An exploration tool of Arabidopsis metabolism

ChloroKB

What is ChloroKB?


ChloroKB is a manually-constructed and curated network of Arabidopsis thaliana metabolism based on a graphical notation system, as proposed in CellDesigner software. ChloroKB initially focused on chloroplast processes now includes processes occurring in other subcellular compartments (mitochondrion, peroxisome, cytosol, etc.) to ensure a comprehensive view of Arabidopsis cell metabolism. The cell represented is a generic cell: all the proteins coded by the genome and involved in a given function are represented.

Proteins and metabolites are represented in their context (position(s) in the network, subcellular localization, presence in protein/metabolite complexes and their control by allosteric effectors binding or by post-translational modifications). Highly connected metabolites are represented as “hubs” where all the inputs and outputs are displayed.

The current version of ChloroKB includes 217 biological processes (referred to as maps) and contains information relating to 1833 proteins with a reviewed status which are included in maps, and 2816 proteins with an unreviewed status which are not yet included in maps. In addition, 318 unknown proteins, 1183 complexes (protein-metabolite and protein-protein complexes), 1367 simple molecules, 16 ions and 105 chemical inhibitors are represented in maps. Annotations reported in ChloroKB are supported by 3933 literature citations.

The following main processes are not included in this release of ChloroKB: ions transport and organic acids transport at the plasma membrane, light reactions and redox processes, cell wall synthesis, protein import processes, protein folding, DNA/RNA synthesis, transcription and translation machineries. For terpene synthesis, users are redirected to the AtIPD database.

Finally, we consider our database to represent a clickable and modifiable review of Arabidopsis thaliana metabolism, and we will welcome contributions from users (through the contribute to ChloroKB page) to help grow and maintain it.