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Wen B, Xiao W, Mu Q, Li D, Chen X, Wu H, Li L, Peng F. How does nitrate regulate plant senescence? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:60-69. [PMID: 33091797 DOI: 10.1016/j.plaphy.2020.08.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 05/19/2023]
Abstract
Nitrogen is an essential macronutrient for plant growth and development and plays an important role in the whole life process of plants. Nitrogen is an important component of amino acids, chlorophyll, plant hormones and secondary metabolites. Nitrogen deficiency leads to early senescence in plants, which is accompanied by changes in gene expression, metabolism, growth, development, and physiological and biochemical traits, which ensures efficient nitrogen recycling and enhances the plant's tolerance to low nitrogen. Therefore, it is very important to understand the adaptation mechanisms of plants under nitrogen deficiency for the efficient utilization of nitrogen and gene regulation. With the popularization of molecular biology, bioinformatics and transgenic technology, the metabolic pathways of nitrogen-deficient plants have been verified, and important progress has been made. However, how the responses of plants to nitrogen deficiency affect the biological processes of the plants is not well understood. The current research also cannot completely explain how the metabolic pathways identified show other reactions or phenotypes through interactions or cascades after nitrogen inhibition. Nitrate is the main form of nitrogen absorption. In this review, we discuss the role of nitrate in plant senescence. Understanding how nitrate inhibition affects nitrate absorption, transport, and assimilation; chlorophyll synthesis; photosynthesis; anthocyanin synthesis; and plant hormone synthesis is key to sustainable agriculture.
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Affiliation(s)
- Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Wei Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Qin Mu
- College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Hongyu Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
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Genome-Wide Differential DNA Methylation and miRNA Expression Profiling Reveals Epigenetic Regulatory Mechanisms Underlying Nitrogen-Limitation-Triggered Adaptation and Use Efficiency Enhancement in Allotetraploid Rapeseed. Int J Mol Sci 2020; 21:ijms21228453. [PMID: 33182819 PMCID: PMC7697602 DOI: 10.3390/ijms21228453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 12/15/2022] Open
Abstract
Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1, NRT1.5, NRT1.7, NRT2.1/NAR2.1, and Gln1;1, and repressed the transcriptional levels of CLCa, NRT1.8, and NIA1. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-SCL6 and miR160-ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.
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Araus V, Swift J, Alvarez JM, Henry A, Coruzzi GM. A balancing act: how plants integrate nitrogen and water signals. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4442-4451. [PMID: 31990028 PMCID: PMC7382378 DOI: 10.1093/jxb/eraa054] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/24/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen (N) and water (W) are crucial inputs for plant survival as well as costly resources for agriculture. Given their importance, the molecular mechanisms that plants rely on to signal changes in either N or W status have been under intense scrutiny. However, how plants sense and respond to the combination of N and W signals at the molecular level has received scant attention. The purpose of this review is to shed light on what is currently known about how plant responses to N are impacted by W status. We review classic studies which detail how N and W combinations have both synergistic and antagonistic effects on key plant traits, such as root architecture and stomatal aperture. Recent molecular studies of N and W interactions show that mutations in genes involved in N metabolism affect drought responses, and vice versa. Specifically, perturbing key N signaling genes may lead to changes in drought-responsive gene expression programs, which is supported by a meta-analysis we conduct on available transcriptomic data. Additionally, we cite studies that show how combinatorial transcriptional responses to N and W status might drive crop phenotypes. Through these insights, we suggest research strategies that could help to develop crops adapted to marginal soils depleted in both N and W, an important task in the face of climate change.
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Affiliation(s)
- Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
| | - Jose M Alvarez
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Amelia Henry
- International Rice Research Institute, Metro Manila, Philippines
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA
- Correspondence:
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Meng X, Li L, Narsai R, De Clercq I, Whelan J, Berkowitz O. Mitochondrial signalling is critical for acclimation and adaptation to flooding in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:227-247. [PMID: 32064696 DOI: 10.1111/tpj.14724] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 01/23/2020] [Accepted: 02/04/2020] [Indexed: 05/23/2023]
Abstract
Mitochondria have critical functions in the acclimation to abiotic and biotic stresses. Adverse environmental conditions lead to increased demands in energy supply and metabolic intermediates, which are provided by mitochondrial ATP production and the tricarboxylic acid (TCA) cycle. Mitochondria also play a role as stress sensors to adjust nuclear gene expression via retrograde signalling with the transcription factor (TF) ANAC017 and the kinase CDKE1 key components to integrate various signals into this pathway. To determine the importance of mitochondria as sensors of stress and their contribution in the tolerance to adverse growth conditions, a comparative phenotypical, physiological and transcriptomic characterisation of Arabidopsis mitochondrial signalling mutants (cdke1/rao1 and anac017/rao2) and a set of contrasting accessions was performed after applying the complex compound stress of submergence. Our results showed that impaired mitochondrial retrograde signalling leads to increased sensitivity to the stress treatments. The multi-factorial approach identified a network of 702 co-expressed genes, including several WRKY TFs, overlapping in the transcriptional responses in the mitochondrial signalling mutants and stress-sensitive accessions. Functional characterisation of two WRKY TFs (WRKY40 and WRKY45), using both knockout and overexpressing lines, confirmed their role in conferring tolerance to submergence. Together, the results revealed that acclimation to submergence is dependent on mitochondrial retrograde signalling, and underlying transcriptional re-programming is used as an adaptation mechanism.
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Affiliation(s)
- Xiangxiang Meng
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Lu Li
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Inge De Clercq
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - James Whelan
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
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Huang CH, Singh GP, Park SH, Chua NH, Ram RJ, Park BS. Early Diagnosis and Management of Nitrogen Deficiency in Plants Utilizing Raman Spectroscopy. FRONTIERS IN PLANT SCIENCE 2020; 11:663. [PMID: 32582235 PMCID: PMC7291773 DOI: 10.3389/fpls.2020.00663] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/29/2020] [Indexed: 05/25/2023]
Abstract
Nutrient deficiency alters growth and development of crop plants and compromises yield. Real-time non-invasive monitoring of the nutritional status of crops would allow timely applications of fertilizers to optimize for growth and yield at different times of the plant's life cycle. Here, we used Raman spectroscopy to characterize Arabidopsis and two varieties of leafy vegetable crops under nitrogen sufficient and deficient conditions. We showed that the 1046 cm-1 Raman peak serves as a specific signature of nitrogen status in planta, which can be used for early diagnosis of nitrogen deficiency in plants before onset of any visible symptoms. Our research can be applied toward crop management for sustainable and precision agriculture.
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Affiliation(s)
- Chung Hao Huang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Gajendra Pratap Singh
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Su Hyun Park
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Rajeev J. Ram
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
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Chardon F, Cueff G, Delannoy E, Aubé F, Lornac A, Bedu M, Gilard F, Pateyron S, Rogniaux H, Gargaros A, Mireau H, Rajjou L, Martin-Magniette ML, Budar F. The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2020; 9:E573. [PMID: 32369924 PMCID: PMC7285260 DOI: 10.3390/plants9050573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/04/2022]
Abstract
Mitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes.
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Affiliation(s)
- Fabien Chardon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Fabien Aubé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Aurélia Lornac
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Magali Bedu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Françoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Stéphanie Pateyron
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France; (H.R.); (A.G.)
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Audrey Gargaros
- INRAE, UR BIA, F-44316 Nantes, France; (H.R.); (A.G.)
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Hakim Mireau
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Loïc Rajjou
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, 91405 Orsay, France; (E.D.); (F.G.); (S.P.); (M.-L.M.-M.)
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91405 Orsay, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Françoise Budar
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (G.C.); (F.A.); (A.L.); (M.B.); (H.M.); (L.R.)
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Ortigosa F, Valderrama-Martín JM, Urbano-Gámez JA, García-Martín ML, Ávila C, Cánovas FM, Cañas RA. Inorganic Nitrogen Form Determines Nutrient Allocation and Metabolic Responses in Maritime Pine Seedlings. PLANTS 2020; 9:plants9040481. [PMID: 32283755 PMCID: PMC7238028 DOI: 10.3390/plants9040481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022]
Abstract
Nitrate and ammonium are the main forms of inorganic nitrogen available to plants. The present study aimed to investigate the metabolic changes caused by ammonium and nitrate nutrition in maritime pine (Pinus pinaster Ait.). Seedlings were grown with five solutions containing different proportions of nitrate and ammonium. Their nitrogen status was characterized through analyses of their biomass, different biochemical and molecular markers as well as a metabolite profile using 1H-NMR. Ammonium-fed seedlings exhibited higher biomass than nitrate-fed-seedlings. Nitrate mainly accumulated in the stem and ammonium in the roots. Needles of ammonium-fed seedlings had higher nitrogen and amino acid contents but lower levels of enzyme activities related to nitrogen metabolism. Higher amounts of soluble sugars and L-arginine were found in the roots of ammonium-fed seedlings. In contrast, L-asparagine accumulated in the roots of nitrate-fed seedlings. The differences in the allocation of nitrate and ammonium may function as metabolic buffers to prevent interference with the metabolism of photosynthetic organs. The metabolite profiles observed in the roots suggest problems with carbon and nitrogen assimilation in nitrate-supplied seedlings. Taken together, this new knowledge contributes not only to a better understanding of nitrogen metabolism but also to improving aspects of applied mineral nutrition for conifers.
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Affiliation(s)
- Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (F.O.); (J.M.V.-M.); (J.A.U.-G.); (C.Á.); (F.M.C.)
| | - José Miguel Valderrama-Martín
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (F.O.); (J.M.V.-M.); (J.A.U.-G.); (C.Á.); (F.M.C.)
| | - José Alberto Urbano-Gámez
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (F.O.); (J.M.V.-M.); (J.A.U.-G.); (C.Á.); (F.M.C.)
| | - María Luisa García-Martín
- BIONAND, Centro Andaluz de Nanomedicina y Biotecnología, Junta de Andalucía, Universidad de Málaga, 29590 Málaga, Spain;
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (F.O.); (J.M.V.-M.); (J.A.U.-G.); (C.Á.); (F.M.C.)
| | - Francisco M. Cánovas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (F.O.); (J.M.V.-M.); (J.A.U.-G.); (C.Á.); (F.M.C.)
| | - Rafael A. Cañas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, 29071 Málaga, Spain; (F.O.); (J.M.V.-M.); (J.A.U.-G.); (C.Á.); (F.M.C.)
- Correspondence: ; Tel.: +34-952-13-4272
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Integrated Transcriptional and Proteomic Profiling Reveals Potential Amino Acid Transporters Targeted by Nitrogen Limitation Adaptation. Int J Mol Sci 2020; 21:ijms21062171. [PMID: 32245240 PMCID: PMC7139695 DOI: 10.3390/ijms21062171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 01/10/2023] Open
Abstract
Nitrogen (N) is essential for plant growth and crop productivity. Organic N is a major form of remobilized N in plants’ response to N limitation. It is necessary to understand the regulatory role of N limitation adaption (NLA) in organic N remobilization for this adaptive response. Transcriptional and proteomic analyses were integrated to investigate differential responses of wild-type (WT) and nla mutant plants to N limitation and to identify the core organic N transporters targeted by NLA. Under N limitation, the nla mutant presented an early senescence with faster chlorophyll loss and less anthocyanin accumulation than the WT, and more N was transported out of the aging leaves in the form of amino acids. High-throughput transcriptomic and proteomic analyses revealed that N limitation repressed genes involved in photosynthesis and protein synthesis, and promoted proteolysis; these changes were higher in the nla mutant than in the WT. Both transcriptional and proteomic profiling demonstrated that LHT1, responsible for amino acid remobilization, were only significantly upregulated in the nla mutant under N limitation. These findings indicate that NLA might target LHT1 and regulate organic N remobilization, thereby improving our understanding of the regulatory role of NLA on N remobilization under N limitation.
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Ueda H, Ito T, Inoue R, Masuda Y, Nagashima Y, Kozuka T, Kusaba M. Genetic Interaction Among Phytochrome, Ethylene and Abscisic Acid Signaling During Dark-Induced Senescence in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:564. [PMID: 32508856 PMCID: PMC7253671 DOI: 10.3389/fpls.2020.00564] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/15/2020] [Indexed: 05/18/2023]
Abstract
Leaf senescence is induced by various internal and external stimuli. Dark-induced senescence has been extensively investigated, but the detailed mechanism underlying it is not well understood. The red light/far-red light receptor phytochrome B and its downstream transcription factors, PYHTOCHROME INTERACTING FACTORs (PIFs) 4 and 5, are known to play an important role in dark-induced senescence. Furthermore, the senescence-inducing phytohormones, ethylene and abscisic acid (ABA) are reported to be involved in dark-induced senescence. In this study, we analyzed the relationship between ethylene, ABA and PIFs in dark-induced leaf senescence. A triple mutant of the core ABA signaling components; SNF1-related protein kinases 2D (SRK2D), SRK2E, and SRK2I, displayed an ABA insensitive phenotype in ABA-induced senescence, whilst the ethylene insensitive mutant ein2 demonstrated low sensitivity to ABA, suggesting that ethylene signaling is involved in ABA-induced senescence. However, the pif4 pif5 mutant did not display low sensitivity to ABA, suggesting that PIF4 and PIF5 act upstream of ABA signaling. Although PIF4 and PIF5 reportedly regulate ethylene production, the triple mutant ein2 pif4 pif5 showed a stronger delayed senescence phenotype than ein2 or pif4 pif5, suggesting that EIN2 and PIF4/PIF5 partially regulate leaf senescence independently of each other. While direct target genes for PIF4 and PIF5, such as LONG HYPOCOTYL IN FAR-RED1 (HFR1) and PHYTOCHROME INTERACTING FACTOR 3-LIKE 1 (PIL1), showed transient upregulation under dark conditions (as is seen in the shade avoidance response), expression of STAY GREEN1 (SGR1), ORESARA1 (ORE1) and other direct target genes of PIF5, continued to increase during dark incubation. It is possible that transcription factors other than PIF4 and PIF5 are involved in the upregulation of SGR1 and ORE1 at a later stage of dark-induced senescence. Possible candidates are senescence-induced senescence regulators (SIRs), which include the NAC transcription factors ORE1 and AtNAP. In fact, ORE1 is known to bind to the SGR1 promoter and promotes its expression. It is therefore inferred that the phytochrome-PIF pathway regulates initial activation of senescence and subsequently, induced SIRs reinforce leaf senescence during dark-induced senescence.
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60
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Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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Lorenzo‐Orts L, Couto D, Hothorn M. Identity and functions of inorganic and inositol polyphosphates in plants. THE NEW PHYTOLOGIST 2020; 225:637-652. [PMID: 31423587 PMCID: PMC6973038 DOI: 10.1111/nph.16129] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 05/08/2023]
Abstract
Inorganic polyphosphates (polyPs) and inositol pyrophosphates (PP-InsPs) form important stores of inorganic phosphate and can act as energy metabolites and signaling molecules. Here we review our current understanding of polyP and inositol phosphate (InsP) metabolism and physiology in plants. We outline methods for polyP and InsP detection, discuss the known plant enzymes involved in their synthesis and breakdown, and summarize the potential physiological and signaling functions for these enigmatic molecules in plants.
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Affiliation(s)
- Laura Lorenzo‐Orts
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Daniel Couto
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
| | - Michael Hothorn
- Structural Plant Biology LaboratoryDepartment of Botany and Plant BiologyUniversity of Geneva30 Quai E. AnsermetGeneva1211Switzerland
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Lu J, Xu Y, Fan Y, Wang Y, Zhang G, Liang Y, Jiang C, Hong B, Gao J, Ma C. Proteome and Ubiquitome Changes during Rose Petal Senescence. Int J Mol Sci 2019; 20:E6108. [PMID: 31817087 PMCID: PMC6940906 DOI: 10.3390/ijms20246108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 12/25/2022] Open
Abstract
Petal senescence involves numerous programmed changes in biological and biochemical processes. Ubiquitination plays a critical role in protein degradation, a hallmark of organ senescence. Therefore, we investigated changes in the proteome and ubiquitome of senescing rose (Rosa hybrida) petals to better understand their involvement in petal senescence. Of 3859 proteins quantified in senescing petals, 1198 were upregulated, and 726 were downregulated during senescence. We identified 2208 ubiquitinated sites, including 384 with increased ubiquitination in 298 proteins and 1035 with decreased ubiquitination in 674 proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that proteins related to peptidases in proteolysis and autophagy pathways were enriched in the proteome, suggesting that protein degradation and autophagy play important roles in petal senescence. In addition, many transporter proteins accumulated in senescing petals, and several transport processes were enriched in the ubiquitome, indicating that transport of substances is associated with petal senescence and regulated by ubiquitination. Moreover, several components of the brassinosteroid (BR) biosynthesis and signaling pathways were significantly altered at the protein and ubiquitination levels, implying that BR plays an important role in petal senescence. Our data provide a comprehensive view of rose petal senescence at the posttranslational level.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Chao Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; (J.L.); (Y.X.); (Y.F.); (Y.W.); (G.Z.); (Y.L.); (C.J.); (B.H.); (J.G.)
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Wen B, Li C, Fu X, Li D, Li L, Chen X, Wu H, Cui X, Zhang X, Shen H, Zhang W, Xiao W, Gao D. Effects of nitrate deficiency on nitrate assimilation and chlorophyll synthesis of detached apple leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:363-371. [PMID: 31398585 DOI: 10.1016/j.plaphy.2019.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 05/10/2023]
Abstract
Nitrogen is one of the most important nutrients for plant growth and development. Nitrate nitrogen (NO3--N) is the main form of nitrogen taken up by plants. Understanding the effects of exogenous NO3--N on nitrogen metabolism at the gene expression and enzyme activity levels during nitrogen assimilation and chlorophyll synthesis is important for increasing nitrogen utilization efficiency. In this study, cell morphology, NO3--N uptake rates, the expression of key genes related to nitrogen assimilation and chlorophyll synthesis and enzyme activity in apple leaves under NO3--N deficiency were investigated. The results showed that the cell morphology of apple leaves was irreversibly deformed due to NO3--N deficiency. NO3--N was absorbed slightly one day after NO3--N deficiency treatment and effluxed after 3 days. The relative expression of genes encoding nitrogen assimilation enzymes and the activity of such enzymes decreased significantly after 1 day of NO3--N deficiency treatment. After treatment for 14 days, gene expression was upregulated, enzyme activity was increased, and NO3--N content was increased. NO3--N deficiency hindered the transformation of 5-aminobilinic acid (ALA) to porphobilinogen (PBG), suggesting a possible route by which NO3--N levels affect chlorophyll synthesis. Collectively, the results indicate that NO3--N deficiency affects enzyme activity by altering the expression of key genes in the nitrogen assimilation pathway, thereby suppressing NO3--N absorption and assimilation. NO3--N deficiency inhibits the synthesis of the chlorophyll precursor PBG, thereby hindering chlorophyll synthesis.
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Affiliation(s)
- Binbin Wen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Chen Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xiude Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Hongyu Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xiaowen Cui
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Xinhao Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Hongyan Shen
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China
| | - Wenqian Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Xintai Modern Agriculture Development Service Center, 819 Qingyun Road, Tai'an, 271200, China
| | - Wei Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
| | - Dongsheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
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Pan W, Wu Y, Xie Q. Regulation of Ubiquitination Is Central to the Phosphate Starvation Response. TRENDS IN PLANT SCIENCE 2019; 24:755-769. [PMID: 31176527 DOI: 10.1016/j.tplants.2019.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 05/22/2023]
Abstract
As sessile organisms, plants have developed numerous strategies to overcome the limiting availability of the essential nutrient phosphate in nature. Recent studies reveal that post-translational modification (PTM) by ubiquitination is an important and central regulation mechanism in the plant phosphate starvation response (PSR). Ubiquitination precisely modulates the stability and trafficking of proteins in response to the heterogeneous phosphate supplement. Induction of autophagy provides novel insights into the molecular mechanisms under phosphate starvation. In this review, we present and discuss novel findings on the regulation of diverse PSRs through ubiquitination. Resolving these regulation mechanisms will pave the way to improve phosphate acquisition and utilization efficiency in crops.
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Affiliation(s)
- Wenbo Pan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Park SH, Jeong JS, Seo JS, Park BS, Chua NH. Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency. THE NEW PHYTOLOGIST 2019; 223:1447-1460. [PMID: 31050353 DOI: 10.1111/nph.15879] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/18/2019] [Indexed: 05/09/2023]
Abstract
Nitrogen deficiency (-N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1. Little is known about post-translational regulation of ORE1 in this process. Here, we show that UBP12/UBP13 (ubiquitin-specific protease 12/13) antagonize the action of NLA (nitrogen limitation adaptation) E3 ligase to maintain ORE1 homeostasis. In vitro pull-down and in vivo co-immunoprecipitation assays demonstrated specific binding between UBP12/UBP13 and ORE1. We further analyzed in various genotypes total Chl content and expression levels of senescence-related genes under -N conditions. We found that UBP12/UBP13 can deubiquitinate polyubiquitinated ORE1 in vitro and increase the stability of ORE1 in vivo in MG132/cycloheximide-chase experiments. Plants overexpressing UBP12/UBP13 display accelerated leaf senescence which is reversed by the ore1 mutation. By contrast, the senescence phenotype of plants overexpressing ORE1 is exacerbated by UBP12/UBP13 overexpression. The expression of senescence-related genes tracks the senescence phenotype. ORE1 protein levels can be elevated by UBP12/UBP13 overexpression but decreased in ubp12-2w/13-3. In conclusion, UBP12/UBP13 deubiquitinate ORE1 to stabilize this transcription factor and promote its activity as a positive regulator for leaf senescence under -N conditions. Our study shows that UBP12/UBP13 counteracts the effect of NLA E3 ligase to accelerate leaf senescence under nitrogen starvation.
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Affiliation(s)
- Su-Hyun Park
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jin Seo Jeong
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Jun Sung Seo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Bong Soo Park
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
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Affiliation(s)
- Salma Balazadeh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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