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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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2
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Jia Y, Zhou M, Chen Y, Luo J, Hu Y. Carbon selection for nitrogen degradation pathway by Stenotrophomonas maltophilia: Based on the balances of nitrogen, carbon and electron. BIORESOURCE TECHNOLOGY 2019; 294:122114. [PMID: 31520854 DOI: 10.1016/j.biortech.2019.122114] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
A novel strain DQ01 capable of simultaneous removal of nitrate and ammonium under the aerobic condition was isolated from the landfill leachate and identified as Stenotrophomonas maltophilia. The result showed that S. maltophilia had carbon selection for the nitrogen removal pathway, and preferred to utilize carboxylate rather than carbohydrate, as carboxylate could directly participate in TCA cycle without Embden Meyerhof Parmas (EMP). Nitrogen and carbon balances confirmed that the ammonium assimilation was the main or even sole removal pathway for S. maltophilia, and carboxylate was more conducive to heterotrophic nitrification-aerobic denitrification (HN-AD) process due to the serious self-alkalization and higher reduction potential of carboxylate, which followed: NH4+ → NO2- → NO3- → NO2- → NO due to the lack of nor and nos. Meanwhile, the higher C/N and nitrate could generate a more powerful ion transport driving force to accelerate the electron transfer in the denitrifying respiratory chain.
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Affiliation(s)
- Yating Jia
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Miaomiao Zhou
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yuancai Chen
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
| | - Jun Luo
- South China Institute of Environmental Science, Ministry of Ecology and Environment of People's Republic of China, Guangzhou 510000, China
| | - Yongyou Hu
- Ministry of Education Key Laboratory of Pollution Control and Ecological Remediation for Industrial Agglomeration Area, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
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3
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Gomes FO, Maia LB, Loureiro JA, Pereira MC, Delerue-Matos C, Moura I, Moura JJ, Morais S. Biosensor for direct bioelectrocatalysis detection of nitric oxide using nitric oxide reductase incorporated in carboxylated single-walled carbon nanotubes/lipidic 3 bilayer nanocomposite. Bioelectrochemistry 2019; 127:76-86. [DOI: 10.1016/j.bioelechem.2019.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 02/07/2023]
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4
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Samhan-Arias AK, Cordas CM, Carepo MS, Maia LB, Gutierrez-Merino C, Moura I, Moura JJG. Ligand accessibility to heme cytochrome b 5 coordinating sphere and enzymatic activity enhancement upon tyrosine ionization. J Biol Inorg Chem 2019; 24:317-330. [PMID: 30838452 DOI: 10.1007/s00775-019-01649-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/21/2019] [Indexed: 01/21/2023]
Abstract
Recently, we observed that at extreme alkaline pH, cytochrome b5 (Cb5) acquires a peroxidase-like activity upon formation of a low spin hemichrome associated with a non-native state. A functional characterization of Cb5, in a wide pH range, shows that oxygenase/peroxidase activities are stimulated in alkaline media, and a correlation between tyrosine ionization and the attained enzymatic activities was noticed, associated with an altered heme spin state, when compared to acidic pH values at which the heme group is released. In these conditions, a competitive assay between imidazole binding and Cb5 endogenous heme ligands revealed the appearance of a binding site for this exogenous ligand that promotes a heme group exposure to the solvent upon ligation. Our results shed light on the mechanism behind Cb5 oxygenase/peroxidase activity stimulation in alkaline media and reveal a role of tyrosinate anion enhancing Cb5 enzymatic activities on the distorted protein before maximum protein unfolding.
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Affiliation(s)
- Alejandro K Samhan-Arias
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal.
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - Marta S Carepo
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - Luisa B Maia
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - Carlos Gutierrez-Merino
- Department of Biochemistry and Molecular Biology, Faculty of Sciences and Institute of Molecular Pathology Biomarkers, University of Extremadura, 06006, Badajoz, Spain
| | - Isabel Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal
| | - José J G Moura
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Lisbon, Portugal.
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5
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Kato M, Nakagawa S, Tosha T, Shiro Y, Masuda Y, Nakata K, Yagi I. Surface-Enhanced Infrared Absorption Spectroscopy of Bacterial Nitric Oxide Reductase under Electrochemical Control Using a Vibrational Probe of Carbon Monoxide. J Phys Chem Lett 2018; 9:5196-5200. [PMID: 30141632 DOI: 10.1021/acs.jpclett.8b02581] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nitric oxide reductases (NORs) reduce nitric oxide to nitrous oxide in the denitrification pathway of the global nitrogen cycle. NORs contain four iron cofactors and the NO reduction occurs at the heme b3/nonheme FeB binuclear active site. The determination of reduction potentials of the iron cofactors will help us elucidate the enzymatic reaction mechanism. However, previous reports on these potentials remain controversial. Herein, we performed electrochemical and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements of Pseudomonas aeruginosa NOR immobilized on gold electrodes. Cyclic voltammograms exhibited two reduction peaks at -0.11 and -0.44 V vs SHE, and a SEIRA spectrum using a vibrational probe of CO showed a characteristic band at 1972 cm-1 at -0.4 V vs SHE, which was assigned to νCO of heme b3-CO. Our results suggest that the reduction of heme b3 initiates the enzymatic NO reduction.
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Affiliation(s)
- Masaru Kato
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN) , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
| | | | - Takehiko Tosha
- RIKEN , SPring-8 Center , Kouto, Sayo , Hyogo 679-5148 , Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science , University of Hyogo , Hyogo 678-1297 , Japan
| | | | | | - Ichizo Yagi
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN) , National Institute for Materials Science (NIMS) , Tsukuba 305-0044 , Japan
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6
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Gomes FO, Maia LB, Cordas C, Moura I, Delerue-Matos C, Moura JJG, Morais S. Electroanalytical characterization of the direct Marinobacter hydrocarbonoclasticus nitric oxide reductase-catalysed nitric oxide and dioxygen reduction. Bioelectrochemistry 2018; 125:8-14. [PMID: 30176545 DOI: 10.1016/j.bioelechem.2018.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 02/07/2023]
Abstract
Understanding the direct electron transfer processes between redox proteins and electrode surface is fundamental to understand the proteins mechanistic properties and for development of novel biosensors. In this study, nitric oxide reductase (NOR) extracted from Marinobacter hydrocarbonoclasticus bacteria was adsorbed onto a pyrolytic graphite electrode (PGE) to develop an unmediated enzymatic biosensor (PGE/NOR)) for characterization of NOR direct electrochemical behaviour and NOR electroanalytical features towards NO and O2. Square-wave voltammetry showed the reduction potential of all the four NOR redox centers: 0.095 ± 0.002, -0.108 ± 0.008, -0.328 ± 0.001 and -0.635 ± 0.004 V vs. SCE for heme c, heme b, heme b3 and non-heme FeB, respectively. The determined sensitivity (-4.00 × 10-8 ± 1.84 × 10-9 A/μM and - 2.71 × 10-8 ± 1.44 × 10-9 A/μM for NO and O2, respectively), limit of detection (0.5 μM for NO and 1.0 μM for O2) and the Michaelis Menten constant (2.1 and 7.0 μM for NO and O2, respectively) corroborated the higher affinity of NOR for its natural substrate (NO). No significant interference on sensitivity towards NO was perceived in the presence of O2, while the O2 reduction was markedly and negatively impacted (3.6 times lower sensitivity) by the presence of NO. These results clearly demonstrate the high potential of NOR for the design of innovative NO biosensors.
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Affiliation(s)
- Filipa O Gomes
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida n° 451, 4249-015 Porto, Portugal; REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Luísa B Maia
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Cristina Cordas
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Isabel Moura
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Cristina Delerue-Matos
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida n° 451, 4249-015 Porto, Portugal
| | - José J G Moura
- REQUIMTE-LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Simone Morais
- REQUIMTE-LAQV, Instituto Superior de Engenharia do Instituto Politécnico do Porto, Rua Dr. António Bernardino de Almeida n° 451, 4249-015 Porto, Portugal.
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7
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Heme redox potentials hold the key to reactivity differences between nitric oxide reductase and heme-copper oxidase. Proc Natl Acad Sci U S A 2018; 115:6195-6200. [PMID: 29802230 DOI: 10.1073/pnas.1720298115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite high structural homology between NO reductases (NORs) and heme-copper oxidases (HCOs), factors governing their reaction specificity remain to be understood. Using a myoglobin-based model of NOR (FeBMb) and tuning its heme redox potentials (E°') to cover the native NOR range, through manipulating hydrogen bonding to the proximal histidine ligand and replacing heme b with monoformyl (MF-) or diformyl (DF-) hemes, we herein demonstrate that the E°' holds the key to reactivity differences between NOR and HCO. Detailed electrochemical, kinetic, and vibrational spectroscopic studies, in tandem with density functional theory calculations, demonstrate a strong influence of heme E°' on NO reduction. Decreasing E°' from +148 to -130 mV significantly impacts electronic properties of the NOR mimics, resulting in 180- and 633-fold enhancements in NO association and heme-nitrosyl decay rates, respectively. Our results indicate that NORs exhibit finely tuned E°' that maximizes their enzymatic efficiency and helps achieve a balance between opposite factors: fast NO binding and decay of dinitrosyl species facilitated by low E°' and fast electron transfer facilitated by high E°'. Only when E°' is optimally tuned in FeBMb(MF-heme) for NO binding, heme-nitrosyl decay, and electron transfer does the protein achieve multiple (>35) turnovers, previously not achieved by synthetic or enzyme-based NOR models. This also explains a long-standing question in bioenergetics of selective cross-reactivity in HCOs. Only HCOs with heme E°' in a similar range as NORs (between -59 and 200 mV) exhibit NOR reactivity. Thus, our work demonstrates efficient tuning of E°' in various metalloproteins for their optimal functionality.
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8
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Hutfless EH, Chaudhari SS, Thomas VC. Emerging Roles of Nitric Oxide Synthase in Bacterial Physiology. Adv Microb Physiol 2018; 72:147-191. [PMID: 29778214 DOI: 10.1016/bs.ampbs.2018.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nitric oxide (NO) is a potent inhibitor of diverse cellular processes in bacteria. Therefore, it was surprising to discover that several bacterial species, primarily Gram-positive organisms, harboured a gene encoding nitric oxide synthase (NOS). Recent attempts to characterize bacterial NOS (bNOS) have resulted in the discovery of structural features that may allow it to function as a NO dioxygenase and produce nitrate in addition to NO. Consistent with this characterization, investigations into the biological function of bNOS have also emphasized a role for NOS-dependent nitrate and nitrite production in aerobic and microaerobic respiration. In this review, we aim to compare, contrast, and summarize the structure, biochemistry, and biological role of bNOS with mammalian NOS and discuss how recent advances in our understanding of bNOS have enabled efforts at designing inhibitors against it.
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Affiliation(s)
| | | | - Vinai C Thomas
- University of Nebraska Medical Center, Omaha, NE, United States.
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9
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Melin F, Xie H, Meyer T, Ahn YO, Gennis RB, Michel H, Hellwig P. The unusual redox properties of C-type oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1892-1899. [PMID: 27664317 DOI: 10.1016/j.bbabio.2016.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/15/2016] [Accepted: 09/19/2016] [Indexed: 10/21/2022]
Abstract
Cytochrome cbb3 (also known as C-type) oxidases belong to the family of heme-copper terminal oxidases which couple at the end of the respiratory chain the reduction of molecular oxygen into water and the pumping of protons across the membrane. They are expressed most often at low pressure of O2 and they exhibit a low homology of sequence with the cytochrome aa3 (A-type) oxidases found in mitochondria. Their binuclear active site comprises a high-spin heme b3 associated with a CuB center. The protein also contains one low-spin heme b and 3 hemes c. We address here the redox properties of cbb3 oxidases from three organisms, Rhodobacter sphaeroides, Vibrio cholerae and Pseudomonas stutzeri by means of electrochemical and spectroscopic techniques. We show that the redox potential of the heme b3 exhibits a relatively low midpoint potential, as in related cytochrome c-dependent nitric oxide reductases. Potential implications for the coupled electron transfer and proton uptake mechanism of C-type oxidases are discussed.
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Affiliation(s)
- Frederic Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg, 1 Rue Blaise Pascal, 67000 Strasbourg, France
| | - Hao Xie
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Thomas Meyer
- Laboratoire de Bioélectrochimie et Spectroscopie, Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg, 1 Rue Blaise Pascal, 67000 Strasbourg, France
| | - Young Ok Ahn
- Department of Biochemistry, University of Illinois at Urbana Champaign, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana Champaign, USA
| | - Hartmut Michel
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, Chimie de la Matière Complexe, UMR 7140, Université de Strasbourg, 1 Rue Blaise Pascal, 67000 Strasbourg, France.
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10
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Blomberg MR, Siegbahn PE. Why is the reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR) not electrogenic? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:826-33. [DOI: 10.1016/j.bbabio.2013.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/27/2013] [Accepted: 04/13/2013] [Indexed: 11/29/2022]
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11
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Electrochemical behaviour of bacterial nitric oxide reductase-evidence of low redox potential non-heme Fe(B) gives new perspectives on the catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:233-8. [PMID: 23142527 DOI: 10.1016/j.bbabio.2012.10.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/26/2012] [Accepted: 10/31/2012] [Indexed: 11/20/2022]
Abstract
Nitric oxide reductase (NOR) is a membrane bound enzyme involved in the metabolic denitrification pathway, reducing nitric oxide (NO) to nitrous oxide (N(2)O), subsequently promoting the formation of the NN bond. Three types of bacterial NOR are known, namely cNOR, qNOR and qCuNOR, that differ on the physiological electron donor. cNOR has been purified as a two subunit complex, the NorC, anchored to the cytoplasmic membrane, with a low-spin heme c, and the NorB subunit showing high structural homology with the HCuO subunit I, comprising a bis-histidine low-spin heme b and a binuclear iron centre. The binuclear iron centre is the catalytic site and it is formed by a heme b(3) coupled to a non-heme iron (Fe(B)) through a μ-oxo bridge. The catalytic mechanism is still under discussion and three hypotheses have been proposed: the trans-mechanism, the cis-Fe(B) and the cis-heme b(3) mechanisms. In the present work, the Pseudomonas nautica cNOR electrochemical behaviour was studied by cyclic voltammetry (CV), using a pyrolytic graphite electrode modified with the immobilised protein. The protein redox centres were observed and the formal redox potentials were determined. The binuclear iron centre presents the lowest redox potential value, and discrimination between the heme b(3) and Fe(B) redox processes was attained. Also, the number of electrons involved and correspondent surface electronic transfer rate constants were estimated. The pH dependence of the observed redox processes was determined and some new insights on the NOR catalytic mechanism are discussed.
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12
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Chen J, Strous M. Denitrification and aerobic respiration, hybrid electron transport chains and co-evolution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:136-44. [PMID: 23044391 DOI: 10.1016/j.bbabio.2012.10.002] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/26/2012] [Accepted: 10/01/2012] [Indexed: 11/18/2022]
Abstract
This paper explores the bioenergetics and potential co-evolution of denitrification and aerobic respiration. The advantages and disadvantages of combining these two pathways in a single, hybrid respiratory chain are discussed and the experimental evidence for the co-respiration of nitrate and oxygen is critically reviewed. A scenario for the co-evolution of the two pathways is presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Jianwei Chen
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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13
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Blomberg MRA, Siegbahn PEM. Mechanism for N2O Generation in Bacterial Nitric Oxide Reductase: A Quantum Chemical Study. Biochemistry 2012; 51:5173-86. [DOI: 10.1021/bi300496e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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14
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Bueno E, Mesa S, Bedmar EJ, Richardson DJ, Delgado MJ. Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. Antioxid Redox Signal 2012; 16:819-52. [PMID: 22098259 PMCID: PMC3283443 DOI: 10.1089/ars.2011.4051] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 12/22/2022]
Abstract
Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, CSIC, Granada, Spain
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15
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Hino T, Nagano S, Sugimoto H, Tosha T, Shiro Y. Molecular structure and function of bacterial nitric oxide reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:680-7. [PMID: 22001779 DOI: 10.1016/j.bbabio.2011.09.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 09/29/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
Abstract
The crystal structure of the membrane-integrated nitric oxide reductase cNOR from Pseudomonas aeruginosa was determined. The smaller NorC subunit of cNOR is comprised of 1 trans-membrane helix and a hydrophilic domain, where the heme c is located, while the larger NorB subunit consists of 12 trans-membrane helices, which contain heme b and the catalytically active binuclear center (heme b(3) and non-heme Fe(B)). The roles of the 5 well-conserved glutamates in NOR are discussed, based on the recently solved structure. Glu211 and Glu280 appear to play an important role in the catalytic reduction of NO at the binuclear center by functioning as a terminal proton donor, while Glu215 probably contributes to the electro-negative environment of the catalytic center. Glu135, a ligand for Ca(2+) sandwiched between two heme propionates from heme b and b(3), and the nearby Glu138 appears to function as a structural factor in maintaining a protein conformation that is suitable for electron-coupled proton transfer from the periplasmic region to the active site. On the basis of these observations, the possible molecular mechanism for the reduction of NO by cNOR is discussed. This article is part of a Special Issue entitled: Respiratory Oxidases.
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