Arabidopsis E3 SUMO ligase SIZ1 (AtSIZ1) controls vegetative growth and development including responses to nutrient deficiency and environment stresses. Here, we analyzed the effect of AtSIZ1 on the stability and amount of seed proteins. Proteomic analysis showed that the amount of three major nutrient reservoir proteins, CRUCIFERIN (CRU) 1, 2 and 3, were decreased in siz1-2 mutants. However, quantitative real-time RT-PCR showed that transcript levels of CRU1, 2 and 3 genes were rather significantly higher in siz1-2 mutants than wild-type plants. Yeast two hybrid analysis revealed that AtSIZ1 interacts with CRU1, CRU2 and CRU3, strongly suggesting that CRU1, 2 and 3 proteins are sumoylated by AtSIZ1. In addition, the analysis of amino acid composition by HPLC showed that the contents of amino acids were a bit high in siz1-2 mutants. Our data indicate that AtSIZ1 plays an important function for accumulation of seed storage proteins through its ligase activity.