Abstract
Many recent high throughput proteomic investigations have focused either on the whole chloroplast or on independent suplastidial fractions. However, these previous studies raised the question of the accurate localization of lots of proteins that were identified in different suplastidial compartments. We recently went a step further into the knowledge of the accurate localization of these proteins within the chloroplast. To achieve this goal, we first obtained highly pure subfractions of envelope, stroma and thylakoids, and evaluated their cross-contaminations using biochemical methods. We then performed a comprehensive analysis of the chloroplast proteome starting from the whole chloroplast and its three main compartments. Then, we assessed the partitioning of each identified protein in the three above-cited compartments using a semi-quantitative proteomic approach (Ferro et al., MCP 2010; AT_Chloro database: http://www.grenoble.prabi.fr/at_chloro/).). An in depth investigation of the proteins identified within the purified envelope fraction allowed new insights over this subplastidial compartment to be revealed (Joyard et al., Mol Plant 2009 & Prog Lipid Res 2010).
