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Scherschel NF, Piercey DG. Nitrodiazene oxides: a unique nitrogen- and oxygen-containing functional group. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231935. [PMID: 38511085 PMCID: PMC10951729 DOI: 10.1098/rsos.231935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/30/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Nitrogen-/oxygen-containing functional groups (N/O groups) may be found in a wide variety of areas such as agriculture, drug design and energetic materials. Exploring the chemistry and synthesis of N/O groups is desirable as compounds containing their functionality may prove to be invaluable in a variety of fields. A unique N/O functional group which may offer additional insight into the design of high-heteroatom content systems is the 2-nitrodiazene-1-N-oxide group (NDO group). While unique on their own, NDOs combine the well-known azoxy (N(O)=N) and nitro (-NO2) groups into a single unique N/O functional group. Although NDOs may offer superior densities and enthalpies of formations relative to their nitro counterparts, NDOs have been significantly less investigated than their nitro-bearing counterparts. This work will discuss NDOs in chemical literature from their initial discovery to modern synthesis techniques, energetic properties and chemical stability.
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Affiliation(s)
- Nicholas F. Scherschel
- School of Materials Engineering, Purdue University, West Lafayette, IN47906, USA
- Purdue Energetics Research Center, Purdue University, West Lafayette, IN47906, USA
| | - Davin G. Piercey
- School of Materials Engineering, Purdue University, West Lafayette, IN47906, USA
- Purdue Energetics Research Center, Purdue University, West Lafayette, IN47906, USA
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, IN47907, USA
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2
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Akutsu Y, Fujiwara T, Suzuki R, Nishigaya Y, Yamazaki T. Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c554. Appl Environ Microbiol 2023; 89:e0129123. [PMID: 38009977 PMCID: PMC10734522 DOI: 10.1128/aem.01291-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Nitrification, the microbial conversion of ammonia to nitrate via nitrite, plays a pivotal role in the global nitrogen cycle. However, the excessive use of ammonium-based fertilizers in agriculture has disrupted this cycle, leading to groundwater pollution and greenhouse gas emissions. In this study, we have demonstrated the inhibitory effects of plant-derived juglone and related 1,4-naphthoquinones on the nitrification process in Nitrosomonas europaea. Notably, the inhibition mechanism is elucidated in which 1,4-naphthoquinones interact with hydroxylamine oxidoreductase, disrupting the electron transfer to cytochrome c554, a physiological electron acceptor. These findings support the notion that phytochemicals can impede nitrification by interfering with the essential electron transfer process in ammonia oxidation. The findings presented in this article offer valuable insights for the development of strategies aimed at the management of nitrification, reduction of fertilizer utilization, and mitigation of greenhouse gas emissions.
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Affiliation(s)
- Yukie Akutsu
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takaaki Fujiwara
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Rintaro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | | | - Toshimasa Yamazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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3
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Ohbayashi T, Wang Y, Aoyagi LN, Hara S, Tago K, Hayatsu M. Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils. Microbes Environ 2023; 38:ME23068. [PMID: 38092410 PMCID: PMC10728637 DOI: 10.1264/jsme2.me23068] [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: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.
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Affiliation(s)
- Tsubasa Ohbayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Luciano Nobuhiro Aoyagi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Shintaro Hara
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
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Wu MR, Miao LL, Liu Y, Qian XX, Hou TT, Ai GM, Yu L, Ma L, Gao XY, Qin YL, Zhu HZ, Du L, Li SY, Tian CL, Li DF, Liu ZP, Liu SJ. Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N 2. J Biol Chem 2022; 298:102372. [PMID: 35970391 PMCID: PMC9478400 DOI: 10.1016/j.jbc.2022.102372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
Nitrogen (N2) gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown that Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed “Dirammox” (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here, we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N2. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated that, in the presence of NADH and FAD, DnfA catalyzed the conversion of 15N-labeled hydroxylamine to 15N2. This conversion did not happen under oxygen (O2)-free conditions. Thus, we concluded that DnfA encodes a hydroxylamine oxidase. We demonstrate that DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a Km of 92.9 ± 3.0 μM for hydroxylamine and a kcat of 0.028 ± 0.001 s−1. Finally, we show that DnfA was localized in the cytoplasm and periplasm as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude that DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N2.
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Affiliation(s)
- Meng-Ru Wu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Qian
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ting-Ting Hou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
| | - Sheng-Ying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China; The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049.
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China.
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5
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Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily. THE ISME JOURNAL 2022; 16:1750-1764. [PMID: 35352015 PMCID: PMC9213671 DOI: 10.1038/s41396-022-01222-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 01/04/2023]
Abstract
Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.
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Soares R, Costa NL, Paquete CM, Andreini C, Louro RO. A new paradigm of multiheme cytochrome evolution by grafting and pruning protein modules. Mol Biol Evol 2022; 39:6609985. [PMID: 35714268 PMCID: PMC9250108 DOI: 10.1093/molbev/msac139] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multiheme cytochromes play key roles in diverse biogeochemical cycles, but understanding the origin and evolution of these proteins is a challenge due to their ancient origin and complex structure. Up until now, the evolution of multiheme cytochromes composed by multiple redox modules in a single polypeptide chain was proposed to occur by gene fusion events. In this context, the pentaheme nitrite reductase NrfA and the tetraheme cytochrome c554 were previously proposed to be at the origin of the extant octa- and nonaheme cytochrome c involved in metabolic pathways that contribute to the nitrogen, sulfur, and iron biogeochemical cycles by a gene fusion event. Here, we combine structural and character-based phylogenetic analysis with an unbiased root placement method to refine the evolutionary relationships between these multiheme cytochromes. The evidence show that NrfA and cytochrome c554 belong to different clades, which suggests that these two multiheme cytochromes are products of truncation of ancestral octaheme cytochromes related to extant octaheme nitrite reductase and MccA, respectively. From our phylogenetic analysis, the last common ancestor is predicted to be an octaheme cytochrome with nitrite reduction ability. Evolution from this octaheme framework led to the great diversity of extant multiheme cytochromes analyzed here by pruning and grafting of protein modules and hemes. By shedding light into the evolution of multiheme cytochromes that intervene in different biogeochemical cycles, this work contributes to our understanding about the interplay between biology and geochemistry across large time scales in the history of Earth.
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Affiliation(s)
- Ricardo Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal.,Instituto Nacional de Investigação Agrária e Veterinária, Portugal
| | - Nazua L Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
| | - Catarina M Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
| | - Claudia Andreini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Portugal
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7
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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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8
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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9
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Akram M, Bock J, Dietl A, Barends TR. Specificity of Small c-Type Cytochromes in Anaerobic Ammonium Oxidation. ACS OMEGA 2021; 6:21457-21464. [PMID: 34471748 PMCID: PMC8388095 DOI: 10.1021/acsomega.1c02275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different "outlet" for electrons on HAO than has traditionally been assumed.
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10
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Duarte AG, Barbosa ACC, Ferreira D, Manteigas G, Domingos RM, Pereira IAC. Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148416. [PMID: 33753023 DOI: 10.1016/j.bbabio.2021.148416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
| | - Ana C C Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Gonçalo Manteigas
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Renato M Domingos
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
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11
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Ferousi C, Schmitz RA, Maalcke WJ, Lindhoud S, Versantvoort W, Jetten MSM, Reimann J, Kartal B. Characterization of a nitrite-reducing octaheme hydroxylamine oxidoreductase that lacks the tyrosine cross-link. J Biol Chem 2021; 296:100476. [PMID: 33652023 PMCID: PMC8042395 DOI: 10.1016/j.jbc.2021.100476] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
The hydroxylamine oxidoreductase (HAO) family consists of octaheme proteins that harbor seven bis-His ligated electron-transferring hemes and one 5-coordinate catalytic heme with His axial ligation. Oxidative HAOs have a homotrimeric configuration with the monomers covalently attached to each other via a unique double cross-link between a Tyr residue and the catalytic heme moiety of an adjacent subunit. This cross-linked active site heme, termed the P460 cofactor, has been hypothesized to modulate enzyme reactivity toward oxidative catalysis. Conversely, the absence of this cross-link is predicted to favor reductive catalysis. However, this prediction has not been directly tested. In this study, an HAO homolog that lacks the heme-Tyr cross-link (HAOr) was purified to homogeneity from the nitrite-dependent anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, and its catalytic and spectroscopic properties were assessed. We show that HAOr reduced nitrite to nitric oxide and also reduced nitric oxide and hydroxylamine as nonphysiological substrates. In contrast, HAOr was not able to oxidize hydroxylamine or hydrazine supporting the notion that cross-link-deficient HAO enzymes are reductases. Compared with oxidative HAOs, we found that HAOr harbors an active site heme with a higher (at least 80 mV) midpoint potential and a much lower degree of porphyrin ruffling. Based on the physiology of anammox bacteria and our results, we propose that HAOr reduces nitrite to nitric oxide in vivo, providing anammox bacteria with NO, which they use to activate ammonium in the absence of oxygen.
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Affiliation(s)
- Christina Ferousi
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter J Maalcke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Simon Lindhoud
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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12
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Abstract
Ammonia-oxidizing bacteria (AOB) convert ammonia (NH3) to nitrite (NO2-) as their primary metabolism and thus provide a blueprint for the use of NH3 as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH2OH) to NO2-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH2OH and were both originally reported to produce NO2-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH2OH oxidation. Under aerobic conditions substoichiometric production of NO2- was observed along with production of nitrous oxide (N2O). Under anaerobic conditions, however, N2O was the exclusive product of NH2OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O2, thus producing NO2- abiotically. Because N2O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO2- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO2- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH2OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH2OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.
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Affiliation(s)
- Rachael E. Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M. Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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13
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Andoralov V, Shleev S, Dergousova N, Kulikova O, Popov V, Tikhonova T. Octaheme nitrite reductase: The mechanism of intramolecular electron transfer and kinetics of nitrite bioelectroreduction. Bioelectrochemistry 2020; 138:107699. [PMID: 33221569 DOI: 10.1016/j.bioelechem.2020.107699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 11/24/2022]
Abstract
Detailed impedance and voltammetric studies of hexameric octaheme nitrite reductase immobilized on carbon-based nanomaterials, specifically nanotubes and nanoparticles, were performed. Well-pronounced bioelectrocatalytic reduction of nitrite on enzyme-modified electrodes was obtained. Analysis of the impedance data indicated the absence of long-lived intermediates involved in the nitrite reduction. Cyclic voltammograms of biomodified electrodes had a bi-sigmoidal shape, which pointed to the presence of two enzyme orientations on carbon supports. The maximum (limiting) catalytic currents were determined and, by applying the correction by the mixed kinetics equation, the Tafel dependences were plotted for each catalytic wave/each enzyme orientation. Finally, two schemes for the rate-limiting processes during bioelectrocatalysis were proposed, viz. for low- and high-potential orientations.
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Affiliation(s)
- Victor Andoralov
- Biomedical Sciences, Health & Society, Malmö University, 205 06 Malmö, Sweden
| | - Sergey Shleev
- Biomedical Sciences, Health & Society, Malmö University, 205 06 Malmö, Sweden; Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Natalia Dergousova
- Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga Kulikova
- Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Vladimir Popov
- Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; Kurchatov NBIC Centre, National Research Centre "Kurchatov Institute", 123182 Moscow, Russia
| | - Tamara Tikhonova
- Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia.
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14
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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15
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Coleman RE, Vilbert AC, Lancaster KM. The Heme-Lys Cross-Link in Cytochrome P460 Promotes Catalysis by Enforcing Secondary Coordination Sphere Architecture. Biochemistry 2020; 59:2289-2298. [PMID: 32525655 DOI: 10.1021/acs.biochem.0c00261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome (cyt) P460 is a c-type monoheme enzyme found in ammonia-oxidizing bacteria (AOB) and methanotrophs; additionally, genes encoding it have been found in some pathogenic bacteria. Cyt P460 is defined by a unique post-translational modification to the heme macrocycle, where a lysine (Lys) residue covalently attaches to the 13' meso carbon of the porphyrin, modifying this heme macrocycle into the enzyme's eponymous P460 cofactor, similar to the cofactor found in the enzyme hydroxylamine oxidoreductase. This cross-link imbues the protein with unique spectroscopic properties, the most obvious of which is the enzyme's green color in solution. Cyt P460 from the AOB Nitrosomonas europaea is a homodimeric redox enzyme that produces nitrous oxide (N2O) from 2 equiv of hydroxylamine. Mutation of the Lys cross-link results in spectroscopic features that are more similar to those of standard cyt c' proteins and renders the enzyme catalytically incompetent for NH2OH oxidation. Recently, the necessity of a second-sphere glutamate (Glu) residue for redox catalysis was established; it plausibly serves as proton relay during the first oxidative half of the catalytic cycle. Herein, we report the first crystal structure of a cross-link deficient cyt P460. This structure shows that the positioning of the catalytically essential Glu changes by approximately 0.8 Å when compared to a cross-linked, catalytically competent cyt P460. It appears that the heme-Lys cross-link affects the relative position of the P460 cofactor with respect to the second-sphere Glu residue, therefore dictating the catalytic competency of the enzyme.
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Affiliation(s)
- Rachael E Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Avery C Vilbert
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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16
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Wendeborn S. Chemie, Biologie und Regulierung der Nitrifikation von Ammonium im Boden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201903014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sebastian Wendeborn
- Fachhochschule Nordwestschweiz FHNWHochschule für Life SciencesInstitut für Chemie und Bioanalytik Hofackerstrasse 30 CH-4132 Muttenz Schweiz
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17
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Tracey JC, Coronado M, Giessen TW, Lau MCY, Silver PA, Ward BB. The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria. Sci Rep 2019; 9:20122. [PMID: 31882935 PMCID: PMC6934571 DOI: 10.1038/s41598-019-56533-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Many prokaryotes encode protein-based encapsulin nanocompartments, including anaerobic ammonium oxidizing (anammox) bacteria. This study expands the list of known anammox encapsulin systems from freshwater species to include the marine genus Scalindua. Two novel systems, identified in "Candidatus Scalindua rubra" and "Candidatus Scalindua sp. SCAELEC01 167" possess different architectures than previously studied freshwater anammox encapsulins. Characterization of the S. rubra encapsulin confirms that it can self-assemble to form compartments when heterologously expressed in Escherichia coli. BLASTp and HMMER searches of additional genomes and metagenomes spanning a range of environments returned 26 additional novel encapsulins, including a freshwater anammox encapsulin identified in "Candidatus Brocadia caroliniensis". Phylogenetic analysis comparing these 28 new encapsulin sequences and cargo to that of their closest known relatives shows that encapsulins cluster by cargo protein type and therefore likely evolved together. Lastly, prokaryotic encapsulins may be more common and diverse than previously thought. Through searching a small sample size of all public metagenomes and genomes, many new encapsulin systems were unearthed by this study. This suggests that many additional encapsulins likely remain to be discovered.
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Affiliation(s)
- John C Tracey
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA.
| | - Maricela Coronado
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA
| | - Tobias W Giessen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Harvard Medical School, Department of Systems Biology, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Maggie C Y Lau
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Pamela A Silver
- Harvard Medical School, Department of Systems Biology, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Bess B Ward
- Princeton University, Department of Geosciences, Guyot Hall, Princeton, NJ, 08544, USA
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18
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Wendeborn S. The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil. Angew Chem Int Ed Engl 2019; 59:2182-2202. [PMID: 31116902 DOI: 10.1002/anie.201903014] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/15/2019] [Indexed: 11/11/2022]
Abstract
Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.
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Affiliation(s)
- Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
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19
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Akram M, Dietl A, Mersdorf U, Prinz S, Maalcke W, Keltjens J, Ferousi C, de Almeida NM, Reimann J, Kartal B, Jetten MSM, Parey K, Barends TRM. A 192-heme electron transfer network in the hydrazine dehydrogenase complex. SCIENCE ADVANCES 2019; 5:eaav4310. [PMID: 31001586 PMCID: PMC6469936 DOI: 10.1126/sciadv.aav4310] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/28/2019] [Indexed: 05/21/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
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Affiliation(s)
- M. Akram
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - A. Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - U. Mersdorf
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - S. Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - W. Maalcke
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - J. Keltjens
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - C. Ferousi
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - N. M. de Almeida
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - J. Reimann
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - B. Kartal
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - M. S. M. Jetten
- Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - K. Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
- Corresponding author. (K.P.); (T.R.M.B.)
| | - T. R. M. Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Corresponding author. (K.P.); (T.R.M.B.)
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20
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Meng J, Li J, He J, Li J, Deng K, Nan J. Nutrient removal from high ammonium swine wastewater in upflow microaerobic biofilm reactor suffered high hydraulic load. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 233:69-75. [PMID: 30557752 DOI: 10.1016/j.jenvman.2018.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/07/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
To understand the ability of an upflow microaerobic biofilm reactor (UMBR) to remove nutrient from manure-free swine wastewater rich in NH4+ with a COD/TN ratio less than 1.00, effect of hydraulic loading rate (HLR) on the microaerobic process was evaluated with a constant reflux ratio of 25 at 25 °C. The results showed that changes in HLR had a remarkable effect on the performance of the UMBR in nutrient removal from the wastewater. With the favorable HLR 3.0 m3/(m3·d) (Hydraulic Retention Time (HRT) 8 h), average removal of COD, NH4+ and TN in the microaerobic process reached 59.3%, 87.7% and 84.7%, respectively, though the COD/TN ratio was as low as 0.84. With an over HLR of 4.0 m3/(m3·d) (HRT decreased to 6 h), bad performance of the UMBR was observed with an average removal of COD, NH4+ and TN as low as 45.0%, 59.0% and 57.5%, respectively. Since the HLR was decreased to 2.4 m3/(m3·d) (HRT 10 h), the microaerobic process regained the efficiency in nutrient removal with a removal of COD, NH4+ and TN averaged 59.0%, 95.3% and 87.8%, respectively. The microaerobic condition allowed anammox bacteria, ammonia-oxidizing bacteria and archaea, nitrite-oxidizing bacteria and denitrifiers to all thrive in the UMBR, resulting in the efficient synchronous removal of organic carbon and nitrogen. As the dominant approach to nitrogen removal, anaerobic ammonium oxidation (anammox) pathway contributing to the TN removal in the microaerobic process exceeded 59.5% at HLR 3.0 m3/(m3·d). The results demonstrated that the UMBR can remove nitrogen and carbon from swine wastewater, with a suitable HLR.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Jiamin He
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China.
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Harbin, 150090, PR China
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21
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Chen JH, Yu LJ, Boussac A, Wang-Otomo ZY, Kuang T, Shen JR. Properties and structure of a low-potential, penta-heme cytochrome c 552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2019; 139:281-293. [PMID: 29691716 DOI: 10.1007/s11120-018-0507-y] [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: 02/28/2018] [Accepted: 03/30/2018] [Indexed: 06/08/2023]
Abstract
The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c', and one of two low-potential cytochrome c552 (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c552 (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.
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Affiliation(s)
- Jing-Hua Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
- University of Chinese Academy of Sciences, Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Long-Jiang Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Alain Boussac
- I2BC, SB2SM, CNRS UMR 9198, CEA Saclay, 91191, Gif-sur-Yvette, France
| | | | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China.
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
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22
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Dietl A, Maalcke WJ, Ferousi C, Jetten MSM, Kartal B, Barends TRM. A 60-heme reductase complex from an anammox bacterium shows an extended electron transfer pathway. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:333-341. [DOI: 10.1107/s2059798318017473] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/10/2018] [Indexed: 11/10/2022]
Abstract
The hydroxylamine oxidoreductase/hydrazine dehydrogenase (HAO/HDH) protein family constitutes an important group of octaheme cytochromes c (OCCs). The majority of these proteins form homotrimers, with their subunits being covalently attached to each other via a rare cross-link between the catalytic heme moiety and a conserved tyrosine residue in an adjacent subunit. This covalent cross-link has been proposed to modulate the active-site heme towards oxidative catalysis by distorting the heme plane. In this study, the crystal structure of a stable complex of an HAO homologue (KsHAOr) with its diheme cytochrome c redox partner (KsDH) from the anammox bacterium Kuenenia stuttgartiensis was determined. KsHAOr lacks the tyrosine cross-link and is therefore tuned to reductive catalysis. The molecular model of the KsHAOr–KsDH complex at 2.6 Å resolution shows a heterododecameric (α6β6) assembly, which was also shown to be the oligomeric state in solution by analytical ultracentrifugation and multi-angle static light scattering. The 60-heme-containing protein complex reveals a unique extended electron transfer pathway and provides deeper insights into catalysis and electron transfer in reductive OCCs.
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23
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Adams HR, Krewson C, Vardanega JE, Fujii S, Moreno-Chicano T, Moreno T, Chicano, Sambongi Y, Svistunenko D, Paps J, Andrew CR, Hough MA. One fold, two functions: cytochrome P460 and cytochrome c'-β from the methanotroph Methylococcus capsulatus (Bath). Chem Sci 2019; 10:3031-3041. [PMID: 30996884 PMCID: PMC6427953 DOI: 10.1039/c8sc05210g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/20/2019] [Indexed: 11/21/2022] Open
Abstract
Nature is adept at utilising highly similar protein folds to carry out very different functions, yet the mechanisms by which this functional divergence occurs remain poorly characterised. In certain methanotrophic bacteria, two homologous pentacoordinate c-type heme proteins have been identified: a cytochrome P460 (cyt P460) and a cytochrome c'-β (cyt cp-β). Cytochromes P460 are able to convert hydroxylamine to nitrous oxide (N2O), a potent greenhouse gas. This reactivity is similar to that of hydroxylamine oxidoreductase (HAO), which is a key enzyme in nitrifying and methanotrophic bacteria. Cyt P460 and HAO both have unusual protein-heme cross-links, formed by a Tyr residue in HAO and a Lys in cyt P460. In contrast, cyts cp-β (the only known cytochromes c' with a β-sheet fold) lack this crosslink and appears to be optimized for binding non-polar molecules (including NO and CO) without enzymatic conversion. Our bioinformatics analysis supports the proposal that cyt cp-β may have evolved from cyt P460 via a gene duplication event. Using high-resolution X-ray crystallography, UV-visible absorption, electron paramagnetic resonance (EPR) and resonance Raman spectroscopy, we have characterized the overall protein folding and active site structures of cyt cp-β and cyt P460 from the obligate methanotroph, Methylococcus capsulatus (Bath). These proteins display a similar β-sheet protein fold, together with a pattern of changes to the heme pocket regions and localised tertiary structure that have converted a hydroxylamine oxidizing enzyme into a gas-binding protein. Structural comparisons provide insights relevant to enzyme redesign for synthetic enzymology and engineering of gas sensor proteins. We also show the widespread occurrence of cyts cp-β and characterise their phylogeny.
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Affiliation(s)
- Hannah R Adams
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Callie Krewson
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Jenny E Vardanega
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Sotaro Fujii
- Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan
| | | | - Tadeo Moreno
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Chicano
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan
| | - Dimitri Svistunenko
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Jordi Paps
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
| | - Colin R Andrew
- Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA .
| | - Michael A Hough
- School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK .
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24
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Holmes DE, Dang Y, Smith JA. Nitrogen cycling during wastewater treatment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:113-192. [PMID: 30798802 DOI: 10.1016/bs.aambs.2018.10.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.
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25
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Paquete CM, Rusconi G, Silva AV, Soares R, Louro RO. A brief survey of the "cytochromome". Adv Microb Physiol 2019; 75:69-135. [PMID: 31655743 DOI: 10.1016/bs.ampbs.2019.07.005] [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] [Indexed: 01/23/2023]
Abstract
Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.
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26
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27
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Barsan MM, Bellemare MJ, Butler IS, Gilson DFR, Bohle DS. Micro-Raman high-pressure investigation on the malaria pigment hematin anhydride (β-hematin). J Inorg Biochem 2018; 189:180-184. [PMID: 30296621 DOI: 10.1016/j.jinorgbio.2018.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/27/2018] [Accepted: 09/15/2018] [Indexed: 10/28/2022]
Abstract
The effect of pressure on the Raman and fluorescence spectra of hematin anhydride (β-hematin) is reported. In a diamond-anvil cell, DAC, with applied pressures up to 41 kbar, the Raman spectrum undergoes a series of intensity enhancements and increases in energy for many of the Raman-active bands up to a pressure of ~27 kbar. At higher pressures, there is either a leveling out or a decrease in the energies of these vibrational modes. The fluorescence bands also undergo a series of pressure- sensitive changes where, up to 10 kbar, there is a marked quenching of the intensity of the emissive bands, which is accompanied by a net increase in energy of the vibrational bands. The results are interpreted in terms of a high-pressure phase change, to account for the Raman shifts, and a separate defect or surface site of the emissive state, which is more efficiently quenched at higher pressure.
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Affiliation(s)
- Mirela M Barsan
- Department of Chemistry, McGill University, 801 Sherbrooke West, Montreal H3A OB8, Canada
| | - Marie-Josée Bellemare
- Department of Chemistry, McGill University, 801 Sherbrooke West, Montreal H3A OB8, Canada
| | - Ian S Butler
- Department of Chemistry, McGill University, 801 Sherbrooke West, Montreal H3A OB8, Canada
| | - Denis F R Gilson
- Department of Chemistry, McGill University, 801 Sherbrooke West, Montreal H3A OB8, Canada
| | - D Scott Bohle
- Department of Chemistry, McGill University, 801 Sherbrooke West, Montreal H3A OB8, Canada.
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28
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Rathnayake RMLD, Oshiki M, Ishii S, Segawa T, Satoh H, Okabe S. Experimental Evidence for in Situ Nitric Oxide Production in Anaerobic Ammonia-Oxidizing Bacterial Granules. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5744-5752. [PMID: 29678110 DOI: 10.1021/acs.est.8b00876] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although nitric oxide (NO) emissions from anaerobic ammonium oxidation (anammox)-based processes were reported previously, the NO production pathways are poorly understood. Here, we investigated the NO production pathways in anammox granules in detail by combining 15N-stable isotope tracer experiments with various inhibitors, microsensor measurements, and transcriptome analysis for key genes of NO2- reduction. NO was emitted from the anammox granules, which account for 0.07% of the N2 emission. 15N-stable isotope-tracer experiments indicated that most of the N2 was produced by anammox bacteria, whereas NO was produced from NO2- reduction by anammox and denitrifying bacteria. The NO emission rate was highest at pH 8.0 and accelerated by increasing NH4+ and NO2- concentrations in the culture media. The microsensor analyses showed the in situ NO production rate was highest in the outer layer of the anammox granule where anammox activity was also highest. The detected in situ NO concentrations of up to 2.7 μM were significantly above physiological thresholds known to affect a wide range of microorganisms present in wastewater. Hence, NO likely plays pivotal roles in the microbial interactions in anammox granules, which needs to be further investigated.
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Affiliation(s)
- Rathnayake M L D Rathnayake
- Department of Civil Engineering, Faculty of Engineering , University of Peradeniya , Peradeniya 20400 , Sri Lanka
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
| | - Mamoru Oshiki
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
- Department of Civil Engineering , National Institute of Technology, Nagaoka College , 888 Nishikatakaimachi , Nagaoka , Niigata 940-8532 , Japan
| | - Satoshi Ishii
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
- Department of Soil, Water and Climate , University of Minnesota , 439 Borlaug Hall, 1991 Upper Buford Circle , St. Paul , Minnesota 55108 , United States
- BioTechnology Institute , University of Minnesota , 140 Gortner Laboratory, 1479 Gortner Avenue , St. Paul , Minnesota 55108 , United States
| | - Takahiro Segawa
- Center for Life Science Research , University of Yamanashi , 1110, Shimokato , Chuo , Yamanashi 409-3898 , Japan
- Transdisciplinary Research Integration Center , National Institute of Polar Research , 10-3 Midori-cho , Tachikawa , Tokyo 190-8518 , Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
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29
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Blum JM, Su Q, Ma Y, Valverde-Pérez B, Domingo-Félez C, Jensen MM, Smets BF. The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2O production. Environ Microbiol 2018; 20:1623-1640. [DOI: 10.1111/1462-2920.14063] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/31/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Jan-Michael Blum
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Qingxian Su
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Yunjie Ma
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Borja Valverde-Pérez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Carlos Domingo-Félez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
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30
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Haase D, Hermann B, Einsle O, Simon J. Epsilonproteobacterial hydroxylamine oxidoreductase (
ε
Hao): characterization of a ‘missing link’ in the multihaem cytochrome
c
family. Mol Microbiol 2017; 105:127-138. [DOI: 10.1111/mmi.13690] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Doreen Haase
- Microbial Energy Conversion and Biotechnology, Department of BiologyTechnische Universität DarmstadtSchnittspahnstraße 1064287Darmstadt Germany
| | - Bianca Hermann
- Lehrstuhl Biochemie, Institut für BiochemieAlbert‐Ludwigs‐Universität FreiburgAlbertstrasse 2179104Freiburg Germany
| | - Oliver Einsle
- Lehrstuhl Biochemie, Institut für BiochemieAlbert‐Ludwigs‐Universität FreiburgAlbertstrasse 2179104Freiburg Germany
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of BiologyTechnische Universität DarmstadtSchnittspahnstraße 1064287Darmstadt Germany
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31
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Toyoda S, Yoshida N, Koba K. Isotopocule analysis of biologically produced nitrous oxide in various environments. MASS SPECTROMETRY REVIEWS 2017; 36:135-160. [PMID: 25869149 DOI: 10.1002/mas.21459] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N2 O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the 15 N-site preference (difference between isotopocule ratios 14 N15 N16 O/14 N14 N16 O and 15 N14 N16 O/14 N14 N16 O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N2 O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.
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Affiliation(s)
- Sakae Toyoda
- Department of Environmental Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
| | - Naohiro Yoshida
- Department of Environmental Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Koba
- Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-City, Tokyo 183-8509, Japan
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32
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Tsujino S, Uematsu C, Dohra H, Fujiwara T. Pyruvic oxime dioxygenase from heterotrophic nitrifier Alcaligenes faecalis is a nonheme Fe (II)-dependent enzyme homologous to class II aldolase. Sci Rep 2017; 7:39991. [PMID: 28059164 PMCID: PMC5216522 DOI: 10.1038/srep39991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/30/2016] [Indexed: 11/09/2022] Open
Abstract
Pyruvic oxime dioxygenase (POD), a key enzyme in heterotrophic nitrification, was purified from Alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. POD was purified as the homotetramer of the subunit whose molecular weight was 30,000. The deduced amino acid sequence of POD was homologous with a class II aldolase that has been regarded as the Zn(II)-dependent enzyme catalyzing aldol reactions. The recombinant protein showed weak POD activity, and was activated by reconstitution with Fe(II). Affinity and catalytic constants were estimated at 470 μM and 4.69 sec-1, respectively. The POD was inactivated by EDTA to remove bound divalent metal cations. A reconstitution experiment demonstrated that Fe(II), not Zn(II), is essential for POD activity and that Mn(II) could partially fulfill the function of Fe(II). A mutant POD with replacement of His183, corresponding to one of three Zn(II)-binding ligands in the class II aldolase, by Asn was purified as a homotetrameric protein but showed no catalytic activities. Those results suggest that the POD is homologous to class II aldolase having non-heme Fe(II) as a catalytic center instead of Zn(II). A possible mechanism of the POD reaction is discussed on the basis of that of a known Fe(II)-dependent dioxygenase.
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Affiliation(s)
- Shuhei Tsujino
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Chisato Uematsu
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka 422-8529, Japan
| | - Hideo Dohra
- Instrumental Research Support Office, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
| | - Taketomo Fujiwara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan
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33
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Is there a pathway for N2O production from hydroxylamine oxidoreductase in ammonia-oxidizing bacteria? Proc Natl Acad Sci U S A 2016; 113:14474-14476. [PMID: 27965392 DOI: 10.1073/pnas.1617953114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Yuan Y, Liu J, Ma B, Liu Y, Wang B, Peng Y. Improving municipal wastewater nitrogen and phosphorous removal by feeding sludge fermentation products to sequencing batch reactor (SBR). BIORESOURCE TECHNOLOGY 2016; 222:326-334. [PMID: 27728835 DOI: 10.1016/j.biortech.2016.09.103] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/22/2016] [Accepted: 09/25/2016] [Indexed: 06/06/2023]
Abstract
This study presents a novel strategy to improve the removal efficiency of nitrogen and phosphorus from municipal wastewater by feeding sequencing batch reactor (SBR) with sludge alkaline fermentation products as carbon sources. The performances of two SBRs treating municipal wastewater (one was fed with sludge fermentation products; F-SBR, and the other without sludge fermentation products; B-SBR) were compared. The removal efficiencies of total nitrogen (TN) and phosphorus (PO43--P) were found to be 82.9% and 96.0% in F-SBR, while the corresponding values in B-SBR were 55.9% (TN) and -6.1% (PO43--P). Illumina MiSeq sequencing indicated that ammonium-oxidizing bacteria (Nitrosomonadaceae and Nitrosomonas) and denitrifying polyphosphate accumulating organisms (Dechloromonas) were enriched in F-SBR, which resulted in NO2--N accumulation and denitrifying phosphorus removal via nitrite (DPRN). Moreover, feeding of sludge fermentation products reduced 862.1mg VSS/d of sludge in the F-SBR system (volume: 10L).
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Affiliation(s)
- Yue Yuan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Jinjin Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Bin Ma
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Ye Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Bo Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, PR China.
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35
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Kartal B, Keltjens JT. Anammox Biochemistry: a Tale of Heme c Proteins. Trends Biochem Sci 2016; 41:998-1011. [DOI: 10.1016/j.tibs.2016.08.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
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36
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Kurth JM, Brito JA, Reuter J, Flegler A, Koch T, Franke T, Klein EM, Rowe SF, Butt JN, Denkmann K, Pereira IAC, Archer M, Dahl C. Electron Accepting Units of the Diheme Cytochrome c TsdA, a Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase. J Biol Chem 2016; 291:24804-24818. [PMID: 27694441 DOI: 10.1074/jbc.m116.753863] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/22/2016] [Indexed: 11/06/2022] Open
Abstract
The enzymes of the thiosulfate dehydrogenase (TsdA) family are wide-spread diheme c-type cytochromes. Here, redox carriers were studied mediating the flow of electrons arising from thiosulfate oxidation into respiratory or photosynthetic electron chains. In a number of organisms, including Thiomonas intermedia and Sideroxydans lithotrophicus, the tsdA gene is immediately preceded by tsdB encoding for another diheme cytochrome. Spectrophotometric experiments in combination with enzymatic assays in solution showed that TsdB acts as an effective electron acceptor of TsdA in vitro when TsdA and TsdB originate from the same source organism. Although TsdA covers a range from -300 to +150 mV, TsdB is redox active between -100 and +300 mV, thus enabling electron transfer between these hemoproteins. The three-dimensional structure of the TsdB-TsdA fusion protein from the purple sulfur bacterium Marichromatium purpuratum was solved by X-ray crystallography to 2.75 Å resolution providing insights into internal electron transfer. In the oxidized state, this tetraheme cytochrome c contains three hemes with axial His/Met ligation, whereas heme 3 exhibits the His/Cys coordination typical for TsdA active sites. Interestingly, thiosulfate is covalently bound to Cys330 on heme 3. In several bacteria, including Allochromatium vinosum, TsdB is not present, precluding a general and essential role for electron flow. Both AvTsdA and the MpTsdBA fusion react efficiently in vitro with high potential iron-sulfur protein from A. vinosum (Em +350 mV). High potential iron-sulfur protein not only acts as direct electron donor to the reaction center in anoxygenic phototrophs but can also be involved in aerobic respiratory chains.
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Affiliation(s)
- Julia M Kurth
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - José A Brito
- the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), 2780-157 Oeiras, Portugal, and
| | - Jula Reuter
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Alexander Flegler
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Tobias Koch
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Thomas Franke
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Eva-Maria Klein
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Sam F Rowe
- the Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Julea N Butt
- the Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Kevin Denkmann
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
| | - Inês A C Pereira
- the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), 2780-157 Oeiras, Portugal, and
| | - Margarida Archer
- the Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), 2780-157 Oeiras, Portugal, and
| | - Christiane Dahl
- From the Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany,
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37
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Parey K, Fielding AJ, Sörgel M, Rachel R, Huber H, Ziegler C, Rajendran C. In meso
crystal structure of a novel membrane-associated octaheme cytochrome c
from the Crenarchaeon Ignicoccus hospitalis. FEBS J 2016; 283:3807-3820. [DOI: 10.1111/febs.13870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/17/2016] [Accepted: 08/31/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Kristian Parey
- Department of Structural Biology; Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Alistair J. Fielding
- School of Chemistry and the Photon Science Institute; University of Manchester; UK
| | - Matthias Sörgel
- Biogeochemistry Department; Max Planck Institute for Chemistry; Mainz Germany
| | - Reinhard Rachel
- Department of Microbiology; University of Regensburg; Germany
| | - Harald Huber
- Department of Microbiology; University of Regensburg; Germany
| | | | - Chitra Rajendran
- Department of Structural Biology; University of Regensburg; Germany
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38
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Meng J, Li J, Li J, Wang C, Deng K, Sun K. Effect of seed sludge on nitrogen removal in a novel upflow microaerobic sludge reactor for treating piggery wastewater. BIORESOURCE TECHNOLOGY 2016; 216:19-27. [PMID: 27218438 DOI: 10.1016/j.biortech.2016.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/08/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Anaerobic activated sludge (AnaS) and aerobic activated sludge (AerS) were used to start up a novel upflow microaerobic sludge reactor (UMSR), respectively, and the nitrogen removal in the two reactors were evaluated when treating low C/N ratio manure-free piggery wastewater with a COD/TN ration of about 0.85. With the same hydraulic retention time 8h and TN loading rate (NLR) 0.42kg/(m(3)d), the UMSR (R2) inoculated with AerS could reach its steady state earlier and obtained a better TN removal than that in the UMSR (R1) inoculated with AnaS. However, the accumulated AnaS made R1 show a better capability in bearing shock load and demonstrated an excellent NH4(+)-N and TN removal with a NLR as high as 1.07kg/(m(3)d). Microbial community structure of the accumulated AerS and AnaS were observable different. The decreased proportion of nitrifiers restricted the ammonium oxidation in R2, and resulting in a decrease in TN removal.
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Affiliation(s)
- Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jiuling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Cheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kai Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
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Maalcke WJ, Reimann J, de Vries S, Butt JN, Dietl A, Kip N, Mersdorf U, Barends TRM, Jetten MSM, Keltjens JT, Kartal B. Characterization of Anammox Hydrazine Dehydrogenase, a Key N2-producing Enzyme in the Global Nitrogen Cycle. J Biol Chem 2016; 291:17077-92. [PMID: 27317665 PMCID: PMC5016112 DOI: 10.1074/jbc.m116.735530] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/07/2016] [Indexed: 11/06/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the oxidation of ammonium with nitrite as the electron acceptor. N2, the end product of this metabolism, is produced from the oxidation of the intermediate, hydrazine (N2H4). Previously, we identified N2-producing hydrazine dehydrogenase (KsHDH) from the anammox organism Kuenenia stuttgartiensis as the gene product of kustc0694 and determined some of its catalytic properties. In the genome of K. stuttgartiensis, kustc0694 is one of 10 paralogs related to octaheme hydroxylamine (NH2OH) oxidoreductase (HAO). Here, we characterized KsHDH as a covalently cross-linked homotrimeric octaheme protein as found for HAO and HAO-related hydroxylamine-oxidizing enzyme kustc1061 from K. stuttgartiensis Interestingly, the HDH trimers formed octamers in solution, each octamer harboring an amazing 192 c-type heme moieties. Whereas HAO and kustc1061 are capable of hydrazine oxidation as well, KsHDH was highly specific for this activity. To understand this specificity, we performed detailed amino acid sequence analyses and investigated the catalytic and spectroscopic (electronic absorbance, EPR) properties of KsHDH in comparison with the well defined HAO and kustc1061. We conclude that HDH specificity is most likely derived from structural changes around the catalytic heme 4 (P460) and of the electron-wiring circuit comprising seven His/His-ligated c-type hemes in each subunit. These nuances make HDH a globally prominent N2-producing enzyme, next to nitrous oxide (N2O) reductase from denitrifying microorganisms.
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Affiliation(s)
- Wouter J Maalcke
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Joachim Reimann
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Simon de Vries
- the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Julea N Butt
- the Centre for Molecular and Structural Biochemistry, School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom, and
| | - Andreas Dietl
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Nardy Kip
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Ulrike Mersdorf
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Mike S M Jetten
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands, the Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands
| | - Jan T Keltjens
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Boran Kartal
- From the Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands,
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Nishigaya Y, Fujimoto Z, Yamazaki T. Optimized inhibition assays reveal different inhibitory responses of hydroxylamine oxidoreductases from beta- and gamma-proteobacterial ammonium-oxidizing bacteria. Biochem Biophys Res Commun 2016; 476:127-33. [DOI: 10.1016/j.bbrc.2016.05.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/08/2016] [Indexed: 10/21/2022]
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Oshiki M, Ali M, Shinyako-Hata K, Satoh H, Okabe S. Hydroxylamine-dependent anaerobic ammonium oxidation (anammox) by “Candidatus
Brocadia sinica”. Environ Microbiol 2016; 18:3133-43. [DOI: 10.1111/1462-2920.13355] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering; National Institute of Technology, Nagaoka College; Nagaoka Niigata 940-8532 Japan
| | - Muhammad Ali
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST),Thuwal; 23955-6900 Saudi Arabia
| | - Kaori Shinyako-Hata
- Tokyo Engineering Consultants Co., Ltd., Kasumigaseki, Chioyadaku, Tokyo 100-0013, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering; Hokkaido University; North-13, West-8 Sapporo Hokkaido 060-8628 Japan
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Li J, Meng J, Li J, Wang C, Deng K, Sun K, Buelna G. The effect and biological mechanism of COD/TN ratio on nitrogen removal in a novel upflow microaerobic sludge reactor treating manure-free piggery wastewater. BIORESOURCE TECHNOLOGY 2016; 209:360-368. [PMID: 26972024 DOI: 10.1016/j.biortech.2016.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 06/05/2023]
Abstract
A novel upflow microaerobic sludge reactor (UMSR) was constructed to treat manure-free piggery wastewater with high NH4(+)-N concentration and low COD/TN ratio, and the effect and biological mechanism of COD/TN ratio on nitrogen removal were investigated at a constant hydraulic retention time of 8h and 35°C. The results showed that the UMSR could treat the wastewater with a better synchronous removal of COD, NH4(+)-N and TN. The microaerobic UMSR allowed nitrifiers, and heterotrophic and autotrophic denitrifiers to thrive in the flocs, revealing a multiple nitrogen removal mechanism in the reactor. Both the nitrifiers and denitrifiers would be restricted by an influent COD/TN ratio more than 0.82, resulting in a decrease of TN removal in the UMSR. To get a TN removal over 80% with a TN load removal above 0.86kg/(m(3)·d) in the UMSR, the influent COD/TN ratio should be less than 0.70.
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Affiliation(s)
- Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China.
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Jiuling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Cheng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kaiwen Deng
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Kai Sun
- State Key Laboratory of Urban Water Resource and Environment, School of Municipal and Environmental Engineering, Harbin Institute of Technology, 73 Huanghe Road, Harbin 150090, PR China
| | - Gerardo Buelna
- Centre de Recherche Industrielle du Québec, 333 Franquet, Québec G1P 4C7, Canada
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43
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Ginn HM, Stuart DI. Recovery of data from perfectly twinned virus crystals revisited. Acta Crystallogr D Struct Biol 2016; 72:817-22. [PMID: 27303802 PMCID: PMC4908870 DOI: 10.1107/s2059798316007117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/27/2016] [Indexed: 11/25/2022] Open
Abstract
Perfect merohedral twinning of crystals is not uncommon and complicates structural analysis. An iterative method for the deconvolution of data from perfectly merohedrally twinned crystals in the presence of noncrystallographic symmetry (NCS) has been reimplemented. It is shown that the method recovers the data effectively using test data, and an independent metric of success, based on special classes of reflections that are unaffected by the twin operator, is now provided. The method was applied to a real problem with fivefold NCS and rather poor-quality diffraction data, and it was found that even in these circumstances the method appears to recover most of the information. The software has been made available in a form that can be applied to other crystal systems.
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Affiliation(s)
- Helen Mary Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David Ian Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
- Diamond House, Harwell Science and Innovation Campus, Fermi Avenue, Didcot OX11 0QX, England
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Song K, Suenaga T, Harper WF, Hori T, Riya S, Hosomi M, Terada A. Effects of aeration and internal recycle flow on nitrous oxide emissions from a modified Ludzak-Ettinger process fed with glycerol. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:19562-19570. [PMID: 26268623 DOI: 10.1007/s11356-015-5129-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/27/2015] [Indexed: 06/04/2023]
Abstract
Nitrous oxide (N2O) is emitted from a modified Ludzak-Ettinger (MLE) process, as a primary activated sludge system, which requires mitigation. The effects of aeration rates and internal recycle flow (IRF) ratios on N2O emission were investigated in an MLE process fed with glycerol. Reducing the aeration rate from 1.5 to 0.5 L/min increased gaseous the N2O concentration from the aerobic tank and the dissolved N2O concentration in the anoxic tank by 54.4 and 53.4 %, respectively. During the period of higher aeration, the N2O-N conversion ratio was 0.9 % and the potential N2O reducers were predominantly Rhodobacter, which accounted for 21.8 % of the total population. Increasing the IRF ratio from 3.6 to 7.2 decreased the N2O emission rate from the aerobic tank and the dissolved N2O concentration in the anoxic tank by 56 and 48 %, respectively. This study suggests effective N2O mitigation strategies for MLE systems.
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Affiliation(s)
- Kang Song
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo, 184-8588, Japan
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Toshikazu Suenaga
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo, 184-8588, Japan
| | - Willie F Harper
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Tomoyuki Hori
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo, 184-8588, Japan
| | - Masaaki Hosomi
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo, 184-8588, Japan
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka, Koganei, Tokyo, 184-8588, Japan.
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45
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Rathnayake RMLD, Oshiki M, Ishii S, Segawa T, Satoh H, Okabe S. Effects of dissolved oxygen and pH on nitrous oxide production rates in autotrophic partial nitrification granules. BIORESOURCE TECHNOLOGY 2015; 197:15-22. [PMID: 26318242 DOI: 10.1016/j.biortech.2015.08.054] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 05/20/2023]
Abstract
The effects of dissolved oxygen (DO) and pH on nitrous oxide (N2O) production rates and pathways in autotrophic partial nitrification (PN) granules were investigated at the granular level. N2O was primarily produced by betaproteobacterial ammonia-oxidizing bacteria, mainly Nitrosomonas europaea, in the oxic surface layer (<200μm) of the autotrophic PN granules. N2O production increased with increasing bulk DO concentration owing to activation of the ammonia (i.e., hydroxylamine) oxidation in this layer. The highest N2O emissions were observed at pH 7.5, although the ammonia oxidation rate was unchanged between pH 6.5 and 8.5. Overall, the results of this study suggest that in situ analyses of PN granules are essential to gaining insight into N2O emission mechanisms in a granule.
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Affiliation(s)
- Rathnayake M L D Rathnayake
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo 060-8628, Japan.
| | - Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo 060-8628, Japan; Department of Civil Engineering, Nagaoka National College of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
| | - Satoshi Ishii
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo 060-8628, Japan; Department of Soil, Water, and Climate, BioTechnology Institute, University of Minnesota, 140 Gortner Laboratory of BioChemistry, 1449 Gortner Avenue, St. Paul, MN 55108-1095, USA.
| | - Takahiro Segawa
- Transdisciplinary Research Integration Center, National Institute of Polar Research, 10-3 Midori-cho, Tachikawa, Tokyo 190-8518, Japan.
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo 060-8628, Japan.
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo 060-8628, Japan.
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47
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Lin YW. The broad diversity of heme-protein cross-links: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:844-59. [DOI: 10.1016/j.bbapap.2015.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/26/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
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Dietl A, Maalcke W, Barends TRM. An unexpected reactivity of the P460cofactor in hydroxylamine oxidoreductase. ACTA ACUST UNITED AC 2015; 71:1708-13. [DOI: 10.1107/s1399004715010706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/03/2015] [Indexed: 11/11/2022]
Abstract
Hydroxylamine oxidoreductases (HAOs) contain a unique haem cofactor called P460that consists of a profoundly ruffledc-type haem with two covalent bonds between the haem porphyrin and a conserved tyrosine. This cofactor is exceptional in that it abstracts electrons from a ligand bound to the haem iron, whereas other haems involved in redox chemistry usually inject electrons into their ligands. The effects of the tyrosine cross-links and of the haem ruffling on the chemistry of this cofactor have been investigated theoretically but are not yet clear. A new crystal structure of an HAO fromCandidatusKuenenia stuttgartiensis, a model organism for anaerobic ammonium oxidation, now shows that its P460cofactor has yet another unexpected reactivity: when ethylene glycol was used as a cryoprotectant, the 1.8 Å resolution electron-density maps showed additional density which could be interpreted as an ethylene glycol molecule covalently bound to the C16atom of the haem ring, opposite the covalent links to the conserved tyrosine. Possible causes for this unexpected reactivity are discussed.
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49
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Stein N, Love D, Judd ET, Elliott SJ, Bennett B, Pacheco AA. Correlations between the Electronic Properties of Shewanella oneidensis Cytochrome c Nitrite Reductase (ccNiR) and Its Structure: Effects of Heme Oxidation State and Active Site Ligation. Biochemistry 2015; 54:3749-58. [PMID: 26042961 DOI: 10.1021/acs.biochem.5b00330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electrochemical properties of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR), a homodimer that contains five hemes per protomer, were investigated by UV-visible and electron paramagnetic resonance (EPR) spectropotentiometries. Global analysis of the UV-vis spectropotentiometric results yielded highly reproducible values for the heme midpoint potentials. These midpoint potential values were then assigned to specific hemes in each protomer (as defined in previous X-ray diffraction studies) by comparing the EPR and UV-vis spectropotentiometric results, taking advantage of the high sensitivity of EPR spectra to the structural microenvironment of paramagnetic centers. Addition of the strong-field ligand cyanide led to a 70 mV positive shift of the active site's midpoint potential, as the cyanide bound to the initially five-coordinate high-spin heme and triggered a high-spin to low-spin transition. With cyanide present, three of the remaining hemes gave rise to distinctive and readily assignable EPR spectral changes upon reduction, while a fourth was EPR-silent. At high applied potentials, interpretation of the EPR spectra in the absence of cyanide was complicated by a magnetic interaction that appears to involve three of five hemes in each protomer. At lower applied potentials, the spectra recorded in the presence and absence of cyanide were similar, which aided global assignment of the signals. The midpoint potential of the EPR-silent heme could be assigned by default, but the assignment was also confirmed by UV-vis spectropotentiometric analysis of the H268M mutant of ccNiR, in which one of the EPR-silent heme's histidine axial ligands was replaced with a methionine.
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Affiliation(s)
- Natalia Stein
- †Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Daniel Love
- †Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | | | | | - Brian Bennett
- §Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - A Andrew Pacheco
- †Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
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50
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The octahaem MccA is a haem c-copper sulfite reductase. Nature 2015; 520:706-9. [PMID: 25642962 DOI: 10.1038/nature14109] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/20/2014] [Indexed: 11/08/2022]
Abstract
The six-electron reduction of sulfite to sulfide is the pivot point of the biogeochemical cycle of the element sulfur. The octahaem cytochrome c MccA (also known as SirA) catalyses this reaction for dissimilatory sulfite utilization by various bacteria. It is distinct from known sulfite reductases because it has a substantially higher catalytic activity and a relatively low reactivity towards nitrite. The mechanistic reasons for the increased efficiency of MccA remain to be elucidated. Here we show that anoxically purified MccA exhibited a 2- to 5.5-fold higher specific sulfite reductase activity than the enzyme isolated under oxic conditions. We determined the three-dimensional structure of MccA to 2.2 Å resolution by single-wavelength anomalous dispersion. We find a homotrimer with an unprecedented fold and haem arrangement, as well as a haem bound to a CX15CH motif. The heterobimetallic active-site haem 2 has a Cu(I) ion juxtaposed to a haem c at a Fe-Cu distance of 4.4 Å. While the combination of metals is reminiscent of respiratory haem-copper oxidases, the oxidation-labile Cu(I) centre of MccA did not seem to undergo a redox transition during catalysis. Intact MccA tightly bound SO2 at haem 2, a dehydration product of the substrate sulfite that was partially turned over due to photoreduction by X-ray irradiation, yielding the reaction intermediate SO. Our data show the biometal copper in a new context and function and provide a chemical rationale for the comparatively high catalytic activity of MccA.
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