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Sorgodb: Superoxide Reductase Gene Ontology Curated Database Lucchetti-Miganeh et al. BMC Microbiology 2011, 11:105 http://www.biomedcentral.com/1471-2180/11/105 DATABASE Open Access SORGOdb: Superoxide Reductase Gene Ontology curated DataBase Céline Lucchetti-Miganeh1*, David Goudenège1, David Thybert1,2, Gilles Salbert1 and Frédérique Barloy-Hubler1 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. Background (called reactive oxygen species or ROS), particularly Two and a half billion years ago, the intense photosyn- hydroxyl radicals (•OH), hydrogen peroxide (H2O2)and thetic activity of cyanobacteria caused the largest envir- superoxide anion radicals (O2-). onmental change in Earth’s history: the oxygenation of The superoxide anion is generated fortuitously by fla- the atmosphere and the oceans, which were hitherto lar- voenzymes such as NADH dehydrogenase II, succinate gely anoxic [1,2]. This profound transformation of the dehydrogenase, fumarate reductase, and sulphite reduc- biosphere exerted an evolutionary selection pressure on tase [3,4]. The superoxide anion is one of the deleterious organisms and led to the development of new pathways, reactive oxygen species: it can damage DNA, proteins including the highly exergonic respiratory chain based and lipids indirectly by releasing iron from damaged on O2 as the terminal electron acceptor. Currently, dehydratase clusters [4,5]. In anaerobes, most of the most living organisms, except anaerobic microbes, essential “central metabolic” redox enzymes (for exam- require oxygen. O2 is used as a substrate by many ple aconitase, fumarase, dihydroxyacid dehydratase, and enzymes involved metabolizing amines, purines and pyruvate:ferredoxin oxidoreductase) contain iron sul- amino acids. Oxygen is a relatively inert molecule due phur [Fe-S] clusters that are rapidly inactivated when to its spin triplet ground state. However, it can be acti- exposed to oxygen [5-8]. vated by photons or by one electron oxidation or reduc- To survive and protect themselves from the toxicity of tion processes to generate reactive oxygen species superoxide anion, many species, and especially anae- robes, have developed defence mechanisms [5]. * Correspondence: [email protected] Superoxide dismutase (SOD) was first isolated by 1CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Mann and Keilis (1938) and its catalytic function, which Beaulieu, 35042 Rennes, France consists to dismutate O2- into molecular oxygen and Full list of author information is available at the end of the article © 2011 Lucchetti-Miganeh et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Lucchetti-Miganeh et al. BMC Microbiology 2011, 11:105 Page 2 of 12 http://www.biomedcentral.com/1471-2180/11/105 hydrogen peroxide, was discovered in 1969 by McCord axial site of the reduced enzyme centre [30]. The addi- and Fridovich [9]. Mammals have two forms of SOD tional N-terminal domain of the 2Fe-SOR contains a isozymes: the manganese SOD (Mn-SOD), present in rubredoxin-like centre, with Fe3+ ligated by four the mitochondria, and the copper/zinc SOD (Cu/Zn-SO), cysteines in a distorted tetrahedral geometry (centre I, present in the cytoplasm [10,11]. In plants, SOD have Fe(Cys)4, [32]). A first classification of these enzymes been classified into three distinct types on the basis of was proposed according to the number of metal centres: their metal cofactor: Cu/Zn-SOD (in the cytosol and neelaredoxin or 1Fe-SOR and desulfoferrodoxin or 2Fe- chloroplasts), Mn-SOD (in mitochondria), and Fe-SOD SOR [33,34]. An additional class was proposed after the (often in chloroplasts) [12-14]. There are three known isolation of a Treponema pallidum SOR that contains SOD in E. coli: MnSOD, FeSOD and CuZnSOD. The two an extended non-iron N-terminal domain of unknown first are located in the cytoplasm and the last in the peri- function [25,35]. In all these three classes, only the plasmic space [15]. A distinct additional fourth class of reduced form of the iron-containing active centre II is - SOD containing nickel (NiSOD) was recently discovered able to react with the superoxide anion O2• . in Streptomyces [16,17] and cyanobacteria [18]. SOD- SOD are found in nearly every living organism except driven dismutation was the only biological mechanism in some strictly anaerobic species [36,37]. Tally et al identified for scavenging superoxide anion radicals until suggested that the diversity in the oxygen tolerance of the early 1990’s. McCord et al. [19] established a correla- anaerobes is generally related to their level of SOD [38]. tion between oxygen tolerance and SOD production and SOR were first thought to be restricted to anaerobic suggested that SOD was the single most important prokaryotes but were subsequently discovered in some enzyme for enabling organisms to survive in the presence micro-aerophilic and micro-aerotolerant Bacteria and of molecular oxygen. They proposed that the hypersensi- Archaea [39,40]. More recently, a SOR encoding gene tivity of obligate anaerobes to oxygen was a consequence was also discovered in an eukaryote, Giardia intestinalis, of SOD deficiency. However, most anaerobic organisms, a microaerophilic protozoan (cited by [41]). Although which indeed lack SOD, show various degrees of toler- SOD and SOR both detoxify superoxide, there is a fun- ance to oxygen when they are occasionally exposed to damental difference in their properties: SOD generate this molecule in their environments. one-half mole of oxygen and one-half mole of hydrogen Two novel iron-sulphur-containing proteins that peroxide per superoxide molecule whereas SOR produce detoxify superoxide molecules were then discovered in only one mole of hydrogen peroxide. The physiological sulphate-reducing and hyperthermophilic anaerobes: conditions, that determine SOR or SOD preference in desulfoferrodoxin (Dfx) in Desulfovibrio desulfuricans, organisms, have not be completely determined, although Desulfovibrio vulgaris Hildenbourgh [20] and Desulfoar- the presence of SOR rather than SOD may be associated culus baarsii [21], neelaredoxin (Nlr) in Desulfovibrio with the amount of redox proteins produced by organ- gigas [22] and superoxide reductase (SOR) in Pyrococcus isms [25]. furiosus [23]. This revealed the existence of alternative Most genomes, even those of anaerobic species, con- mechanisms for ROS detoxification in anaerobes. The tain both SOD and SOR although some species have function of these proteins was first studied in 1996 by only one of the two enzymes. The increasing number of Dfx complementation of superoxide detoxication activity sequenced genomes makes allows comparative genomic in E. coli SOD mutants [24]. Later, Nlr from Treponema analyses, to elucidate the evolutionary or functional pro- pallidum [25] and D. gigas [26] were also shown to cesses of SOR. Unfortunately, there are several problems complement such SOD mutants. Liochev and Fridovich with the annotation of superoxide reductase genes, [27] suggested that Dfx catalyzes the reduction of super- partly a consequence of heterogeneous transfer of anno- oxide rather than its dismutation, and that it uses cellu- tations from previously characterized neelaredoxin, lar reductants such as NAD(P)H. Subsequently, the Dfx desulfoferrodoxin, superoxide reductase or rubredoxin enzyme was confirmed as an oxidoreductase [23-25,27]. oxidase. Moreover, due to the absence of updating or Finally, the superoxide reductase activity of those pro- correction of databases, many sor genes remained anon- teins were established by two groups [21,23]. ymous because of the transfer of annotations from SOR Dfx and Nlr proteins have different numbers of iron genes initially annotated as “hypothetical”, “function sites: both contain a similar C-terminal single iron- unknown” or “putative activity”.Also,SORaresmall containing site (centre II) but also has Dfx a second N- proteins, ca. 200 amino acids
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