Peroxisomes are single-membrane subcellular organelles, present in most eukaryotic cells and organisms. This organelle fulfils essential metabolic functions in lipid metabolism and free radical detoxification. Fatal disorders are related to defective peroxisomal function or biogenesis.
The aim of Peroxisome database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathways they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of 37 genomes to a total of 2706 peroxisomal homolog proteins. PeroxisomeDB integrates the peroxisomal metabolome of whole microbody family, including the glycosome proteomes of trypanosomatids and the glyoxysome proteome of Arabidopsis thaliana.
Features of PeroxisomeDB include:
-
1. The peroxisomal proteome from 37 eukaryotic genomes. Using a comparative genomics approach, we designed 139 different peroxisomal protein families or core functional units. These core units were used to capture 2706 peroxisomal homolog proteins from all kingdoms of life, from human to trypanosomatids.
-
2. The global peroxisomal metabolome. We aim at integration into a comprehensive and complete metabolomic picture of the most relevant peroxisomal metabolic pathways. We are including the putative peroxisomal homologs assigned to their respective protein families as deduced from the comparative genomics analysis. In addition, organism-specific metabolic pathways are provided on detail.
-
3. Each of the 2,706 proteins has a database entry that includes information on the assigned protein family, functional category, and subcellular localization, as well as links to reference databases and Pubmed. For each peroxisomal entry, a phylogenetic alignment and tree building is provided, to facilitate comprehension of their evolutionary history. In addition, a peroxisomal Targeting Signal (PTS) Prediction is included for each peroxisomal protein.
-
4. Enzyme entries are linked through the ontology-based mediator used by SBMM Assistant (www.sbmm.uma.es) to the reference databases Brenda, CheBI and Sabio-RK, which provide updated kinetic and biochemical information for peroxisomal enzymes.
-
5. Peroxisome related disease: a total of 22 disorders sorted by clinical criteria and classified into peroxisome biogenesis disorders (PBD) and single peroxisomal protein deficiencies. Moreover, PeroxisomeDB contains comprehensible flow charts for diagnosis.
-
6. Two different predictive tools allowing the in silico peroxisome presence identification in genomes (Organelle predictor), and Peroxisomal Targeting Signal (PTS1, PTS2, PEX19BS) recognition in proteins (PTSs predictor).
PeroxisomeDB aims at becoming the database of reference for basic researchers and clinicians working on peroxisomes and metabolic disease.
