1
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Zhuo M, Sakuraba Y, Yanagisawa S. Dof1.7 and NIGT1 transcription factors mediate multilayered transcriptional regulation for different expression patterns of NITRATE TRANSPORTER2 genes under nitrogen deficiency stress. THE NEW PHYTOLOGIST 2024; 242:2132-2147. [PMID: 38523242 DOI: 10.1111/nph.19695] [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: 10/31/2023] [Accepted: 03/01/2024] [Indexed: 03/26/2024]
Abstract
Elucidating the mechanisms regulating nitrogen (N) deficiency responses in plants is of great agricultural importance. Previous studies revealed that decreased expression of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) transcriptional repressor genes upon N deficiency is involved in N deficiency-inducible gene expression in Arabidopsis thaliana. However, our knowledge of the mechanisms controlling N deficiency-induced changes in gene expression is still limited. Through the identification of Dof1.7 as a direct target of NIGT1 repressors and a novel N deficiency response-related transcriptional activator gene, we here show that NIGT1 and Dof1.7 transcription factors (TFs) differentially regulate N deficiency-inducible expression of three high-affinity nitrate transporter genes, NRT2.1, NRT2.4, and NRT2.5, which are responsible for most of the soil nitrate uptake activity of Arabidopsis plants under N-deficient conditions. Unlike NIGT1 repressors, which directly suppress NRT2.1, NRT2.4, and NRT2.5 under N-sufficient conditions, Dof1.7 directly activated only NRT2.5 but indirectly and moderately activated NRT2.1 and NRT2.4 under N-deficient conditions, probably by indirectly decreasing NIGT1 expression. Thus, Dof1.7 converted passive transcriptional activation into active and potent transcriptional activation, further differentially enhancing the expression of NRT2 genes. These findings clarify the mechanism underlying different expression patterns of NRT2 genes upon N deficiency, suggesting that time-dependent multilayered transcriptional regulation generates complicated expression patterns of N deficiency-inducible genes.
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Affiliation(s)
- Mengna Zhuo
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhito Sakuraba
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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2
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Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: it's about time and space. THE PLANT CELL 2024; 36:1482-1503. [PMID: 38366121 PMCID: PMC11062454 DOI: 10.1093/plcell/koae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
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Affiliation(s)
- Carly M Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Rothkegel
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - Chia-Yi Cheng
- Department of Life Science, National Taiwan University, Taipei 10663, Taiwan
| | - José M Alvarez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés Bello, 8370035 Santiago, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Rodrigo A Gutiérrez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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3
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Derrien V, André E, Bernad S. Peroxidase activity of rice (Oryza sativa) hemoglobin: distinct role of tyrosines 112 and 151. J Biol Inorg Chem 2023; 28:613-626. [PMID: 37507628 DOI: 10.1007/s00775-023-02014-0] [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: 02/03/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Five non-symbiotic hemoglobins (nsHb) have been identified in rice (Oryza sativa). Previous studies have shown that stress conditions can induce their overexpression, but the role of those globins is still unclear. To better understand the functions of nsHb, the reactivity of rice Hb1 toward hydrogen peroxide (H2O2) has been studied in vitro. Our results show that recombinant rice Hb1 dimerizes through dityrosine cross-links in the presence of H2O2. By site-directed mutagenesis, we suggest that tyrosine 112 located in the FG loop is involved in this dimerization. Interestingly, this residue is not conserved in the sequence of the five rice non-symbiotic hemoglobins. Stopped-flow spectrophotometric experiments have been performed to measure the catalytic constants of rice Hb and its variants using the oxidation of guaiacol. We have shown that Tyrosine112 is a residue that enhances the peroxidase activity of rice Hb1, since its replacement by an alananine leads to a decrease of guaiacol oxidation. In contrast, tyrosine 151, a conserved residue which is buried inside the heme pocket, reduces the protein reactivity. Indeed, the variant Tyr151Ala exhibits a higher peroxidase activity than the wild type. Interestingly, this residue affects the heme coordination and the replacement of the tyrosine by an alanine leads to the loss of the distal ligand. Therefore, even if the amino acid at position 151 does not participate to the formation of the dimer, this residue modulates the peroxidase activity and plays a role in the hexacoordinated state of the heme.
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Affiliation(s)
- Valérie Derrien
- Institut de Chimie Physique, UMR8000, Université Paris-Saclay, CNRS, Avenue Jean Perrin. Bat 350, 91405, Orsay, France.
| | - Eric André
- Institut de Chimie Physique, UMR8000, Université Paris-Saclay, CNRS, Avenue Jean Perrin. Bat 350, 91405, Orsay, France
| | - Sophie Bernad
- Institut de Chimie Physique, UMR8000, Université Paris-Saclay, CNRS, Avenue Jean Perrin. Bat 350, 91405, Orsay, France
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4
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Nakagami S, Notaguchi M, Kondo T, Okamoto S, Ida T, Sato Y, Higashiyama T, Tsai AYL, Ishida T, Sawa S. Root-knot nematode modulates plant CLE3-CLV1 signaling as a long-distance signal for successful infection. SCIENCE ADVANCES 2023; 9:eadf4803. [PMID: 37267361 PMCID: PMC10413670 DOI: 10.1126/sciadv.adf4803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/28/2023] [Indexed: 06/04/2023]
Abstract
Plants use many long-distance and systemic signals to modulate growth and development, as well as respond to biotic and abiotic stresses. Parasitic nematodes infect host plant roots and cause severe damage to crop plants. However, the molecular mechanisms that regulate parasitic nematode infections are still unknown. Here, we show that plant parasitic root-knot nematodes (RKNs), Meloidogyne incognita, modulate the host CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE)-CLV1 signaling module to promote the infection progression. Plants deficient in the CLE signaling pathway show enhanced RKN resistance, whereas CLE overexpression leads to increased susceptibility toward RKN. Grafting analysis shows that CLV1 expression in the shoot alone is sufficient to positively regulate RKN infection. Together with results from the split-root culture system, infection assays, and CLE3-CLV1 binding assays, we conclude that mobile root-derived CLE signals are perceived by CLV1 in the shoot, which subsequently produce systemic signals to promote gall formation and RKN reproduction.
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Affiliation(s)
- Satoru Nakagami
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan
| | - Tatsuhiko Kondo
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Satoru Okamoto
- Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama, 332-0012, Japan
| | - Takanori Ida
- Department of Bioactive Peptides, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Allen Yi-Lun Tsai
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
- International Research Center for Agricultural & Environmental Biology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto 860-8555, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
- International Research Center for Agricultural & Environmental Biology, Kumamoto University, Kumamoto 860-8555, Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto 860-8555, Japan
- Institute of Industrial Nanomaterial (IINA), Kumamoto University, Kumamoto 860-8555, Japan
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5
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Durand M, Brehaut V, Clement G, Kelemen Z, Macé J, Feil R, Duville G, Launay-Avon A, Roux CPL, Lunn JE, Roudier F, Krapp A. The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply. THE PLANT CELL 2023; 35:1429-1454. [PMID: 36752317 PMCID: PMC10118280 DOI: 10.1093/plcell/koad025] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Whereas several transcriptional regulators of nitrate signaling have been identified, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN7 (NLP7), additional regulators are expected to fine-tune this pivotal physiological response. Here, we characterized Arabidopsis NLP2 as a top-tier transcriptional regulator of the early nitrate response gene regulatory network. NLP2 interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, DNA-binding motif, and some target genes with NLP7. Genetic, genomic, and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multitiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production.
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Affiliation(s)
- Mickaël Durand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
- UMR CNRS 7267, EBI Ecologie et Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Virginie Brehaut
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Gilles Clement
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Zsolt Kelemen
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Julien Macé
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm D-14476, Germany
| | - Garry Duville
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm D-14476, Germany
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Anne Krapp
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
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6
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Wu H, Li J, Pu Q, Mi C, Zeng G, Chen Y, Kong D, Zuo X, Hu X, Li O. Physiological and transcriptome analysis of Dendrobium officinale under low nitrogen stress. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:314-334. [PMID: 36872310 DOI: 10.1071/fp22061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen (N) is the main nutrient of plants, and low nitrogen usually affects plant growth and crop yield. The traditional Chinese herbal medicine Dendrobium officinale Kimura et. Migo is a typical low nitrogen-tolerant plant, and its mechanism in response to low nitrogen stress has not previously been reported. In this study, physiological measurements and RNA-Seq analysis were used to analyse the physiological changes and molecular responses of D. officinale under different nitrogen concentrations. The results showed that under low nitrogen levels, the growth, photosynthesis and superoxide dismutase activity were found to be significantly inhibited, while the activities of peroxidase and catalase, the content of polysaccharides and flavonoids significantly increased. Differentially expressed genes (DEGs) analysis showed that nitrogen and carbon metabolisms, transcriptional regulation, antioxidative stress, secondary metabolite synthesis and signal transduction all made a big difference in low nitrogen stress. Therefore, copious polysaccharide accumulation, efficient assimilation and recycling of nitrogen, as well as rich antioxidant components play critical roles. This study is helpful for understanding the response mechanism of D. officinale to low nitrogen levels, which might provide good guidance for practical production of high quality D. officinale .
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Affiliation(s)
- Hangtao Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Jin Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Qian Pu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Chunyi Mi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Guohong Zeng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Ying Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Dedong Kong
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310018, P. R. China
| | - Xiaorong Zuo
- Xi'an Ande Pharmaceutical Co., Ltd, Zhenping Branch, Xi'an 710000, P. R. China
| | - Xiufang Hu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
| | - Ou Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, P. R. China
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7
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Iron Source and Medium pH Affect Nutrient Uptake and Pigment Content in Petunia hybrida ‘Madness Red’ Cultured In Vitro. Int J Mol Sci 2022; 23:ijms23168943. [PMID: 36012209 PMCID: PMC9409069 DOI: 10.3390/ijms23168943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Deficiency or excess of iron (Fe) and improper medium pH will inhibit the growth and development of plants, reduce the transfer and utilization of energy from the root to the leaf, and affect the utilization efficiency of inorganic nutrients. The most common symptom of Fe deficiency in plants is chlorosis of the young leaves. In this study, the effects of the iron source, in combination with the medium pH, on plant growth and development, plant pigment synthesis, and nutrient uptake in a model plant Petunia hybrida cultured in vitro were investigated. Iron sulfate (FeSO4·7H2O) or iron chelated with ethylenediaminetetraacetic acid (Fe-EDTA) were supplemented to the MNS (a multipurpose nutrient solution) medium at a concentration of 2.78 mg·L−1 Fe, and the treatment without any Fe was used as the control. The pH of the agar-solidified medium was adjusted to either 4.70, 5.70, or 6.70 before autoclaving. The experiment was carried out in an environmentally controlled culture room with a temperature of 24 °C with 100 µmol·m−2·s−1 photosynthetic photon flux density (PPFD) supplied by white light emitting diodes (LEDs) during a photoperiod of 16 h a day, 18 °C for 8 h a day in the dark, and 70% relative humidity. Regardless of the Fe source including the control, the greatest number of leaves was observed at pH 4.70. However, the greatest lengths of the leaf and root were observed in the treatment with Fe-EDTA combined with pH 5.70. The contents of the chlorophyll, carotenoid, and anthocyanin decreased with increasing medium pH, and contents of these plant pigments were positively correlated with the leaf color. The highest soluble protein content and activities of APX and CAT were observed in the Fe-EDTA under pH 5.70. However, the GPX activity was the highest in the control under pH 4.70. In addition, the highest contents of ammonium (NH4+) and nitrate (NO3−) were measured in the FeSO4-4.7 and EDTA-5.7, respectively. More than that, the treatment of Fe-EDTA combined with pH 5.70 (EDTA-5.7) enhanced nutrient absorption, as proven by the highest tissue contents of P, K, Ca, Mg, Fe, and Mn. The genes’ ferric reduction oxidase 1 and 8 (PhFRO1 and PhFRO8), iron-regulated transporter 1 (PhIRT1), nitrate transporter 2.5 (PhNRT2.5), and deoxyhypusine synthase (PhDHS) were expressed at the highest levels in this treatment as well. In the treatment of EDTA-5.7, the reduction and transport of chelated iron in P. hybrida leaves were enhanced, which also affected the transport of nitrate and catalyzed chlorophyll level in leaves. In conclusion, when the medium pH was adjusted to 5.70, supplementation of chelated Fe-EDTA was more conducive to promoting the growth and development of, and absorption of mineral nutrients by, the plant and the expression of related genes in the leaves.
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8
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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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9
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Liao HS, Chung YH, Hsieh MH. Glutamate: A multifunctional amino acid in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111238. [PMID: 35351313 DOI: 10.1016/j.plantsci.2022.111238] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Glutamate (Glu) is a versatile metabolite and a signaling molecule in plants. Glu biosynthesis is associated with the primary nitrogen assimilation pathway. The conversion between Glu and 2-oxoglutarate connects Glu metabolism to the tricarboxylic acid cycle, carbon metabolism, and energy production. Glu is the predominant amino donor for transamination reactions in the cell. In addition to protein synthesis, Glu is a building block for tetrapyrroles, glutathione, and folate. Glu is the precursor of γ-aminobutyric acid that plays an important role in balancing carbon/nitrogen metabolism and various cellular processes. Glu can conjugate to the major auxin indole 3-acetic acid (IAA), and IAA-Glu is destined for oxidative degradation. Glu also conjugates with isochorismate for the production of salicylic acid. Accumulating evidence indicates that Glu functions as a signaling molecule to regulate plant growth, development, and defense responses. The ligand-gated Glu receptor-like proteins (GLRs) mediate some of these responses. However, many of the Glu signaling events are GLR-independent. The receptor perceiving extracellular Glu as a danger signal is still unknown. In addition to GLRs, Glu may act on receptor-like kinases or receptor-like proteins to trigger immune responses. Glu metabolism and Glu signaling may entwine to regulate growth, development, and defense responses in plants.
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Affiliation(s)
- Hong-Sheng Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hsin Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan; Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan.
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10
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Zang L, Tarkowski ŁP, Morère-Le Paven MC, Zivy M, Balliau T, Clochard T, Bahut M, Balzergue S, Pelletier S, Landès C, Limami AM, Montrichard F. The Nitrate Transporter MtNPF6.8 Is a Master Sensor of Nitrate Signal in the Primary Root Tip of Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:832246. [PMID: 35371178 PMCID: PMC8971838 DOI: 10.3389/fpls.2022.832246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/12/2023]
Abstract
Nitrate is not only an essential nutrient for plants, but also a signal involved in plant development. We have previously shown in the model legume Medicago truncatula, that the nitrate signal, which restricts primary root growth, is mediated by MtNPF6.8, a nitrate transporter. Nitrate signal also induces changes in reactive oxygen species accumulation in the root tip due to changes in cell wall peroxidase (PODs) activity. Thus, it was interesting to determine the importance of the role of MtNPF6.8 in the regulation of the root growth by nitrate and identify the POD isoforms responsible for the changes in POD activity. For this purpose, we compared in M. truncatula a npf6.8 mutant and nitrate insensitive line deficient in MtNPF6.8 and the corresponding wild and sensitive genotype for their transcriptomic and proteomic responses to nitrate. Interestingly, only 13 transcripts and no protein were differently accumulated in the primary root tip of the npf6.8-3 mutant line in response to nitrate. The sensitivity of the primary root tip to nitrate appeared therefore to be strongly linked to the integrity of MtNPF6.8 which acts as a master mediator of the nitrate signal involved in the control of the root system architecture. In parallel, 7,259 and 493 genes responded, respectively, at the level of transcripts or proteins in the wild type, 196 genes being identified by both their transcript and protein. By focusing on these 196 genes, a concordance of expression was observed for most of them with 143 genes being up-regulated and 51 being down-regulated at the two gene expression levels. Their ontology analysis uncovered a high enrichment in POD genes, allowing the identification of POD candidates involved in the changes in POD activity previously observed in response to nitrate.
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Affiliation(s)
- Lili Zang
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | | | | | - Michel Zivy
- PAPPSO, GQE – Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Balliau
- PAPPSO, GQE – Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Clochard
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | | | - Sandrine Balzergue
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Sandra Pelletier
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Claudine Landès
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Anis M. Limami
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
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11
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Singh P, Kumar K, Jha AK, Yadava P, Pal M, Rakshit S, Singh I. Global gene expression profiling under nitrogen stress identifies key genes involved in nitrogen stress adaptation in maize (Zea mays L.). Sci Rep 2022; 12:4211. [PMID: 35273237 PMCID: PMC8913646 DOI: 10.1038/s41598-022-07709-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Maize is a heavy consumer of fertilizer nitrogen (N) which not only results in the high cost of cultivation but may also lead to environmental pollution. Therefore, there is a need to develop N-use efficient genotypes, a prerequisite for which is a greater understanding of N-deficiency stress adaptation. In this study, comparative transcriptome analysis was performed using leaf and root tissues from contrasting inbred lines, viz., DMI 56 (tolerant to N stress) and DMI 81 (susceptible to N stress) to delineate the differentially expressed genes (DEGs) under low-N stress. The contrasting lines were grown hydroponically in modified Hoagland solution having either sufficient- or deficient-N, followed by high-throughput RNA-sequencing. A total of 8 sequencing libraries were prepared and 88–97% of the sequenced raw reads were mapped to the reference B73 maize genome. Genes with a p value ≤ 0.05 and fold change of ≥ 2.0 or ≤ − 2 were considered as DEGs in various combinations performed between susceptible and tolerant genotypes. DEGs were further classified into different functional categories and pathways according to their putative functions. Gene Ontology based annotation of these DEGs identified three different functional categories: biological processes, molecular function, and cellular component. The KEGG and Mapman based analysis revealed that most of the DEGs fall into various metabolic pathways, biosynthesis of secondary metabolites, signal transduction, amino acid metabolism, N-assimilation and metabolism, and starch metabolism. Some of the key genes involved in N uptake (high-affinity nitrate transporter 2.2 and 2.5), N assimilation and metabolism (glutamine synthetase, asparagine synthetase), redox homeostasis (SOD, POX), and transcription factors (MYB36, AP2-EREBP) were found to be highly expressed in the tolerant genotype compared to susceptible one. The candidate genes identified in the present study might be playing a pivotal role in low-N stress adaptation in maize and hence could be useful in augmenting further research on N metabolism and development of N-deficiency tolerant maize cultivars.
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Affiliation(s)
- Prabha Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India.,Indian Council of Agricultural Research-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Krishan Kumar
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Abhishek Kumar Jha
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pranjal Yadava
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Madan Pal
- Indian Council of Agricultural Research-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Sujay Rakshit
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Ishwar Singh
- Indian Council of Agricultural Research-Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India.
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12
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The Regulation of Nitrate Reductases in Response to Abiotic Stress in Arabidopsis. Int J Mol Sci 2022; 23:ijms23031202. [PMID: 35163124 PMCID: PMC8835330 DOI: 10.3390/ijms23031202] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
The two homologous genes, NIA1 and NIA2, encode nitrate reductases in Arabidopsis, which govern the reduction of nitrate to nitrite. This step is the rate-limiting step of the nitrate assimilation and utilization. Therefore, the regulation of NIA1 and NIA2 is important for plant development and growth. Although they are similar in sequence and structure, their regulations are different. Genetic analysis uncovers that NIA1, rather than NIA2, plays a predominant role in adopting to ABA stress. Although both long-term stress conditions can cause an improvement in NIA1 levels, a decrease in NIA1 levels under short-term treatments seems to be necessary for plants to switch from the growth status into the adopting status. Interestingly, the downregulation of the NR is distinct under different stress conditions. Under ABA treatment, the NR proteins are degraded via a 26S-proteasome dependent manner, while the transcriptional regulation is the main manner to rapidly reduce the NIA1 levels under nitrogen deficiency and NaCl stress conditions. These results indicate that under stress conditions, the regulation of NIA1 is complex, and it plays a key role in regulating the balance between growth and adaptation.
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13
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Song J, Zou X, Liu P, Cardoso JA, Schultze-Kraft R, Liu G, Luo L, Chen Z. Differential expressions and enzymatic properties of malate dehydrogenases in response to nutrient and metal stresses in Stylosanthes guianensis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:325-337. [PMID: 34954567 DOI: 10.1016/j.plaphy.2021.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Malate dehydrogenase (MDH, EC 1.1.1.37) is a key enzyme that catalyzes a reversible NAD-dependent dehydrogenase reaction from oxaloacetate (OAA) to malate. Although MDH has been documented to participate in cellular metabolism and redox homeostasis in plants, the roles of MDH members in the tropical legume Stylosanthes guianensis (stylo) remain less definitive. In this study, except SgMDH1 that had been previously characterized, six novel MDH genes were isolated from stylo and were then designated as SgMDH2 to SgMDH7. All of the SgMDH proteins possessed the common features of NAD binding, dimerization interface and substrate binding sites. Expression analysis showed that three SgMDHs exhibited preferential expressions in leaves, and one SgMDH was mainly expressed in roots. Furthermore, SgMDHs were regulated by nutrient deficiencies in stylo roots, especially for phosphorus (-P) and potassium (-K) deficiencies. Differential responses of SgMDHs to trace metal stress and heavy metal toxicity were observed in stylo roots, suggesting the involvement of SgMDHs in the response of stylo to metal stresses. The six novel SgMDHs were subsequently expressed and purified from Escherichia coli to analyze their biochemical properties. Although SgMDHs exhibited variations in subcellular localizations, each SgMDH protein displayed a high level of catalytic efficiency towards OAA and NADH but a low level of catalytic efficiency towards malate and NAD+. In addition, the activities of recombinant SgMDH proteins were pH-dependent and temperature-sensitive, and exhibited differential regulations by various metal ions. These results together suggest the potential roles of SgMDHs in stylo coping with nutrient and metal stresses.
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Affiliation(s)
- Jianling Song
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570110, China
| | - Xiaoyan Zou
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570110, China
| | - Pandao Liu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Juan Andres Cardoso
- Alliance of Biodiversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Rainer Schultze-Kraft
- Alliance of Biodiversity International and International Center for Tropical Agriculture, Cali, A.A.6713, Colombia
| | - Guodao Liu
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Lijuan Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570110, China.
| | - Zhijian Chen
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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14
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Wani SH, Vijayan R, Choudhary M, Kumar A, Zaid A, Singh V, Kumar P, Yasin JK. Nitrogen use efficiency (NUE): elucidated mechanisms, mapped genes and gene networks in maize ( Zea mays L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2875-2891. [PMID: 35035142 PMCID: PMC8720126 DOI: 10.1007/s12298-021-01113-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 11/22/2021] [Accepted: 12/07/2021] [Indexed: 05/22/2023]
Abstract
UNLABELLED Nitrogen, the vital primary plant growth nutrient at deficit soil conditions, drastically affects the growth and yield of a crop. Over the years, excess use of inorganic nitrogenous fertilizers resulted in pollution, eutrophication and thereby demanding the reduction in the use of chemical fertilizers. Being a C4 plant with fibrous root system and high NUE, maize can be deployed to be the best candidate for better N uptake and utilization in nitrogen deficient soils. The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits. Adoption of single cross maize hybrids as well as inherent property of high NUE has helped maize cultivars to achieve the highest growth rate among the cereals during last decade. Further, considering the high cost of nitrogenous fertilizers, adverse effects on soil health and environmental impact, maize improvement demands better utilization of existing genetic variation for NUE via introgression of novel allelic combinations in existing cultivars. Marker assisted breeding efforts need to be supplemented with introgression of genes/QTLs related to NUE in ruling varieties and thereby enhancing the overall productivity of maize in a sustainable manner. To achieve this, we need mapped genes and network of interacting genes and proteins to be elucidated. Identified genes may be used in screening ideal maize genotypes in terms of better physiological functionality exhibiting high NUE. Future genome editing may help in developing lines with increased productivity under low N conditions in an environment of optimum agronomic practices. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01113-z.
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Affiliation(s)
- Shabir H. Wani
- Genetics and Plant Breeding, Mountain Research Centre For Field Crops, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Anantnag, J&K 192101 India
| | - Roshni Vijayan
- Regional Agricultural Research Station-Central Zone, Kerala Agricultural University, MelePattambi, Palakkad, Kerala 679306 India
| | | | - Anuj Kumar
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002 India
| | - Vishal Singh
- Department of Plants, Soils and Climate, Utah State University, 4820 Old Main Hill, Logan, UT 84322 USA
| | - Pardeep Kumar
- ICAR-Indian Institute of Maize Research, Ludhiana, 141001 India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012 India
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15
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Camut L, Gallova B, Jilli L, Sirlin-Josserand M, Carrera E, Sakvarelidze-Achard L, Ruffel S, Krouk G, Thomas SG, Hedden P, Phillips AL, Davière JM, Achard P. Nitrate signaling promotes plant growth by upregulating gibberellin biosynthesis and destabilization of DELLA proteins. Curr Biol 2021; 31:4971-4982.e4. [PMID: 34614391 DOI: 10.1016/j.cub.2021.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Nitrate, one of the main nitrogen (N) sources for crops, acts as a nutrient and key signaling molecule coordinating gene expression, metabolism, and various growth processes throughout the plant life cycle. It is widely accepted that nitrate-triggered developmental programs cooperate with hormone synthesis and transport to finely adapt plant architecture to N availability. Here, we report that nitrate, acting through its signaling pathway, promotes growth in Arabidopsis and wheat, in part by modulating the accumulation of gibberellin (GA)-regulated DELLA growth repressors. We show that nitrate reduces the abundance of DELLAs by increasing GA contents through activation of GA metabolism gene expression. Consistently, the growth restraint conferred by nitrate deficiency is partially rescued in global-DELLA mutant that lacks all DELLAs. At the cellular level, we show that nitrate enhances both cell proliferation and elongation in a DELLA-dependent and -independent manner, respectively. Our findings establish a connection between nitrate and GA signaling pathways that allow plants to adapt their growth to nitrate availability.
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Affiliation(s)
- Lucie Camut
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Barbora Gallova
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Lucas Jilli
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Mathilde Sirlin-Josserand
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 Valencia, Spain
| | - Lali Sakvarelidze-Achard
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Sandrine Ruffel
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stephen G Thomas
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Peter Hedden
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK; Laboratory of Growth Regulators, Institute of Experimental Botany and Palacky University, 78371 Olomouc, Czech Republic
| | - Andrew L Phillips
- Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Jean-Michel Davière
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Patrick Achard
- Institut de Biologie Moléculaire des Plantes, CNRS, University of Strasbourg, 67084 Strasbourg, France.
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16
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Heerah S, Molinari R, Guerrier S, Marshall-Colon A. Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis. BIOINFORMATICS (OXFORD, ENGLAND) 2021; 37:2450-2460. [PMID: 33693548 DOI: 10.1101/2020.06.15.152819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
MOTIVATION Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signalling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues of Arabidopsis thaliana in response to a nitrogen signal. RESULTS This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model's dependence structure to the specific sampling time. Using maximum-likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to the A.thaliana data, the proposed approach produced 3078 significant interactions, in which 2012 interactions have root causal genes and 1066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signalling, including genes encoding transcription factors, hormones and signalling peptides. Of the 1007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signalling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signalling. AVAILABILITY AND IMPLEMENTATION The method was developed with the R statistical software and is made available through the R package 'irg' hosted on the GitHub repository https://github.com/SMAC-Group/irg where also a running example vignette can be found (https://smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete A.thaliana data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sachin Heerah
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Roberto Molinari
- Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849, USA
| | - Stéphane Guerrier
- Faculty of Science & Geneva School of Economics and Management, University of Geneva, Geneva 1205, Switzerland
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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17
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Del Castello F, Foresi N, Nejamkin A, Lindermayr C, Buegger F, Lamattina L, Correa-Aragunde N. Cyanobacterial NOS expression improves nitrogen use efficiency, nitrogen-deficiency tolerance and yield in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 307:110860. [PMID: 33902845 DOI: 10.1016/j.plantsci.2021.110860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Developing strategies to improve nitrogen (N) use efficiency (NUE) in plants is a challenge to reduce environmental problems linked to over-fertilization. The nitric oxide synthase (NOS) enzyme from the cyanobacteria Synechococcus PCC 7335 (SyNOS) has been recently identified and characterized. SyNOS catalyzes the conversion of arginine to citrulline and nitric oxide (NO), and then approximately 75 % of the produced NO is rapidly oxidized to nitrate by an unusual globin domain in the N-terminus of the enzyme. In this study, we assessed whether SyNOS expression in plants affects N metabolism, NUE and yield. Our results showed that SyNOS-expressing transgenic Arabidopsis plants have greater primary shoot length and shoot branching when grown under N-deficient conditions and higher seed production both under N-sufficient and N-deficient conditions. Moreover, transgenic plants showed significantly increased NUE in both N conditions. Although the uptake of N was not modified in the SyNOS lines, they showed an increase in the assimilation/remobilization of N under conditions of low N availability. In addition, SyNOS lines have greater N-deficiency tolerance compared to control plants. Our results support that SyNOS expression generates a positive effect on N metabolism and seed production in Arabidopsis, and it might be envisaged as a strategy to improve productivity in crops under adverse N environments.
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Affiliation(s)
- Fiorella Del Castello
- Instituto de Investigaciones Biológicas-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Deán Funes 3350, CC 1245, 7600 Mar del Plata, Argentina.
| | - Noelia Foresi
- Instituto de Investigaciones Biológicas-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Deán Funes 3350, CC 1245, 7600 Mar del Plata, Argentina.
| | - Andrés Nejamkin
- Instituto de Investigaciones Biológicas-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Deán Funes 3350, CC 1245, 7600 Mar del Plata, Argentina.
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg/Munich, Germany.
| | - Franz Buegger
- Institute of Soil Ecology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg/Munich, Germany.
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Deán Funes 3350, CC 1245, 7600 Mar del Plata, Argentina.
| | - Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Deán Funes 3350, CC 1245, 7600 Mar del Plata, Argentina.
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18
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Heerah S, Molinari R, Guerrier S, Marshall-Colon A. Granger-Causal Testing for Irregularly Sampled Time Series with Application to Nitrogen Signaling in Arabidopsis. Bioinformatics 2021; 37:2450-2460. [PMID: 33693548 PMCID: PMC8388030 DOI: 10.1093/bioinformatics/btab126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/05/2022] Open
Abstract
Motivation Identification of system-wide causal relationships can contribute to our understanding of long-distance, intercellular signalling in biological organisms. Dynamic transcriptome analysis holds great potential to uncover coordinated biological processes between organs. However, many existing dynamic transcriptome studies are characterized by sparse and often unevenly spaced time points that make the identification of causal relationships across organs analytically challenging. Application of existing statistical models, designed for regular time series with abundant time points, to sparse data may fail to reveal biologically significant, causal relationships. With increasing research interest in biological time series data, there is a need for new statistical methods that are able to determine causality within and between time series data sets. Here, a statistical framework was developed to identify (Granger) causal gene-gene relationships of unevenly spaced, multivariate time series data from two different tissues of Arabidopsis thaliana in response to a nitrogen signal. Results This work delivers a statistical approach for modelling irregularly sampled bivariate signals which embeds functions from the domain of engineering that allow to adapt the model’s dependence structure to the specific sampling time. Using maximum-likelihood to estimate the parameters of this model for each bivariate time series, it is then possible to use bootstrap procedures for small samples (or asymptotics for large samples) in order to test for Granger-Causality. When applied to the A.thaliana data, the proposed approach produced 3078 significant interactions, in which 2012 interactions have root causal genes and 1066 interactions have shoot causal genes. Many of the predicted causal and target genes are known players in local and long-distance nitrogen signalling, including genes encoding transcription factors, hormones and signalling peptides. Of the 1007 total causal genes (either organ), 384 are either known or predicted mobile transcripts, suggesting that the identified causal genes may be directly involved in long-distance nitrogen signalling through intercellular interactions. The model predictions and subsequent network analysis identified nitrogen-responsive genes that can be further tested for their specific roles in long-distance nitrogen signalling. Availability and implementation The method was developed with the R statistical software and is made available through the R package ‘irg’ hosted on the GitHub repository https://github.com/SMAC-Group/irg where also a running example vignette can be found (https://smac-group.github.io/irg/articles/vignette.html). A few signals from the original data set are made available in the package as an example to apply the method and the complete A.thaliana data can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sachin Heerah
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Roberto Molinari
- Department of Mathematics and Statistics, Auburn University, Auburn, AL, USA
| | - Stéphane Guerrier
- Faculty of Science & Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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19
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Akhatar J, Goyal A, Kaur N, Atri C, Mittal M, Singh MP, Kaur R, Rialch I, Banga SS. Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss. Sci Rep 2021; 11:4278. [PMID: 33608616 PMCID: PMC7896068 DOI: 10.1038/s41598-021-83689-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/05/2021] [Indexed: 11/09/2022] Open
Abstract
Timely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.
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Affiliation(s)
- Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anna Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Navneet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Meenakshi Mittal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mohini Prabha Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Rimaljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Indu Rialch
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
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20
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Manrique-Gil I, Sánchez-Vicente I, Torres-Quezada I, Lorenzo O. Nitric oxide function during oxygen deprivation in physiological and stress processes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:904-916. [PMID: 32976588 PMCID: PMC7876777 DOI: 10.1093/jxb/eraa442] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/16/2020] [Indexed: 05/07/2023]
Abstract
Plants are aerobic organisms that have evolved to maintain specific requirements for oxygen (O2), leading to a correct respiratory energy supply during growth and development. There are certain plant developmental cues and biotic or abiotic stress responses where O2 is scarce. This O2 deprivation known as hypoxia may occur in hypoxic niches of plant-specific tissues and during adverse environmental cues such as pathogen attack and flooding. In general, plants respond to hypoxia through a complex reprogramming of their molecular activities with the aim of reducing the impact of stress on their physiological and cellular homeostasis. This review focuses on the fine-tuned regulation of hypoxia triggered by a network of gaseous compounds that includes O2, ethylene, and nitric oxide. In view of recent scientific advances, we summarize the molecular mechanisms mediated by phytoglobins and by the N-degron proteolytic pathway, focusing on embryogenesis, seed imbibition, and germination, and also specific structures, most notably root apical and shoot apical meristems. In addition, those biotic and abiotic stresses that comprise hypoxia are also highlighted.
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Affiliation(s)
- Isabel Manrique-Gil
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
| | - Inmaculada Sánchez-Vicente
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
| | - Isabel Torres-Quezada
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
| | - Oscar Lorenzo
- Departamento de Botánica y Fisiología Vegetal, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Facultad de Biología, Universidad de Salamanca. C/ Río Duero 12, Salamanca, Spain
- Correspondence:
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21
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Grabsztunowicz M, Rantala M, Ivanauskaite A, Blomster T, Koskela MM, Vuorinen K, Tyystjärvi E, Burow M, Overmyer K, Mähönen AP, Mulo P. Root-type ferredoxin-NADP + oxidoreductase isoforms in Arabidopsis thaliana: Expression patterns, location and stress responses. PLANT, CELL & ENVIRONMENT 2021; 44:548-558. [PMID: 33131061 DOI: 10.1111/pce.13932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
In Arabidopsis, two leaf-type ferredoxin-NADP+ oxidoreductase (LFNR) isoforms function in photosynthetic electron flow in reduction of NADP+ , while two root-type FNR (RFNR) isoforms catalyse reduction of ferredoxin in non-photosynthetic plastids. As the key to understanding, the function of RFNRs might lie in their spatial and temporal distribution in different plant tissues and cell types, we examined expression of RFNR1 and RFNR2 genes using β-glucuronidase (GUS) reporter lines and investigated accumulation of distinct RFNR isoforms using a GFP approach and Western blotting upon various stresses. We show that while RFNR1 promoter is active in leaf veins, root tips and in the stele of roots, RFNR2 promoter activity is present in leaf tips and root stele, epidermis and cortex. RFNR1 protein accumulates as a soluble protein within the plastids of root stele cells, while RFNR2 is mainly present in the outer root layers. Ozone treatment of plants enhanced accumulation of RFNR1, whereas low temperature treatment specifically affected RFNR2 accumulation in roots. We further discuss the physiological roles of RFNR1 and RFNR2 based on characterization of rfnr1 and rfnr2 knock-out plants and show that although the function of these proteins is partly redundant, the RFNR proteins are essential for plant development and survival.
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Affiliation(s)
- Magda Grabsztunowicz
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Marjaana Rantala
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Aiste Ivanauskaite
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Tiina Blomster
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Minna M Koskela
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Katariina Vuorinen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kirk Overmyer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ari P Mähönen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Paula Mulo
- Department of Biochemistry, Molecular Plant Biology, University of Turku, Turku, Finland
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22
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Takehisa H, Sato Y. Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. BREEDING SCIENCE 2021; 71:76-88. [PMID: 33762878 PMCID: PMC7973498 DOI: 10.1270/jsbbs.20098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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23
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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24
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Maurya J, Bandyopadhyay T, Prasad M. Transcriptional regulators of nitrate metabolism: Key players in improving nitrogen use in crops. J Biotechnol 2020; 324:121-133. [PMID: 33031844 DOI: 10.1016/j.jbiotec.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/19/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
Green revolution has boosted crop yields by the development of varieties which rely on high fertilizer application. Since then, higher productivity has largely witnessed excessive nitrogen (N) fertilizer application resulting in many environmentally and agronomically unsustainable consequences. One possible solution to this problem is to develop varieties with efficient N use endowed with genetically superior N metabolizing machinery, thereby significantly reducing N loss in soil and facilitating gainful yield performance at lower N conditions. Nitrate (NO3-) is the major form of N acquired by plants in aerobic soils. Hence, its efficient acquisition, transport, assimilation into complex organic compounds, and overall homeostasis is crucial to ensure productivity under optimal and suboptimal N conditions. Transcription factors are prime regulators of these processes, and insights into their mechanism of action and the resultant effect on N metabolism are crucial to generating crops with efficient and durable nitrogen use efficiency. The present review, therefore, presents a comprehensive updated account of major N responsive transcription factor families, their cross-talk with other growth factors, and explores existing and potential areas of their biotechnological application to maximize crop yields.
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Affiliation(s)
- Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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25
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Astegno A, Conter C, Bertoldi M, Dominici P. Structural Insights into the Heme Pocket and Oligomeric State of Non-Symbiotic Hemoglobins from Arabidopsis thaliana. Biomolecules 2020; 10:E1615. [PMID: 33260415 PMCID: PMC7761212 DOI: 10.3390/biom10121615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 11/18/2022] Open
Abstract
Non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana are hexacoordinate heme-proteins that likely have different biological roles, in view of diverse tissue localization, expression pattern, and ligand binding properties. Herein, we expand upon previous biophysical studies on these isoforms, focusing on their oligomeric states and circular dichroism (CD) characteristics. We found that AHb1 exists in solution in a concentration-dependent monomer-dimer equilibrium, while AHb2 is present only as a monomer. The quaternary structure of AHb1 affects its degree of hexacoordination with the formation of the dimer that enhances pentacoordination. Accordingly, the mutant of a conserved residue within the dimeric interface, AHb1-T45A, which is mostly monomeric in solution, has an equilibrium that is shifted toward a hexacoordinate form compared to the wild-type protein. CD studies further support differences in the globin's structure and heme moiety. The Soret CD spectra for AHb2 are opposite in sense to those for AHb1, reflecting different patterns of heme-protein side chain contacts in the two proteins. Moreover, the smaller contribution of the heme to the near-UV CD in AHb2 compared to AHb1 suggests a weaker heme-protein association in AHb2. Our data corroborate the structural diversity of AHb1 and AHb2 and confirm the leghemoglobin-like structural properties of AHb2.
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Affiliation(s)
- Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, 8, 37134 Verona, Italy;
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy; (A.A.); (C.C.)
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26
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Fukuda M, Fujiwara T, Nishida S. Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants. Int J Mol Sci 2020; 21:ijms21228508. [PMID: 33198163 PMCID: PMC7696010 DOI: 10.3390/ijms21228508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development; therefore, N deficiency is a major limiting factor in crop production. Plants have evolved mechanisms to cope with N deficiency, and the role of protein-coding genes in these mechanisms has been well studied. In the last decades, regulatory non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long ncRNAs (lncRNAs), have emerged as important regulators of gene expression in diverse biological processes. Recent advances in technologies for transcriptome analysis have enabled identification of N-responsive ncRNAs on a genome-wide scale. Characterization of these ncRNAs is expected to improve our understanding of the gene regulatory mechanisms of N response. In this review, we highlight recent progress in identification and characterization of N-responsive ncRNAs in Arabidopsis thaliana and several other plant species including maize, rice, and Populus.
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Affiliation(s)
- Makiha Fukuda
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA;
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
| | - Sho Nishida
- Department of Bioresource Science, Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
- Correspondence: ; Tel.: +81-952-28-8720
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27
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Wen B, Li J, Luo Y, Zhang X, Wang K, Liu Z, Huang J. Identification and expression profiling of MYB transcription factors related to l-theanine biosynthesis in Camellia sinensis. Int J Biol Macromol 2020; 164:4306-4317. [PMID: 32861783 DOI: 10.1016/j.ijbiomac.2020.08.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
The MYB proteins belong to a large family of transcription factors in plant genomes and play significant roles in primary and secondary metabolism. Although several CsMYB genes have been identified in Camellia sinensis, few CsMYBs involved in l-theanine biosynthesis have been analyzed. In this study, we screened and identified 20 CsMYBs related to l-theanine biosynthesis. Transcriptomic analysis revealed that the expression profiles of the CsMYBs were positively or negatively related to dynamic changes in the l-theanine content. Validation of selected l-theanine biosynthetic and CsMYB genes was conducted by qRT-PCR. The results illustrated that most of the structural and CsMYB genes were downregulated with a decrease in the l-theanine levels. Protein-protein interaction networks of CsMYB5, CsMYB12 and CsMYB94 proteins demonstrated that they might form complexes with bHLH and WD 40 proteins. Multiple DNA-binding sites of the R2R3-MYB protein were observed in promoter regions of structural genes, indicating CsMYB family proteins might be involved in l-theanine metabolism via the attachment of AC elements. Moreover, CsMYB73 demonstrated binding specificity to the promoter region of CsGDH2 (CsGDH2-pro). These findings provide fundamental understanding of specific members of the CsMYBs related to the l-theanine biosynthesis pathway.
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Affiliation(s)
- Beibei Wen
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, PR China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Co-innovation Center for Utilization of Botanical Functional Ingredients and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Yong Luo
- School of Chemistry, Biology and Environmental Engineering, Xiangnan University, Chenzhou, Hunan 423000, PR China
| | - Xiangna Zhang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Kunbo Wang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, PR China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Co-innovation Center for Utilization of Botanical Functional Ingredients and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, PR China.
| | - Zhonghua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, PR China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Co-innovation Center for Utilization of Botanical Functional Ingredients and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, PR China.
| | - Jianan Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan 410128, PR China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Co-innovation Center for Utilization of Botanical Functional Ingredients and Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan 410128, PR China.
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28
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Liu KH, Diener A, Lin Z, Liu C, Sheen J. Primary nitrate responses mediated by calcium signalling and diverse protein phosphorylation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4428-4441. [PMID: 31985788 PMCID: PMC7382375 DOI: 10.1093/jxb/eraa047] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/24/2020] [Indexed: 05/04/2023]
Abstract
Nitrate, the major source of inorganic nitrogen for plants, is a critical signal controlling nutrient transport and assimilation and adaptive growth responses throughout the plant. Understanding how plants perceive nitrate and how this perception is transduced into responses that optimize growth are important for the rational improvement of crop productivity and for mitigating pollution from the use of fertilizers. This review highlights recent findings that reveal key roles of cytosolic-nuclear calcium signalling and dynamic protein phosphorylation via diverse mechanisms in the primary nitrate response (PNR). Nitrate-triggered calcium signatures as well as the critical functions of subgroup III calcium-sensor protein kinases, a specific protein phosphatase 2C, and RNA polymerase II C-terminal domain phosphatase-like 3 are discussed. Moreover, genome-wide meta-analysis of nitrate-regulated genes encoding candidate protein kinases and phosphatases for modulating critical phosphorylation events in the PNR are elaborated. We also consider how phosphoproteomics approaches can contribute to the identification of putative regulatory protein kinases in the PNR. Exploring and integrating experimental strategies, new methodologies, and comprehensive datasets will further advance our understanding of the molecular and cellular mechanisms underlying the complex regulatory processes in the PNR.
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Affiliation(s)
- Kun-Hsiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
- Correspondence:
| | - Andrew Diener
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ziwei Lin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Cong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
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29
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Vidal EA, Alvarez JM, Araus V, Riveras E, Brooks MD, Krouk G, Ruffel S, Lejay L, Crawford NM, Coruzzi GM, Gutiérrez RA. Nitrate in 2020: Thirty Years from Transport to Signaling Networks. THE PLANT CELL 2020; 32:2094-2119. [PMID: 32169959 PMCID: PMC7346567 DOI: 10.1105/tpc.19.00748] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/05/2020] [Accepted: 03/10/2020] [Indexed: 05/18/2023]
Abstract
Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research.
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Affiliation(s)
- Elena A Vidal
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
| | - José M Alvarez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 8580745
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Viviana Araus
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Eleodoro Riveras
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
| | - Matthew D Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Gabriel Krouk
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Sandrine Ruffel
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Laurence Lejay
- Biochemistry and Plant Molecular Physiology, CNRS, INRA, Montpellier SupAgro, Universite Montpellier, Montpellier, France, 34060
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, 92093
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rodrigo A Gutiérrez
- Millennium Institute for Integrative Biology, Santiago, Chile, 7500565
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile, 8331150
- FONDAP Center for Genome Regulation, Santiago, Chile, 8370415
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Chaput V, Martin A, Lejay L. Redox metabolism: the hidden player in carbon and nitrogen signaling? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3816-3826. [PMID: 32064525 DOI: 10.1093/jxb/eraa078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/12/2020] [Indexed: 05/05/2023]
Abstract
While decades of research have considered redox metabolism as purely defensive, recent results show that reactive oxygen species (ROS) are necessary for growth and development. Close relationships have been found between the regulation of nitrogen metabolism and ROS in response to both carbon and nitrogen availability. Root nitrate uptake and nitrogen metabolism have been shown to be regulated by a signal from the oxidative pentose phosphate pathway (OPPP) in response to carbon signaling. As a major source of NADP(H), the OPPP is critical to maintaining redox balance under stress situations. Furthermore, recent results suggest that at least part of the regulation of the root nitrate transporter by nitrogen signaling is also linked to the redox status of the plant. This leads to the question of whether there is a more general role of redox metabolism in the regulation of nitrogen metabolism by carbon and nitrogen. This review highlights the role of the OPPP in carbon signaling and redox metabolism, and the interaction between redox and nitrogen metabolism. We discuss how redox metabolism could be an important player in the regulation of nitrogen metabolism in response to carbon/nitrogen interaction and the implications for plant adaptation to extreme environments and future crop development.
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Affiliation(s)
- Valentin Chaput
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Antoine Martin
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Laurence Lejay
- BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
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31
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Transcriptome Analysis of High-NUE (T29) and Low-NUE (T13) Genotypes Identified Different Responsive Patterns Involved in Nitrogen Stress in Ramie ( Boehmeria nivea (L.) Gaudich). PLANTS 2020; 9:plants9060767. [PMID: 32575463 PMCID: PMC7356044 DOI: 10.3390/plants9060767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/22/2022]
Abstract
Nitrogen-use efficiency (NUE) has significant impacts on plant growth and development. NUE in plants differs substantially in physiological resilience to nitrogen stress; however, the molecular mechanisms underlying enhanced resilience of high-NUE plants to nitrogen deficiency remains unclear. We compared transcriptome-wide gene expression between high-NUE and low-NUE ramie (Boehmeria nivea (L.) Gaudich) genotypes under nitrogen (N)-deficient and normal conditions to identify the transcriptomic expression patterns that contribute to ramie resilience to nitrogen deficiency. Two ramie genotypes with contrasting NUE were used in the study, including T29 (NUE = 46.01%) and T13 (NUE = 15.81%). Our results showed that high-NUE genotypes had higher gene expression under the control condition across 94 genes, including frontloaded genes such as GDSL esterase and lipase, gibberellin, UDP-glycosyltransferase, and omega-6 fatty acid desaturase. Seventeen stress-tolerance genes showed lower expression levels and varied little in response to N-deficiency stress in high-NUE genotypes. In contrast, 170 genes were upregulated under N deficiency in high-NUE genotypes but downregulated in low-NUE genotypes compared with the controls. Furthermore, we identified the potential key genes that enable ramie to maintain physiological resilience under N-deficiency stress, and categorized these genes into three groups based on the transcriptome and their expression patterns. The transcriptomic and clustering analysis of these nitrogen-utilization-related genes could provide insight to better understand the mechanism of linking among the three gene classes that enhance resilience in high-NUE ramie genotypes.
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32
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Xu N, Yu B, Chen R, Li S, Zhang G, Huang J. OsNAR2.2 plays a vital role in the root growth and development by promoting nitrate uptake and signaling in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:159-169. [PMID: 32070909 DOI: 10.1016/j.plaphy.2020.02.004] [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: 10/29/2019] [Revised: 02/02/2020] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Plants in soil faces great fluctuations of external mineral nutrient availability, and they have developed sophisticated nutrient sensing systems to regulate their physiological responses to prevent nutrient deficiency. However, complete knowledge of the regulatory system is required to maximize inorganic nitrogen (N) uptake and utilization. In this study, we report a partner protein for high-affinity nitrate transport, OsNAR2.2. OsNAR2.2 was involved in the root growth in a nitrate-dependent manner in rice, and this process was closely associated with auxin. Expression analysis showed that OsNAR2.2 responded to nitrate and various plant hormone signals. Knockdown of OsNAR2.2 by T-DNA insertion not only significantly repressed the primary root elongation, but also severely reduced the number of lateral root and adventitious root. Further research indicated that the size of meristematic zone and epidermal cell length of mature zone in the primary root tip were remarkably reduced, and the formation of lateral root primordial was constrained in osnar2.2 mutant. Interestingly, the repression of root growth in osnar2.2 mutant was observed when NO3- but not NH4+ was used as N source in the medium. The NO3- content in osnar2.2 root was significantly reduced under NO3- conditions, in comparison with that of wild type. Meanwhile, the free IAA accumulation as well as the expression of auxin biosynthesis and transport genes was altered in osnar2.2 root, suggesting there might be a crosslink between the nitrate and auxin signaling. Together, OsNAR2.2 plays a vital role in rice root growth and development in a nitrate-dependent manner, which might be associated with auxin signaling.
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Affiliation(s)
- Ning Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, PR China
| | - Bo Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, PR China
| | - Rongrong Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, PR China
| | - Shuaiting Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, PR China
| | - Guochao Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, PR China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400030, PR China.
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33
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Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. MOLECULAR PLANT 2019; 12:1545-1560. [PMID: 31526863 DOI: 10.1016/j.molp.2019.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 05/13/2023]
Abstract
Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
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Affiliation(s)
- José M Alvarez
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tao Zhang
- Yangzhou University, Yangzhou, China
| | - Diana E Gras
- Instituto de Agrobiotecnologia del Litoral, CONICET, Santa Fe, Argentina
| | - Francisco J Herrera
- University of California, Berkeley, CA, USA; Trancura Biosciences, Inc., San Francisco, CA 94158, USA
| | - Viviana Araus
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - José A O'Brien
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Plant Biology and Horticulture, Michigan State University, MI 48824, USA
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34
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Mur LAJ, Kumari A, Brotman Y, Zeier J, Mandon J, Cristescu SM, Harren F, Kaiser WM, Fernie AR, Gupta KJ. Nitrite and nitric oxide are important in the adjustment of primary metabolism during the hypersensitive response in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4571-4582. [PMID: 31173640 DOI: 10.1093/jxb/erz161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
Nitrate and ammonia deferentially modulate primary metabolism during the hypersensitive response in tobacco. In this study, tobacco RNAi lines with low nitrite reductase (NiRr) levels were used to investigate the roles of nitrite and nitric oxide (NO) in this process. The lines accumulate NO2-, with increased NO generation, but allow sufficient reduction to NH4+ to maintain plant viability. For wild-type (WT) and NiRr plants grown with NO3-, inoculation with the non-host biotrophic pathogen Pseudomonas syringae pv. phaseolicola induced an accumulation of nitrite and NO, together with a hypersensitive response (HR) that resulted in decreased bacterial growth, increased electrolyte leakage, and enhanced pathogen resistance gene expression. These responses were greater with increases in NO or NO2- levels in NiRr plants than in the WT under NO3- nutrition. In contrast, WT and NiRr plants grown with NH4+ exhibited compromised resistance. A metabolomic analysis detected 141 metabolites whose abundance was differentially changed as a result of exposure to the pathogen and in response to accumulation of NO or NO2-. Of these, 13 were involved in primary metabolism and most were linked to amino acid and energy metabolism. HR-associated changes in metabolism that are often linked with primary nitrate assimilation may therefore be influenced by nitrite and NO production.
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Affiliation(s)
- Luis A J Mur
- Institute of Environmental and Rural Science, Aberystwyth University, Edward Llwyd Building, Aberystwyth, UK
| | - Aprajita Kumari
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Yariv Brotman
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Golm-Potsdam, Germany
| | - Jurgen Zeier
- Institute of Plant Molecular Ecophysiology, Heinrich-Heine-Universität Universitätsstrasse, Düsseldorf, Germany
| | - Julien Mandon
- Radboud University, Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, GL Nijmegen, The Netherlands
| | - Simona M Cristescu
- Radboud University, Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, GL Nijmegen, The Netherlands
| | - Frans Harren
- Radboud University, Life Science Trace Gas Facility, Molecular and Laser Physics, Institute for Molecules and Materials, GL Nijmegen, The Netherlands
| | - Werner M Kaiser
- Julius-von-Sachs-Institut für Biowissenschaften; Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik; Julius-von-Sachs-Platz, Wuerzburg, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, Golm-Potsdam, Germany
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35
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Kumar M, Le DT, Hwang S, Seo PJ, Kim HU. Role of the INDETERMINATE DOMAIN Genes in Plants. Int J Mol Sci 2019; 20:ijms20092286. [PMID: 31075826 PMCID: PMC6539433 DOI: 10.3390/ijms20092286] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Dung Thi Le
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
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36
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Abstract
Symbiotic legume nodules and lateral roots arise away from the root meristem via dedifferentiation events. While these organs share some morphological and developmental similarities, whether legume nodules are modified lateral roots is an open question. We dissected emerging nodules, mature nodules, emerging lateral roots and young lateral roots, and constructed strand-specific RNA sequencing (RNAseq) libraries using polyA-enriched RNA preparations. Root sections above and below these organs, devoid of any lateral organs, were used to construct respective control tissue libraries. High sequence quality, predominant mapping to coding sequences, and consistency between replicates indicated that the RNAseq libraries were of a very high quality. We identified genes enriched in emerging nodules, mature nodules, emerging lateral roots and young lateral roots in soybean by comparing global gene expression profiles between each of these organs and adjacent root segments. Potential uses for this high quality transcriptome data set include generation of global gene regulatory networks to identify key regulators; metabolic pathway analyses and comparative analyses of key gene families to discover organ-specific biological processes; and identification of organ-specific alternate spliced transcripts. When combined with other similar datasets, especially from leguminous plants, these analyses can help answer questions on the evolutionary origins of root nodules and relationships between the development of different plant lateral organs.
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37
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El-Shehawi AM, Elseehy MM. Gene Expression Profiling during Life Cycle of Potato (Solanum tuberosum) Tubers by Microarray. CYTOL GENET+ 2019. [DOI: 10.3103/s009545271901002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Chen G, Li X, Chen Q, Wang L, Qi K, Yin H, Qiao X, Wang P, Zhang S, Wu J, Huang Z. Dynamic transcriptome analysis of root nitrate starvation and re-supply provides insights into nitrogen metabolism in pear (Pyrus bretschneideri). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:322-333. [PMID: 30466597 DOI: 10.1016/j.plantsci.2018.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/29/2018] [Accepted: 10/06/2018] [Indexed: 06/09/2023]
Abstract
Pear (Pyrus bretschneideri) is a popular fruit worldwide, but the irrational utilization of nitrogen as a fertilizer not only greatly affects the fruit' quality, but also wastes resources and results in serious environmental pollution. To better understand the molecular mechanism in pear responsible for the regulation of nitrate transport and assimilation, RNA-seq was performed on samples collected in response to nitrate treatments. Here, 10,273 differentially expressed genes were obtained and annotated into 49 GO terms, 45 clusters having co-expression trends that involved 18 KEGG-defined significantly overrepresented pathways. The KEGG pathways revealed that 15 unigenes, including one NRT gene, two NR genes, one NiR gene, two GDH genes, six GS genes and three GOGAT genes, were related to nitrogen metabolism and significantly differentially expressed in response to nitrate starvation and a nitrate re-supply treatment. Furthermore, 449 transcription factors belonging to 35 different families were identified during the nitrate treatments. The expression patterns of 14 randomly selected differentially expressed genes were validated by qRT-PCR. This study provides valuable resources for investigating the genetics of the nitrogen metabolic pathways and improving nitrogen utilization efficiency in pear.
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Affiliation(s)
- Guodong Chen
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaolong Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Chen
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijie Qi
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yin
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Qiao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhi Huang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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39
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Samuilov S, Brilhaus D, Rademacher N, Flachbart S, Arab L, Alfarraj S, Kuhnert F, Kopriva S, Weber APM, Mettler-Altmann T, Rennenberg H. The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:1709. [PMID: 30559749 PMCID: PMC6284229 DOI: 10.3389/fpls.2018.01709] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/02/2018] [Indexed: 05/24/2023]
Abstract
This study was aimed at elucidating the significance of photorespiratory serine (Ser) production for cysteine (Cys) biosynthesis. For this purpose, sulfur (S) metabolism and its crosstalk with nitrogen (N) and carbon (C) metabolism were analyzed in wildtype Arabidopsis and its photorespiratory bou-2 mutant with impaired glycine decarboxylase (GDC) activity. Foliar glycine and Ser contents were enhanced in the mutant at day and night. The high Ser levels in the mutant cannot be explained by transcript abundances of genes of the photorespiratory pathway or two alternative pathways of Ser biosynthesis. Despite enhanced foliar Ser, reduced GDC activity mediated a decline in sulfur flux into major sulfur pools in the mutant, as a result of deregulation of genes of sulfur reduction and assimilation. Still, foliar Cys and glutathione contents in the mutant were enhanced. The use of Cys for methionine and glucosinolates synthesis was reduced in the mutant. Reduced GDC activity in the mutant downregulated Calvin Cycle and nitrogen assimilation genes, upregulated key enzymes of glycolysis and the tricarboxylic acid (TCA) pathway and modified accumulation of sugars and TCA intermediates. Thus, photorespiratory Ser production can be replaced by other metabolic Ser sources, but this replacement deregulates the cross-talk between S, N, and C metabolism.
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Affiliation(s)
- Sladjana Samuilov
- Chair of Tree Physiology, Institute of Forest Sciences, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg im Breisgau, Germany
| | - Dominik Brilhaus
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Nadine Rademacher
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Samantha Flachbart
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Leila Arab
- Chair of Tree Physiology, Institute of Forest Sciences, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg im Breisgau, Germany
| | - Saleh Alfarraj
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Franziska Kuhnert
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg im Breisgau, Germany
- College of Sciences, King Saud University, Riyadh, Saudi Arabia
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40
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Gaudinier A, Rodriguez-Medina J, Zhang L, Olson A, Liseron-Monfils C, Bågman AM, Foret J, Abbitt S, Tang M, Li B, Runcie DE, Kliebenstein DJ, Shen B, Frank MJ, Ware D, Brady SM. Transcriptional regulation of nitrogen-associated metabolism and growth. Nature 2018; 563:259-264. [PMID: 30356219 DOI: 10.1038/s41586-018-0656-3] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/22/2018] [Indexed: 11/09/2022]
Abstract
Nitrogen is an essential macronutrient for plant growth and basic metabolic processes. The application of nitrogen-containing fertilizer increases yield, which has been a substantial factor in the green revolution1. Ecologically, however, excessive application of fertilizer has disastrous effects such as eutrophication2. A better understanding of how plants regulate nitrogen metabolism is critical to increase plant yield and reduce fertilizer overuse. Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. Genetic perturbation of a subset of these transcription factors revealed coordinate transcriptional regulation of enzymes involved in nitrogen metabolism. Transcriptional regulators in the network are transcriptionally modified by feedback via genetic perturbation of nitrogen metabolism. The network, genes and gene-regulatory modules identified here will prove critical to increasing agricultural productivity.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Joel Rodriguez-Medina
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | | | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Jessica Foret
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Michelle Tang
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.,Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.,DynaMo Center of Excellence, University of Copenhagen, Frederiksberg C, Denmark
| | - Bo Shen
- DuPont Pioneer, Johnston, IA, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA.,US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.
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41
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Dos Santos TB, Soares JDM, Lima JE, Silva JC, Ivamoto ST, Baba VY, Souza SGH, Lorenzetti APR, Paschoal AR, Meda AR, Nishiyama Júnior MY, de Oliveira ÚC, Mokochinski JB, Guyot R, Junqueira-de-Azevedo ILM, Figueira AVO, Mazzafera P, Júnior OR, Vieira LGE, Pereira LFP, Domingues DS. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses. Funct Integr Genomics 2018; 19:151-169. [PMID: 30196429 DOI: 10.1007/s10142-018-0634-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 01/09/2023]
Abstract
Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.
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Affiliation(s)
- Tiago Benedito Dos Santos
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil. .,Universidade do Oeste Paulista, Rodovia Raposo Tavares Km 572, Presidente Prudente, 19067-175, Brazil.
| | - João D M Soares
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil
| | - Joni E Lima
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13400-970, Brazil.,Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Juliana C Silva
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Programa de pós-graduação em Bioinformática, Universidade Tecnológica Federal do Paraná, Cornélio Procópio, 86300-000, Brazil
| | - Suzana T Ivamoto
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil
| | - Viviane Y Baba
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil
| | - Silvia G H Souza
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, 87502-210, Brazil
| | - Alan P R Lorenzetti
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina, Londrina, 86057-970, Brazil
| | - Alexandre R Paschoal
- Programa de pós-graduação em Bioinformática, Universidade Tecnológica Federal do Paraná, Cornélio Procópio, 86300-000, Brazil
| | - Anderson R Meda
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil
| | | | - Úrsula C de Oliveira
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, 05503-900, Brazil
| | - João B Mokochinski
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-970, Brazil
| | - Romain Guyot
- IRD, UMR IPME, COFFEEADAPT, BP 64501, 34394, Montpellier Cedex 5, France
| | | | - Antônio V O Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13400-970, Brazil
| | - Paulo Mazzafera
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-970, Brazil
| | - Osvaldo R Júnior
- Life Sciences Core Facility (LaCTAD), Universidade Estadual de Campinas, Campinas, 13083-886, Brazil
| | - Luiz G E Vieira
- Universidade do Oeste Paulista, Rodovia Raposo Tavares Km 572, Presidente Prudente, 19067-175, Brazil
| | - Luiz F P Pereira
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Embrapa Café, Brasília, 70770-901, Brazil
| | - Douglas S Domingues
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil.,Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil
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42
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Gu J, Li Z, Mao Y, Struik PC, Zhang H, Liu L, Wang Z, Yang J. Roles of nitrogen and cytokinin signals in root and shoot communications in maximizing of plant productivity and their agronomic applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:320-331. [PMID: 30080619 DOI: 10.1016/j.plantsci.2018.06.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 05/03/2023]
Abstract
Nitrogen is an essential, often limiting, factor in plant growth and development. To regulate growth under limited nitrogen supply, plants sense the internal and external nitrogen status, and coordinate various metabolic processes and developmental programs accordingly. This coordination requires the transmission of various signaling molecules that move across the entire plant. Cytokinins, phytohormones derived from adenine and synthesized in various parts of the plant, are considered major local and long-distance messengers. Cytokinin metabolism and signaling are closely associated with nitrogen availability. They are systemically transported via the vasculature from plant roots to shoots, and vice versa, thereby coordinating shoot and root development. Tight linkage exists between the nitrogen signaling network and cytokinins during diverse developmental and physiological processes. However, the cytokinin-nitrogen interactions and the communication systems involved in sensing rhizospheric nitrogen status and in regulating canopy development remain obscure. We review current knowledge on cytokinin biosynthesis, transport and signaling, nitrogen acquisition, metabolism and signaling, and their interactive roles in regulating root-shoot morphological and physiological characteristics. We also discuss the role of spatio-temporal regulation of cytokinins in enhancing beneficial crop traits of yield and nitrogen use efficiency.
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Affiliation(s)
- Junfei Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhikang Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yiqi Mao
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Science, Wageningen University, PO Box 430, Wageningen, 6700 AK, The Netherlands
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Lijun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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43
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Hsieh PH, Kan CC, Wu HY, Yang HC, Hsieh MH. Early molecular events associated with nitrogen deficiency in rice seedling roots. Sci Rep 2018; 8:12207. [PMID: 30111825 PMCID: PMC6093901 DOI: 10.1038/s41598-018-30632-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/31/2018] [Indexed: 11/16/2022] Open
Abstract
Nitrogen (N) deficiency is one of the most common problems in rice. The symptoms of N deficiency are well documented, but the underlying molecular mechanisms are largely unknown in rice. Here, we studied the early molecular events associated with N starvation (−N, 1 h), focusing on amino acid analysis and identification of −N-regulated genes in rice roots. Interestingly, levels of glutamine rapidly decreased within 15 min of −N treatment, indicating that part of the N-deficient signals could be mediated by glutamine. Transcriptome analysis revealed that genes involved in metabolism, plant hormone signal transduction (e.g. abscisic acid, auxin, and jasmonate), transporter activity, and oxidative stress responses were rapidly regulated by −N. Some of the −N-regulated genes encode transcription factors, protein kinases and protein phosphatases, which may be involved in the regulation of early −N responses in rice roots. Previously, we used similar approaches to identify glutamine-, glutamate-, and ammonium nitrate-responsive genes. Comparisons of the genes induced by different forms of N with the −N-regulated genes identified here have provided a catalog of potential N regulatory genes for further dissection of the N signaling pathwys in rice.
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Affiliation(s)
- Ping-Han Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Cheng Kan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsin-Yu Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsiu-Chun Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
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44
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Molecular Regulation of Nitrate Responses in Plants. Int J Mol Sci 2018; 19:ijms19072039. [PMID: 30011829 PMCID: PMC6073361 DOI: 10.3390/ijms19072039] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022] Open
Abstract
Nitrogen is an essential macronutrient that affects plant growth and development. Improving the nitrogen use efficiency of crops is of great importance for the economic and environmental sustainability of agriculture. Nitrate (NO3−) is a major form of nitrogen absorbed by most crops and also serves as a vital signaling molecule. Research has identified key molecular components in nitrate signaling mainly by employing forward and reverse genetics as well as systems biology. In this review, we focus on advances in the characterization of genes involved in primary nitrate responses as well as the long-term effects of nitrate, especially in terms of how nitrate regulates root development.
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45
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Zubimendi JP, Martinatto A, Valacco MP, Moreno S, Andreo CS, Drincovich MF, Tronconi MA. The complex allosteric and redox regulation of the fumarate hydratase and malate dehydratase reactions of Arabidopsis thaliana Fumarase 1 and 2 gives clues for understanding the massive accumulation of fumarate. FEBS J 2018; 285:2205-2224. [PMID: 29688630 DOI: 10.1111/febs.14483] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/22/2018] [Accepted: 04/19/2018] [Indexed: 11/30/2022]
Abstract
Arabidopsis thaliana possesses two fumarase genes (FUM), AtFUM1 (At2g47510) encoding for the mitochondrial Krebs cycle-associated enzyme and AtFUM2 (At5g50950) for the cytosolic isoform required for fumarate massive accumulation. Here, the comprehensive biochemical studies of AtFUM1 and AtFUM2 shows that they are active enzymes with similar kinetic parameters but differential regulation. For both enzymes, fumarate hydratase (FH) activity is favored over the malate dehydratase (MD) activity; however, MD is the most regulated activity with several allosteric activators. Oxalacetate, glutamine, and/or asparagine are modulators causing the MD reaction to become preferred over the FH reaction. Activity profiles as a function of pH suggest a suboptimal FUM activity in Arabidopsis cells; moreover, the direction of the FUM reaction is sensitive to pH changes. Under mild oxidation conditions, AtFUMs form high mass molecular aggregates, which present both FUM activities decreased to a different extent. The biochemical properties of oxidized AtFUMs (oxAtFUMs) were completely reversed by NADPH-supplied Arabidopsis leaf extracts, suggesting that the AtFUMs redox regulation can be accomplished in vivo. Mass spectrometry analyses indicate the presence of an active site-associated intermolecular disulfide bridge in oxAtFUMs. Finally, a phylogenetic approach points out that other plant species may also possess cytosolic FUM2 enzymes mainly encoded by paralogous genes, indicating that the evolutionary history of this trait has been drawn through a process of parallel evolution. Overall, according to our results, a multilevel regulatory pattern of FUM activities emerges, supporting the role of this enzyme as a carbon flow monitoring point through the organic acid metabolism in plants.
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Affiliation(s)
- Juan P Zubimendi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - Andrea Martinatto
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - Maria P Valacco
- Departamento de Química Biológica, Facultad de Ciencias exactas y Naturales, Universidad de Buenos Aires (UBA), Argentina
| | - Silvia Moreno
- Departamento de Química Biológica, Facultad de Ciencias exactas y Naturales, Universidad de Buenos Aires (UBA), Argentina
| | - Carlos S Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - María F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
| | - Marcos A Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Santa Fe, Argentina
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46
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Goel P, Sharma NK, Bhuria M, Sharma V, Chauhan R, Pathania S, Swarnkar MK, Chawla V, Acharya V, Shankar R, Singh AK. Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L. Sci Rep 2018; 8:7451. [PMID: 29748645 PMCID: PMC5945678 DOI: 10.1038/s41598-018-25826-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/01/2018] [Indexed: 11/09/2022] Open
Abstract
Nitrate is the main source of inorganic nitrogen for plants, which also act as signaling molecule. Present study was aimed to understand nitrate regulatory mechanism in Brassica juncea cultivars, with contrasting nitrogen-use-efficiency (NUE) viz. Pusa Bold (PB, high-NUE) and Pusa Jai Kisan (PJK, low-NUE), employing RNA-seq approach. A total of 4031, 3874 and 3667 genes in PB and 2982, 2481 and 2843 genes in PJK were differentially expressed in response to early, low (0.25 mM KNO3), medium (2 mM KNO3) and high (4 mM KNO3) nitrate treatments, respectively, as compared to control (0 mM KNO3). Genes of N-uptake (NRT1.1, NRT1.8, and NRT2.1), assimilation (NR1, NR2, NiR, GS1.3, and Fd-GOGAT) and remobilization (GDH2, ASN2–3 and ALaT) were highly-upregulated in PB than in PJK in response to early nitrate treatments. We have also identified transcription factors and protein kinases that were rapidly induced in response to nitrate, suggesting their involvement in nitrate-mediated signaling. Co-expression network analysis revealed four nitrate specific modules in PB, enriched with GO terms like, “Phenylpropanoid pathway”, “Nitrogen compound metabolic process” and “Carbohydrate metabolism”. The network analysis also identified HUB transcription factors like mTERF, FHA, Orphan, bZip and FAR1, which may be the key regulators of nitrate-mediated response in B. juncea.
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Affiliation(s)
- Parul Goel
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Nitesh Kumar Sharma
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Monika Bhuria
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Vishal Sharma
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Rohit Chauhan
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India
| | - Shivalika Pathania
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India
| | - Mohit Kumar Swarnkar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India
| | - Vandna Chawla
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India
| | - Vishal Acharya
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India
| | - Ravi Shankar
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India. .,Academy of Scientific and Innovative Research, New Delhi, India.
| | - Anil Kumar Singh
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, (HP), India. .,Academy of Scientific and Innovative Research, New Delhi, India. .,ICAR-Indian Institute of Agricultural Biotechnology, PDU Campus, IINRG, Namkum, Ranchi, 834010, India.
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47
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Elevation of cytosolic Ca2+ in response to energy deficiency in plants: the general mechanism of adaptation to low oxygen stress. Biochem J 2018; 475:1411-1425. [DOI: 10.1042/bcj20180169] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
Abstract
Ca2+ can be released from cell compartments to the cytosol during stress conditions. We discuss here the causes of Ca2+ release under conditions of ATP concentration decline that result in the suppression of ATPases and activation of calcium ion channels. The main signaling and metabolic consequences of Ca2+ release are considered for stressed plant cells. The signaling function includes generation and spreading of calcium waves, while the metabolic function results in the activation of particular enzymes and genes. Ca2+ is involved in the activation of glutamate decarboxylase, initiating the γ-aminobutyric acid shunt and triggering the formation of alanine, processes which play a role, in particular, in pH regulation. Ca2+ activates the transcription of several genes, e.g. of plant hemoglobin (phytoglobin, Pgb) which scavenges nitric oxide and regulates redox and energy balance through the Pgb–nitric oxide cycle. This cycle involves NADH and NADPH oxidation from the cytosolic side of mitochondria, in which Ca2+- and low pH-activated external NADH and NADPH dehydrogenases participate. Ca2+ can also activate the genes of alcohol dehydrogenase and pyruvate decarboxylase stimulating hypoxic fermentation. It is concluded that calcium is a primary factor that causes the metabolic shift under conditions of oxygen deficiency.
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48
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Guan X, Chen S, Voon CP, Wong KB, Tikkanen M, Lim BL. FdC1 and Leaf-Type Ferredoxins Channel Electrons From Photosystem I to Different Downstream Electron Acceptors. FRONTIERS IN PLANT SCIENCE 2018; 9:410. [PMID: 29670639 PMCID: PMC5893904 DOI: 10.3389/fpls.2018.00410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/14/2018] [Indexed: 05/24/2023]
Abstract
Plant-type ferredoxins in Arabidopsis transfer electrons from the photosystem I to multiple redox-driven enzymes involved in the assimilation of carbon, nitrogen, and sulfur. Leaf-type ferredoxins also modulate the switch between the linear and cyclic electron routes of the photosystems. Recently, two novel ferredoxin homologs with extra C-termini were identified in the Arabidopsis genome (AtFdC1, AT4G14890; AtFdC2, AT1G32550). FdC1 was considered as an alternative electron acceptor of PSI under extreme ferredoxin-deficient conditions. Here, we showed that FdC1 could interact with some, but not all, electron acceptors of leaf-type Fds, including the ferredoxin-thioredoxin reductase (FTR), sulfite reductase (SiR), and nitrite reductase (NiR). Photoreduction assay on cytochrome c and enzyme assays confirmed its capability to receive electrons from PSI and donate electrons to the Fd-dependent SiR and NiR but not to the ferredoxin-NADP+ oxidoreductase (FNR). Hence, FdC1 and leaf-type Fds may play differential roles by channeling electrons from photosystem I to different downstream electron acceptors in photosynthetic tissues. In addition, the median redox potential of FdC1 may allow it to receive electrons from FNR in non-photosynthetic plastids.
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Affiliation(s)
- Xiaoqian Guan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shuai Chen
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chia Pao Voon
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Bo Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Mikko Tikkanen
- Department of Biochemistry and Food Chemistry, Molecular Plant Biology, University of Turku, Turku, Finland
| | - Boon L. Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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49
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Abstract
Nitrogen (N) fertilizer has a major influence on the yield and quality. Understanding and optimising the response of crop plants to nitrogen fertilizer usage is of central importance in enhancing food security and agricultural sustainability. In this study, the analysis of gene regulatory networks reveals multiple genes and biological processes in response to N. Two microarray studies have been used to infer components of the nitrogen-response network. Since they used different array technologies, a map linking the two probe sets to the maize B73 reference genome has been generated to allow comparison. Putative Arabidopsis homologues of maize genes were used to query the Biological General Repository for Interaction Datasets (BioGRID) network, which yielded the potential involvement of three transcription factors (TFs) (GLK5, MADS64 and bZIP108) and a Calcium-dependent protein kinase. An Artificial Neural Network was used to identify influential genes and retrieved bZIP108 and WRKY36 as significant TFs in both microarray studies, along with genes for Asparagine Synthetase, a dual-specific protein kinase and a protein phosphatase. The output from one study also suggested roles for microRNA (miRNA) 399b and Nin-like Protein 15 (NLP15). Co-expression-network analysis of TFs with closely related profiles to known Nitrate-responsive genes identified GLK5, GLK8 and NLP15 as candidate regulators of genes repressed under low Nitrogen conditions, while bZIP108 might play a role in gene activation.
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50
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Understanding nitrate uptake, signaling and remobilisation for improving plant nitrogen use efficiency. Semin Cell Dev Biol 2018; 74:89-96. [DOI: 10.1016/j.semcdb.2017.08.034] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022]
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