PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease

Abstract

Peroxisomes are essential organelles of eukaryotic origin, ubiquitously distributed in cells and organisms, playing key roles in lipid and antioxidant metabolism. Loss or malfunction of peroxisomes causes more than 20 fatal inherited conditions. We have created a peroxisomal database (http://www.peroxisomeDB.org) that includes the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae, by gathering, updating and integrating the available genetic and functional information on peroxisomal genes. PeroxisomeDB is structured in interrelated sections 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases', that include hyperlinks to selected features of NCBI, ENSEMBL and UCSC databases. We have designed graphical depictions of the main peroxisomal metabolic routes and have included updated flow charts for diagnosis. Precomputed BLAST, PSI-BLAST, multiple sequence alignment (MUSCLE) and phylogenetic trees are provided to assist in direct multispecies comparison to study evolutionary conserved functions and pathways. Highlights of the PeroxisomeDB include new tools developed for facilitating (i) identification of novel peroxisomal proteins, by means of identifying proteins carrying peroxisome targeting signal (PTS) motifs, (ii) detection of peroxisomes in silico, particularly useful for screening the deluge of newly sequenced genomes. PeroxisomeDB should contribute to the systematic characterization of the peroxisomal proteome and facilitate system biology approaches on the organelle.

Figure 1

One of the six interactive schemes displayed in PeroxisomeDB: ‘Peroxins and other PMPs (peroxisome membrane proteins)’.

Figure 2

Gene Page for a given peroxisomal gene, including a brief description, localization, functional role, disease caused by malfunction if any, tools for functional genomics and selected links to reference databases (Gene Info).

Figure 3

Bayesian tree of a peroxisomal protein (PEX12) displayed in ATV [A Tree Viewer (21)]. Numbers at the nodes indicate the posterior probability of the corresponding partition. ^***Indicate query sequence.

Figure 4

Target Signal Predictor. Tool for the prediction of the three peroxisomal target signals: PTS1, PTS2 and PEX19BS. Motifs within the query sequence are identified using ‘Do-It-YourSelf Block Search’ in BLOCKS server.

Figure 5

Peroxisome Identification Tool. It is based on the detection of four peroxisomal markers, by launching BLAST processes. The 119 different eukaryotic genomes provided by ‘genomic Blast with eukaryotic genomes page’ from NCBI, can be automatically blasted against the four markers.