Nitrogen Assimilation
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Phosphoenolpyruvate Carboxylase Intrinsically Located in the Chloroplast of Rice Plays a Crucial Role in Ammonium Assimilation
Phosphoenolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation Chisato Masumotoa,1, Shin-Ichi Miyazawaa,1, Hiroshi Ohkawaa,2, Takuya Fukudaa, Yojiro Taniguchia,3, Seiji Murayamaa,4, Miyako Kusanob, Kazuki Saitob, Hiroshi Fukayamaa,5, and Mitsue Miyaoa,6 aPhotobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Kannondai, Tsukuba 305-8602, Japan; and bRIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan Edited by Elisabeth Gantt, University of Maryland, College Park, MD, and approved February 4, 2010 (received for review November 12, 2009) Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of primary encoded by a small gene family (5). Treatments that lead to ele- metabolism in bacteria, algae, and vascular plants, and is believed to vation of the PEPC activity, such as enhanced nitrogen assimilation Oryza sativa be cytosolic. Here we show that rice ( L.) has a plant-type and Pi starvation in C3 plant leaves (6, 7), induce expression of PEPC, Osppc4, that is targeted to the chloroplast. Osppc4 was ex- PEPC kinase gene(s) and phosphorylation of PEPC (8, 9). These pressed in all organs tested and showed high expression in the leaves. mechanisms strictly regulate PEPC activity, which is essential for Its expression in the leaves was confined to mesophyll cells, and plants because of the irreversible nature of the reaction. Osppc4 accounted for approximately one-third of total PEPC protein In addition to the plant-type PEPC, vascular plants have in theleaf blade.RecombinantOsppc4 wasactivein thePEPCreaction, another isozyme, a bacterial-type PEPC that lacks the conserved V showing max comparable to cytosolic isozymes. -
Nitrogen Assimilation in the Highly Salt- and Boron-Tolerant Ecotype Zea Mays L
plants Article Nitrogen Assimilation in the Highly Salt- and Boron-Tolerant Ecotype Zea mays L. Amylacea Teresa Fuertes-Mendizábal 1 , Elizabeth Irica Bastías 2, Carmen González-Murua 1 and a 1, M¯ Begoña González-Moro * 1 Departamento de Biología Vegetal y Ecología, Facultad de Ciencia y Tecnología, Universidad del País Vasco/EHU, Apdo. 644, E-48080 Bilbao, Spain; [email protected] (T.F.-M.); [email protected] (C.G.-M.) 2 Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile; [email protected] * Correspondence: [email protected]; Tel.: +34-4-946-01-53-19 Received: 13 January 2020; Accepted: 27 February 2020; Published: 4 March 2020 Abstract: The Lluta Valley in Northern Chile is an important agricultural area affected by both salinity and boron (B) toxicity. Zea mays L. amylacea, an ecotype arisen because of the seed selection practiced in this valley, shows a high tolerance to salt and B levels. In the present study the interaction between B and salt was studied after 20 days of treatment at low (100 mM) and high salinity (430 mM NaCl), assessing changes in nitrogen metabolites and in the activity of key nitrogen-assimilating enzymes. Under non-saline conditions, the presence of excessive B favored higher nitrate and ammonium mobilization to leaves, increasing nitrate reductase (NR) activity but not glutamine synthetase (GS). Thus, the increment of nitrogen use efficiency by B application would contribute partially to maintain the biomass production in this ecotype. Positive relationships between NR activity, nitrate, and stomatal conductance were observed in leaves. -
In Nitrogen Assimilation (Plant Mutant/Biochemical Genetics/Ammonia Assimilation/Gene Expression) ROSANA MELO-OLIVEIRA, IGOR CUNHA OLIVEIRA, and GLORIA M
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 4718-4723, May 1996 Plant Biology Arabidopsis mutant analysis and gene regulation define a nonredundant role for glutamate dehydrogenase in nitrogen assimilation (plant mutant/biochemical genetics/ammonia assimilation/gene expression) ROSANA MELO-OLIVEIRA, IGOR CUNHA OLIVEIRA, AND GLORIA M. CORUZZI Department of Biology, New York University, New York, NY 10003 Communicated by William L. Ogren, Champaign, IL, December 18, 1995 (received for review June 2, 1995) ABSTRACT Glutamate dehydrogenase (GDH) is ubiqui- similating photorespiratory ammonia (6). However, several tous to all organisms, yet its role in higher plants remains pieces of data argue against this proposed role. Inhibitors of enigmatic. To better understand the role of GDH in plant GS, such as phosphinothricin, specifically kill plants grown nitrogen metabolism, we have characterized an Arabidopsis under photorespiratory growth conditions (4, 10, 11). Second, mutant (gdhl-1) defective in one of two GDH gene products the characterization of photorespiratory mutants has sup- and have studied GDHI gene expression. GDHI mRNA accu- ported a major role for GS/GOGAT in this process. Plant mulates to highest levels in dark-adapted or sucrose-starved mutants deficient in chloroplast GS2 or ferredoxin-dependent plants, and light or sucrose treatment each repress GDHI GOGAT are chlorotic when grown under photorespiratory mRNA accumulation. These results suggest that the GDHI conditions (in air), yet they display a normal phenotype when gene product functions in the direction of glutamate catabo- grown under conditions that suppress photorespiration (high lism under carbon-limiting conditions. Low levels of GDHI CO2) (12-15). Together these data suggest that GDH plays a mRNA present in leaves of light-grown plants can be induced minor role, if any, in the reassimilation of photorespiratory by exogenously supplied ammonia. -
Supplementary Material Temporal Dynamics of Bacterial Communities
Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2017 Supplementary Material Temporal dynamics of bacterial communities and predicted nitrogen metabolism genes in a full-scale wastewater treatment plant Xiao-Yan Fan, Jing-Feng Gao *, Kai-Ling Pan, Ding-Chang Li, Hui-Hui Dai, Xing Li National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China *Corresponding author: Dr. Jingfeng Gao, E-mail: [email protected] or [email protected], Tel.: 0086-10-67391918; Fax: 0086-10-67391983. Tel: +86-10-6739-2627(office); Fax: +86-10-6739-1983 E-mail: [email protected] or [email protected] Contents 1. Tables Table S1 Detailed information concerning variation of water quality indexes (WQI), operational parameters (OP) and temperature (T) during sampling period. Table S2 Primers, thermal programs and standard curves of qPCR in this study. Table S3 The KOs of nitrogen cycle. Table S4 Raw and effective reads, plus numbers of OTUs, Good’s coverage, Shannon, Chao1, ACE, and Simpson of the five Groups. 2. Figures Fig. S1 Bacterial communitiy difference across 12 activated sludge samples collected from different seasons as revealed by cluster analysis. Fig. S2 Shifts in bacterial functions as revealed by PCoA. Fig. S3 Relative abundance of different bacterial functions across 12 activated sludge samples. Fig. S4 Top 35 potential functions of the microbes in different Groups. Table S1 Detailed information -
Nitrogen Fertilizer Induced Alterations in the Root Proteome of Two Rice Cultivars
Article Nitrogen Fertilizer Induced Alterations in The Root Proteome of Two Rice Cultivars Jichao Tang 1, Zhigui Sun 1, Qinghua Chen 1, Rebecca Njeri Damaris 2 and Bilin Lu 1,* and Zhengrong Hu 2,* 1 Hubei Collaborative Innovation Center for Grain Industry, Agricultural college, Yangtze University, Jingzhou 434025, China 2 State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China * Correspondence: [email protected] (B.L.); [email protected] (Z.H.) Received: 4 June 2019; Accepted: 24 July 2019; Published: 26 July 2019 Abstract: Nitrogen (N) is an essential nutrient for plants and a key limiting factor of crop production. However, excessive application of N fertilizers and the low nitrogen use efficiency (NUE) have brought in severe damage to the environment. Therefore, improving NUE is urgent and critical for the reductions of N fertilizer pollution and production cost. In the present study, we investigated the effects of N nutrition on the growth and yield of the two rice (Oryza sativa L.) cultivars, conventional rice Huanghuazhan and indica hybrid rice Quanliangyou 681, which were grown at three levels of N fertilizer (including 135, 180 and 225 kg/hm2, labeled as N9, N12, N15, respectively). Then, a proteomic approach was employed in the roots of the two rice cultivars treated with N fertilizer at the level of N15. A total of 6728 proteins were identified, among which 6093 proteins were quantified, and 511 differentially expressed proteins were found in the two rice cultivars after N fertilizer treatment. These differentially expressed proteins were mainly involved in ammonium assimilation, amino acid metabolism, carbohydrate metabolism, lipid metabolism, signal transduction, energy production/regulation, material transport, and stress/defense response. -
Supplementary Informations SI2. Supplementary Table 1
Supplementary Informations SI2. Supplementary Table 1. M9, soil, and rhizosphere media composition. LB in Compound Name Exchange Reaction LB in soil LBin M9 rhizosphere H2O EX_cpd00001_e0 -15 -15 -10 O2 EX_cpd00007_e0 -15 -15 -10 Phosphate EX_cpd00009_e0 -15 -15 -10 CO2 EX_cpd00011_e0 -15 -15 0 Ammonia EX_cpd00013_e0 -7.5 -7.5 -10 L-glutamate EX_cpd00023_e0 0 -0.0283302 0 D-glucose EX_cpd00027_e0 -0.61972444 -0.04098397 0 Mn2 EX_cpd00030_e0 -15 -15 -10 Glycine EX_cpd00033_e0 -0.0068175 -0.00693094 0 Zn2 EX_cpd00034_e0 -15 -15 -10 L-alanine EX_cpd00035_e0 -0.02780553 -0.00823049 0 Succinate EX_cpd00036_e0 -0.0056245 -0.12240603 0 L-lysine EX_cpd00039_e0 0 -10 0 L-aspartate EX_cpd00041_e0 0 -0.03205557 0 Sulfate EX_cpd00048_e0 -15 -15 -10 L-arginine EX_cpd00051_e0 -0.0068175 -0.00948672 0 L-serine EX_cpd00054_e0 0 -0.01004986 0 Cu2+ EX_cpd00058_e0 -15 -15 -10 Ca2+ EX_cpd00063_e0 -15 -100 -10 L-ornithine EX_cpd00064_e0 -0.0068175 -0.00831712 0 H+ EX_cpd00067_e0 -15 -15 -10 L-tyrosine EX_cpd00069_e0 -0.0068175 -0.00233919 0 Sucrose EX_cpd00076_e0 0 -0.02049199 0 L-cysteine EX_cpd00084_e0 -0.0068175 0 0 Cl- EX_cpd00099_e0 -15 -15 -10 Glycerol EX_cpd00100_e0 0 0 -10 Biotin EX_cpd00104_e0 -15 -15 0 D-ribose EX_cpd00105_e0 -0.01862144 0 0 L-leucine EX_cpd00107_e0 -0.03596182 -0.00303228 0 D-galactose EX_cpd00108_e0 -0.25290619 -0.18317325 0 L-histidine EX_cpd00119_e0 -0.0068175 -0.00506825 0 L-proline EX_cpd00129_e0 -0.01102953 0 0 L-malate EX_cpd00130_e0 -0.03649016 -0.79413596 0 D-mannose EX_cpd00138_e0 -0.2540567 -0.05436649 0 Co2 EX_cpd00149_e0 -
A Robust Nitrifying Community in a Bioreactor at 50&Thinsp;&Deg;C Opens up the Path for Thermophilic Nitrogen Removal
The ISME Journal (2016) 10, 2293–2303 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE A robust nitrifying community in a bioreactor at 50°C opens up the path for thermophilic nitrogen removal Emilie NP Courtens1, Eva Spieck2, Ramiro Vilchez-Vargas1, Samuel Bodé3, Pascal Boeckx3, Stefan Schouten4, Ruy Jauregui5, Dietmar H Pieper5, Siegfried E Vlaeminck1,6,7 and Nico Boon1,7 1Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Gent, Belgium; 2Biocenter Klein Flottbek and Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany; 3Isotope Bioscience Laboratory, Ghent University, Gent, Belgium; 4Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands; 5Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany and 6Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Antwerpen, Belgium The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to ‘Candidatus Nitrososphaera gargensis’, and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. -
Review NH4 Toxicity in Higher Plants
J. Plant Physiol. 159. 567–584 (2002) Urban & Fischer Verlag http://www.urbanfischer.de/journals/jpp Review + NH4 toxicity in higher plants: a critical review Dev T. Britto, Herbert J. Kronzucker* Division of Life Sciences, University of Toronto, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada Received December 14, 2001 · Accepted February 22, 2002 Abstract + Ammonium (NH4 ) toxicity is an issue of global ecological and economic importance. In this review, + + we discuss the major themes of NH4 toxicity, including the occurrence of NH4 in the biosphere, + response differences to NH4 nutrition among wild and domesticated species, symptoms and pro- posed mechanisms underlying toxicity, and means by which it can be alleviated. Where possible, – nitrate (NO3 ) nutrition is used as point of comparison. Particular emphasis is placed on issues of + cellular pH, ionic balance, relationships with carbon biochemistry, and bioenergetics of primary NH4 transport. Throughout, we attempt to identify areas that are controversial, and areas that are in need of further examination. I. Introduction universal biological phenomenon, as it has also been ob- served in many animal systems (Petit et al. 1990, Kosenko et + al. 1991, 1995, Tremblay and Bradley 1992, Gardner et al. Ammonium (NH4 ) is a paradoxical nutrient ion in that, al- though it is a major nitrogen (N) source whose oxidation state 1994), including humans, where it has been implicated in par- eliminates the need for its reduction in the plant cell (Salsac ticular in neurological disorders (Marcaida et al. 1992, Mira- et al. 1987), and although it is an intermediate in many meta- bet et al. 1997, Butterworth 1998, Haghighat et al. -
Drought-Induced Responses of Nitrogen Metabolism in Ipomoea Batatas
plants Article Drought-Induced Responses of Nitrogen Metabolism in Ipomoea batatas Houqiang Xia y, Tao Xu y , Jing Zhang y, Ke Shen, Zongyun Li * and Jingran Liu * Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221116, China; [email protected] (H.X.); [email protected] (T.X.); [email protected] (J.Z.); [email protected] (K.S.) * Correspondence: [email protected] (Z.L.); [email protected] (J.L.) These authors contributed equally to this paper. y Received: 20 September 2020; Accepted: 8 October 2020; Published: 11 October 2020 Abstract: This study investigated the effect of water stress, simulated by the polyethylene glycol (PEG-6000) method, on nitrogen (N) metabolism in leaves and roots of hydroponically grown sweet potato seedlings, Xushu 32 (X32) and Ningzishu 1 (N1). The concentrations of PEG-6000 treatments were 0%, 5% and 10% (m/v). The results showed that the drought-treated plants showed a decline leaf relative water content, and revealed severe growth inhibition, compared with the 0% treatment. Under drought stress, the decline in biomass of the leaf and stem was more noticeable than in root biomass for X32, leading to a higher root to shoot ratio. Drought stress increased the nitrate nitrogen (NO3−-N) and protein in leaves, but reduced all the activities of N-metabolism enzymes and the transcriptional levels of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase + (GOGAT); in roots, NO3−-N and NR had opposite trends. The leaf ammonium nitrogen (NH4 -N), GS and amino acid had different trends between X32 and N1 under drought stress. -
Tansley Review Biological Stoichiometry of Plant Production: Metabolism, Scaling and Ecological Response to Global Change
New Phytologist Review Tansley review Biological stoichiometry of plant production: metabolism, scaling and ecological response to global change Author for correspondence: J. J. Elser1, W. F. Fagan2, A. J. Kerkhoff3, N. G. Swenson4 J. J. Elser 5,6,7 Tel: +1 480 965 9747 and B. J. Enquist Email: [email protected] 1School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; 2Department of Biology, 3 Received: 19 May 2009 University of Maryland, College Park, MD 20742, USA; Department of Biology and Department of Accepted: 4 January 2010 Mathematics, Kenyon College, Gambier, OH 43022, USA; 4Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; 5Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA; 6The Santa Fe Institute, Santa Fe, NM 87501, USA; 7Center for Applied Biodiversity Science, Conservation International, Arlington, VA 22202, USA Contents Summary 1 V. Applications: large-scale patterns and processes 9 associated with plant stoichiometry I. Introduction 2 VI. Global change and plants: a stoichiometric scaling 11 II. Variation in plant C : N : P ratios: how much and what are 3 perspective the sources? VII. Synthesis and summary 12 III. The growth rate hypothesis in terrestrial plants and the 5 scaling of whole-plant N : P stoichiometry Acknowledgements 13 and production References 13 IV. Scaling from tissues to whole plants 7 Summary New Phytologist (2010) Biological stoichiometry theory considers the balance of multiple chemical ele- doi: 10.1111/j.1469-8137.2010.03214.x ments in living systems, whereas metabolic scaling theory considers how size affects metabolic properties from cells to ecosystems. -
Nitrate Assimilation in Soils
January, 1931 Research Bulletin No. 135 Nitrate Assimilation in Soils By 1<'. B. SMITH AND P . E. BROWN AGRICUDTURAL EXPERIMENT STATION IOWA ,STATE COLLEGE OF AGRICULTURE AND MECHANIC ARTS C. F . CURTISS, Director AGRONOMY SECTION SOILS AMES, IOWA CONTENTS Page Discussion and Summary 36 Introduction 37 Historical . 38 Depressing Effect of Straw and Manure on Crop Yields 38 Nitrate Assimilation in Soils 40 Microorganisms Capable of Utilizing Nitrate Nitrogen 43 Experimental 45 Part I. The Nitrate-Assimilating Power of the Soil 45 1. Solution Studies 45 2. Soil Studies 45 3. Effect of Varying the Amount of Ni trates Added and the Length of Incuba- tion Period 46 4. Nitrate-Assimilating Power of Some Iowa ~ili ~ Part II. Effect of Soil Treatment on the Nitrate Assimi- lating Power of the Soil . 48 Carrington Loam 48 Marshall Silt Loam and Grundy Silt Loam 49 Effect of Artificial Manures and F'arm Manure on Nitrate Assimilating Power of Carrington Loam 51 Nitrate Assimilating Power Under Con tinuous Corn and a Three-Year Rotation 51 Part III. Nitrate Assimilation by Soil Microorganisms 53 Isolation of the Organisms 53 Description of the Organisms . 53 Nitrate Assimilation and Denitrification by Pure Cultures of Microorganisms 54 Literature Cited 59 DISCUSSION AND SUMMARY Preliminary work with solution cultures inoculated with soil showed that 20.83 mgm. of nitrate nitrogen disappeared in eight days, while the total nitrogen increased. The results obtained with soil cultures were very similar to those obtained with the solution cultures. Treating the soil with straw in the greenhouse brought about a complete utilization of the nitrates, while there was a small accumulation of nitrate in the soil treated with farm manure. -
Discovery of Industrially Relevant Oxidoreductases
DISCOVERY OF INDUSTRIALLY RELEVANT OXIDOREDUCTASES Thesis Submitted for the Degree of Master of Science by Kezia Rajan, B.Sc. Supervised by Dr. Ciaran Fagan School of Biotechnology Dublin City University Ireland Dr. Andrew Dowd MBio Monaghan Ireland January 2020 Declaration I hereby certify that this material, which I now submit for assessment on the programme of study leading to the award of Master of Science, is entirely my own work, and that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge breach any law of copyright, and has not been taken from the work of others save and to the extent that such work has been cited and acknowledged within the text of my work. Signed: ID No.: 17212904 Kezia Rajan Date: 03rd January 2020 Acknowledgements I would like to thank the following: God, for sending me angels in the form of wonderful human beings over the last two years to help me with any- and everything related to my project. Dr. Ciaran Fagan and Dr. Andrew Dowd, for guiding me and always going out of their way to help me. Thank you for your patience, your advice, and thank you for constantly believing in me. I feel extremely privileged to have gotten an opportunity to work alongside both of you. Everything I’ve learnt and the passion for research that this project has sparked in me, I owe it all to you both. Although I know that words will never be enough to express my gratitude, I still want to say a huge thank you from the bottom of my heart.