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Open Access Database

OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes

David Thybert, Stéphane Avner, Céline Lucchetti-Miganeh, Angélique Chéron and Frédérique Barloy-Hubler*

Author Affiliations

CNRS UMR 6026, Interactions Cellulaires et Moléculaires, Equipe B@SIC, Université de Rennes 1, IFR140 GFAS, Campus de Beaulieu, Av. du Général Leclerc, 35042 Rennes, France

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BMC Genomics 2008, 9:637  doi:10.1186/1471-2164-9-637

Published: 31 December 2008

Abstract

Background

Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description.

Description

In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface.

Conclusion

OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software webcite