dThe encystation of Acanthamoeba leads to the formation of resilient cysts from vegetative trophozoites. This process is essential for parasite survival under unfavorable conditions, such as those associated with starvation, low temperatures, and biocides. Furthermore, cysteine proteases have been implicated in the massive turnover of intracellular components required for encystation. Thus, strict modulation of the activities of cysteine proteases is required to protect Acanthamoeba from intracellular damage. However, mechanisms underlying the control of protease activity during encystation have not been established in Acanthamoeba. In the present study, we identified and characterized Acanthamoeba cysteine protease inhibitor (AcStefin), which was found to be highly expressed during encystation and to be associated with lysosomes by fluorescence microscopy. Recombinant AcStefin inhibited various cysteine proteases, including human cathepsin B, human cathepsin L, and papain. Transfection with small interfering RNA against AcStefin increased cysteine protease activity during encystation and resulted in incomplete cyst formation, reduced excystation efficiency, and a significant reduction in cytoplasmic area. Taken together, these results indicate that AcStefin is involved in the modulation of cysteine proteases and that it plays an essential role during the encystation of Acanthamoeba.A canthamoeba is the causative agent of granulomatous amoebic encephalitis (GAE) and amoebic keratitis. The life cycle of Acanthamoeba is divided into two stages, that is, the vegetative trophozoite stage and the dormant cystic stage. Under challenging conditions, such as those associated with starvation, low temperatures, and biocide treatment, the trophozoite converts to the resilient cyst form (1-5). This differentiation, which is termed encystation, protects Acanthamoeba against host immune responses and allows it to evade the effect of chemical treatments, and thus, encystation decreases treatment efficacies (3, 6). Therefore, the inhibition of encystation during medical treatment could lead to outcomes that are more favorable in cases of amoebic infection. However, this goal is hindered by a lack of information about the encystation mechanism involved.The cysteine proteases are regarded as major drug targets, and the papain family of cysteine proteases, such as cathepsin B and cathepsin L, are localized in lysosomes for intracellular protein degradation (7,8). Previous studies on Giardia and Entamoeba have shown that cysteine proteases are implicated in parasite survival under nutrient-limited conditions and during developmental differentiation (9-14). In Acanthamoeba, the cysteine protease inhibitor E64d was found to slow encystment (15), and in a previous study, we detected the upregulations of various proteases, including cysteine proteases, by cDNA microarray analysis and comparative expression analysis of expressed sequence tags (ESTs) during encystation (16,17). Cysteine proteases in lysosomes cause massive proteolytic de...