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Harland JB, Samanta S, Lehnert N. Bacterial nitric oxide reductase (NorBC) models employing click chemistry. J Inorg Biochem 2023; 246:112280. [PMID: 37352656 DOI: 10.1016/j.jinorgbio.2023.112280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
Bacterial NO Reductase (NorBC or cNOR) is a membrane-bound enzyme found in denitrifying bacteria that catalyzes the two-electron reduction of NO to N2O and water. The mechanism by which NorBC operates is highly debated, due to the fact that this enzyme is difficult to work with, and no intermediates of the NO reduction reaction could have been identified so far. The unique active site of NorBC consists of a heme b3/non-heme FeB diiron center. Synthetic model complexes provide the opportunity to obtain insight into possible mechanistic alternatives for this enzyme. In this paper, we present three new synthetic model systems for NorBC, consisting of a tetraphenylporphyrin-derivative clicked to modified BMPA-based ligands (BMPA = bis(methylpyridyl)amine) that model the non-heme site in the enzyme. These complexes have been characterized by EPR, IR and UV-Vis spectroscopy. The reactivity with NO was then investigated, and it was found that the complex with the BMPA-carboxylate ligand as the non-heme component has a very low affinity for NO at the non-heme iron site. If the carboxylate functional group is replaced with a phenolate or pyridine group, reactivity is restored and formation of a diiron dinitrosyl complex was observed. Upon one-electron reduction of the nitrosylated complexes, following the semireduced pathway for NO reduction, formation of dinitrosyl iron complexes (DNICs) was observed in all three cases, but no N2O could be detected.
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Affiliation(s)
- Jill B Harland
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Subhra Samanta
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States.
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2
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Merakeb L, Bennaamane S, De Freitas J, Clot E, Mézailles N, Robert M. Molecular Electrochemical Reductive Splitting of Dinitrogen with a Molybdenum Complex. Angew Chem Int Ed Engl 2022; 61:e202209899. [PMID: 35941077 PMCID: PMC9804441 DOI: 10.1002/anie.202209899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 01/05/2023]
Abstract
Nitrogen reduction under mild conditions (room T and atmospheric P), using a non-fossil source of hydrogen remains a challenge. Molecular metal complexes, notably Mo based, have recently been shown to be active for such nitrogen fixation. We report electrochemical N2 splitting with a MoIII triphosphino complex [(PPP)MoI3 ], at room temperature and a moderately negative potential. A MoIV nitride species was generated, which is confirmed by electrochemistry and NMR studies. The reaction goes through two successive one electron reductions of the starting Mo species, coordination of a N2 molecule, and further splitting to a MoIV nitride complex. Preliminary DFT studies support the formation of a bridging MoI N2 MoI dinitrogen dimer evolving to the Mo nitride via a low energy transition state. This example joins a short list of molecular complexes for N2 electrochemical reductive cleavage. It opens a door to electrochemical proton-coupled electron transfer (PCET) conversion studies of N2 to NH3 .
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Affiliation(s)
- Lydia Merakeb
- Laboratoire d'Electrochimie Moléculaire—UMR 7591Université Paris Cité15, rue Jean Antoine de Baïf75013ParisFrance
| | - Soukaina Bennaamane
- Laboratoire Hétérochimie Fondamentale et Appliquée—UMR 5069Université Toulouse III—Paul Sabatier118, route de Narbonne, Bât 2R131062ToulouseFrance
| | - Jérémy De Freitas
- Laboratoire d'Electrochimie Moléculaire—UMR 7591Université Paris Cité15, rue Jean Antoine de Baïf75013ParisFrance
| | - Eric Clot
- ICGMUniv MontpellierCNRSENSCM34000MontpellierFrance
| | - Nicolas Mézailles
- Laboratoire Hétérochimie Fondamentale et Appliquée—UMR 5069Université Toulouse III—Paul Sabatier118, route de Narbonne, Bât 2R131062ToulouseFrance
| | - Marc Robert
- Laboratoire d'Electrochimie Moléculaire—UMR 7591Université Paris Cité15, rue Jean Antoine de Baïf75013ParisFrance
- Institut Universitaire de France (IUF)75005ParisFrance
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3
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Venturin B, Rodrigues HC, Bonassa G, Hollas CE, Bolsan AC, Antes FG, De Prá MC, Fongaro G, Treichel H, Kunz A. Key enzymes involved in anammox-based processes for wastewater treatment: An applied overview. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10780. [PMID: 36058650 DOI: 10.1002/wer.10780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The anaerobic ammonium oxidation (anammox) process has attracted significant attention as an economic, robustness, and sustainable method for the treatment of nitrogen (N)-rich wastewater. Anammox bacteria (AnAOB) coexist with other microorganisms, and particularly with ammonia-oxidizing bacteria (AOB) and/or heterotrophic bacteria (HB), in symbiosis in favor of the substrate requirement (ammonium and nitrite) of the AnAOB being supplied by these other organisms. The dynamics of these microbial communities have a significant effect on the N-removal performance, but the corresponding metabolic pathways are still not fully understood. These processes involve many common metabolites that may act as key factors to control the symbiotic interactions between these organisms, to maximize N-removal efficiency from wastewater. Therefore, this work overviews the current state of knowledge about the metabolism of these microorganisms including key enzymes and intermediate metabolites and summarizes already reported experiences based on the employment of certain metabolites for the improvement of N-removal using anammox-based processes. PRACTITIONER POINTS: Approaches knowledge about the biochemistry and metabolic pathways involved in anammox-based processes. Some molecular tools can be used to determine enzymatic activity, serving as an optimization in nitrogen removal processes. Enzymatic evaluation allied to the physical-chemical and biomolecular analysis of the nitrogen removal processes expands the application in different effluents.
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Affiliation(s)
- Bruno Venturin
- Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
| | | | - Gabriela Bonassa
- Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
| | | | | | | | | | - Gislaine Fongaro
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Helen Treichel
- Universidade Federal da Fronteira Sul, Erechim, Rio Grande do Sul, Brazil
| | - Airton Kunz
- Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- Universidade Federal da Fronteira Sul, Erechim, Rio Grande do Sul, Brazil
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4
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Merakeb L, Bennaamane S, De Freitas J, Clot E, Mézailles N, Robert M. Molecular Electrochemical Reductive Splitting of Dinitrogen with a Molybdenum Complex. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - Eric Clot
- Université Montpellier 1: Universite de Montpellier Chemistry FRANCE
| | | | - Marc Robert
- Universite Paris Cité - Laboraoire Electrochimie Moleculaire - UMR CNRS 7591 Chemistry Department 15 rue Jean de Baif 75013 Paris FRANCE
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5
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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6
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Wang YY, Ding XL, Gurti JI, Chen Y, Huang XQ, Li W, Wang X. Facile N≡N Bond Cleavage by Anionic Trimetallic Clusters V 3-x Ta x C 4 - (x=0-3): A DFT Study. Chemphyschem 2021; 23:e202100771. [PMID: 34821022 DOI: 10.1002/cphc.202100771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Indexed: 11/08/2022]
Abstract
Activation of N2 on anionic trimetallic V3-x Tax C4 - (x=0-3) clusters was theoretically studied employing density functional theory. For all studied clusters, initial adsorption of N2 (end-on) on one of the metal atoms (denoted as Site 1) is transferred to an of end-on: side-on: side-on coordination on three metal atoms, prior to N2 dissociation. The whole reaction is exothermic and has no global energy barriers, indicating that the dissociation of N2 is facile under mild conditions. The reaction process can be divided into two processes: N2 transfer (TRF) and N-N dissociation (DIS). For V-series clusters, which has a V atom on Site 1, the rate-determining step is DIS, while for Ta-series clusters with a Ta on Site 1, TRF may be the rate-determining step or has energy barriers similar to those of DIS. The overall energy barriers for heteronuclear V2 TaC4 - and VTa2 C4 - clusters are lower than those for homonuclear V3 C4 - and Ta3 C4 - , showing that the doping effect is beneficial for the activation and dissociation of N2 . In particular, V-Ta2 C4 - has low energy barriers in both TRF and DIS, and it has the highest N2 adsorption energy and a high reaction heat release. Therefore, a trimetallic heteronuclear V-series cluster, V-Ta2 C4 - , is suggested to have high reactivity to N2 activation, and may serve as a prototype for designing related catalysts at a molecular level.
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Affiliation(s)
- Ya-Ya Wang
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,School of New Energy, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
| | - Xun-Lei Ding
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
| | - Joseph Israel Gurti
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
| | - Yan Chen
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,School of New Energy, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
| | - Xue-Qian Huang
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
| | - Wei Li
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
| | - Xin Wang
- School of Mathematics and Physics, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China.,Institute of Clusters and Low Dimensional Nanomaterials, North China Electric Power University, Beinong Road 2, Huilongguan, Beijing, 102206, P. R. China
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7
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Choi H, Yi T, Ha SH. Diversity of Plastid Types and Their Interconversions. FRONTIERS IN PLANT SCIENCE 2021; 12:692024. [PMID: 34220916 PMCID: PMC8248682 DOI: 10.3389/fpls.2021.692024] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/24/2021] [Indexed: 05/03/2023]
Abstract
Plastids are pivotal subcellular organelles that have evolved to perform specialized functions in plant cells, including photosynthesis and the production and storage of metabolites. They come in a variety of forms with different characteristics, enabling them to function in a diverse array of organ/tissue/cell-specific developmental processes and with a variety of environmental signals. Here, we have comprehensively reviewed the distinctive roles of plastids and their transition statuses, according to their features. Furthermore, the most recent understanding of their regulatory mechanisms is highlighted at both transcriptional and post-translational levels, with a focus on the greening and non-greening phenotypes.
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Affiliation(s)
| | | | - Sun-Hwa Ha
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
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8
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Zakaria NN, Gomez-Fuentes C, Abdul Khalil K, Convey P, Roslee AFA, Zulkharnain A, Sabri S, Shaharuddin NA, Cárdenas L, Ahmad SA. Statistical Optimisation of Diesel Biodegradation at Low Temperatures by an Antarctic Marine Bacterial Consortium Isolated from Non-Contaminated Seawater. Microorganisms 2021; 9:microorganisms9061213. [PMID: 34205164 PMCID: PMC8227063 DOI: 10.3390/microorganisms9061213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
Hydrocarbon pollution is widespread around the globe and, even in the remoteness of Antarctica, the impacts of hydrocarbons from anthropogenic sources are still apparent. Antarctica’s chronically cold temperatures and other extreme environmental conditions reduce the rates of biological processes, including the biodegradation of pollutants. However, the native Antarctic microbial diversity provides a reservoir of cold-adapted microorganisms, some of which have the potential for biodegradation. This study evaluated the diesel hydrocarbon-degrading ability of a psychrotolerant marine bacterial consortium obtained from the coast of the north-west Antarctic Peninsula. The consortium’s growth conditions were optimised using one-factor-at-a-time (OFAT) and statistical response surface methodology (RSM), which identified optimal growth conditions of pH 8.0, 10 °C, 25 ppt NaCl and 1.5 g/L NH4NO3. The predicted model was highly significant and confirmed that the parameters’ salinity, temperature, nitrogen concentration and initial diesel concentration significantly influenced diesel biodegradation. Using the optimised values generated by RSM, a mass reduction of 12.23 mg/mL from the initial 30.518 mg/mL (4% (w/v)) concentration of diesel was achieved within a 6 d incubation period. This study provides further evidence for the presence of native hydrocarbon-degrading bacteria in non-contaminated Antarctic seawater.
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Affiliation(s)
- Nur Nadhirah Zakaria
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (A.F.A.R.); (N.A.S.)
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes, Punta Arenas 01855, Región de Magallanes y Antártica Chilena, Chile;
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas 01855, Región de Magallanes y Antártica Chilena, Chile
| | - Khalilah Abdul Khalil
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam 40450, Selangor, Malaysia;
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK;
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Ahmad Fareez Ahmad Roslee
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (A.F.A.R.); (N.A.S.)
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minumaku, Saitama 337-8570, Japan;
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (A.F.A.R.); (N.A.S.)
| | - Leyla Cárdenas
- Centro Fondap Ideal, Insituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile;
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (N.N.Z.); (A.F.A.R.); (N.A.S.)
- Center for Research and Antarctic Environmental Monitoring (CIMAA), Universidad de Magallanes, Avda. Bulnes, Punta Arenas 01855, Región de Magallanes y Antártica Chilena, Chile
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence:
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9
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Li P, Gao S, Liu Q, Ding P, Wu Y, Wang C, Yu S, Liu W, Wang Q, Chen S. Recent Progress of the Design and Engineering of Bismuth Oxyhalides for Photocatalytic Nitrogen Fixation. ADVANCED ENERGY AND SUSTAINABILITY RESEARCH 2021. [DOI: 10.1002/aesr.202000097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peishen Li
- Laboratory for Micro-sized Functional Materials College of Elementary Education Department of Chemistry Capital Normal University Beijing 100048 China
- Beijing Innovation Center for Engineering Science and Advanced Technology (BIC-ESAT) Key Laboratory of Water and Sediment Sciences (Ministry of Education) College of Environmental Sciences and Engineering Peking University Beijing 100871 China
| | - Shuai Gao
- Laboratory for Micro-sized Functional Materials College of Elementary Education Department of Chemistry Capital Normal University Beijing 100048 China
| | - Qiming Liu
- Department of Chemistry and Biochemistry University of California 1156 High Street Santa Cruz CA 95064 USA
| | - Peiren Ding
- Laboratory for Micro-sized Functional Materials College of Elementary Education Department of Chemistry Capital Normal University Beijing 100048 China
| | - Yunyun Wu
- Laboratory for Micro-sized Functional Materials College of Elementary Education Department of Chemistry Capital Normal University Beijing 100048 China
| | - Changzheng Wang
- Beijing Key Laboratory of Functional Materials for Building Structure and Environmental Remediation Beijing University of Civil Engineering and Architecture Beijing 100044 China
| | - Shaobin Yu
- Beijing Key Laboratory of Functional Materials for Building Structure and Environmental Remediation Beijing University of Civil Engineering and Architecture Beijing 100044 China
| | - Wen Liu
- Beijing Innovation Center for Engineering Science and Advanced Technology (BIC-ESAT) Key Laboratory of Water and Sediment Sciences (Ministry of Education) College of Environmental Sciences and Engineering Peking University Beijing 100871 China
| | - Qiang Wang
- Laboratory for Micro-sized Functional Materials College of Elementary Education Department of Chemistry Capital Normal University Beijing 100048 China
| | - Shaowei Chen
- Department of Chemistry and Biochemistry University of California 1156 High Street Santa Cruz CA 95064 USA
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10
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Abstract
In this Viewpoint, we address some of the limitations within our current understanding of the complex chemistry of the enzymes used in the Nitrogen Cycle. Further understanding of these chemical processes will play a large role in limiting the anthropogenic effects on our environment.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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11
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Mechanical coupling in the nitrogenase complex. PLoS Comput Biol 2021; 17:e1008719. [PMID: 33661889 PMCID: PMC7963043 DOI: 10.1371/journal.pcbi.1008719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 03/16/2021] [Accepted: 01/18/2021] [Indexed: 11/19/2022] Open
Abstract
The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.
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12
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Chen P, Liu Y, Mo C, Jiang Z, Yang J, Lin J. Microbial mechanism of biochar addition on nitrogen leaching and retention in tea soils from different plantation ages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143817. [PMID: 33246734 DOI: 10.1016/j.scitotenv.2020.143817] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/01/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
The effect of biochar additions on N leaching and retention in tea soils and its microbial mechanism are still unclear. In this study, effects of biochar additions at rates of 0, 3% and 6% on N leaching, N retention and microbial responses in two tea soils with 20- and 60-year plantation ages were investigated under application with 15N-labeled urea. The results showed that cumulative mass of leached NH4+-N, NO3--N and TN was reduced by 20.9%-91.9%, 35.1%-66.9% and 40.0%-72.8% under biochar additions, respectively. The retention of TN in soil was increased by 1.2%-5.8% under biochar amendment. Fertilizer-N in the leachate was reduced by 28.8%-62.1%, while fertilizer-N retention in the soils was enhanced by 3.2%-23.9% with biochar application. Biochar addition of 6% showed the highest mitigation of N leaching and enhancement of TN retention across the two soils. Biochar additions increased soil microbial biomass and enzyme activities and changed the bacterial community composition, indicating that biochar addition increased the microbial N requirement, stimulated soil N cycling, including nitrification and denitrification processes, and enhanced microbial N immobilization in the tea soils. Those microbial responses to biochar addition were higher in 60-year-old soil relative to 20-year-old soil, leading to a higher enhancement of N retention and mitigation of N leaching. Soil pH was the prime factor that influenced soil microbes, and it strongly correlated with microbial biomass, enzyme activity, the relative abundance of dominant phyla and α-diversity indices. Therefore, the enhancement of microbial biomass, activity and shifts of bacterial community composition related to N cycling in response to biochar additions that increased the soil pH could be an important mechanism to better understand the biochar-induced N leaching mitigation and N retention enhancement in tea soils under different plantation ages.
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Affiliation(s)
- Pengfei Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yizhen Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chaoyang Mo
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Zhenhui Jiang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Jingping Yang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Jingdong Lin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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13
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Zhang S, Wang M, Jiang S, Wang H. The Activation and Reduction of N
2
by Single/Double‐Atom Electrocatalysts: A First‐Principle Study. ChemistrySelect 2021. [DOI: 10.1002/slct.202100057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shishi Zhang
- Institute for Advanced Study School of Materials Science and Engineering Nanchang University Xuefu Road 999 Nanchang City 330031 PR China
| | - Mingda Wang
- Institute for Advanced Study School of Materials Science and Engineering Nanchang University Xuefu Road 999 Nanchang City 330031 PR China
| | - Sheng Jiang
- Institute for Advanced Study School of Materials Science and Engineering Nanchang University Xuefu Road 999 Nanchang City 330031 PR China
| | - Hongming Wang
- Institute for Advanced Study School of Materials Science and Engineering Nanchang University Xuefu Road 999 Nanchang City 330031 PR China
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14
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Molybdenum-Containing Metalloenzymes and Synthetic Catalysts for Conversion of Small Molecules. Catalysts 2021. [DOI: 10.3390/catal11020217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The energy deficiency and environmental problems have motivated researchers to develop energy conversion systems into a sustainable pathway, and the development of catalysts holds the center of the research endeavors. Natural catalysts such as metalloenzymes have maintained energy cycles on Earth, thus proving themselves the optimal catalysts. In the previous research results, the structural and functional analogs of enzymes and nano-sized electrocatalysts have shown promising activities in energy conversion reactions. Mo ion plays essential roles in natural and artificial catalysts, and the unique electrochemical properties render its versatile utilization as an electrocatalyst. In this review paper, we show the current understandings of the Mo-enzyme active sites and the recent advances in the synthesis of Mo-catalysts aiming for high-performing catalysts.
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15
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Saha P, Amanullah S, Dey A. Electrocatalytic Reduction of Nitrogen to Hydrazine Using a Trinuclear Nickel Complex. J Am Chem Soc 2020; 142:17312-17317. [PMID: 33006899 DOI: 10.1021/jacs.0c08785] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Activation and reduction of N2 have been a major challenge to chemists and the focus since now has mostly been on the synthesis of NH3. Alternatively, reduction of N2 to hydrazine is desirable because hydrazine is an excellent energy vector that can release the stored energy very conveniently without the need for catalysts. To date, only one molecular catalyst has been reported to be able to reduce N2 to hydrazine chemically. A trinuclear T-shaped nickel thiolate molecular complex has been designed to activate dinitrogen. The electrochemically generated all Ni(I) state of this molecule can reduce N2 in the presence of PhOH as a proton donor. Hydrazine is detected as the only nitrogen-containing product of the reaction, along with gaseous H2. The complex reported here is selective for the 4e-/4H+ reduction of nitrogen to hydrazine with a minor overpotential of ∼300 mV.
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Affiliation(s)
- Paramita Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Sk Amanullah
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
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16
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Suga M, Shimada A, Akita F, Shen JR, Tosha T, Sugimoto H. Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA. Biochim Biophys Acta Gen Subj 2019; 1864:129466. [PMID: 31678142 DOI: 10.1016/j.bbagen.2019.129466] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach. SCOPE OF REVIEW Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described. MAJOR CONCLUSIONS XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data. GENERAL SIGNIFICANCE XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
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Affiliation(s)
- Michihiro Suga
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan..
| | - Atsuhiro Shimada
- Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan..
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Takehiko Tosha
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan..
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17
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Lydon BR, Lee CC, Tanifuji K, Sickerman NS, Newcomb MP, Hu Y, Ribbe MW, Yang JY. Electrochemical Characterization of Isolated Nitrogenase Cofactors from Azotobacter vinelandii. Chembiochem 2019; 21:1773-1778. [PMID: 31392810 DOI: 10.1002/cbic.201900425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Indexed: 11/09/2022]
Abstract
The nitrogenase cofactors are structurally and functionally unique in biological chemistry. Despite a substantial amount of spectroscopic characterization of protein-bound and isolated nitrogenase cofactors, electrochemical characterization of these cofactors and their related species is far from complete. Herein we present voltammetric studies of three isolated nitrogenase cofactor species: the iron-molybdenum cofactor (M-cluster), iron-vanadium cofactor (V-cluster), and a homologue to the iron-iron cofactor (L-cluster). We observe two reductive events in the redox profiles of all three cofactors. Of the three, the V-cluster is the most reducing. The reduction potentials of the isolated cofactors are significantly more negative than previously measured values within the molybdenum-iron and vanadium-iron proteins. The outcome of this study provides insight into the importance of the heterometal identity, the overall ligation of the cluster, and the impact of the protein scaffolds on the overall electronic structures of the cofactors.
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Affiliation(s)
- Brian R Lydon
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA, 92697, USA
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, 3205 McGaugh Hall, Irvine, CA, 92697, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, 3205 McGaugh Hall, Irvine, CA, 92697, USA
| | - Nathaniel S Sickerman
- Department of Molecular Biology and Biochemistry, University of California, 3205 McGaugh Hall, Irvine, CA, 92697, USA
| | - Megan P Newcomb
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA, 92697, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, 3205 McGaugh Hall, Irvine, CA, 92697, USA
| | - Markus W Ribbe
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, 3205 McGaugh Hall, Irvine, CA, 92697, USA
| | - Jenny Y Yang
- Department of Chemistry, University of California, 1102 Natural Sciences II, Irvine, CA, 92697, USA
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18
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Epp Schmidt DJ, Kotze DJ, Hornung E, Setälä H, Yesilonis I, Szlavecz K, Dombos M, Pouyat R, Cilliers S, Tóth Z, Yarwood S. Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use: N Catabolism, Methanogenesis, and Nutrient Acquisition. Front Microbiol 2019; 10:2330. [PMID: 31649656 PMCID: PMC6795690 DOI: 10.3389/fmicb.2019.02330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023] Open
Abstract
Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.
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Affiliation(s)
- Dietrich J. Epp Schmidt
- Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, United States
| | - David Johan Kotze
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Erzsébet Hornung
- Department of Ecology, University of Veterinary Science, Budapest, Hungary
| | - Heikki Setälä
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Ian Yesilonis
- Baltimore Ecosystem Study, USDA Forest Service, Baltimore, MD, United States
| | - Katalin Szlavecz
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Miklós Dombos
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Richard Pouyat
- Northern Research Station, University of Delaware, Newark, DE, United States
| | - Sarel Cilliers
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Zsolt Tóth
- Department of Ecology, University of Veterinary Science, Budapest, Hungary
| | - Stephanie Yarwood
- Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, United States
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19
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Lehnert N, Fujisawa K, Camarena S, Dong HT, White CJ. Activation of Non-Heme Iron-Nitrosyl Complexes: Turning Up the Heat. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kiyoshi Fujisawa
- Department of Chemistry, Ibaraki University, Mito 310-8512, Japan
| | - Stephanie Camarena
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Hai T. Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Corey J. White
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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20
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Campos PC, Gomes MTR, Marinho FAV, Guimarães ES, de Moura Lodi Cruz MGF, Oliveira SC. Brucella abortus nitric oxide metabolite regulates inflammasome activation and IL-1β secretion in murine macrophages. Eur J Immunol 2019; 49:1023-1037. [PMID: 30919410 DOI: 10.1002/eji.201848016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/20/2019] [Accepted: 03/25/2019] [Indexed: 11/07/2022]
Abstract
NLRP3 inflammasome is a protein complex crucial to caspase-1 activation and IL-1β and IL-18 maturation. This receptor participates in innate immune responses to different pathogens, including the bacteria of genus Brucella. Our group recently demonstrated that Brucella abortus-induced IL-1β secretion involves NLRP3 inflammasome and it is partially dependent on mitochondrial ROS production. However, other factors could be involved, such as P2X7-dependent potassium efflux, membrane destabilization, and cathepsin release. Moreover, there is increasing evidence that nitric oxide acts as a modulator of NLRP3 inflammasome. The aim of this study was to unravel the mechanism of NLRP3 inflammasome activation induced by B. abortus, as well as the involvement of bacterial nitric oxide (NO) as a modulator of this inflammasome pathway. We demonstrated that NO produced by B. abortus can be used by the bacteria to modulate IL-1β secretion in infected murine macrophages. Additionally, our results suggest that B. abortus-induced IL-1β secretion depends on a P2X7-independent potassium efflux, lysosomal acidification, cathepsin release, mechanisms clearly associated to NLRP3 inflammasome. In summary, our results help to elucidate the molecular mechanisms of NLRP3 activation and regulation during an intracellular bacterial infection.
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Affiliation(s)
- Priscila Carneiro Campos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marco Túlio Ribeiro Gomes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fábio Antônio Vitarelli Marinho
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Erika Sousa Guimarães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Sergio Costa Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais (INCT-DT), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Ministério de Ciência, Tecnologia e Inovação, Salvador, Bahia, Brazil
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21
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Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
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Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
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22
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McQuarters AB, Blaesi EJ, Kampf JW, Alp EE, Zhao J, Hu M, Krebs C, Lehnert N. Synthetic Model Complex of the Key Intermediate in Cytochrome P450 Nitric Oxide Reductase. Inorg Chem 2019; 58:1398-1413. [PMID: 30623648 DOI: 10.1021/acs.inorgchem.8b02947] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fungal denitrification plays a crucial role in the nitrogen cycle and contributes to the total N2O emission from agricultural soils. Here, cytochrome P450 NO reductase (P450nor) reduces two NO to N2O using a single heme site. Despite much research, the exact nature of the critical "Intermediate I" responsible for the key N-N coupling step in P450nor is unknown. This species likely corresponds to a Fe-NHOH-type intermediate with an unknown electronic structure. Here we report a new strategy to generate a model system for this intermediate, starting from the iron(III) methylhydroxylamide complex [Fe(3,5-Me-BAFP)(NHOMe)] (1), which was fully characterized by 1H NMR, UV-vis, electron paramagnetic resonance, and vibrational spectroscopy (rRaman and NRVS). Our data show that 1 is a high-spin ferric complex with an N-bound hydroxylamide ligand that is strongly coordinated (Fe-N distance, 1.918 Å; Fe-NHOMe stretch, 558 cm-1). Simple one-electron oxidation of 1 at -80 °C then cleanly generates the first model system for Intermediate I, [Fe(3,5-Me-BAFP)(NHOMe)]+ (1+). UV-vis, resonance Raman, and Mössbauer spectroscopies, in comparison to the chloro analogue [Fe(3,5-Me-BAFP)(Cl)]+, demonstrate that 1+ is best described as an FeIII-(NHOMe)• complex with a bound NHOMe radical. Further reactivity studies show that 1+ is highly reactive toward NO, a reaction that likely proceeds via N-N bond formation, following a radical-radical-type coupling mechanism. Our results therefore provide experimental evidence, for the first time, that an FeIII-(NHOMe)• electronic structure is indeed a reasonable electronic description for Intermediate I and that this electronic structure is advantageous for P450nor catalysis because it can greatly facilitate N-N bond formation and, ultimately, N2O generation.
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Affiliation(s)
- Ashley B McQuarters
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Elizabeth J Blaesi
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Jeff W Kampf
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - E Ercan Alp
- Advanced Photon Source (APS) , Argonne National Laboratory (ANL) , Argonne , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source (APS) , Argonne National Laboratory (ANL) , Argonne , Illinois 60439 , United States
| | - Michael Hu
- Advanced Photon Source (APS) , Argonne National Laboratory (ANL) , Argonne , Illinois 60439 , United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109 , United States
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23
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24
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Van Stappen C, Lehnert N. Mechanism of N–N Bond Formation by Transition Metal–Nitrosyl Complexes: Modeling Flavodiiron Nitric Oxide Reductases. Inorg Chem 2018; 57:4252-4269. [DOI: 10.1021/acs.inorgchem.7b02333] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Casey Van Stappen
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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25
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McQuarters AB, Kampf JW, Alp EE, Hu M, Zhao J, Lehnert N. Ferric Heme-Nitrosyl Complexes: Kinetically Robust or Unstable Intermediates? Inorg Chem 2017; 56:10513-10528. [PMID: 28825299 DOI: 10.1021/acs.inorgchem.7b01493] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have determined a convenient method for the bulk synthesis of high-purity ferric heme-nitrosyl complexes ({FeNO}6 in the Enemark-Feltham notation); this method is based on the chemical or electrochemical oxidation of corresponding {FeNO}7 precursors. We used this method to obtain the five- and six-coordinate complexes [Fe(TPP)(NO)]+ (TPP2- = tetraphenylporphyrin dianion) and [Fe(TPP)(NO)(MI)]+ (MI = 1-methylimidazole) and demonstrate that these complexes are stable in solution in the absence of excess NO gas. This is in stark contrast to the often-cited instability of such {FeNO}6 model complexes in the literature, which is likely due to the common presence of halide impurities (although other impurities could certainly also play a role). This is avoided in our approach for the synthesis of {FeNO}6 complexes via oxidation of pure {FeNO}7 precursors. On the basis of these results, {FeNO}6 complexes in proteins do not show an increased stability toward NO loss compared to model complexes. We also prepared the halide-coordinated complexes [Fe(TPP)(NO)(X)] (X = Cl-, Br-), which correspond to the elusive, key reactive intermediate in the so-called autoreduction reaction, which is frequently used to prepare {FeNO}7 complexes from ferric precursors. All of the complexes were characterized using X-ray crystallography, UV-vis, IR, and nuclear resonance vibrational spectroscopy (NRVS). On the basis of the vibrational data, further insight into the electronic structure of these {FeNO}6 complexes, in particular with respect to the role of the axial ligand trans to NO, is obtained.
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Affiliation(s)
- Ashley B McQuarters
- Department of Chemistry and Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeff W Kampf
- Department of Chemistry and Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - E Ercan Alp
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Michael Hu
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
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26
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Ascenzi P, Ciaccio C, Gasperi T, Pesce A, Caporaso L, Coletta M. Hydroxylamine-induced oxidation of ferrous carbonylated truncated hemoglobins from Mycobacterium tuberculosis and Campylobacter jejuni is limited by carbon monoxide dissociation. J Biol Inorg Chem 2017. [PMID: 28646425 DOI: 10.1007/s00775-017-1476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydroxylamine (HA) is an oxidant of ferrous globins and its action has been reported to be inhibited by CO, even though this mechanism has not been clarified. Here, kinetics of the HA-mediated oxidation of ferrous carbonylated Mycobacterium tuberculosis truncated hemoglobin N and O (Mt-trHbN(II)-CO and Mt-trHbO(II)-CO, respectively) and Campylobacter jejuni truncated hemoglobin P (Cj-trHbP(II)-CO), at pH 7.2 and 20.0 °C, are reported. Mixing Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO solution with the HA solution brings about absorption spectral changes reflecting the disappearance of the ferrous carbonylated derivatives with the concomitant formation of the ferric species. HA oxidizes irreversibly Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO with the 1:2 stoichiometry. The dissociation of CO turns out to be the rate-limiting step for the oxidation of Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO by HA. Values of the second-order rate constant for HA-mediated oxidation of Mt-trHbN(II)-CO, Mt-trHbO(II)-CO, and Cj-trHbP(II)-CO range between 8.8 × 104 and 8.6 × 107 M-1 s-1, reflecting different structural features of the heme distal pocket. This study (1) demonstrates that the inhibitory effect of CO is linked to the dissociation of this ligand, giving a functional basis to previous studies, (2) represents the first comparative investigation of the oxidation of ferrous carbonylated bacterial 2/2 globins belonging to the N, O, and P groups by HA, (3) casts light on the correlation between kinetics of HA-mediated oxidation and carbonylation of globins, and (4) focuses on structural determinants modulating the HA-induced oxidation process.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, 00146, Rome, Italy.
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", 00133, Rome, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, 70126, Bari, Italy
| | - Tecla Gasperi
- Department of Sciences, Roma Tre University, 00146, Rome, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, 16146, Genoa, Italy
| | - Lucia Caporaso
- Department of Mathematics and Physics, Roma Tre University, 00146, Rome, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", 00133, Rome, Italy.,Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, 70126, Bari, Italy
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Hinrichsen S, Kindjajev A, Adomeit S, Krahmer J, Näther C, Tuczek F. Molybdenum(0) Dinitrogen Complexes Supported by Pentadentate Tetrapodal Phosphine Ligands: Structure, Synthesis, and Reactivity toward Acids. Inorg Chem 2016; 55:8712-22. [PMID: 27526268 DOI: 10.1021/acs.inorgchem.6b01255] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Svea Hinrichsen
- Christian-Albrechts-Universität Kiel, Institute of Inorganic Chemistry, Max-Eyth-Straße 2, D-24118 Kiel, Germany
| | - Andrei Kindjajev
- Christian-Albrechts-Universität Kiel, Institute of Inorganic Chemistry, Max-Eyth-Straße 2, D-24118 Kiel, Germany
| | - Sven Adomeit
- Leibniz-Institut für Katalyse, Albert-Einstein-Straße 29a, D-18059 Rostock, Germany
| | - Jan Krahmer
- Christian-Albrechts-Universität Kiel, Institute of Inorganic Chemistry, Max-Eyth-Straße 2, D-24118 Kiel, Germany
| | - Christian Näther
- Christian-Albrechts-Universität Kiel, Institute of Inorganic Chemistry, Max-Eyth-Straße 2, D-24118 Kiel, Germany
| | - Felix Tuczek
- Christian-Albrechts-Universität Kiel, Institute of Inorganic Chemistry, Max-Eyth-Straße 2, D-24118 Kiel, Germany
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28
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Deka H, Ghosh S, Saha S, Gogoi K, Mondal B. Effect of ligand denticity on the nitric oxide reactivity of cobalt(ii) complexes. Dalton Trans 2016; 45:10979-88. [DOI: 10.1039/c6dt01169a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NO reactivity of three Co(ii) complexes, 1, 2 and 3 have been studied in degassed methanol solution. The complexes differ from each other in terms of denticity and flexibility of the ligand fameworks. Complex 1 undergoes reductive nitrosylation of the metal ion; 2 results in corresponding [CoIII(NO−)] complex; whereas 3 does not react with NO.
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Affiliation(s)
- Hemanta Deka
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Assam-781039
- India
| | - Somnath Ghosh
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Assam-781039
- India
| | - Soumen Saha
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Assam-781039
- India
| | - Kuldeep Gogoi
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Assam-781039
- India
| | - Biplab Mondal
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Assam-781039
- India
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29
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Lehnert N, Peters JC. Preface for Small-Molecule Activation: From Biological Principles to Energy Applications. Part 2: Small Molecules Related to the Global Nitrogen Cycle. Inorg Chem 2015; 54:9229-33. [DOI: 10.1021/acs.inorgchem.5b02124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry, The University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| | - Jonas C. Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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30
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Kalita A, Kumar V, Mondal B. Nitric oxide reactivity of copper(II) complexes of bidentate amine ligands. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2015.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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Ravcheev DA, Thiele I. Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota. Front Microbiol 2014; 5:674. [PMID: 25538694 PMCID: PMC4257093 DOI: 10.3389/fmicb.2014.00674] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/19/2014] [Indexed: 11/13/2022] Open
Abstract
Because of the specific anatomical and physiological properties of the human intestine, a specific oxygen gradient builds up within this organ that influences the intestinal microbiota. The intestinal microbiome has been intensively studied in recent years, and certain respiratory substrates used by gut inhabiting microbes have been shown to play a crucial role in human health. Unfortunately, a systematic analysis has not been previously performed to determine the respiratory capabilities of human gut microbes (HGM). Here, we analyzed the distribution of aerobic and anaerobic respiratory reductases in 254 HGM genomes. In addition to the annotation of known enzymes, we also predicted a novel microaerobic reductase and novel thiosulfate reductase. Based on this comprehensive assessment of respiratory reductases in the HGM, we proposed a number of exchange pathways among different bacteria involved in the reduction of various nitrogen oxides. The results significantly expanded our knowledge of HGM metabolism and interactions in bacterial communities.
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Affiliation(s)
- Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg ; Division 6: Comparative Genomics of Regulation System, A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
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32
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Poser A, Vogt C, Knöller K, Ahlheim J, Weiss H, Kleinsteuber S, Richnow HH. Stable sulfur and oxygen isotope fractionation of anoxic sulfide oxidation by two different enzymatic pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9094-9102. [PMID: 25003498 DOI: 10.1021/es404808r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The microbial oxidation of sulfide is a key reaction of the microbial sulfur cycle, recycling sulfur in its most reduced valence state back to more oxidized forms usable as electron acceptors. Under anoxic conditions, nitrate is a preferential electron acceptor for this process. Two enzymatic pathways have been proposed for sulfide oxidation under nitrate reducing conditions, the sulfide:quinone oxidoreductase (SQR) pathway and the Sox (sulfur oxidation) system. In experiments with the model strains Thiobacillus denitrificans and Sulfurimonas denitrificans, both pathways resulted in a similar small sulfur and oxygen isotope fractionation of -2.4 to -3.6‰ for (34)S and -2.4 to -3.4‰ for (18)O. A similar pattern was detected during the oxidation of sulfide in a column percolated with sulfidic, nitrate amended groundwater. In experiments with (18)O-labeled water, a strong oxygen isotope fractionation was observed for T. denitrificans and S. denitrificans, indicating a preferential incorporation of (18)O-depleted oxygen released as water by nitrate reduction to nitrogen. The study indicates that nitrate-dependent sulfide oxidation might be monitored in the environment by analysis of (18)O-depleted sulfate.
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Affiliation(s)
- Alexander Poser
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research UFZ , Permoserstraße 15, 04318 Leipzig, Germany
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Streptomyces griseusEnhances Denitrification byRalstonia pickettiiK50, Which Is Possibly Mediated by Histidine Produced during Co-Culture. Biosci Biotechnol Biochem 2014; 72:163-70. [DOI: 10.1271/bbb.70528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Hoffman BM, Lukoyanov D, Yang ZY, Dean DR, Seefeldt LC. Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 2014; 114:4041-62. [PMID: 24467365 PMCID: PMC4012840 DOI: 10.1021/cr400641x] [Citation(s) in RCA: 979] [Impact Index Per Article: 97.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Brian M Hoffman
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
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Saggar S, Jha N, Deslippe J, Bolan NS, Luo J, Giltrap DL, Kim DG, Zaman M, Tillman RW. Denitrification and N2O:N2 production in temperate grasslands: processes, measurements, modelling and mitigating negative impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 465:173-95. [PMID: 23260378 DOI: 10.1016/j.scitotenv.2012.11.050] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/11/2012] [Accepted: 11/12/2012] [Indexed: 05/02/2023]
Abstract
In this review we explore the biotic transformations of nitrogenous compounds that occur during denitrification, and the factors that influence denitrifier populations and enzyme activities, and hence, affect the production of nitrous oxide (N2O) and dinitrogen (N2) in soils. Characteristics of the genes related to denitrification are also presented. Denitrification is discussed with particular emphasis on nitrogen (N) inputs and dynamics within grasslands, and their impacts on the key soil variables and processes regulating denitrification and related gaseous N2O and N2 emissions. Factors affecting denitrification include soil N, carbon (C), pH, temperature, oxygen supply and water content. We understand that the N2O:N2 production ratio responds to the changes in these factors. Increased soil N supply, decreased soil pH, C availability and water content generally increase N2O:N2 ratio. The review also covers approaches to identify and quantify denitrification, including acetylene inhibition, (15)N tracer and direct N2 quantification techniques. We also outline the importance of emerging molecular techniques to assess gene diversity and reveal enzymes that consume N2O during denitrification and the factors affecting their activities and consider a process-based approach that can be used to quantify the N2O:N2 product ratio and N2O emissions with known levels of uncertainty in soils. Finally, we explore strategies to reduce the N2O:N2 product ratio during denitrification to mitigate N2O emissions. Future research needs to focus on evaluating the N2O-reducing ability of the denitrifiers to accelerate the conversion of N2O to N2 and the reduction of N2O:N2 ratio during denitrification.
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Affiliation(s)
- Surinder Saggar
- Ecosystems & Global Change Team, Landcare Research, Private Bag 11052, Palmerston North 4442, New Zealand.
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37
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Lee DJ, Wong BT. Methanogenic activities of sulfide and nitric oxide amended mesophilic, methanogenic culture: role of nitrososufides complex. BIORESOURCE TECHNOLOGY 2013; 142:63-68. [PMID: 23743421 DOI: 10.1016/j.biortech.2013.05.035] [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: 04/09/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 06/02/2023]
Abstract
Sulfide (S(2-)) and nitric oxide (NO) can be formed in anaerobic digester if nitrate and sulfate were presented in the influent streams. This study noted by 4,5-diaminofluorescein diacetate (DAF-2DA) staining and confocal laser scanning microscopy (CLSM) the presence of nitrososulfides (SNO) complex in the S(2-)+NO-amended methanogenic sludge. Kinetic analysis suggested two-step kinetics involving chemical equilibrium between S(2-), NO and SNO as step 1 and the slow conversion from SNO to N2O as step 2. The SNO complex was claimed to have higher inhibition effect than S(2-) or NO alone on the methangenic activities. Comments were made on the role of SNO complex for the interactions between sulfur, nitrogen and carbon metabolisms in anaerobic digestion.
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Affiliation(s)
- Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan.
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38
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McQuarters AB, Goodrich LE, Goodrich CM, Lehnert N. Disproportionation of O-Benzylhydroxylamine Catalyzed by a Ferric Bis-Picket Fence Porphyrin Complex. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Kumar P, Kalita A, Mondal B. Nitric oxide reactivity of Cu(ii) complexes of tetra- and pentadentate ligands: structural influence in deciding the reduction pathway. Dalton Trans 2013; 42:5731-9. [DOI: 10.1039/c3dt32580f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Shoun H, Fushinobu S, Jiang L, Kim SW, Wakagi T. Fungal denitrification and nitric oxide reductase cytochrome P450nor. Philos Trans R Soc Lond B Biol Sci 2012; 367:1186-94. [PMID: 22451104 DOI: 10.1098/rstb.2011.0335] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have shown that many fungi (eukaryotes) exhibit distinct denitrifying activities, although occurrence of denitrification was previously thought to be restricted to bacteria (prokaryotes), and have characterized the fungal denitrification system. It comprises NirK (copper-containing nitrite reductase) and P450nor (a cytochrome P450 nitric oxide (NO) reductase (Nor)) to reduce nitrite to nitrous oxide (N(2)O). The system is localized in mitochondria functioning during anaerobic respiration. Some fungal systems further contain and use dissimilatory and assimilatory nitrate reductases to denitrify nitrate. Phylogenetic analysis of nirK genes showed that the fungal-denitrifying system has the same ancestor as the bacterial counterpart and suggested a possibility of its proto-mitochondrial origin. By contrast, fungi that have acquired a P450 from bacteria by horizontal transfer of the gene, modulated its function to give a Nor activity replacing the original Nor with P450nor. P450nor receives electrons directly from nicotinamide adenine dinucleotide to reduce NO to N(2)O. The mechanism of this unprecedented electron transfer has been extensively studied and thoroughly elucidated. Fungal denitrification is often accompanied by a unique phenomenon, co-denitrification, in which a hybrid N(2) or N(2)O species is formed upon the combination of nitrogen atoms of nitrite with a nitrogen donor (amines and imines). Possible involvement of NirK and P450nor is suggested.
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Affiliation(s)
- Hirofumi Shoun
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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41
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Pro D, Arkoun M, Huguet S, Daniellou R, Nugier-Chauvin C, Morvan J, Wolbert D, Ourry A, Yvin JC, Ferrières V. Impact of glycosylation on physico–chemical and biological properties of nitrification inhibitors. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Sarma M, Mondal B. Nitric oxide reactivity of copper(II) complexes of bidentate amine ligands: effect of substitution on ligand nitrosation. Dalton Trans 2012; 41:2927-34. [PMID: 22266544 DOI: 10.1039/c2dt11082b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three copper(ii) complexes with bidentate ligands L(1), L(2) and L(3) [L(1), N,N(/)-dimethylethylenediamine; L(2), N,N(/)-diethylethylenediamine and L(3), N,N(/)-diisobutylethylenediamine], respectively, were synthesized as their perchlorate salts. The single crystal structures for all the complexes were determined. The nitric oxide reactivity of the complexes was studied in acetonitrile solvent. The formation of thermally unstable [Cu(II)-NO] intermediate on reaction of the complexes with nitric oxide in acetonitrile solution was observed prior to the reduction of copper(II) centres to copper(I). The reduction was found to result with a simultaneous mono- and di-nitrosation at the secondary amine sites of the ligand. All the nitrosation products were isolated and characterized. The ratio of the yield of mono- and di-nitrosation product was found to be dependent on the N-substitution present in the ligand framework.
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Affiliation(s)
- Moushumi Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, India
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43
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Sarma M, Kumar V, Kalita A, Deka RC, Mondal B. Nitric oxide reactivity of copper(ii) complexes of bidentate amine ligands: effect of chelate ring size on the stability of a [CuII–NO] intermediate. Dalton Trans 2012; 41:9543-52. [DOI: 10.1039/c2dt30721a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Kalita A, Kumar P, Deka RC, Mondal B. First example of a Cu(i)–(η2-O,O)nitrite complex derived from Cu(ii)–nitrosyl. Chem Commun (Camb) 2012; 48:1251-3. [DOI: 10.1039/c1cc16316g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Doctorovich F, Bikiel D, Pellegrino J, Suárez SA, Larsen A, Martí MA. Nitroxyl (azanone) trapping by metalloporphyrins. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.04.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Tabares LC, Kostrz D, Elmalk A, Andreoni A, Dennison C, Aartsma TJ, Canters GW. Fluorescence lifetime analysis of nitrite reductase from Alcaligenes xylosoxidans at the single-molecule level reveals the enzyme mechanism. Chemistry 2011; 17:12015-9. [PMID: 21922585 DOI: 10.1002/chem.201102063] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Leandro C Tabares
- Leiden Institute of Physics, Huygens Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands.
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Wu H, Yuan Y, Ma J, Gao Y. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of NifH1 from Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:565-567. [PMID: 21543862 PMCID: PMC3087641 DOI: 10.1107/s1744309111007408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 02/26/2011] [Indexed: 05/30/2023]
Abstract
Nitrogen fixation is catalyzed by the nitrogenase complex in Azotobacter, which is composed of dinitrogenase and dinitrogenase reductase. Dinitrogenase is an α(2)β(2) heterotetramer of the proteins NifD and NifK. Dinitrogenase reductase is a homodimer of the protein NifH. The expression of NifD/K and NifH nitrogenase homologues (named NflD/K and NflH for Nif-like D and H, respectively) has been detected in the non-nitrogen-fixing hyperthermophilic methanogen Methanocaldococcus jannaschii. Solving the structure of MjNifH1 may help in better understanding its function and may supply some clues to understanding the evolution of nitrogenase. The full-length protein with an additional His(6) tag at the C-terminus was expressed, purified and crystallized by the hanging-drop vapour-diffusion method at 287 K. An X-ray diffraction data set was collected to a resolution of 3.3 Å. The crystal belonged to space group P4(1)32, with unit-cell parameters a = b = c = 139.45 Å, and was estimated to contain one protein molecule per asymmetric unit.
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Affiliation(s)
- Hao Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Ye Yuan
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Jinming Ma
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
| | - Yongxiang Gao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027, People’s Republic of China
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Sarma M, Mondal B. Nitric Oxide Reduction of Copper(II) Complexes: Spectroscopic Evidence of Copper(II)−Nitrosyl Intermediate. Inorg Chem 2011; 50:3206-12. [DOI: 10.1021/ic1011988] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Moushumi Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Biplab Mondal
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India
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Abstract
The nitrogen cycle describes the processes through which nitrogen is converted between its various chemical forms. These transformations involve both biological and abiotic redox processes. The principal processes involved in the nitrogen cycle are nitrogen fixation, nitrification, nitrate assimilation, respiratory reduction of nitrate to ammonia, anaerobic ammonia oxidation (anammox) and denitrification. All of these are carried out by micro-organisms, including bacteria, archaea and some specialized fungi. In the present article, we provide a brief introduction to both the biochemical and ecological aspects of these processes and consider how human activity over the last 100 years has changed the historic balance of the global nitrogen cycle.
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Abstract
Nitrogenase is the enzyme responsible for biological reduction of dinitrogen (N(2)) to ammonia, a form usable for life. Playing a central role in the global biogeochemical nitrogen cycle, this enzyme has been the focus of intensive research for over 60 years. This chapter provides an overview of the features of nitrogenase as a background to the subsequent chapters of this volume that detail the many methods that have been applied in an attempt to gain a deeper understanding of this complex enzyme.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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