How phytoplankton rule the oceans
20th June 2017

An exploration tool for chloroplast metabolism connected with other cell compartments


How phytoplankton rule the oceans
Cell metabolism is extremely complex especially in plants but as most molecular components are now well characterized it appears possible in a near future to predict its behavior. However, this can only be done thanks to dedicated software.

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.

References

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)

Links

http://chlorokb.fr
http://big.cea.fr/drf/big/pages/actualites/resultats-scientifiques/l56_gcurien.aspx