To this purpose we developed a web-application dedicated to the model plant Arabidopsis thaliana (freely available at http://chlorokb.fr ). The main originality of ChloroKB is a graphical representation of the cellular context (subcellular localization of proteins and metabolites, proteins inside protein-protein complexes, fine regulations). Thanks to this tool it is now possible to explore interactively the metabolic network of the chloroplast and its inter-connections with cellular metabolism.
This network was reconstructed manually integrating more than 1200 proteins, 1900 metabolites and 800 complexes, localized in 5 subcellular compartments. ChloroKB generates graphical maps based on CellDesigner modeling standard and allows dynamic navigation in these maps (vectorial format) representing metabolic pathways, assembly processes, and regulatory mechanisms. ChloroKB is a very original tool in the present landscape of biological metabolic databases and represents an essential resource for quantitative modeling of plant metabolism. ChloroKB will also serve as a platform for the reconstruction of other metabolic networks, especially in microalgae (MoMix project, ANR-DFG grant, 2018).
This work has been funded by Labex GRAL.
Gloaguen P, Bournais S, Alban C, Ravanel S, Seigneurin- Berny D, Matringe M, Tardif M, Kuntz M, Ferro M, Bruley C, Rolland N, Vandenbrouck Y and Curien G (2017). ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network.
Plant Physiology, 8, 174(2), 922–934 (PMID:28442501)