Cysteine proteases are known to be important pathogenicity factors of the protozoan parasite Entamoeba histolytica. So far, a total of eight genes coding for cysteine proteases have been identified in E. histolytica, two of which are absent in the closely related nonpathogenic species E. dispar. However, present knowledge is restricted to enzymes expressed during in vitro cultivation of the parasite, which might represent only a subset of the entire repertoire. Taking advantage of the current E. histolytica genome-sequencing efforts, we analyzed databases containing more than 99% of all ameba gene sequences for the presence of cysteine protease genes. A total of 20 full-length genes was identified (including all eight genes previously reported), which show 10 to 86% sequence identity. The various genes obviously originated from two separate ancestors since they form two distinct clades. Despite cathepsin B-like substrate specificities, all of the ameba polypeptides are structurally related to cathepsin L-like enzymes. None of the previously described enzymes but 7 of the 12 newly identified proteins are unique compared to cathepsins of higher eukaryotes in that they are predicted to have transmembrane or glycosylphosphatidylinositol anchor attachment domains. Southern blot analysis revealed that orthologous sequences for all of the newly identified proteases are present in E. dispar. Interestingly, the majority of the various cysteine protease genes are not expressed in E. histolytica or E. dispar trophozoites during in vitro cultivation. Therefore, it is likely that at least some of these enzymes are required for infection of the human host and/or for completion of the parasite life cycle.Cysteine proteases (EC 3.4.22) of the papain superfamily occur in a wide range of organisms including bacteria, plants, invertebrates, and vertebrates (7). In mammals, they are well documented as intracellular enzymes involved in protein turnover within lysosomes. In addition, extracellular cysteine proteases have been implicated in various physiological and pathophysiological processes, including tumor invasion and metastasis (33,43). Cysteine proteases are important virulence factors of various infectious agents and the main proteolytic enzymes in many protozoon parasites (22,29). The protozoan Entamoeba histolytica, the causative agent of human amoebiasis, is characterized by its great capacity to destroy host tissue, leading to potentially life-threatening diseases such as ulcerative colitis or liver abscess. Convincing evidence exists that cysteine proteases are essential for E. histolytica-induced pathology. Treatment of the ameba with sublethal doses of a specific cysteine protease inhibitor or the addition of laminin, which blocks the substrate-binding pocket of cysteine proteases, greatly reduces its ability to produce liver abscesses in laboratory animals (18, 37). Likewise, liver abscess formation was totally blocked and significantly less gut inflammation and damage to the intestinal permeability barrier were obser...