Ubiquitin/proteasome-mediated proteolysis plays an important role in the response to several environmental stresses. Here, we described the relationship of the proteolysis in the flooding stress in soybean (Glycine max L. cultivar Enrei), Immunoblot analyses were performed using antibodies against two subunits of 26S proteasome, Rpt5 and Rpn10, 20S proteasome and two subunits of COP9 signalosome (CSN), CSN4 and CSN5, to compare between flooded and untreated roots. We also examined their protein amounts in the condition of low oxygen. Moreover, crude extracts from flooded or untreated roots incubated with or without a proteasome inhibitor MG132 were analyzed by proteomics technique. We revealed that the amount of ubiquitinated proteins in soybean roots decreased after flooding treatment and increased to levels similar to controls after de-submergence. Both CSN4 and CSN5 accumulated following flooding treatment, although no significant difference was observed in proteasome. Low oxygen had no effect on the amount of ubiquitinated proteins or CSN4. By 2D-PAGE, the amount of 6 proteins changed significantly following MG132 treatment in flooding stressed plants. We conclude that the accumulation of CSN proteins might enhance the degradation of ubiquitinated proteins independent of hypoxia caused by flooding, thereby lowering their abundance during flooding stress. (c) 2011 Elsevier Ireland Ltd. All rights reserved