Abstract
BackgroundOxidative 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.DescriptionIn 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.ConclusionOxyGene 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:
Highlights
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
OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes
To improve the annotation of reactive oxygen species (ROS)/RNS response subsystems and to bypass previous inaccurate computer-assisted annotations, we have developed a platform named Oxy-Gene and an embedded supervised database (OxyDB) with a new ontology and unambiguous anchor-based signatures for 37 ROS/RNS detoxification enzymes
Summary
The 21st century is going to be a fruitful period with the start of the "genome" era. All authors participated in data curation and in writing the manuscript For this reason, we have developed OxyGene, an innovative platform that allows ab initio annotation and comparative analysis of detoxification subsystems in whole prokaryotic genomes. The OxyGene GUI allows rapid and reliable identification of all genes encoding detoxification enzymes in complete genomes (even those that were previously not or misannotated), and comparison of detoxification subsystems, maps and chromosomal locations. No equivalent free software is currently available, and OxyGene is the first tool dedicated to oxidative stress. These ROS/RNS stresses are frequent in cells and the resulting imbalance between the generation and elimination of oxidants often leads to cell damage or death.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
