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Fortunato S, Nigro D, Lasorella C, Marcotuli I, Gadaleta A, de Pinto MC. The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals. Biomolecules 2023; 13:1771. [PMID: 38136642 PMCID: PMC10742212 DOI: 10.3390/biom13121771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.
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Affiliation(s)
- Stefania Fortunato
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Cecilia Lasorella
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
| | - Ilaria Marcotuli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.N.); (I.M.)
| | - Maria Concetta de Pinto
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (S.F.)
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2
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Wu F, Yu P, Mao L. Multi-Spatiotemporal Probing of Neurochemical Events by Advanced Electrochemical Sensing Methods. Angew Chem Int Ed Engl 2023; 62:e202208872. [PMID: 36284258 DOI: 10.1002/anie.202208872] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 11/05/2022]
Abstract
Neurochemical events involving biosignals of different time and space dimensionalities constitute the complex basis of neurological functions and diseases. In view of this fact, electrochemical measurements enabling real-time quantification of neurochemicals at multiple levels of spatiotemporal resolution can provide informative clues to decode the molecular networks bridging vesicles and brains. This Minireview focuses on how scientific questions regarding the properties of single vesicles, neurotransmitter release kinetics, interstitial neurochemical dynamics, and multisignal interconnections in vivo have driven the design of electrochemical nano/microsensors, sensing interface engineering, and signal/data processing. An outlook for the future frontline in this realm will also be provided.
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Affiliation(s)
- Fei Wu
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
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3
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Iron–Sulfur Clusters toward Stresses: Implication for Understanding and Fighting Tuberculosis. INORGANICS 2022. [DOI: 10.3390/inorganics10100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) remains the leading cause of death due to a single pathogen, accounting for 1.5 million deaths annually on the global level. Mycobacterium tuberculosis, the causative agent of TB, is persistently exposed to stresses such as reactive oxygen species (ROS), reactive nitrogen species (RNS), acidic conditions, starvation, and hypoxic conditions, all contributing toward inhibiting bacterial proliferation and survival. Iron–sulfur (Fe-S) clusters, which are among the most ancient protein prosthetic groups, are good targets for ROS and RNS, and are susceptible to Fe starvation. Mtb holds Fe-S containing proteins involved in essential biological process for Mtb. Fe-S cluster assembly is achieved via complex protein machineries. Many organisms contain several Fe-S assembly systems, while the SUF system is the only one in some pathogens such as Mtb. The essentiality of the SUF machinery and its functionality under the stress conditions encountered by Mtb underlines how it constitutes an attractive target for the development of novel anti-TB.
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4
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Han Z, Wu F, Yu P, Mao L. Computer-Aided Rational Construction of Mediated Bioelectrocatalysis with π-Conjugated (Hetero)cyclic Molecules: Toward Promoted Distant Electron Tunneling and Improved Biosensing. Anal Chem 2022; 94:8033-8040. [PMID: 35604848 DOI: 10.1021/acs.analchem.2c01289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Highly π-conjugated (hetero)cyclic molecules having delocalized orbitals and tunable charge mobilities are attractive redox relays for mediated bioelectrocatalysis in manifold applications. As rigid molecules, their dynamics within the soft but confined intraprotein space becomes the crucial determinant of the enzyme-mediator electron-tunneling efficiency. However, it is rarely investigated in designing the mediated interface with a particular biocatalyst (e.g., oxidoreductase), which remains an empirical but try-and-error process. Herein, we present the computer-aided exploration of interactions between a flavin-containing reductive synthase and structurally diverse π-extended (hetero)cyclic mediators to realize reversed bioelectrocatalytic oxidation at low overpotentials. Compared to ring-fused systems with unbroken molecular planarity, heteroatom-bridged cyclic, and rotatable conjugated structures (e.g., indophenols) can experience unusually large dynamic torsion under biased forces of hydrogen bonding with enzyme residues. This behavior led to fast intraprotein reorientation (<50 ps) that shortened the electron-tunneling distance from 12 to 9 Å. Meanwhile, the lowest unoccupied molecular orbital level upon molecular torsion was decreased by 0.5 eV to further promote electron abstraction from the reduced flavin cofactor. An efficient distant electron tunneling also obviated mediator transport through the substrate channel, thus avoiding competitive inhibition on enzyme kinetics to broaden the operating concentration range. The resulting bioelectrocatalytic interface enables low-potential biosensing of glutamate with improved selectivity. Our finding provides new structural insights into constructing efficient long-range heterogeneous charge transport with biomacromolecular catalysts.
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Affiliation(s)
- Zhongjie Han
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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5
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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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Vanoni MA. Iron-sulfur flavoenzymes: the added value of making the most ancient redox cofactors and the versatile flavins work together. Open Biol 2021; 11:210010. [PMID: 33947244 PMCID: PMC8097209 DOI: 10.1098/rsob.210010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) flavoproteins form a broad and growing class of complex, multi-domain and often multi-subunit proteins coupling the most ancient cofactors (the Fe-S clusters) and the most versatile coenzymes (the flavin coenzymes, FMN and FAD). These enzymes catalyse oxidoreduction reactions usually acting as switches between donors of electron pairs and acceptors of single electrons, and vice versa. Through selected examples, the enzymes' structure−function relationships with respect to rate and directionality of the electron transfer steps, the role of the apoprotein and its dynamics in modulating the electron transfer process will be discussed.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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7
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Glutacetine ® Biostimulant Applied on Wheat under Contrasting Field Conditions Improves Grain Number Leading to Better Yield, Upgrades N-Related Traits and Changes Grain Ionome. PLANTS 2021; 10:plants10030456. [PMID: 33670931 PMCID: PMC7997451 DOI: 10.3390/plants10030456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022]
Abstract
Wheat is one of the most important cereals for human nutrition, but nitrogen (N) losses during its cultivation cause economic problems and environmental risks. In order to improve N use efficiency (NUE), biostimulants are increasingly used. The present study aimed to evaluate the effects of Glutacetine®, a biostimulant sprayed at 5 L ha−1 in combination with fertilizers (urea or urea ammonium nitrate (UAN)), on N-related traits, grain yield components, and the grain quality of winter bread wheat grown at three field sites in Normandy (France). Glutacetine® improved grain yield via a significant increase in the grain number per spike and per m2, which also enhanced the thousand grain weight, especially with urea. The total N in grains and the NUE tended to increase in response to Glutacetine®, irrespective of the site or the form of N fertilizer. Depending on the site, spraying Glutacetine® can also induce changes in the grain ionome (analyzed by X-ray fluorescence), with a reduction in P content observed (site 2 under urea nutrition) or an increase in Mn content (site 3 under UAN nutrition). These results provide a roadmap for utilizing Glutacetine® biostimulant to enhance wheat production and flour quality in a temperate climate.
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8
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Anas M, Liao F, Verma KK, Sarwar MA, Mahmood A, Chen ZL, Li Q, Zeng XP, Liu Y, Li YR. Fate of nitrogen in agriculture and environment: agronomic, eco-physiological and molecular approaches to improve nitrogen use efficiency. Biol Res 2020; 53:47. [PMID: 33066819 PMCID: PMC7565752 DOI: 10.1186/s40659-020-00312-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/20/2020] [Indexed: 11/10/2022] Open
Abstract
Nitrogen is the main limiting nutrient after carbon, hydrogen and oxygen for photosynthetic process, phyto-hormonal, proteomic changes and growth-development of plants to complete its lifecycle. Excessive and inefficient use of N fertilizer results in enhanced crop production costs and atmospheric pollution. Atmospheric nitrogen (71%) in the molecular form is not available for the plants. For world's sustainable food production and atmospheric benefits, there is an urgent need to up-grade nitrogen use efficiency in agricultural farming system. The nitrogen use efficiency is the product of nitrogen uptake efficiency and nitrogen utilization efficiency, it varies from 30.2 to 53.2%. Nitrogen losses are too high, due to excess amount, low plant population, poor application methods etc., which can go up to 70% of total available nitrogen. These losses can be minimized up to 15-30% by adopting improved agronomic approaches such as optimal dosage of nitrogen, application of N by using canopy sensors, maintaining plant population, drip fertigation and legume based intercropping. A few transgenic studies have shown improvement in nitrogen uptake and even increase in biomass. Nitrate reductase, nitrite reductase, glutamine synthetase, glutamine oxoglutarate aminotransferase and asparagine synthetase enzyme have a great role in nitrogen metabolism. However, further studies on carbon-nitrogen metabolism and molecular changes at omic levels are required by using "whole genome sequencing technology" to improve nitrogen use efficiency. This review focus on nitrogen use efficiency that is the major concern of modern days to save economic resources without sacrificing farm yield as well as safety of global environment, i.e. greenhouse gas emissions, ammonium volatilization and nitrate leaching.
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Affiliation(s)
- Muhammad Anas
- College of Agriculture, Guangxi University, Nanning, 530005, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | | | - Aamir Mahmood
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Qiang Li
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Xu-Peng Zeng
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yang Liu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007, China.
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, 530005, China.
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
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9
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Iqbal A, Qiang D, Alamzeb M, Xiangru W, Huiping G, Hengheng Z, Nianchang P, Xiling Z, Meizhen S. Untangling the molecular mechanisms and functions of nitrate to improve nitrogen use efficiency. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:904-914. [PMID: 31612486 DOI: 10.1002/jsfa.10085] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/01/2019] [Accepted: 10/10/2019] [Indexed: 05/19/2023]
Abstract
A huge amount of nitrogenous fertilizer is used to increase crop production. This leads to an increase in the cost of production, and to human and environmental problems. It is therefore necessary to improve nitrogen use efficiency (NUE) and to design agronomic, biotechnological and breeding strategies for better fertilizer use. Nitrogen use efficiency relies primarily on how plants extract, uptake, transport, assimilate, and remobilize nitrogen. Many plants use nitrate as a preferred nitrogen source. It acts as a signaling molecule in the various important physiological processes required for growth and development. As nitrate is the main source of nitrogen in the soil, root nitrate transporters are important subjects for study. The latest reports have also discussed how nitrate transporter and assimilation genes can be used as molecular tools to improve NUE in crops. The purpose of this review is to describe the mechanisms and functions of nitrate as a specific factor that can be addressed to increase NUE. Improving factors such as nitrate uptake, transport, assimilation, and remobilization through activation by signaling, sensing, and regulatory processes will improve plant growth and NUE. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Asif Iqbal
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Dong Qiang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Madeeha Alamzeb
- Standardization of cotton planting technology, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Wang Xiangru
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Gui Huiping
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Zhang Hengheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Pang Nianchang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Zhang Xiling
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Song Meizhen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
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10
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Dey S, Kundu R, Gopal G, Mukherjee A, Nag A, Paul S. Enhancement of nitrogen assimilation and photosynthetic efficiency by novel iron pulsing technique in Oryza sativa L. var Pankaj. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:207-221. [PMID: 31586721 DOI: 10.1016/j.plaphy.2019.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/21/2019] [Accepted: 09/22/2019] [Indexed: 06/10/2023]
Abstract
Rice is a major food crop. Due to urbanization and climate change, rice production is declining, posing a threat to the increasing food demand. For this, a modified technique of priming is used to enhance plant vigor. In the present study an endogenous rice cultivar was treated with two different iron salts for 72 h and grown for 14 days in nutrient solution. This increased the iron content of the samples which further escalated the photosynthetic efficiency and carbon assimilation in the treated plants. Photosynthesis being correlated to nitrogen assimilation, nitrogen assimilation intermediates and protein content were also elevated in treated plants. Plants showed no symptoms of stress as evident from low malondialdehyde content and increased antioxidant enzymes' activity. From this study it can be inferred that, treatment with iron during germination, helps to trigger growth by facilitating photosynthesis and nitrogen assimilation.
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Affiliation(s)
- Swarnali Dey
- Centre of Advance Study, Department of Botany, University of Calcutta, Kolkata, 700019, India
| | - Rita Kundu
- Centre of Advance Study, Department of Botany, University of Calcutta, Kolkata, 700019, India
| | - Geetha Gopal
- Centre for NanoBiotechnology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Amitava Mukherjee
- Centre for NanoBiotechnology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Anish Nag
- Department of Life Sciences, CHRIST (Deemed to be University), Bangalore, 560029, India
| | - Subhabrata Paul
- Department of Life Sciences, Presidency University, Kolkata, 700073, India.
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11
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Pereira PN, Cushman JC. Exploring the Relationship between Crassulacean Acid Metabolism (CAM) and Mineral Nutrition with a Special Focus on Nitrogen. Int J Mol Sci 2019; 20:E4363. [PMID: 31491972 PMCID: PMC6769741 DOI: 10.3390/ijms20184363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 09/02/2019] [Indexed: 01/09/2023] Open
Abstract
Crassulacean acid metabolism (CAM) is characterized by nocturnal CO2 uptake and concentration, reduced photorespiration, and increased water-use efficiency (WUE) when compared to C3 and C4 plants. Plants can perform different types of CAM and the magnitude and duration of CAM expression can change based upon several abiotic conditions, including nutrient availability. Here, we summarize the abiotic factors that are associated with an increase in CAM expression with an emphasis on the relationship between CAM photosynthesis and nutrient availability, with particular focus on nitrogen, phosphorus, potassium, and calcium. Additionally, we examine nitrogen uptake and assimilation as this macronutrient has received the greatest amount of attention in studies using CAM species. We also discuss the preference of CAM species for different organic and inorganic sources of nitrogen, including nitrate, ammonium, glutamine, and urea. Lastly, we make recommendations for future research areas to better understand the relationship between macronutrients and CAM and how their interaction might improve nutrient and water-use efficiency in order to increase the growth and yield of CAM plants, especially CAM crops that may become increasingly important as global climate change continues.
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Affiliation(s)
- Paula Natália Pereira
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
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12
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Wu F, Yu P, Yang X, Han Z, Wang M, Mao L. Exploring Ferredoxin-Dependent Glutamate Synthase as an Enzymatic Bioelectrocatalyst. J Am Chem Soc 2018; 140:12700-12704. [DOI: 10.1021/jacs.8b08020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Xiaoti Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Zhongjie Han
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Ming Wang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
- University of CAS, Beijing 100049, China
- CAS Research/Education Center for Excellence in Molecule Science, Beijing 100190, China
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13
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins. J Struct Biol 2018; 202:250-263. [DOI: 10.1016/j.jsb.2018.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/11/2018] [Accepted: 01/29/2018] [Indexed: 01/27/2023]
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14
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García-Gutiérrez Á, Cánovas FM, Ávila C. Glutamate synthases from conifers: gene structure and phylogenetic studies. BMC Genomics 2018; 19:65. [PMID: 29351733 PMCID: PMC5775586 DOI: 10.1186/s12864-018-4454-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/15/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants. In conifers, partial cDNA sequences for GOGATs have been isolated and used for gene expression studies. However, knowledge of the gene structure and of phylogenetic relationships with other plant enzymes is quite scant. RESULTS Technological advances in conifer megagenomes sequencing have made it possible to obtain full-length cDNA sequences encoding Fd- and NADH-GOGAT from maritime pine, as well as BAC clones containing sequences for NADH-GOGAT and Fd-GOGAT genes. In the current study, we studied the genomic organization of pine GOGAT genes, the size of their exons/introns, copy numbers in the pine genome and relationships with other plant genes. Phylogenetic analysis was performed, and the degree of preservation and dissimilarity of key domains for the catalytic activities of these enzymes in different taxa were determined. CONCLUSIONS Fd- and NADH-GOGAT are encoded by single-copy genes in the maritime pine genome. The Fd-GOGAT gene is extremely large spanning more than 330 kb and the presence of very long introns highlights the important contribution of LTR retrotransposons to the gene size in conifers. In contrast, the structure of the NADH-GOGAT gene is similar to the orthologous genes in angiosperms. Our phylogenetic analysis indicates that these two genes had different origins during plant evolution. The results provide new insights into the structure and molecular evolution of these essential genes.
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Affiliation(s)
- Ángel García-Gutiérrez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
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Hirasawa M, Solis J, Vaidyanathan N, Srivastava AP, Wynn RM, Sutton RB, Knaff DB. Identification of the ferredoxin interaction sites on ferredoxin-dependent glutamate synthase from Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2017; 134:317-328. [PMID: 28975508 DOI: 10.1007/s11120-017-0446-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Based on in silico docking methods, five amino acids in glutamate synthase (Gln-467, His-1144, Asn-1147, Arg-1162, and Trp-676) likely constitute key binding residues in the interface of a glutamate synthase:ferredoxin complex. Although all interfacial mutants studied showed the ability to form a complex under low ionic strength, these docking mutations showed significantly less ferredoxin-dependent activities, while still retaining enzymatic activity. Furthermore, isothermal titration calorimetry showed a possible 1:2 molar ratio between the wild-type glutamate synthase and ferredoxin. However, each of our interfacial mutants showed only a 1:1 complex with ferredoxin, suggesting that the mutations directly affect the glutamate synthase:ferredoxin heterodimer interface.
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Affiliation(s)
- Masakazu Hirasawa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Jacaranda Solis
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Science Center, Lubbock, TX, 79430-6591, USA
| | - Nanditha Vaidyanathan
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
- Depuy Synthes Companies, 1302 Wrights Lane East, West Chester, PA, 19380, USA
| | - Anurag P Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinoi, 60064, USA
| | - R Max Wynn
- Departments of Internal Medicine and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9038, USA.
| | - Roger B Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech Health Science Center, Lubbock, TX, 79430-6551, USA
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
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16
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The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Yang X, Nian J, Xie Q, Feng J, Zhang F, Jing H, Zhang J, Dong G, Liang Y, Peng J, Wang G, Qian Q, Zuo J. Rice Ferredoxin-Dependent Glutamate Synthase Regulates Nitrogen-Carbon Metabolomes and Is Genetically Differentiated between japonica and indica Subspecies. MOLECULAR PLANT 2016; 9:1520-1534. [PMID: 27677460 DOI: 10.1016/j.molp.2016.09.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 09/11/2016] [Accepted: 09/18/2016] [Indexed: 05/03/2023]
Abstract
Plants assimilate inorganic nitrogen absorbed from soil into organic forms as Gln and Glu through the glutamine synthetase/glutamine:2-oxoglutarate amidotransferase (GS/GOGAT) cycle. Whereas GS catalyzes the formation of Gln from Glu and ammonia, GOGAT catalyzes the transfer of an amide group from Gln to 2-oxoglutarate to produce two molecules of Glu. However, the regulatory role of the GS/GOGAT cycle in the carbon-nitrogen balance is not well understood. Here, we report the functional characterization of rice ABNORMAL CYTOKININ RESPONSE 1 (ABC1) gene that encodes a ferredoxin-dependent (Fd)-GOGAT. The weak mutant allele abc1-1 mutant shows a typical nitrogen-deficient syndrome, whereas the T-DNA insertional mutant abc1-2 is seedling lethal. Metabolomics analysis revealed the accumulation of an excessive amount of amino acids with high N/C ratio (Gln and Asn) and several intermediates in the tricarboxylic acid cycle in abc1-1, suggesting that ABC1 plays a critical role in nitrogen assimilation and carbon-nitrogen balance. Five non-synonymous single-nucleotide polymorphisms were identified in the ABC1 coding region and characterized as three distinct haplotypes, which have been highly and specifically differentiated between japonica and indica subspecies. Collectively, these results suggest that ABC1/OsFd-GOGAT is essential for plant growth and development by modulating nitrogen assimilation and the carbon-nitrogen balance.
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Affiliation(s)
- Xiaolu Yang
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinqiang Nian
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingjun Xie
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Feng
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongwei Jing
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhang
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juli Peng
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Gaufichon L, Rothstein SJ, Suzuki A. Asparagine Metabolic Pathways in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:675-89. [PMID: 26628609 DOI: 10.1093/pcp/pcv184] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/18/2015] [Indexed: 05/03/2023]
Abstract
Inorganic nitrogen in the form of ammonium is assimilated into asparagine via multiple steps involving glutamine synthetase (GS), glutamate synthase (GOGAT), aspartate aminotransferase (AspAT) and asparagine synthetase (AS) in Arabidopsis. The asparagine amide group is liberated by the reaction catalyzed by asparaginase (ASPG) and also the amino group of asparagine is released by asparagine aminotransferase (AsnAT) for use in the biosynthesis of amino acids. Asparagine plays a primary role in nitrogen recycling, storage and transport in developing and germinating seeds, as well as in vegetative and senescence organs. A small multigene family encodes isoenzymes of each step of asparagine metabolism in Arabidopsis, except for asparagine aminotransferase encoded by a single gene. The aim of this study is to highlight the structure of the genes and encoded enzyme proteins involved in asparagine metabolic pathways; the regulation and role of different isogenes; and kinetic and physiological properties of encoded enzymes in different tissues and developmental stages.
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Affiliation(s)
- Laure Gaufichon
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Steven J Rothstein
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, Ontario, Canada N1G 2W1
| | - Akira Suzuki
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
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19
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Vanoni MA. Glutamate synthase: A case-study for in silico drug screening on a complex iron–sulfur flavoenzyme? Gene X 2015; 564:233-5. [DOI: 10.1016/j.gene.2015.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/01/2015] [Indexed: 10/23/2022] Open
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20
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Yoneyama T, Fujimori T, Yanagisawa S, Hase T, Suzuki A. 15N Tracing Studies on In Vitro Reactions of Ferredoxin-Dependent Nitrite Reductase and Glutamate Synthase Using Reconstituted Electron Donation Systems. PLANT & CELL PHYSIOLOGY 2015; 56:1154-1161. [PMID: 25745028 DOI: 10.1093/pcp/pcv039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
It is known that plants contain ferredoxin (Fd)-dependent nitrite reductase (NiR) and glutamate synthase (GOGAT). The Fd-NiR reaction produces ammonia from nitrite, and the activity is usually measured by nitrite disappearance. The Fd-GOGAT reaction forms two glutamates of different origin, from glutamine and 2-oxoglutarate, and the activity is measured by the oxidation of reductant (NADPH) or by formation of total glutamate. Here, a quantitative probe of the products and efficiency of the process was conducted using (15)N tracing techniques on these reactions in vitro. We quantified the reduction of (15)N-labeled [Formula: see text] to [Formula: see text] and the formation of [(15)N]glutamate and [(14)N]glutamate from [5-(15)N-amide]glutamine plus 2-oxoglutarate by NiR and GOGAT, respectively, with the reductant-Fd-NADP(+) oxidoreductase (FNR)-Fd system as the sequential electron donors. The supply of dithionite or NADPH to recombinant cyanobacterial NiR led to electron donation system-dependent formation of [(15)N]ammonium from [(15)N]nitrite. Addition of 20 mM NaCl and 20 mM Na-ascorbate accelerated nitrite reduction under high concentrations of NADPH. A sufficient supply of NADPH to recombinant Zea mays Fd-GOGAT generated complete GOGAT activity (transferring the [5-(15)N]amide of glutamine to 2-oxoglutarate to form [(15)N]glutamate), whereas a shortage of NADPH resulted in glutaminase activity only, which removed the amide from glutamine and released ammonia and [(14)N]glutamate. We conclude that although the recombinant Fd-GOGAT enzyme has two forms of glutamate synthesis, the first by glutaminase (ammonia release by glutamine amidotransferase) and the second by glutamate synthase (coupling of the ammonia and exogenously applied 2-oxoglutarate), the first works without NADPH, while the second is strictly dependent on NADPH availability.
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Affiliation(s)
- Tadakatsu Yoneyama
- Department of Applied Biological Chemistry, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Tamaki Fujimori
- Department of Applied Biological Chemistry, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Shuichi Yanagisawa
- Department of Applied Biological Chemistry, the University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Toshiharu Hase
- Laboratory of Regulation of Biological Reaction, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871 Japan
| | - Akira Suzuki
- INRA, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
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21
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Wang M, Shen Q, Xu G, Guo S. New insight into the strategy for nitrogen metabolism in plant cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 310:1-37. [PMID: 24725423 DOI: 10.1016/b978-0-12-800180-6.00001-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitrogen (N) is one of the most important mineral nutrients required by higher plants. Primary N absorbed by higher plants includes nitrate (NO3(-)), ammonium (NH4(+)), and organic N. Plants have developed several mechanisms for regulating their N metabolism in response to N availability and environmental conditions. Numerous transporters have been characterized and the mode of N movement within plants has been demonstrated. For further assimilation of N, various enzymes are involved in the key processes of NO3(-) or NH4(+) assimilation. N and carbon (C) metabolism are tightly coordinated in the fundamental biochemical pathway that permits plant growth. As N and C metabolism are the fundamental constituents of plant life, understanding N regulation is essential for growing plants and improving crop production. Regulation of N metabolism at the transcriptional and posttranscriptional levels provides important perceptions in the complex regulatory network of plants to adapt to changing N availability. In this chapter, recent advances in elucidating molecular mechanisms of N metabolism processes and regulation strategy, as well as interactions between C and N, are discussed. This review provides new insights into the strategy for studying N metabolism at the cellular level for optimum plant growth in different environments.
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Affiliation(s)
- Min Wang
- Key Lab of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Agricultural Ministry, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China; Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Qirong Shen
- Key Lab of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Agricultural Ministry, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China; Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Guohua Xu
- Key Lab of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Agricultural Ministry, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China; Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Shiwei Guo
- Key Lab of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Agricultural Ministry, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China; Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu Province, China.
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22
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Nitrate signals determine the sensing of nitrogen through differential expression of genes involved in nitrogen uptake and assimilation in finger millet. Funct Integr Genomics 2013; 13:179-90. [PMID: 23435937 DOI: 10.1007/s10142-013-0311-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 01/30/2013] [Accepted: 02/04/2013] [Indexed: 10/27/2022]
Abstract
In order to understand the molecular basis of high nitrogen use efficiency of finger millet, five genes (EcHNRT2, EcLNRT1, EcNADH-NR, EcGS, and EcFd-GOGAT) involved in nitrate uptake and assimilation were isolated using conserved primer approaches. Expression profiles of these five genes along with the previously isolated EcDof1 was studied under increased KNO3 concentrations (0.15 to 1,500 μM) for 2 h as well as at 1.5 μM for 24 h in the roots and shoots of 25 days old nitrogen deprived two contrasting finger millet genotypes (GE-3885 and GE-1437) differing in grain protein content (13.76 and 6.15 %, respectively). Time kinetics experiment revealed that, all the five genes except EcHNRT2 in the leaves of GE-3885 were induced within 30 min of nitrate exposure indicating that there might be a greater nitrogen deficit in leaves and therefore quick transportation of nitrate signals to the leaves. Exposing the plants to increasing nitrate concentrations for 2 h showed that in roots of GE-3885, NR was strongly induced while GS was repressed; however, the pattern was found to be reversed in leaves of GE-1437 indicating that in GE-3885, most of the nitrate might be reduced in the roots but assimilated in leaves and vice-versa. Furthermore, compared with the low-protein genotype, expression of HNRT2 was strongly induced in both roots and shoots of high-protein genotype at the least nitrate concentration supplied. This further indicates that GE-3885 is a quick sensor of nitrogen compared with the low-protein genotype. Furthermore, expression of EcDof1 was also found to overlap the expression of NR, GS, and GOGAT indicating that Dof1 probably regulates the expression of these genes under different conditions by sensing the nitrogen fluctuations around the root zone.
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23
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Betti M, García-Calderón M, Pérez-Delgado CM, Credali A, Estivill G, Galván F, Vega JM, Márquez AJ. Glutamine synthetase in legumes: recent advances in enzyme structure and functional genomics. Int J Mol Sci 2012; 13:7994-8024. [PMID: 22942686 PMCID: PMC3430217 DOI: 10.3390/ijms13077994] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 01/12/2023] Open
Abstract
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N(2) fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism.
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Affiliation(s)
- Marco Betti
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-95-4556917; Fax: +34-95-4626853
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24
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Shinmura K, Muraki N, Yoshida A, Hase T, Kurisu G. Crystallization and preliminary X-ray studies of an electron-transfer complex of ferredoxin and ferredoxin-dependent glutamate synthase from the cyanobacterium Leptolyngbya boryana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:324-7. [PMID: 22442234 PMCID: PMC3310542 DOI: 10.1107/s1744309112003387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 11/11/2022]
Abstract
Ferredoxin (Fd) dependent glutamate synthase (Fd-GOGAT) is a key enzyme involved in nitrogen assimilation that catalyzes the two-electron reductive conversion of Gln and 2-oxoglutarate to two molecules of Glu. Fd serves as an electron donor for Fd-GOGAT and the two proteins form a transient electron-transfer complex. In this study, these two proteins were cocrystallized using the hanging-drop vapour-diffusion method. Diffraction data were collected and processed at 2.65 Å resolution. The crystals belonged to space group P4(3), with unit-cell parameters a = b = 84.95, c = 476.31 Å.
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Affiliation(s)
- Kanako Shinmura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norifumi Muraki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ayako Yoshida
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiharu Hase
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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25
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Meguro M, Ito H, Takabayashi A, Tanaka R, Tanaka A. Identification of the 7-hydroxymethyl chlorophyll a reductase of the chlorophyll cycle in Arabidopsis. THE PLANT CELL 2011; 23:3442-53. [PMID: 21934147 PMCID: PMC3203437 DOI: 10.1105/tpc.111.089714] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/23/2011] [Accepted: 09/02/2011] [Indexed: 05/18/2023]
Abstract
The interconversion of chlorophyll a and chlorophyll b, referred to as the chlorophyll cycle, plays a crucial role in the processes of greening, acclimation to light intensity, and senescence. The chlorophyll cycle consists of three reactions: the conversions of chlorophyll a to chlorophyll b by chlorophyllide a oxygenase, chlorophyll b to 7-hydroxymethyl chlorophyll a by chlorophyll b reductase, and 7-hydroxymethyl chlorophyll a to chlorophyll a by 7-hydroxymethyl chlorophyll a reductase. We identified 7-hydroxymethyl chlorophyll a reductase, which is the last remaining unidentified enzyme of the chlorophyll cycle, from Arabidopsis thaliana by genetic and biochemical methods. Recombinant 7-hydroxymethyl chlorophyll a reductase converted 7-hydroxymethyl chlorophyll a to chlorophyll a using ferredoxin. Both sequence and biochemical analyses showed that 7-hydroxymethyl chlorophyll a reductase contains flavin adenine dinucleotide and an iron-sulfur center. In addition, a phylogenetic analysis elucidated the evolution of 7-hydroxymethyl chlorophyll a reductase from divinyl chlorophyllide vinyl reductase. A mutant lacking 7-hydroxymethyl chlorophyll a reductase was found to accumulate 7-hydroxymethyl chlorophyll a and pheophorbide a. Furthermore, this accumulation of pheophorbide a in the mutant was rescued by the inactivation of the chlorophyll b reductase gene. The downregulation of pheophorbide a oxygenase activity is discussed in relation to 7-hydroxymethyl chlorophyll a accumulation.
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Affiliation(s)
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
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Macheroux P, Kappes B, Ealick SE. Flavogenomics--a genomic and structural view of flavin-dependent proteins. FEBS J 2011; 278:2625-34. [PMID: 21635694 DOI: 10.1111/j.1742-4658.2011.08202.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Riboflavin (vitamin B(2)) serves as the precursor for FMN and FAD in almost all organisms that utilize the redox-active isoalloxazine ring system as a coenzyme in enzymatic reactions. The role of flavin, however, is not limited to redox processes, as ∼ 10% of flavin-dependent enzymes catalyze nonredox reactions. Moreover, the flavin cofactor is also widely used as a signaling and sensing molecule in biological processes such as phototropism and nitrogen fixation. Here, we present a study of 374 flavin-dependent proteins analyzed with regard to their function, structure and distribution among 22 archaeal, eubacterial, protozoan and eukaryotic genomes. More than 90% of flavin-dependent enzymes are oxidoreductases, and the remaining enzymes are classified as transferases (4.3%), lyases (2.9%), isomerases (1.4%) and ligases (0.4%). The majority of enzymes utilize FAD (75%) rather than FMN (25%), and bind the cofactor noncovalently (90%). High-resolution structures are available for about half of the flavoproteins. FAD-containing proteins predominantly bind the cofactor in a Rossmann fold (∼ 50%), whereas FMN-containing proteins preferably adopt a (βα)(8)-(TIM)-barrel-like or flavodoxin-like fold. The number of genes encoding flavin-dependent proteins varies greatly in the genomes analyzed, and covers a range from ∼ 0.1% to 3.5% of the predicted genes. It appears that some species depend heavily on flavin-dependent oxidoreductases for degradation or biosynthesis, whereas others have minimized their flavoprotein arsenal. An understanding of 'flavin-intensive' lifestyles, such as in the human pathogen Mycobacterium tuberculosis, may result in valuable new intervention strategies that target either riboflavin biosynthesis or uptake.
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Affiliation(s)
- Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria.
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Masclaux-Daubresse C, Daniel-Vedele F, Dechorgnat J, Chardon F, Gaufichon L, Suzuki A. Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture. ANNALS OF BOTANY 2010; 105:1141-57. [PMID: 20299346 PMCID: PMC2887065 DOI: 10.1093/aob/mcq028] [Citation(s) in RCA: 675] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/13/2009] [Accepted: 12/17/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Productive agriculture needs a large amount of expensive nitrogenous fertilizers. Improving nitrogen use efficiency (NUE) of crop plants is thus of key importance. NUE definitions differ depending on whether plants are cultivated to produce biomass or grain yields. However, for most plant species, NUE mainly depends on how plants extract inorganic nitrogen from the soil, assimilate nitrate and ammonium, and recycle organic nitrogen. Efforts have been made to study the genetic basis as well as the biochemical and enzymatic mechanisms involved in nitrogen uptake, assimilation, and remobilization in crops and model plants. The detection of the limiting factors that could be manipulated to increase NUE is the major goal of such research. SCOPE An overall examination of the physiological, metabolic, and genetic aspects of nitrogen uptake, assimilation and remobilization is presented in this review. The enzymes and regulatory processes manipulated to improve NUE components are presented. Results obtained from natural variation and quantitative trait loci studies are also discussed. CONCLUSIONS This review presents the complexity of NUE and supports the idea that the integration of the numerous data coming from transcriptome studies, functional genomics, quantitative genetics, ecophysiology and soil science into explanatory models of whole-plant behaviour will be promising.
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Nedelcu AM, Blakney AJC, Logue KD. Functional replacement of a primary metabolic pathway via multiple independent eukaryote-to-eukaryote gene transfers and selective retention. J Evol Biol 2009; 22:1882-94. [PMID: 19619164 DOI: 10.1111/j.1420-9101.2009.01797.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although lateral gene transfer (LGT) is now recognized as a major force in the evolution of prokaryotes, the contribution of LGT to the evolution and diversification of eukaryotes is less understood. Notably, transfers of complete pathways are believed to be less likely between eukaryotes, because the successful transfer of a pathway requires the physical clustering of functionally related genes. Here, we report that in one of the closest unicellular relatives of animals, the choanoflagellate, Monosiga, three genes whose products work together in the glutamate synthase cycle are of algal origin. The concerted retention of these three independently acquired genes is best explained as the consequence of a series of adaptive replacement events. More generally, this study argues that (i) eukaryote-to-eukaryote transfers of entire metabolic pathways are possible, (ii) adaptive functional replacements of primary pathways can occur, and (iii) functional replacements involving eukaryotic genes are likely to have also contributed to the evolution of eukaryotes. Lastly, these data underscore the potential contribution of algal genes to the evolution of nonphotosynthetic lineages.
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Affiliation(s)
- A M Nedelcu
- Biology Department, University of New Brunswick, Fredericton, NB, Canada.
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29
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Glass JB, Wolfe-Simon F, Anbar AD. Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae. GEOBIOLOGY 2009; 7:100-23. [PMID: 19320747 DOI: 10.1111/j.1472-4669.2009.00190.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Marine primary producers adapted over eons to the changing chemistry of the oceans. Because a number of metalloenzymes are necessary for N assimilation, changes in the availability of transition metals posed a particular challenge to the supply of this critical nutrient that regulates marine biomass and productivity. Integrating recently developed geochemical, biochemical, and genetic evidence, we infer that the use of metals in N assimilation - particularly Fe and Mo - can be understood in terms of the history of metal availability through time. Anoxic, Fe-rich Archean oceans were conducive to the evolution of Fe-using enzymes that assimilate abiogenic NH(4)(+) and NO(2)(-). The N demands of an expanding biosphere were satisfied by the evolution of biological N(2) fixation, possibly utilizing only Fe. Trace O(2) in late Archean environments, and the eventual 'Great Oxidation Event' c. 2.3 Ga, mobilized metals such as Mo, enabling the evolution of Mo (or V)-based N(2) fixation and the Mo-dependent enzymes for NO(3)(-) assimilation and denitrification by prokaryotes. However, the subsequent onset of deep-sea euxinia, an increasingly-accepted idea, may have kept ocean Mo inventories low and depressed Fe, limiting the rate of N(2) fixation and the supply of fixed N. Eukaryotic ecosystems may have been particularly disadvantaged by N scarcity and the high Mo requirement of eukaryotic NO(3)(-) assimilation. Thorough ocean oxygenation in the Neoproterozoic led to Mo-rich oceans, possibly contributing to the proliferation of eukaryotes and thus the Cambrian explosion of metazoan life. These ideas can be tested by more intensive study of the metal requirements in N assimilation and the biological strategies for metal uptake, regulation, and storage.
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Affiliation(s)
- J B Glass
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA.
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Vanoni MA, Curti B. Structure-function studies of glutamate synthases: a class of self-regulated iron-sulfur flavoenzymes essential for nitrogen assimilation. IUBMB Life 2008; 60:287-300. [PMID: 18421771 DOI: 10.1002/iub.52] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Glutamate synthases play with glutamine synthetase an essential role in nitrogen assimilation processes in microorganisms, plants, and lower animals by catalyzing the net synthesis of one molecule of L-glutamate from L-glutamine and 2-oxoglutarate. They exhibit a modular architecture with a common subunit or region, which is responsible for the L-glutamine-dependent glutamate synthesis from 2-oxoglutarate. Here, a PurF- (Type II- or Ntn-) type amidotransferase domain is coupled to the synthase domain, a (beta/alpha)8 barrel containing FMN and one [3Fe-4S]0,+1 cluster, through a approximately 30 angstroms-long intramolecular tunnel for the transfer of ammonia between the sites. In bacterial and eukaryotic GltS, reducing equivalents are provided by reduced pyridine nucleotides thanks to the stable association with a second subunit or region, which acts as a FAD-dependent NAD(P)H oxidoreductase and is responsible for the formation of the two low potential [4Fe-4S]+1,+2 clusters of the enzyme. In photosynthetic cells, reduced ferredoxin is the physiological reductant. This review focus on the mechanism of cross-activation of the synthase and glutaminase reactions in response to the bound substrates and the redox state of the enzyme cofactors, as well as on recent information on the structure of the alphabeta protomer of the NADPH-dependent enzyme, which sheds light on the intramolecular electron transfer pathway between the flavin cofactors.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, Milano, Italy.
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Lintner RE, Mishra PK, Srivastava P, Martinez-Vaz BM, Khodursky AB, Blumenthal RM. Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio. BMC Microbiol 2008; 8:60. [PMID: 18405378 PMCID: PMC2374795 DOI: 10.1186/1471-2180-8-60] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 04/11/2008] [Indexed: 02/03/2023] Open
Abstract
Background Bacterial genome sequences are being determined rapidly, but few species are physiologically well characterized. Predicting regulation from genome sequences usually involves extrapolation from better-studied bacteria, using the hypothesis that a conserved regulator, conserved target gene, and predicted regulator-binding site in the target promoter imply conserved regulation between the two species. However many compared organisms are ecologically and physiologically diverse, and the limits of extrapolation have not been well tested. In E. coli K-12 the leucine-responsive regulatory protein (Lrp) affects expression of ~400 genes. Proteus mirabilis and Vibrio cholerae have highly-conserved lrp orthologs (98% and 92% identity to E. coli lrp). The functional equivalence of Lrp from these related species was assessed. Results Heterologous Lrp regulated gltB, livK and lrp transcriptional fusions in an E. coli background in the same general way as the native Lrp, though with significant differences in extent. Microarray analysis of these strains revealed that the heterologous Lrp proteins significantly influence only about half of the genes affected by native Lrp. In P. mirabilis, heterologous Lrp restored swarming, though with some pattern differences. P. mirabilis produced substantially more Lrp than E. coli or V. cholerae under some conditions. Lrp regulation of target gene orthologs differed among the three native hosts. Strikingly, while Lrp negatively regulates its own gene in E. coli, and was shown to do so even more strongly in P. mirabilis, Lrp appears to activate its own gene in V. cholerae. Conclusion The overall similarity of regulatory effects of the Lrp orthologs supports the use of extrapolation between related strains for general purposes. However this study also revealed intrinsic differences even between orthologous regulators sharing >90% overall identity, and 100% identity for the DNA-binding helix-turn-helix motif, as well as differences in the amounts of those regulators. These results suggest that predicting regulation of specific target genes based on genome sequence comparisons alone should be done on a conservative basis.
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Affiliation(s)
- Robert E Lintner
- Department of Medical Microbiology and Immunology, University of Toledo Health Sciences Center, Toledo, OH 43614-2598, USA.
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Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol 2008; 74:3559-72. [PMID: 18390676 DOI: 10.1128/aem.02722-07] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.
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Kameya M, Ikeda T, Nakamura M, Arai H, Ishii M, Igarashi Y. A novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium Hydrogenobacter thermophilus TK-6. J Bacteriol 2007; 189:2805-12. [PMID: 17237175 PMCID: PMC1855818 DOI: 10.1128/jb.01360-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glutamate synthases are classified according to their specificities for electron donors. Ferredoxin-dependent glutamate synthases had been found only in plants and cyanobacteria, whereas many bacteria have NADPH-dependent glutamate synthases. In this study, Hydrogenobacter thermophilus, a hydrogen-oxidizing chemoautotrophic bacterium, was shown to possess a ferredoxin-dependent glutamate synthase like those of phototrophs. This is the first observation, to our knowledge, of a ferredoxin-dependent glutamate synthase in a nonphotosynthetic organism. The purified enzyme from H. thermophilus was shown to be a monomer of a 168-kDa polypeptide homologous to ferredoxin-dependent glutamate synthases from phototrophs. In contrast to known ferredoxin-dependent glutamate synthases, the H. thermophilus glutamate synthase exhibited glutaminase activity. Furthermore, this glutamate synthase did not react with a plant-type ferredoxin (Fd3 from this bacterium) containing a [2Fe-2S] cluster but did react with bacterial ferredoxins (Fd1 and Fd2 from this bacterium) containing [4Fe-4S] clusters. Interestingly, the H. thermophilus glutamate synthase was activated by some of the organic acids in the reductive tricarboxylic acid cycle, the central carbon metabolic pathway of this organism. This type of activation has not been reported for any other glutamate synthases, and this property may enable the control of nitrogen assimilation by carbon metabolism.
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Affiliation(s)
- Masafumi Kameya
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Agnelli P, Dossena L, Colombi P, Mulazzi S, Morandi P, Tedeschi G, Negri A, Curti B, Vanoni MA. The unexpected structural role of glutamate synthase [4Fe-4S](+1,+2) clusters as demonstrated by site-directed mutagenesis of conserved C residues at the N-terminus of the enzyme beta subunit. Arch Biochem Biophys 2005; 436:355-66. [PMID: 15797248 DOI: 10.1016/j.abb.2005.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2005] [Revised: 02/02/2005] [Indexed: 12/19/2022]
Abstract
Azospirillum brasilense glutamate synthase (GltS) is a complex iron-sulfur flavoprotein whose catalytically active alphabeta protomer (alpha subunit, 162kDa; beta subunit, 52.3 kDa) contains one FAD, one FMN, one [3Fe-4S](0,+1), and two [4Fe-4S](+1,+2) clusters. The structure of the alpha subunit has been determined providing information on the mechanism of ammonia transfer from L-glutamine to 2-oxoglutarate through a 30 A-long intramolecular tunnel. On the contrary, details of the electron transfer pathway from NADPH to the postulated 2-iminoglutarate intermediate through the enzyme flavin co-factors and [Fe-S] clusters are largely indirect. To identify the location and role of each one of the GltS [4Fe-4S] clusters, we individually substituted the four cysteinyl residues forming the first of two conserved C-rich regions at the N-terminus of GltS beta subunit with alanyl residues. The engineered genes encoding the beta subunit variants (and derivatives carrying C-terminal His6-tags) were co-expressed with the wild-type alpha subunit gene. In all cases the C/A substitutions prevented alpha and beta subunits association to yield the GltS alphabeta protomer. This result is consistent with the fact that these residues are responsible for the formation of glutamate synthase [4Fe-4S](+1,+2) clusters within the N-terminal region of the beta subunit, and that these clusters are implicated not only in electron transfer between the GltS flavins, but also in alphabeta heterodimer formation by structuring an N-terminal [Fe-S] beta subunit interface subdomain, as suggested by the three-dimensional structure of dihydropyrimidine dehydrogenase, an enzyme containing an N-terminal beta subunit-like domain.
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Affiliation(s)
- Paola Agnelli
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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Suzuki A, Knaff DB. Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism. PHOTOSYNTHESIS RESEARCH 2005; 83:191-217. [PMID: 16143852 DOI: 10.1007/s11120-004-3478-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Accepted: 09/20/2004] [Indexed: 05/03/2023]
Abstract
Ammonium ion assimilation constitutes a central metabolic pathway in many organisms, and glutamate synthase, in concert with glutamine synthetase (GS, EC 6.3.1.2), plays the primary role of ammonium ion incorporation into glutamine and glutamate. Glutamate synthase occurs in three forms that can be distinguished based on whether they use NADPH (NADPH-GOGAT, EC 1.4.1.13), NADH (NADH-GOGAT, EC 1.4.1.14) or reduced ferredoxin (Fd-GOGAT, EC 1.4.7.1) as the electron donor for the (two-electron) conversion of L-glutamine plus 2-oxoglutarate to L-glutamate. The distribution of these three forms of glutamate synthase in different tissues is quite specific to the organism in question. Gene structures have been determined for Fd-, NADH- and NADPH-dependent glutamate synthases from different organisms, as shown by searches in nucleic acid sequence data banks. Fd-glutamate synthase contains two electron-carrying prosthetic groups, the redox properties of which are discussed. A description of the ferredoxin binding by Fd-glutamate synthase is also presented. In plants, including nitrogen-fixing legumes, Fd-glutamate synthase and NADH-glutamate synthase supply glutamate during the nitrogen assimilation and translocation. The biological functions of Fd-glutamate synthase and NADH-glutamate synthase, which show a highly tissue-specific distribution pattern, are tightly related to the regulation by the light and metabolite sensing systems. Analysis of mutants and transgenic studies have provided insights into the primary individual functions of Fd-glutamate synthase and NADH-glutamate synthase. These studies also provided evidence that glutamate dehydrogenase (NADH-GDH, EC 1.4.1.2) does not represent a significant alternate route for glutamate formation in plants. Taken together, biochemical analysis and genetic and molecular data imply that Fd-glutamate synthase incorporates photorespiratory and non-photorespiratory ammonium and provides nitrogen for transport to maintain nitrogen status in plants. Fd-glutamate synthase also plays a role that is redundant, in several important aspects, to that played by NADH-glutamate synthase in ammonium assimilation and nitrogen transport.
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Affiliation(s)
- Akira Suzuki
- Unité de Nutrition Azotée des Plantes, Institut National de la Recherche Agronomique, Route de Saint-Cyr, 78026 Versailles cedex, France.
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Coiro VM, Di Nola A, Vanoni MA, Aschi M, Coda A, Curti B, Roccatano D. Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates. Protein Sci 2004; 13:2979-91. [PMID: 15498940 PMCID: PMC2286594 DOI: 10.1110/ps.04863104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 08/04/2004] [Accepted: 08/04/2004] [Indexed: 10/26/2022]
Abstract
Glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive transfer of L-glutamine amide group to the C2 carbon of 2-oxoglutarate yielding two molecules of L-glutamate. Molecular dynamics calculations in explicit solvent were carried out to gain insight into the conformational flexibility of GltS and into the role played by the enzyme substrates in regulating the catalytic cycle. We have modelled the free (unliganded) form of Azospirillum brasilense GltS alpha subunit and the structure of the reduced enzyme in complex with the L-glutamine and 2-oxoglutarate substrates starting from the crystallographically determined coordinates of the GltS alpha subunit in complex with L-methionine sulphone and 2-oxoglutarate. The present 4-ns molecular dynamics calculations reveal that the GltS glutaminase site may exist in a catalytically inactive conformation unable to bind glutamine, and in a catalytically competent conformation, which is stabilized by the glutamine substrate. Substrates binding also induce (1) closure of the loop formed by residues 263-271 with partial shielding of the glutaminase site from solvent, and (2) widening of the ammonia tunnel entrance at the glutaminase end to allow for ammonia diffusion toward the synthase site. The Q-loop of glutamate synthase, which acts as an active site lid in other amidotransferases, seems to maintain an open conformation. Finally, binding of L-methionine sulfone, a glutamine analog that mimics the tetrahedral transient species occurring during its hydrolysis, causes a coordinated rigid-body motion of segments of the glutaminase domain that results in the inactive conformation observed in the crystal structure of GltS alpha subunit.
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Affiliation(s)
- Vincenza M Coiro
- Department of Chemistry, University of Rome La Sapienza, Piazzale Aldo Moro 5, Rome 00185, Italy.
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