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Ye C, Huang S, Sha C, Wu J, Cui C, Su J, Ruan J, Tan J, Tang H, Xue J. Changes of bacterial community in arable soil after short-term application of fresh manures and organic fertilizer. ENVIRONMENTAL TECHNOLOGY 2022; 43:824-834. [PMID: 32757721 DOI: 10.1080/09593330.2020.1807608] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The application of animal manure is highly recommended in agricultural production. However, the effect of different kinds of manures on bacterial community in farmland still remains unclear. In this study, a short-term field experiment was conducted to investigate the rapid effects of pig manure (PM), chicken manure (CM) and organic fertilizer (OF, composted by pig manure) application on soil physicochemical properties and soil bacterial community. The results showed that the application of CM and OF significantly increased soil bacterial richness (p < 0.05), mainly correlated with the increase of soil total nitrogen. Compared with CM and PM, OF had the greatest disturbance to soil bacterial structure. And total phosphorus showed the highest correlation with bacterial community. Meanwhile, the application of OF reduced the relative abundance of Actinobacteria, the organic matter synthetic bacteria, and Nitrospirae, the nitrifying bacteria, by 17.18% and 40.00%, respectively. 16S functional prediction analysis results shows that the application of OF increased the relative abundance of genes encoding Ribulose-1,5-bisphosphate carboxylase/oxyg (RuBsiCO), the genes involved in soil Calvin cycling, by 20.51%, and increased the relative abundance of genes encoding nitrous-oxide reductase by 44.86%. In conclusion, Short-term application of OF had greater disturbance to soil bacteria than CM and PM, and it had a significant influence on soil functional bacteria and genes involved in soil carbon and nitrogen cycling.
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Affiliation(s)
- Chunmei Ye
- College of Environmental Science and Engineering, Donghua University, Shanghai, People's Republic of China
| | - Shenfa Huang
- College of Environmental Science and Engineering, Donghua University, Shanghai, People's Republic of China
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Chenyan Sha
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Jinghua Su
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Junjie Ruan
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Juan Tan
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Hao Tang
- Shanghai Academy of Environmental Sciences, Shanghai, People's Republic of China
| | - Jiajia Xue
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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2
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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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3
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Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
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Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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4
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Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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5
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Tosha T, Yamagiwa R, Sawai H, Shiro Y. NO Dynamics in Microbial Denitrification System. CHEM LETT 2021. [DOI: 10.1246/cl.200629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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6
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Cytochrome c oxidase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148335. [PMID: 33171185 DOI: 10.1016/j.bbabio.2020.148335] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Cytochrome c oxidase (COX) deficiency is characterized by a high degree of genetic and phenotypic heterogeneity, partly reflecting the extreme structural complexity, multiple post-translational modification, variable, tissue-specific composition, and the high number of and intricate connections among the assembly factors of this enzyme. In fact, decreased COX specific activity can manifest with different degrees of severity, affect the whole organism or specific tissues, and develop a wide spectrum of disease natural history, including disease onsets ranging from birth to late adulthood. More than 30 genes have been linked to COX deficiency, but the list is still incomplete and in fact constantly updated. We here discuss the current knowledge about COX in health and disease, focusing on genetic aetiology and link to clinical manifestations. In addition, information concerning either fundamental biological features of the enzymes or biochemical signatures of its defects have been provided by experimental in vivo models, including yeast, fly, mouse and fish, which expanded our knowledge on the functional features and the phenotypical consequences of different forms of COX deficiency.
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7
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Takeda H, Kimura T, Nomura T, Horitani M, Yokota A, Matsubayashi A, Ishii S, Shiro Y, Kubo M, Tosha T. Timing of NO Binding and Protonation in the Catalytic Reaction of Bacterial Nitric Oxide Reductase as Established by Time-Resolved Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan
| | - Azusa Yokota
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Akiko Matsubayashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Shoko Ishii
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
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8
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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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9
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Jones SM, Heppner DE, Vu K, Kosman DJ, Solomon EI. Rapid Decay of the Native Intermediate in the Metallooxidase Fet3p Enables Controlled Fe II Oxidation for Efficient Metabolism. J Am Chem Soc 2020; 142:10087-10101. [PMID: 32379440 DOI: 10.1021/jacs.0c02384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The multicopper oxidases (MCOs) couple four 1e- oxidations of substrate to the 4e- reduction of O2 to H2O. These divide into two groups: those that oxidize organic substrates with high turnover frequencies (TOFs) up to 560 s-1 and those that oxidize metal ions with low TOFs, ∼1 s-1 or less. The catalytic mechanism of the organic oxidases has been elucidated, and the high TOF is achieved through rapid intramolecular electron transfer (IET) to the native intermediate (NI), which only slowly decays to the resting form. Here, we uncover the factors that govern the low TOF in Fet3p, a prototypical metallooxidase, in the context of the MCO mechanism. We determine that the NI decays rapidly under optimal turnover conditions, and the mechanism thereby becomes rate-limited by slow IET to the resting enzyme. Development of a catalytic model leads to the important conclusions that proton delivery to the NI controls the mechanism and enables the slow turnover in Fet3p that is functionally significant in Fe metabolism enabling efficient ferroxidase activity while avoiding ROS generation.
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Affiliation(s)
- Stephen M Jones
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, California 94305, United States
| | - David E Heppner
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, California 94305, United States
| | - Kenny Vu
- Department of Biochemistry, The University at Buffalo, 140 Farber Hall, 3435 Main Street, Buffalo, New York 14214, United States
| | - Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, 140 Farber Hall, 3435 Main Street, Buffalo, New York 14214, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive Stanford, California 94305, United States
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10
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Kwon H, Basran J, Devos JM, Suardíaz R, van der Kamp MW, Mulholland AJ, Schrader TE, Ostermann A, Blakeley MP, Moody PCE, Raven EL. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Proc Natl Acad Sci U S A 2020; 117:6484-6490. [PMID: 32152099 PMCID: PMC7104402 DOI: 10.1073/pnas.1918936117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.
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Affiliation(s)
- Hanna Kwon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Juliette M Devos
- Life Sciences Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Reynier Suardíaz
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Tobias E Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, D-85748 Garching, Germany
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 38000 Grenoble, France
| | - Peter C E Moody
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, United Kingdom;
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Emma L Raven
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
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11
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Mahinthichaichan P, Gennis RB, Tajkhorshid E. Bacterial denitrifying nitric oxide reductases and aerobic respiratory terminal oxidases use similar delivery pathways for their molecular substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:712-724. [PMID: 29883591 DOI: 10.1016/j.bbabio.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/05/2018] [Accepted: 06/04/2018] [Indexed: 10/14/2022]
Abstract
The superfamily of heme‑copper oxidoreductases (HCOs) include both NO and O2 reductases. Nitric oxide reductases (NORs) are bacterial membrane enzymes that catalyze an intermediate step of denitrification by reducing nitric oxide (NO) to nitrous oxide (N2O). They are structurally similar to heme‑copper oxygen reductases (HCOs), which reduce O2 to water. The experimentally observed apparent bimolecular rate constant of NO delivery to the deeply buried catalytic site of NORs was previously reported to approach the diffusion-controlled limit (108-109 M-1 s-1). Using the crystal structure of cytochrome-c dependent NOR (cNOR) from Pseudomonas aeruginosa, we employed several protocols of molecular dynamics (MD) simulation, which include flooding simulations of NO molecules, implicit ligand sampling and umbrella sampling simulations, to elucidate how NO in solution accesses the catalytic site of this cNOR. The results show that NO partitions into the membrane, enters the enzyme from the lipid bilayer and diffuses to the catalytic site via a hydrophobic tunnel that is resolved in the crystal structures. This is similar to what has been found for O2 diffusion through the closely related O2 reductases. The apparent second order rate constant approximated using the simulation data is ~5 × 108 M-1 s-1, which is optimized by the dynamics of the amino acid side chains lining in the tunnel. It is concluded that both NO and O2 reductases utilize well defined hydrophobic tunnels to assure that substrate diffusion to the buried catalytic sites is not rate limiting under physiological conditions.
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Affiliation(s)
- Paween Mahinthichaichan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Street, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, 405 North Mathews Avenue, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, 179 Looomis, MC-704, 1110 Green Street, Urbana, IL 61801, USA.
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12
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Yamagiwa R, Kurahashi T, Takeda M, Adachi M, Nakamura H, Arai H, Shiro Y, Sawai H, Tosha T. Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:333-341. [PMID: 29499184 DOI: 10.1016/j.bbabio.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/18/2018] [Accepted: 02/24/2018] [Indexed: 11/30/2022]
Abstract
Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N2O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO2-) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies.
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Affiliation(s)
- Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takuya Kurahashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mariko Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mayuho Adachi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Hiro Nakamura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroyuki Arai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
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Ter Beek J, Kahle M, Ädelroth P. Modulation of protein function in membrane mimetics: Characterization of P. denitrificans cNOR in nanodiscs or liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1951-1961. [PMID: 28668220 DOI: 10.1016/j.bbamem.2017.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/03/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
For detailed functional characterization, membrane proteins are usually studied in detergent. However, it is becoming clear that detergent micelles are often poor mimics of the lipid environment in which these proteins function. In this work we compared the catalytic properties of the membrane-embedded cytochrome c-dependent nitric oxide reductase (cNOR) from Paracoccus (P.) denitrificans in detergent, lipid/protein nanodiscs, and proteoliposomes. We used two different lipid mixtures, an extract of soybean lipids and a defined mix of synthetic lipids mimicking the original P. denitrificans membrane. We show that the catalytic activity of detergent-solubilized cNOR increased threefold upon reconstitution from detergent into proteoliposomes with the P. denitrificans lipid mixture, and above two-fold when soybean lipids were used. In contrast, there was only a small activity increase in nanodiscs. We further show that binding of the gaseous ligands CO and O2 are affected differently by reconstitution. In proteoliposomes the turnover rates are affected much more than in nanodiscs, but CO-binding is more significantly accelerated in liposomes with soybean lipids, while O2-binding is faster with the P. denitrificans lipid mix. We also investigated proton-coupled electron transfer during the reaction between fully reduced cNOR and O2, and found that the pKa of the internal proton donor was increased in proteoliposomes but not in nanodiscs. Taking our results together, the liposome-reconstituted enzyme shows significant differences to detergent-solubilized protein. Nanodiscs show much more subtle effects, presumably because of their much lower lipid to protein ratio. Which of these two membrane-mimetic systems best mimics the native membrane is discussed.
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Affiliation(s)
- Josy Ter Beek
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
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14
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Carvalheda CA, Pisliakov AV. Insights into proton translocation in cbb 3 oxidase from MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:396-406. [PMID: 28259641 DOI: 10.1016/j.bbabio.2017.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/03/2017] [Accepted: 02/27/2017] [Indexed: 01/18/2023]
Abstract
Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb3) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom molecular dynamics simulations and continuum electrostatics calculations to obtain atomic-level insights into the hydration and dynamics of a cbb3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chemical" and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337.
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Affiliation(s)
- Catarina A Carvalheda
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom; Physics, School of Sciences and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN, United Kingdom.
| | - Andrei V Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom; Physics, School of Sciences and Engineering, University of Dundee, Nethergate, Dundee, DD1 4HN, United Kingdom.
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15
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Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans. PLoS One 2016; 11:e0152745. [PMID: 27030968 PMCID: PMC4816578 DOI: 10.1371/journal.pone.0152745] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/18/2016] [Indexed: 01/22/2023] Open
Abstract
Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed.
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Torres M, Simon J, Rowley G, Bedmar E, Richardson D, Gates A, Delgado M. Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms. Adv Microb Physiol 2016; 68:353-432. [PMID: 27134026 DOI: 10.1016/bs.ampbs.2016.02.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.
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Al-Attar S, de Vries S. An electrogenic nitric oxide reductase. FEBS Lett 2015; 589:2050-7. [PMID: 26149211 DOI: 10.1016/j.febslet.2015.06.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
Nitric oxide reductases (Nors) are members of the heme-copper oxidase superfamily that reduce nitric oxide (NO) to nitrous oxide (N₂O). In contrast to the proton-pumping cytochrome oxidases, Nors studied so far have neither been implicated in proton pumping nor have they been experimentally established as electrogenic. The copper-A-dependent Nor from Bacillus azotoformans uses cytochrome c₅₅₁ as electron donor but lacks menaquinol activity, in contrast to our earlier report (Suharti et al., 2001). Employing reduced phenazine ethosulfate (PESH) as electron donor, the main NO reduction pathway catalyzed by Cu(A)Nor reconstituted in liposomes involves transmembrane cycling of the PES radical. We show that Cu(A)Nor reconstituted in liposomes generates a proton electrochemical gradient across the membrane similar in magnitude to cytochrome aa₃, highlighting that bacilli using Cu(A)Nor can exploit NO reduction for increased cellular ATP production compared to organisms using cNor.
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Affiliation(s)
- Sinan Al-Attar
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, The Netherlands
| | - Simon de Vries
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, The Netherlands.
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Terasaka E, Okada N, Sato N, Sako Y, Shiro Y, Tosha T. Characterization of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus: enzymatic activity and active site structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1019-26. [PMID: 24569054 DOI: 10.1016/j.bbabio.2014.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 10/25/2022]
Abstract
Nitric oxide reductase (NOR) catalyzes the reduction of nitric oxide to generate nitrous oxide. We recently reported on the crystal structure of a quinol-dependent NOR (qNOR) from Geobacillus stearothermophilus [Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita and Y. Shiro, Nat. Struct. Mol. Biol. 19 (2012) 238-246], and suggested that a water channel from the cytoplasm, which is not observed in cytochrome c-dependent NOR (cNOR), functions as a pathway transferring catalytic protons. Here, we further investigated the functional and structural properties of qNOR, and compared the findings with those for cNOR. The pH optimum for the enzymatic reaction of qNOR was in the alkaline range, whereas Pseudomonas aeruginosa cNOR showed a higher activity at an acidic pH. The considerably slower reduction rate, and a correlation of the pH dependence for enzymatic activity and the reduction rate suggest that the reduction process is the rate-determining step for the NO reduction by qNOR, while the reduction rate for cNOR was very fast and therefore is unlikely to be the rate-determining step. A close examination of the heme/non-heme iron binuclear center by resonance Raman spectroscopy indicated that qNOR has a more polar environment at the binuclear center compared with cNOR. It is plausible that a water channel enhances the accessibility of the active site to solvent water, creating a more polar environment in qNOR. This structural feature could control certain properties of the active site, such as redox potential, which could explain the different catalytic properties of the two NORs. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Erina Terasaka
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Norihiro Okada
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Nozomi Sato
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshihiko Sako
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitsugu Shiro
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
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Fischer N, Raunest M, Schmidt TH, Koch DC, Kandt C. Efflux pump-mediated antibiotics resistance: Insights from computational structural biology. Interdiscip Sci 2014; 6:1-12. [DOI: 10.1007/s12539-014-0191-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 09/03/2013] [Accepted: 11/18/2013] [Indexed: 01/08/2023]
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20
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Sato N, Ishii S, Sugimoto H, Hino T, Fukumori Y, Sako Y, Shiro Y, Tosha T. Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes. Proteins 2014; 82:1258-71. [PMID: 24338896 DOI: 10.1002/prot.24492] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 11/07/2022]
Abstract
Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N2O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non-heme Fe center. We report herein on the structures of the reduced and ligand-bound forms of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3-2.7 Å, to elucidate structure-function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO-bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH3-CH=N-OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ∼0.5 Å increase in the heme/non-heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton-pumping activity in cNOR, because redox-coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non-heme Fe distance even in the bulky ligand-bound form of cNOR (∼4.5 Å) than the heme/Cu distance in CCO (∼5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N-N coupling to produce a hyponitrite intermediate for the generation of N2O.
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Affiliation(s)
- Nozomi Sato
- Biometal Science Laboratory, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Ter Beek J, Krause N, Reimann J, Lachmann P, Ädelroth P. The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway. J Biol Chem 2013; 288:30626-30635. [PMID: 24014024 DOI: 10.1074/jbc.m113.497347] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The NO reductase from Paracoccus denitrificans reduces NO to N2O (2NO + 2H(+) + 2e(-) → N2O + H2O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O2-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O2 reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O2. We further show that electron transfer during single-turnover reduction of O2 is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.
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Affiliation(s)
- Josy Ter Beek
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Nils Krause
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Joachim Reimann
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Lachmann
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- From the Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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Characterization of the nitric oxide reductase from Thermus thermophilus. Proc Natl Acad Sci U S A 2013; 110:12613-8. [PMID: 23858452 DOI: 10.1073/pnas.1301731110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas implicated in climate change. The dominant source of atmospheric N2O is incomplete biological dentrification, and the enzymes responsible for the release of N2O are NO reductases. It was recently reported that ambient emissions of N2O from the Great Boiling Spring in the United States Great Basin are high, and attributed to incomplete denitrification by Thermus thermophilus and related bacterial species [Hedlund BP, et al. (2011) Geobiology 9(6)471-480]. In the present work, we have isolated and characterized the NO reductase (NOR) from T. thermophilus. The enzyme is a member of the cNOR family of enzymes and belongs to a phylogenetic clade that is distinct from previously examined cNORs. Like other characterized cNORs, the T. thermophilus cNOR consists of two subunits, NorB and NorC, and contains a one heme c, one Ca(2+), a low-spin heme b, and an active site consisting of a high-spin heme b and FeB. The roles of conserved residues within the cNOR family were investigated by site-directed mutagenesis. The most important and unexpected result is that the glutamic acid ligand to FeB is not essential for function. The E211A mutant retains 68% of wild-type activity. Mutagenesis data and the pattern of conserved residues suggest that there is probably not a single pathway for proton delivery from the periplasm to the active site that is shared by all cNORs, and that there may be multiple pathways within the T. thermophilus cNOR.
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Brzezinski P, Öjemyr LN, Ädelroth P. Intermediates generated during the reaction of reduced Rhodobacter sphaeroides cytochrome c oxidase with dioxygen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:843-7. [DOI: 10.1016/j.bbabio.2013.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
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Detection of an intermediary, protonated water cluster in photosynthetic oxygen evolution. Proc Natl Acad Sci U S A 2013; 110:10634-9. [PMID: 23757501 DOI: 10.1073/pnas.1306532110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In photosynthesis, photosystem II evolves oxygen from water by the accumulation of photooxidizing equivalents at the oxygen-evolving complex (OEC). The OEC is a Mn4CaO5 cluster, and its sequentially oxidized states are termed the Sn states. The dark-stable state is S1, and oxygen is released during the transition from S3 to S0. In this study, a laser flash induces the S1 to S2 transition, which corresponds to the oxidation of Mn(III) to Mn(IV). A broad infrared band, at 2,880 cm(-1), is produced during this transition. Experiments using ammonia and (2)H2O assign this band to a cationic cluster of internal water molecules, termed "W5(+)." Observation of the W5(+) band is dependent on the presence of calcium, and flash dependence is observed. These data provide evidence that manganese oxidation during the S1 to S2 transition results in a coupled proton transfer to a substrate-containing, internal water cluster in the OEC hydrogen-bonded network.
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Tosha T, Shiro Y. Crystal structures of nitric oxide reductases provide key insights into functional conversion of respiratory enzymes. IUBMB Life 2013; 65:217-26. [DOI: 10.1002/iub.1135] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 12/25/2012] [Indexed: 11/08/2022]
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