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Li F, Thananusak R, Raethong N, Yang J, Wei M, Zhao X, Laoteng K, Song Y, Vongsangnak W. Dissecting Holistic Metabolic Acclimatization of Mucor circinelloides WJ11 Defective in Carotenoid Biosynthesis. BIOLOGY 2024; 13:276. [PMID: 38666888 PMCID: PMC11048425 DOI: 10.3390/biology13040276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain's economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. To dissect the metabolic mechanism underlying lipid and carotenoid biosynthesis, transcriptome analysis and reporter metabolites identification were implemented between the wild-type (WJ11) and ΔcarRP WJ11 strains of M. circinelloides. As a result, transcriptome analysis revealed 10,287 expressed genes, with 657 differentially expressed genes (DEGs) primarily involved in amino acid, carbohydrate, and energy metabolism. Integration with a genome-scale metabolic model (GSMM) identified reporter metabolites in the ΔcarRP WJ11 strain, highlighting metabolic pathways crucial for amino acid, energy, and nitrogen metabolism. Notably, the downregulation of genes associated with carotenoid biosynthesis and acetyl-CoA generation suggests a coordinated relationship between the carotenoid and fatty acid biosynthesis pathways. Despite disruptions in the carotenoid pathway, lipid production remains stagnant due to reduced acetyl-CoA availability, emphasizing the intricate metabolic interplay. These findings provide insights into the coordinated relationship between carotenoid and fatty acid biosynthesis in M. circinelloides that are valuable in applied research to design optimized strains for producing desired bioproducts through emerging technology.
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Affiliation(s)
- Fanyue Li
- Interdisciplinary Graduate Programs in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Colin Rateledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun West Road, Zibo 255000, China
| | - Roypim Thananusak
- Omics Center for Agriculture, Bioresources, Food, and Health Kasetsart University (OmiKU), Bangkok 10900, Thailand;
| | - Nachon Raethong
- Institute of Nutrition, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Junhuan Yang
- Department of Food Sciences, College of Food Science and Engineering, Lingnan Normal University, Zhanjiang 524048, China;
| | - Mingyue Wei
- College of Ecology, Resources and Environment, Dezhou University, Dezhou 253000, China;
| | - Xingtang Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China;
| | - Kobkul Laoteng
- Industrial Bioprocess Technology Research Team, Functional Ingredient and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
| | - Yuanda Song
- Colin Rateledge Center for Microbial Lipids, School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun West Road, Zibo 255000, China
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health Kasetsart University (OmiKU), Bangkok 10900, Thailand;
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Yu J, Yin K, Liu Y, Li Y, Zhang J, Han X, Tong Z. Co-expression network analysis reveals PbTGA4 and PbAPRR2 as core transcription factors of drought response in an important timber species Phoebe bournei. FRONTIERS IN PLANT SCIENCE 2024; 14:1297235. [PMID: 38259934 PMCID: PMC10800493 DOI: 10.3389/fpls.2023.1297235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Phoebe bournei is one of the main afforestation tree species in subtropical regions of China and is famous for its timber. Its distribution and growth are significantly impaired by water conditions. Thus, it is essential to understand the mechanism of the stress response in P. bournei. Here, we analyzed the phenotypic changes and transcriptomic rearrangement in the leaves and roots of P. bournei seedlings grown for 0 h, 1 h, 24 h, and 72 h under simulated drought conditions (10% PEG 6000). The results showed that drought stress inhibited plant photosynthesis and increased oxidoreductase activity and abscisic acid (ABA) accumulation. Spatio-temporal transcriptomic analysis identified 2836 and 3704 differentially expressed genes (DEGs) in leaves and roots, respectively. The responsive genes in different organs presented various expression profiles at different times. Gene co-expression network analysis identified two core transcription factors, TGA4 and APRR2, from two modules that showed a strong positive correlation with ABA accumulation. Our study investigated the different responses of aboveground and belowground organs of P. bournei to drought stress and provides critical information for improving the drought resistance of this timber species.
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Affiliation(s)
| | | | | | | | | | - Xiao Han
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Baud S, Corso M, Debeaujon I, Dubreucq B, Job D, Marion-Poll A, Miquel M, North H, Rajjou L, Lepiniec L. Recent progress in molecular genetics and omics-driven research in seed biology. C R Biol 2023; 345:61-110. [PMID: 36847120 DOI: 10.5802/crbiol.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.
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Hodin J, Lind C, Marmagne A, Espagne C, Bianchi MW, De Angeli A, Abou-Choucha F, Bourge M, Chardon F, Thomine S, Filleur S. Proton exchange by the vacuolar nitrate transporter CLCa is required for plant growth and nitrogen use efficiency. THE PLANT CELL 2023; 35:318-335. [PMID: 36409008 PMCID: PMC9806559 DOI: 10.1093/plcell/koac325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Nitrate is a major nutrient and osmoticum for plants. To deal with fluctuating nitrate availability in soils, plants store this nutrient in their vacuoles. Chloride channel a (CLCa), a 2NO3-/1H+ exchanger localized to the vacuole in Arabidopsis (Arabidopsis thaliana), ensures this storage process. CLCa belongs to the CLC family, which includes anion/proton exchangers and anion channels. A mutation in a glutamate residue conserved across CLC exchangers is likely responsible for the conversion of exchangers to channels. Here, we show that CLCa with a mutation in glutamate 203 (E203) behaves as an anion channel in its native membrane. We introduced the CLCaE203A point mutation to investigate its physiological importance into the Arabidopsis clca knockout mutant. These CLCaE203A mutants displayed a growth deficit linked to the disruption of water homeostasis. Additionally, CLCaE203A expression failed to complement the defect in nitrate accumulation of clca and favored higher N-assimilation at the vegetative stage. Further analyses at the post-flowering stages indicated that CLCaE203A expression results in an increase in N uptake allocation to seeds, leading to a higher nitrogen use efficiency compared to the wild-type. Altogether, these results point to the critical function of the CLCa exchanger on the vacuole for plant metabolism and development.
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Affiliation(s)
- Julie Hodin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, F-75205 Paris Cedex 13, France
| | - Christof Lind
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Anne Marmagne
- AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, 78000 Versailles, France
| | - Christelle Espagne
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- Université Paris-Est-Créteil-Val-de-Marne, 94010 Creteil Cedex, France
| | - Alexis De Angeli
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Fadi Abou-Choucha
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Fabien Chardon
- AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, 78000 Versailles, France
| | - Sebastien Thomine
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Sophie Filleur
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, F-75205 Paris Cedex 13, France
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Hoffmann B, Aubry E, Marmagne A, Dinant S, Chardon F, Le Hir R. Impairment of sugar transport in the vascular system acts on nitrogen remobilization and nitrogen use efficiency in Arabidopsis. PHYSIOLOGIA PLANTARUM 2022; 174:e13830. [PMID: 36437708 DOI: 10.1111/ppl.13830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Carbon (C) and nitrogen (N) metabolisms have long been known to be coupled, and this is required for adjusting nitrogen use efficiency (NUE). Despite this intricate relationship, it is still unclear how deregulation of sugar transport impacts N allocation. Here, we investigated in Arabidopsis the consequences of the simultaneous downregulation of the genes coding for the sugar transporters SWEET11, SWEET12, SWEET16, and SWEET17 on various anatomical and physiological traits ranging from the stem's vascular system development to plant biomass production, seed yield, and N remobilization and use efficiency. Our results show that intracellular sugar exchanges mediated by SWEET16 and SWEET17 proteins specifically impact vascular development but do not play a significant role in the distribution of N. Most importantly, we showed that the double mutant swt11 swt12, which has an impacted vascular development, displays an improved NUE and nitrogen remobilization to the seeds. In addition, a significant negative correlation between sugar and amino acids contents and the inflorescence stem radial growth exists, highlighting the complex interaction between the maintenance of C/N homeostasis and the inflorescence stem development. Our results thus deepen the link between sugar transport, C/N allocation, and vascular system development.
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Affiliation(s)
- Beate Hoffmann
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Emilie Aubry
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Anne Marmagne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sylvie Dinant
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Rozenn Le Hir
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Marmagne A, Masclaux-Daubresse C, Chardon F. Modulation of plant nitrogen remobilization and postflowering nitrogen uptake under environmental stresses. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153781. [PMID: 36029571 DOI: 10.1016/j.jplph.2022.153781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 07/16/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Plants are sessile organisms that take up nitrogen (N) from the soil for growth and development. At the postflowering stage, N that plants require for seed growth and filling derives from either root uptake or shoot remobilization. The balance between N uptake and N remobilization determines the final carbon (C) and N composition of the seed. The N uptake and N remobilization mechanisms are regulated by endogenous signals, including hormones, developmental stage, and carbon/nitrogen ratio, and by environmental factors. The cellular responses to the environment are relatively well known. However, the effects of environmental stresses on the balance between N uptake and N remobilization are still poorly understood. Thus, this study aims to analyze the impact of environmental stresses (drought, heat, darkness, triggered defense, and low nitrate) on N fluxes within plants during seed filling. Using publicly available Arabidopsis transcriptome data, expression of several marker genes involved in N assimilation, transport, and recycling was analyzed in relation to stress. Results showed that the responses of genes encoding inorganic N transporters, N assimilation, and N recycling are mainly regulated by N limitation, the genes encoding housekeeping proteases are principally sensitive to C limitation, and the response of genes involved in the transport of organic N is controlled by both C and N limitations. In addition, 15N data were used to examine the effects of severe environmental stresses on N remobilization and N uptake, and a schematic representation of the major factors that regulate the balance between N remobilization and N uptake under the stress and control conditions was provided.
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Affiliation(s)
- Anne Marmagne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Céline Masclaux-Daubresse
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
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Huang W, Ma D, Hao X, Li J, Xia L, Zhang E, Wang P, Wang M, Guo F, Wang Y, Ni D, Zhao H. CsATG101 Delays Growth and Accelerates Senescence Response to Low Nitrogen Stress in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:880095. [PMID: 35620698 PMCID: PMC9127664 DOI: 10.3389/fpls.2022.880095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
For tea plants, nitrogen (N) is a foundational element and large quantities of N are required during periods of roundly vigorous growth. However, the fluctuation of N in the tea garden could not always meet the dynamic demand of the tea plants. Autophagy, an intracellular degradation process for materials recycling in eukaryotes, plays an important role in nutrient remobilization upon stressful conditions and leaf senescence. Studies have proven that numerous autophagy-related genes (ATGs) are involved in N utilization efficiency in Arabidopsis thaliana and other species. Here, we identified an ATG gene, CsATG101, and characterized the potential functions in response to N in A. thaliana. The expression patterns of CsATG101 in four categories of aging gradient leaves among 24 tea cultivars indicated that autophagy mainly occurred in mature leaves at a relatively high level. Further, the in planta heterologous expression of CsATG101 in A. thaliana was employed to investigate the response of CsATG101 to low N stress. The results illustrated a delayed transition from vegetative to reproductive growth under normal N conditions, while premature senescence under N deficient conditions in transgenic plants vs. the wild type. The expression profiles of 12 AtATGs confirmed the autophagy process, especially in mature leaves of transgenic plants. Also, the relatively high expression levels for AtAAP1, AtLHT1, AtGLN1;1, and AtNIA1 in mature leaves illustrated that the mature leaves act as the source leaves in transgenic plants. Altogether, the findings demonstrated that CsATG101 is a candidate gene for improving annual fresh tea leaves yield under both deficient and sufficient N conditions via the autophagy process.
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Affiliation(s)
- Wei Huang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Danni Ma
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Xulei Hao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Jia Li
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Li Xia
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - E. Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Pu Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Mingle Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Fei Guo
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yu Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Hua Zhao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
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Jasinski S, Fabrissin I, Masson A, Marmagne A, Lécureuil A, Bill L, Chardon F. ACCELERATED CELL DEATH 6 Acts on Natural Leaf Senescence and Nitrogen Fluxes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 11:611170. [PMID: 33488657 PMCID: PMC7817547 DOI: 10.3389/fpls.2020.611170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/23/2020] [Indexed: 05/30/2023]
Abstract
As the last step of leaf development, senescence is a molecular process involving cell death mechanism. Leaf senescence is trigged by both internal age-dependent factors and environmental stresses. It must be tightly regulated for the plant to adopt a proper response to environmental variation and to allow the plant to recycle nutrients stored in senescing organs. However, little is known about factors that regulate both nutrients fluxes and plant senescence. Taking advantage of variation for natural leaf senescence between Arabidopsis thaliana accessions, Col-0 and Ct-1, we did a fine mapping of a quantitative trait loci for leaf senescence and identified ACCELERATED CELL DEATH 6 (ACD6) as the causal gene. Using two near-isogeneic lines, differing solely around the ACD6 locus, we showed that ACD6 regulates rosette growth, leaf chlorophyll content, as well as leaf nitrogen and carbon percentages. To unravel the role of ACD6 in N remobilization, the two isogenic lines and acd6 mutant were grown and labeled with 15N at the vegetative stage in order to determine 15N partitioning between plant organs at harvest. Results showed that N remobilization efficiency was significantly lower in all the genotypes with lower ACD6 activity irrespective of plant growth and productivity. Measurement of N uptake at vegetative and reproductive stages revealed that ACD6 did not modify N uptake efficiency but enhanced nitrogen translocation from root to silique. In this study, we have evidenced a new role of ACD6 in regulating both sequential and monocarpic senescences and disrupting the balance between N remobilization and N uptake that is required for a good seed filling.
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Xu G, Takahashi H. Improving nitrogen use efficiency: from cells to plant systems. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4359-4364. [PMID: 32710784 DOI: 10.1093/jxb/eraa309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- China MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing, China
| | - Hideki Takahashi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
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