Macro-autophagy (hereafter referred to as autophagy) is a universal mechanism in eukaryotic cells that facilitates the degradation of unwanted cell constituents. Autophagy is induced in plant under nitrate limiting conditions and autophagy-defective plants are hypersensitive to starvations. Shotgun proteomic analyses were performed on root extracts from atg5 and atg7 mutants harvested after flowering time, when nitrogen remobilization is induced in the leaves as in the roots. The aim of analysis was to clarify the roles of autophagy in the roots when nitrogen recycling and remobilization are enhanced. Study was performed on both nitrate sufficient and nitrate limiting conditions.