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Superoxide Anion Chemistry-Its Role at the Core of the Innate Immunity. Int J Mol Sci 2023; 24:ijms24031841. [PMID: 36768162 PMCID: PMC9916283 DOI: 10.3390/ijms24031841] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Classically, superoxide anion O2•- and reactive oxygen species ROS play a dual role. At the physiological balance level, they are a by-product of O2 reduction, necessary for cell signalling, and at the pathological level they are considered harmful, as they can induce disease and apoptosis, necrosis, ferroptosis, pyroptosis and autophagic cell death. This revision focuses on understanding the main characteristics of the superoxide O2•-, its generation pathways, the biomolecules it oxidizes and how it may contribute to their modification and toxicity. The role of superoxide dismutase, the enzyme responsible for the removal of most of the superoxide produced in living organisms, is studied. At the same time, the toxicity induced by superoxide and derived radicals is beneficial in the oxidative death of microbial pathogens, which are subsequently engulfed by specialized immune cells, such as neutrophils or macrophages, during the activation of innate immunity. Ultimately, this review describes in some depth the chemistry related to O2•- and how it is harnessed by the innate immune system to produce lysis of microbial agents.
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Martins MC, Romão CV, Folgosa F, Borges PT, Frazão C, Teixeira M. How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes. Free Radic Biol Med 2019; 140:36-60. [PMID: 30735841 DOI: 10.1016/j.freeradbiomed.2019.01.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O2 and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O2 and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.
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Affiliation(s)
- Maria C Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Filipe Folgosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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3
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Horch M. Rational redox tuning of transition metal sites: learning from superoxide reductase. Chem Commun (Camb) 2019; 55:9148-9151. [PMID: 31304493 DOI: 10.1039/c9cc04004h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using superoxide reductase as a model system, a computational approach reveals how histidine tautomerism tunes the redox properties of metalloenzymes to enable their catalytic function. Inspired by these experimentally inaccessible insights, non-canonical histidine congeners are introduced as new versatile tools for the rational engineering of biological transition metal sites.
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Affiliation(s)
- Marius Horch
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK.
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4
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Romão CV, Matias PM, Sousa CM, Pinho FG, Pinto AF, Teixeira M, Bandeiras TM. Insights into the Structures of Superoxide Reductases from the Symbionts Ignicoccus hospitalis and Nanoarchaeum equitans. Biochemistry 2018; 57:5271-5281. [PMID: 29939726 DOI: 10.1021/acs.biochem.8b00334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Superoxide reductases (SORs) are enzymes that detoxify the superoxide anion through its reduction to hydrogen peroxide and exist in both prokaryotes and eukaryotes. The substrate is transformed at an iron catalytic center, pentacoordinated in the ferrous state by four histidines and one cysteine. SORs have a highly conserved motif, (E)(K)HxP-, in which the glutamate is associated with a redox-driven structural change, completing the octahedral coordination of the iron in the ferric state, whereas the lysine may be responsible for stabilization and donation of a proton to catalytic intermediates. We aimed to understand at the structural level the role of these two residues, by determining the X-ray structures of the SORs from the hyperthermophilic archaea Ignicoccus hospitalis and Nanoarchaeum equitans that lack the quasi-conserved lysine and glutamate, respectively, but have catalytic rate constants similar to those of the canonical enzymes, as we previously demonstrated. Furthermore, we have determined the crystal structure of the E23A mutant of I. hospitalis SOR, which mimics several enzymes that lack both residues. The structures revealed distinct structural arrangements of the catalytic center that simulate several catalytic cycle intermediates, namely, the reduced and the oxidized forms, and the glutamate-free and deprotonated ferric forms. Moreover, the structure of the I. hospitalis SOR provides evidence for the presence of an alternative lysine close to the iron center in the reduced state that may be a functional substitute for the "canonical" lysine.
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Affiliation(s)
- Célia V Romão
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal
| | - Pedro M Matias
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal.,iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
| | - Cristiana M Sousa
- iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
| | - Filipa G Pinho
- iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
| | - Ana F Pinto
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal
| | - Miguel Teixeira
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal
| | - Tiago M Bandeiras
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier , Universidade Nova de Lisboa , Av. da República , 2780-157 Oeiras , Portugal.,iBET , Instituto de Biologia Experimental e Tecnológica , Apartado 12 , 2781-901 Oeiras , Portugal
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5
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Horch M, Utesch T, Hildebrandt P, Mroginski MA, Zebger I. Domain motions and electron transfer dynamics in 2Fe-superoxide reductase. Phys Chem Chem Phys 2016; 18:23053-66. [DOI: 10.1039/c6cp03666j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical studies on 2Fe-superoxide reductase provide mechanistic insights into structural dynamics and electron transfer efficiencies.
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Affiliation(s)
- Marius Horch
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Tillmann Utesch
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | - Peter Hildebrandt
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
| | | | - Ingo Zebger
- Institut für Chemie
- Technische Universität Berlin
- D-10623 Berlin
- Germany
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6
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Olszewski M, Balsewicz J, Nowak M, Maciejewska N, Cyranka-Czaja A, Zalewska-Piątek B, Piątek R, Kur J. Characterization of a Single-Stranded DNA-Binding-Like Protein from Nanoarchaeum equitans--A Nucleic Acid Binding Protein with Broad Substrate Specificity. PLoS One 2015; 10:e0126563. [PMID: 25973760 PMCID: PMC4431734 DOI: 10.1371/journal.pone.0126563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/03/2015] [Indexed: 11/18/2022] Open
Abstract
Background SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized, obligatory parasite/symbiont of Ignicoccus hospitalis. Results This paper reports on the ssb-like gene cloning, gene expression and characterization of a novel nucleic acid binding protein from Nanoarchaeum equitans archaeon (NeqSSB-like protein). This protein consists of 243 amino acid residues and one OB fold per monomer. It is biologically active as a monomer like as SSBs from some viruses. The NeqSSB-like protein displays a low sequence similarity to the Escherichia coli SSB, namely 10% identity and 29% similarity, and is the most similar to the Sulfolobus solfataricus SSB (14% identity and 32% similarity). The NeqSSB-like protein binds to ssDNA, although it can also bind mRNA and, surprisingly, various dsDNA forms, with no structure-dependent preferences as evidenced by gel mobility shift assays. The size of the ssDNA binding site, which was estimated using fluorescence spectroscopy, is 7±1 nt. No salt-dependent binding mode transition was observed. NeqSSB-like protein probably utilizes a different model for ssDNA binding than the SSB proteins studied so far. This protein is highly thermostable; the half-life of the ssDNA binding activity is 5 min at 100°C and melting temperature (Tm) is 100.2°C as shown by differential scanning calorimetry (DSC) analysis. Conclusion NeqSSB-like protein is a novel highly thermostable protein which possesses a unique broad substrate specificity and is able to bind all types of nucleic acids.
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Affiliation(s)
- Marcin Olszewski
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
- * E-mail:
| | - Jan Balsewicz
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Marta Nowak
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Natalia Maciejewska
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Anna Cyranka-Czaja
- University of Wroclaw, Faculty of Biotechnology, Department of Protein Engineering, 50–138, Wrocław, Poland
| | - Beata Zalewska-Piątek
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Rafał Piątek
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Józef Kur
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
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7
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Pinto AF, Romão CV, Pinto LC, Huber H, Saraiva LM, Todorovic S, Cabelli D, Teixeira M. Superoxide reduction by a superoxide reductase lacking the highly conserved lysine residue. J Biol Inorg Chem 2015; 20:155-164. [PMID: 25476860 DOI: 10.1007/s00775-014-1222-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/26/2014] [Indexed: 01/12/2023]
Abstract
Superoxide reductases (SORs) are the most recently identified superoxide detoxification systems, being found in microorganisms from the three domains of life. These enzymes are characterized by a catalytic mononuclear iron site, with one cysteine and four histidine ligands of the ferrous active form. A lysine residue in the -EKHVP- motif, located close to the active site, has been considered to be essential for the enzyme function, by contributing to the positive surface patch that attracts the superoxide anion and by controlling the chemistry of the catalytic mechanism through a hydrogen bond network. However, we show here that this residue is substituted by non-equivalent amino acids in several putative SORs from Archaea and unicellular Eukarya. In this work, we focus on mechanistic and spectroscopic studies of one of these less common enzymes, the SOR from the hyperthermophilic Crenarchaeon Ignicoccus hospitalis. We employ pulse radiolysis fast kinetics and spectroscopic approaches to study the wild-type enzyme (-E23T24HVP-), and two mutants, T24K and E23A, the later mimicking enzymes lacking both the lysine and glutamate (a ferric ion ligand) of the motif. The efficiency of the wild-type protein and mutants in reducing superoxide is comparable to other SORs, revealing the robustness of these enzymes to single mutations.
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Affiliation(s)
- Ana F Pinto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177, Stockholm, Sweden
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Liliana C Pinto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Harald Huber
- Lehrstuhl fuer Mikrobiologie, Universität Regensburg, 93053, Regensburg, Germany
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Smilja Todorovic
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal
| | - Diane Cabelli
- Chemistry Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Apartado 127, 2781-901, Oeiras, Portugal.
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8
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Sheng Y, Abreu IA, Cabelli DE, Maroney MJ, Miller AF, Teixeira M, Valentine JS. Superoxide dismutases and superoxide reductases. Chem Rev 2014; 114:3854-918. [PMID: 24684599 PMCID: PMC4317059 DOI: 10.1021/cr4005296] [Citation(s) in RCA: 600] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Yuewei Sheng
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
| | - Isabel A. Abreu
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto
de Biologia Experimental e Tecnológica, Av. da República,
Qta. do Marquês, Estação Agronómica Nacional,
Edificio IBET/ITQB, 2780-157, Oeiras, Portugal
| | - Diane E. Cabelli
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael J. Maroney
- Department
of Chemistry, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Anne-Frances Miller
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Miguel Teixeira
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Joan Selverstone Valentine
- Department
of Chemistry and Biochemistry, University
of California Los Angeles, Los
Angeles, California 90095, United States
- Department
of Bioinspired Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
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9
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Horch M, Pinto AF, Mroginski MA, Teixeira M, Hildebrandt P, Zebger I. Metal-induced histidine deprotonation in biocatalysis? Experimental and theoretical insights into superoxide reductase. RSC Adv 2014. [DOI: 10.1039/c4ra11976b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An experimental and theoretical case study on superoxide reductase explores the protonation states of iron-bound histidines and their relevance for metalloenzyme catalysis.
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Affiliation(s)
- Marius Horch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - Ana Filipa Pinto
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- P-2780-157 Oeiras, Portugal
| | | | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- P-2780-157 Oeiras, Portugal
| | - Peter Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
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10
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Horch M, Pinto AF, Utesch T, Mroginski MA, Romão CV, Teixeira M, Hildebrandt P, Zebger I. Reductive activation and structural rearrangement in superoxide reductase: a combined infrared spectroscopic and computational study. Phys Chem Chem Phys 2014; 16:14220-30. [DOI: 10.1039/c4cp00884g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Local and global structural changes that enable reductive activation of superoxide reductase are revealed by a combined approach of infrared difference spectroscopy and computational methods.
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Affiliation(s)
- M. Horch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - A. F. Pinto
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - T. Utesch
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - M. A. Mroginski
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - C. V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - M. Teixeira
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- Av. da República (EAN)
- P-2780-157 Oeiras, Portugal
| | - P. Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
| | - I. Zebger
- Technische Universität Berlin
- Institut für Chemie
- 10623 Berlin, Germany
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11
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Almeida RM, Turano P, Moura I, Moura JJG, Pauleta SR. Superoxide Reductase: Different Interaction Modes with its Two Redox Partners. Chembiochem 2013; 14:1858-66. [DOI: 10.1002/cbic.201300196] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Indexed: 11/08/2022]
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12
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Testa F, Mastronicola D, Cabelli DE, Bordi E, Pucillo LP, Sarti P, Saraiva LM, Giuffrè A, Teixeira M. The superoxide reductase from the early diverging eukaryote Giardia intestinalis. Free Radic Biol Med 2011; 51:1567-74. [PMID: 21839165 DOI: 10.1016/j.freeradbiomed.2011.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/02/2011] [Accepted: 07/20/2011] [Indexed: 12/13/2022]
Abstract
Unlike superoxide dismutases (SODs), superoxide reductases (SORs) eliminate superoxide anion (O(2)(•-)) not through its dismutation, but via reduction to hydrogen peroxide (H(2)O(2)) in the presence of an electron donor. The microaerobic protist Giardia intestinalis, responsible for a common intestinal disease in humans, though lacking SOD and other canonical reactive oxygen species-detoxifying systems, is among the very few eukaryotes encoding a SOR yet identified. In this study, the recombinant SOR from Giardia (SOR(Gi)) was purified and characterized by pulse radiolysis and stopped-flow spectrophotometry. The protein, isolated in the reduced state, after oxidation by superoxide or hexachloroiridate(IV), yields a resting species (T(final)) with Fe(3+) ligated to glutamate or hydroxide depending on pH (apparent pK(a)=8.7). Although showing negligible SOD activity, reduced SOR(Gi) reacts with O(2)(•-) with a pH-independent second-order rate constant k(1)=1.0×10(9) M(-1) s(-1) and yields the ferric-(hydro)peroxo intermediate T(1); this in turn rapidly decays to the T(final) state with pH-dependent rates, without populating other detectable intermediates. Immunoblotting assays show that SOR(Gi) is expressed in the disease-causing trophozoite of Giardia. We propose that the superoxide-scavenging activity of SOR in Giardia may promote the survival of this air-sensitive parasite in the fairly aerobic proximal human small intestine during infection.
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Affiliation(s)
- Fabrizio Testa
- Department of Biochemical Sciences, CNR Institute of Molecular Biology and Pathology, Sapienza Università di Roma, I-00185 Rome, Italy
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13
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Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F. SORGOdb: Superoxide Reductase Gene Ontology curated DataBase. BMC Microbiol 2011; 11:105. [PMID: 21575179 PMCID: PMC3116461 DOI: 10.1186/1471-2180-11-105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 05/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated. DESCRIPTION SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010). CONCLUSIONS SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.
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Affiliation(s)
- Céline Lucchetti-Miganeh
- CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France.
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14
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Pinho FG, Pinto AF, Pinto LC, Huber H, Romão CV, Teixeira M, Matias PM, Bandeiras TM. Superoxide reductase from Nanoarchaeum equitans: expression, purification, crystallization and preliminary X-ray crystallographic analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:591-5. [PMID: 21543869 PMCID: PMC3087648 DOI: 10.1107/s1744309111009432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 03/11/2011] [Indexed: 11/10/2022]
Abstract
Superoxide reductases (SORs) are the most recent oxygen-detoxification system to be identified in anaerobic and microaerobic bacteria and archaea. SORs are metalloproteins that are characterized by their possession of a catalytic nonhaem iron centre in the ferrous form coordinated by four histidine ligands and one cysteine ligand. Ignicoccus hospitalis, a hyperthermophilic crenarchaeon, is the only organism known to date to serve as a host for Nanoarchaeum equitans, a nanosized hyperthermophilic archaeon isolated from a submarine hot vent which completely depends on the presence of and contact with I. hospitalis cells for growth to occur. Similarly to I. hospitalis, N. equitans has a neelaredoxin (a 1Fe-type SOR) that keeps toxic oxygen species under control, catalysing the one-electron reduction of superoxide to hydrogen peroxide. Blue crystals of recombinant N. equitans SOR in the oxidized form (12.7 kDa, 109 residues) were obtained using polyethylene glycol (PEG 2000 MME) as precipitant. These crystals diffracted to 1.9 Å resolution at 100 K and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 51.88, b = 82.01, c = 91.30 Å. Cell-content analysis suggested the presence of four monomers in the asymmetric unit. The Matthews coefficient (V(M)) was determined to be 1.9 Å(3) Da(-1), corresponding to an estimated solvent content of 36%. Self-rotation function and native Patterson calculations suggested a tetramer with 222 point-group symmetry, similar to other 1Fe-SORs. The three-dimensional structure will be determined by the molecular-replacement method.
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Affiliation(s)
- Filipa G. Pinho
- Instituto de Biologia Experimental e Tecnológica, Universidade Nova de Lisboa, Apartado 12, 2701-901 Oeiras, Portugal
| | - Ana F. Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Liliana C. Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Harald Huber
- Lehrstuhl für Mikrobiologie, Universität Regensburg, 93053 Regensburg, Germany
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Tiago M. Bandeiras
- Instituto de Biologia Experimental e Tecnológica, Universidade Nova de Lisboa, Apartado 12, 2701-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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Rodrigues JV, Gomes CM. Enhanced superoxide and hydrogen peroxide detection in biological assays. Free Radic Biol Med 2010; 49:61-6. [PMID: 20332022 DOI: 10.1016/j.freeradbiomed.2010.03.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 02/24/2010] [Accepted: 03/16/2010] [Indexed: 11/28/2022]
Abstract
Superoxide reductase (SOR) is an enzyme that converts superoxide into hydrogen peroxide at a twofold higher yield than canonical superoxide dismutases (SOD). Superoxide radical detection was investigated using the Amplex red (AR)/peroxidase system to measure the difference in hydrogen peroxide production yield in the presence of SOR or SOD. We found that reduced SOR reacts with the AR oxidation intermediate, a one-electron reduced AR(*) radical, by reducing this intermediate back to the initial AR leuco compound. Ascorbate also quenched this radical in a concentration-dependent manner and could be used to compete efficiently with SOR; at concentrations of ascorbate higher than 5 microM, SOR no longer interfered with the detection of H(2)O(2). By using xanthine/xanthine oxidase as a superoxide-generating system, it was possible to successfully quantify superoxide and hydrogen peroxide in vitro using the AR/peroxidase/SOR system, either by visible absorption or by fluorescence emission, with a considerable low detection limit of 10nM/min. The use of enzymes with diffusion-limited reactivity toward superoxide substantially increases specificity and detection threshold for superoxide and turns this approach into a powerful system to detect ROS in biological systems.
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Affiliation(s)
- João V Rodrigues
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida República, EAN, 2785-572 Oeiras, Portugal
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16
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Bandeiras TM, Romão CV, Rodrigues JV, Teixeira M, Matias PM. Purification, crystallization and X-ray crystallographic analysis of Archaeoglobus fulgidus neelaredoxin. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:316-9. [PMID: 20208170 PMCID: PMC2833046 DOI: 10.1107/s1744309110000916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 01/07/2010] [Indexed: 11/10/2022]
Abstract
Neelaredoxins are a type of superoxide reductase (SOR), which are blue 14 kDa metalloproteins with a catalytic nonhaem iron centre coordinated by four histidines and one cysteine in the ferrous form. Anaerobic organisms such as Archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, have developed defence mechanisms against toxic oxygen species in which superoxide reductases play a key role. SOR is responsible for scavenging toxic superoxide anion radicals (O(2)(*-)), catalysing the one-electron reduction of superoxide to hydrogen peroxide. Crystals of recombinant A. fulgidus neelaredoxin in the oxidized form (13.7 kDa, 125 residues) were obtained using polyethylene glycol and ammonium sulfate. These crystals diffracted to 1.9 A resolution and belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 75.72, c = 185.44 A. Cell-content analysis indicated the presence of a tetramer in the asymmetric unit, with a Matthews coefficient (V(M)) of 2.36 A(3) Da(-1) and an estimated solvent content of 48%. The three-dimensional structure was determined by the MAD method and is currently under refinement.
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Affiliation(s)
- Tiago M Bandeiras
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.
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17
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Pinto AF, Rodrigues JV, Teixeira M. Reductive elimination of superoxide: Structure and mechanism of superoxide reductases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:285-97. [PMID: 19857607 DOI: 10.1016/j.bbapap.2009.10.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 10/12/2009] [Accepted: 10/14/2009] [Indexed: 10/20/2022]
Abstract
Superoxide anion is among the deleterious reactive oxygen species, towards which all organisms have specialized detoxifying enzymes. For quite a long time, superoxide elimination was thought to occur through its dismutation, catalyzed by Fe, Cu, and Mn or, as more recently discovered, by Ni-containing enzymes. However, during the last decade, a novel type of enzyme was established that eliminates superoxide through its reduction: the superoxide reductases, which are spread among anaerobic and facultative microorganisms, from the three life kingdoms. These enzymes share the same unique catalytic site, an iron ion bound to four histidines and a cysteine that, in its reduced form, reacts with superoxide anion with a diffusion-limited second order rate constant of approximately 10(9) M(-1) s(-1). In this review, the properties of these enzymes will be thoroughly discussed.
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Affiliation(s)
- Ana Filipa Pinto
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal
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Todorovic S, Rodrigues JV, Pinto AF, Thomsen C, Hildebrandt P, Teixeira M, Murgida DH. Resonance Raman study of the superoxide reductase from Archaeoglobus fulgidus, E12 mutants and a ‘natural variant’. Phys Chem Chem Phys 2009; 11:1809-15. [DOI: 10.1039/b815489a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moura I, Pauleta SR, Moura JJG. Enzymatic activity mastered by altering metal coordination spheres. J Biol Inorg Chem 2008; 13:1185-95. [PMID: 18719950 DOI: 10.1007/s00775-008-0414-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 08/01/2008] [Indexed: 11/24/2022]
Abstract
Metalloenzymes control enzymatic activity by changing the characteristics of the metal centers where catalysis takes place. The conversion between inactive and active states can be tuned by altering the coordination number of the metal site, and in some cases by an associated conformational change. These processes will be illustrated using heme proteins (cytochrome c nitrite reductase, cytochrome c peroxidase and cytochrome cd1 nitrite reductase), non-heme proteins (superoxide reductase and [NiFe]-hydrogenase), and copper proteins (nitrite and nitrous oxide reductases) as examples. These examples catalyze electron transfer reactions that include atom transfer, abstraction and insertion.
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Affiliation(s)
- Isabel Moura
- REQUIMTE, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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