PeroxisomeDB

PeroxisomeDB catalogs peroxisomal proteomes and metabolomes across eukaryotes, including Homo sapiens, Saccharomyces cerevisiae, 35 newly sequenced eukaryotic genomes (fungi, yeasts, plants, and lower eukaryotes), trypanosomatid glycosomes, and the Arabidopsis thaliana glyoxysome, to support comparative, evolutionary and metabolic analyses.

Key Features:

• Species and organelle coverage: Includes peroxisomal data for Homo sapiens, Saccharomyces cerevisiae, 35 newly sequenced eukaryotic genomes across fungi, yeasts, plants and lower eukaryotes, plus glycosome and glyoxysome proteomes.
• Peroxisomal protein families: Identifies a core ensemble of 139 peroxisomal protein families.
• Putative homolog identification: Reports 2706 putative peroxisomal protein homologs across the included genomes.
• Peroxisome targeting signal (PTS) annotation: Annotates putative PTS in approximately 37% of the identified homologs.
• Phylogenetic resources: Provides phylogenetic trees for 2386 peroxisomal proteins to enable evolutionary comparisons.
• Metabolome integration: Incorporates the peroxisomal metabolome of the microbody family and includes glycosome and glyoxysome metabolomic/proteomic data.
• Enzyme kinetics integration: Captures and links kinetic information from Brenda, CheBI, and Sabio-RK.
• Literature corpus: Aggregates over 1400 selected bibliographic references relevant to peroxisomal biology.

Scientific Applications:

• Comparative genomics: Enables cross-species comparison of peroxisomal proteomes and metabolomes to study conservation and divergence.
• Evolutionary analysis: Supports exploration of evolutionary relationships and functional diversification via phylogenetic trees for peroxisomal proteins.
• Metabolic pathway and enzyme study: Facilitates analysis of peroxisomal metabolic pathways and enzyme kinetics through integration with Brenda, CheBI, and Sabio-RK.
• Functional genomics and systems analysis: Supports systems-level studies of peroxisome roles in redox signaling, lipid homeostasis, and broader metabolism.
• Disease research: Provides resources for investigating genetic and functional mechanisms underlying peroxisomal diseases.

Methodology:

Identification and cataloging of 139 peroxisomal protein families and 2706 putative homologs with annotation of putative PTS; generation of phylogenetic trees for 2386 peroxisomal proteins; and capture/integration of kinetic information from Brenda, CheBI, and Sabio-RK.