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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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Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all Crenarchaeota described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). The Thermoproteales are highlighted in red, the Sulfolobales in blue and the Desulfurococcales in green. Organisms having at least one SOR, or one SOD or none of both (any SOD and any SOR) are respectively represented in red, blue and dark.
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Figure 4: Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all Crenarchaeota described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). The Thermoproteales are highlighted in red, the Sulfolobales in blue and the Desulfurococcales in green. Organisms having at least one SOR, or one SOD or none of both (any SOD and any SOR) are respectively represented in red, blue and dark.

Mentions: According to 16S rRNA gene sequences, the Crenarchaeota group can be subdivided into three orders, the Thermoproteales, the Sulfolobales and the Desulfurococcales [64]. All Sulfolobales and Thermoproteoles genomes studied encode a single SOD, with the single exception of the unique member of the Thermofilaceae familly, Thermofilum pendens, an anaerobic commensal that encodes a SOR. By contrast, all Desulfurococcales genomes available encode a SOR but not a SOD, except Aeropyrum pernix that has the particularity to be strictly aerobic [65] and that encodes an extremely thermostable Mn/Fe superoxide dismutase [66] and Ignisphaera aggregans, a novel deep-branching member of the Desulfurococcaceae lineage of strict anaerobes (as even trace quantities of oxygen inhibited its growth, [67] ) the genome of which carries neither SOR or SOD genes. Other Desulfurococcales studied (Figure 4) have all a gene encoding a centre II mono-domain SOR-type enzyme. Interestingly, two recent genomes have been made available since the last update of SORGOdb (May 2010) and both contain annotation for SOR-like genes: Tagg_0590, described as a Desulfoferrodoxin ferrous iron-binding protein of Thermosphaera aggregans DSM 11486 and Shell_0770 for Staphylothermus hellenicus DSM 12710, annotated as a twin-arginine secreted superoxide reductase, by homology with Geobacter metallireducens GS-15 Gmet_2613 SOR. Using the SORGOdb "search by BlastP", we could confirm that both ORFs are true SOR (ten best e-value from e-59 to e-34) and belong to the SOR-type class. This analysis contradicts the annotation of Shell_0770 in NCBI as TAT-SOR; the absence of a significant TAT targeting signal in Shell_0770 was tested and confirmed by TatFind [68] and TatP [69] predictions. The SORGOdb "search by BlastP" tool therefore allows the accuracy of public SOR annotations to be checked and allows suggestions of their possible SORGOdb classification.


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 Crenarchaeota described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). The Thermoproteales are highlighted in red, the Sulfolobales in blue and the Desulfurococcales in green. Organisms having at least one SOR, or one SOD or none of both (any SOD and any SOR) are respectively represented in red, blue and dark.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Repartition of superoxide reductase (SOR) and superoxide dismutase (SOD) genes regarding the 16S rRNA gene distance tree of all Crenarchaeota described in SORGOdb. All of the sequences were retrieved from SILVA [60] when available or GenBank (http://www.ncbi.nlm.nih.gov/). The Thermoproteales are highlighted in red, the Sulfolobales in blue and the Desulfurococcales in green. Organisms having at least one SOR, or one SOD or none of both (any SOD and any SOR) are respectively represented in red, blue and dark.
Mentions: According to 16S rRNA gene sequences, the Crenarchaeota group can be subdivided into three orders, the Thermoproteales, the Sulfolobales and the Desulfurococcales [64]. All Sulfolobales and Thermoproteoles genomes studied encode a single SOD, with the single exception of the unique member of the Thermofilaceae familly, Thermofilum pendens, an anaerobic commensal that encodes a SOR. By contrast, all Desulfurococcales genomes available encode a SOR but not a SOD, except Aeropyrum pernix that has the particularity to be strictly aerobic [65] and that encodes an extremely thermostable Mn/Fe superoxide dismutase [66] and Ignisphaera aggregans, a novel deep-branching member of the Desulfurococcaceae lineage of strict anaerobes (as even trace quantities of oxygen inhibited its growth, [67] ) the genome of which carries neither SOR or SOD genes. Other Desulfurococcales studied (Figure 4) have all a gene encoding a centre II mono-domain SOR-type enzyme. Interestingly, two recent genomes have been made available since the last update of SORGOdb (May 2010) and both contain annotation for SOR-like genes: Tagg_0590, described as a Desulfoferrodoxin ferrous iron-binding protein of Thermosphaera aggregans DSM 11486 and Shell_0770 for Staphylothermus hellenicus DSM 12710, annotated as a twin-arginine secreted superoxide reductase, by homology with Geobacter metallireducens GS-15 Gmet_2613 SOR. Using the SORGOdb "search by BlastP", we could confirm that both ORFs are true SOR (ten best e-value from e-59 to e-34) and belong to the SOR-type class. This analysis contradicts the annotation of Shell_0770 in NCBI as TAT-SOR; the absence of a significant TAT targeting signal in Shell_0770 was tested and confirmed by TatFind [68] and TatP [69] predictions. The SORGOdb "search by BlastP" tool therefore allows the accuracy of public SOR annotations to be checked and allows suggestions of their possible SORGOdb classification.

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