745233 PMCID: PMC8567078 DOI: 10.3389/fgene.2021.769888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
The major facilitator superfamily (MFS) is one of the largest known membrane transporter families. MFSs are involved in many essential functions, but studies on the MFS family in poplar have not yet been reported. Here, we identified 41 MFS genes from Populus trichocarpa (PtrMFSs). We built a phylogenetic tree, which clearly divided members of PtrMFS into six groups with specific gene structures and protein motifs/domains. The promoter regions contain various cis-acting elements involved in stress and hormone responsiveness. Genes derived from segmental duplication events are unevenly distributed in 17 poplar chromosomes. Collinearity analysis showed that PtrMFS genes are conserved and homologous to corresponding genes from four other species. Transcriptome data indicated that 40 poplar MFS genes were differentially expressed when treated with Fusarium oxysporum. Co-expression networks and gene function annotations of MFS genes showed that MFS genes tightly co-regulated and closely related in function of transmembrane transport. Taken together, we systematically analyzed structure and function of genes and proteins in the PtrMFS family. Evidence indicated that poplar MFS genes play key roles in plant development and response to a biological stressor.
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Affiliation(s)
- Jian Diao
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Shuxuan Li
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Ling Ma
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Ping Zhang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Jianyang Bai
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Jiaqi Wang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqian Ma
- Institute of Forest Protection, Heilongjiang Academy of Forestry, Harbin, China
| | - Wei Ma
- College of Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
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26
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Wang W, Li A, Zhang Z, Chu C. Posttranslational Modifications: Regulation of Nitrogen Utilization and Signaling. PLANT & CELL PHYSIOLOGY 2021; 62:543-552. [PMID: 33493288 PMCID: PMC8462382 DOI: 10.1093/pcp/pcab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/07/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen is the most important macroelement required for the composition of key molecules, such as nucleic acids, proteins and other organic compounds. As sessile organisms, plants have evolved sophisticated mechanisms to acquire nitrogen for their normal growth and development. Besides the transcriptional and translational regulation of nitrogen uptake, assimilation, remobilization and signal transduction, posttranslational modifications (PTMs) are shown to participate in these processes in plants. In addition to alterations in protein abundance, PTMs may dramatically increase the complexity of the proteome without the concomitant changes in gene transcription and have emerged as an important type of protein regulation in terms of protein function, subcellular localization and protein activity and stability. Herein, we briefly summarize recent advances on the posttranslational regulation of nitrogen uptake, assimilation, remobilization and nitrogen signaling and discuss the underlying mechanisms of PTMs as well as the signal output of such PTMs. Understanding these regulation mechanisms will provide novel insights for improving the nitrogen use efficiency of plants.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Aifu Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihua Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chengcai Chu
- * Corresponding author: E-mail, ; Fax, +86-10-64806608
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27
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Li K, Wang J, Kuang L, Tian Z, Wang X, Dun X, Tu J, Wang H. Genome-wide association study and transcriptome analysis reveal key genes affecting root growth dynamics in rapeseed. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:178. [PMID: 34507599 PMCID: PMC8431925 DOI: 10.1186/s13068-021-02032-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/30/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND In terms of global demand, rapeseed is the third-largest oilseed crop after soybeans and palm, which produces vegetable oil for human consumption and biofuel for industrial production. Roots are vital organs for plant to absorb water and attain mineral nutrients, thus they are of great importance to plant productivity. However, the genetic mechanisms regulating root development in rapeseed remain unclear. In the present study, seven root-related traits and shoot biomass traits in 280 Brassica napus accessions at five continuous vegetative stages were measured to establish the genetic basis of root growth in rapeseed. RESULTS The persistent and stage-specific genetic mechanisms were revealed by root dynamic analysis. Sixteen persistent and 32 stage-specific quantitative trait loci (QTL) clusters were identified through genome-wide association study (GWAS). Root samples with contrasting (slow and fast) growth rates throughout the investigated stages and those with obvious stage-specific changes in growth rates were subjected to transcriptome analysis. A total of 367 differentially expressed genes (DEGs) with persistent differential expressions throughout root development were identified, and these DEGs were significantly enriched in GO terms, such as energy metabolism and response to biotic or abiotic stress. Totally, 485 stage-specific DEGs with different expressions at specific stage were identified, and these DEGs were enriched in GO terms, such as nitrogen metabolism. Four candidate genes were identified as key persistent genetic factors and eight as stage-specific ones by integrating GWAS, weighted gene co-expression network analysis (WGCNA), and differential expression analysis. These candidate genes were speculated to regulate root system development, and they were less than 100 kb away from peak SNPs of QTL clusters. The homologs of three genes (BnaA03g52990D, BnaA06g37280D, and BnaA09g07580D) out of 12 candidate genes have been reported to regulate root development in previous studies. CONCLUSIONS Sixteen QTL clusters and four candidate genes controlling persistently root development, and 32 QTL clusters and eight candidate genes stage-specifically regulating root growth in rapeseed were detected in this study. Our results provide new insights into the temporal genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.
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Affiliation(s)
- Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430062 China
| | - Jie Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Lieqiong Kuang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Ze Tian
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430062 China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
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Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective. PLANTS 2021; 10:plants10040681. [PMID: 33916130 PMCID: PMC8066207 DOI: 10.3390/plants10040681] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022]
Abstract
Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H+-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.
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29
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Affiliation(s)
- Brent N Kaiser
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia.
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30
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Ohkubo Y, Kuwata K, Matsubayashi Y. A type 2C protein phosphatase activates high-affinity nitrate uptake by dephosphorylating NRT2.1. NATURE PLANTS 2021; 7:310-316. [PMID: 33686225 DOI: 10.1038/s41477-021-00870-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The nitrate transporter NRT2.1, which plays a central role in high-affinity nitrate uptake in roots, is activated at the post-translational level in response to nitrogen (N) starvation1,2. However, the critical enzymes required for the post-translational activation of NRT2.1 remain to be identified. Here, we show that a type 2C protein phosphatase, designated CEPD-induced phosphatase (CEPH), activates high-affinity nitrate uptake by directly dephosphorylating Ser501 of NRT2.1, a residue that functions as a negative phospho-switch in Arabidopsis2. CEPH is predominantly expressed in epidermal and cortex cells in roots and is upregulated by N starvation via a CEPDL2/CEPD1/2-mediated long-distance signalling from shoots3,4. The loss of CEPH leads to marked decreases in high-affinity nitrate uptake, tissue nitrate content and plant biomass. Collectively, our results identify CEPH as a crucial enzyme in the N-starvation-dependent activation of NRT2.1 and provide molecular and mechanistic insights into how plants regulate high-affinity nitrate uptake at the post-translational level in response to the N environment.
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Affiliation(s)
- Yuri Ohkubo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.
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31
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Affiliation(s)
- Moona Rahikainen
- Molecular Plant Biology, University of Turku, Turku, FI-20014, Finland
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