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SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.

Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F - BMC Microbiol. (2011)

Bottom Line: 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.These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous.SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France. celine.lucchetti@univ-rennes1.fr

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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Related in: MedlinePlus

Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all archaeal described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). SOR are represented with a single green arrow, Dx-SOR with a double khaki arrow, Fe-Mn SOD by a light blue dot and Cu-Zn SOD by a dark blue dot. SOD-type genes were determined using OxyGene [36]. Scale bar: 3% difference. Crenarchaeota (in red) are developed in Figure 4.
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Figure 3: Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all archaeal described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). SOR are represented with a single green arrow, Dx-SOR with a double khaki arrow, Fe-Mn SOD by a light blue dot and Cu-Zn SOD by a dark blue dot. SOD-type genes were determined using OxyGene [36]. Scale bar: 3% difference. Crenarchaeota (in red) are developed in Figure 4.

Mentions: Using the "Browse by phylogeny" option of SORGOdb, we collected the names of all Archaea that possess at least one SOR gene in their complete or partial genomes. Then, we generated a 16S-based phylogenetic tree for these organisms, using ClustalW [46] and sequences recovered from the SILVA comprehensible ribosomal RNA databases [60] (http://www.arb-silva.de/), clustered by Maximum Likelihood and Neighborhood joining algorithms (Neighborhood joining tree is not shown). This tree was annotated with the class of SOR and the presence of SOD on the genome (Maximum Likelihood Tree; Figure 3).


SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.

Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F - BMC Microbiol. (2011)

Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all archaeal described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). SOR are represented with a single green arrow, Dx-SOR with a double khaki arrow, Fe-Mn SOD by a light blue dot and Cu-Zn SOD by a dark blue dot. SOD-type genes were determined using OxyGene [36]. Scale bar: 3% difference. Crenarchaeota (in red) are developed in Figure 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116461&req=5

Figure 3: Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all archaeal described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). SOR are represented with a single green arrow, Dx-SOR with a double khaki arrow, Fe-Mn SOD by a light blue dot and Cu-Zn SOD by a dark blue dot. SOD-type genes were determined using OxyGene [36]. Scale bar: 3% difference. Crenarchaeota (in red) are developed in Figure 4.
Mentions: Using the "Browse by phylogeny" option of SORGOdb, we collected the names of all Archaea that possess at least one SOR gene in their complete or partial genomes. Then, we generated a 16S-based phylogenetic tree for these organisms, using ClustalW [46] and sequences recovered from the SILVA comprehensible ribosomal RNA databases [60] (http://www.arb-silva.de/), clustered by Maximum Likelihood and Neighborhood joining algorithms (Neighborhood joining tree is not shown). This tree was annotated with the class of SOR and the presence of SOD on the genome (Maximum Likelihood Tree; Figure 3).

Bottom Line: 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.These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous.SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France. celine.lucchetti@univ-rennes1.fr

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.

Show MeSH
Related in: MedlinePlus