The standard reference for pathogenic and nonpathogenic amoebae is the human parasite Entamoeba histolytica; a direct correlation between virulence and protease expression has been demonstrated for this amoeba. Traditionally, proteases are considered virulence factors, including those that produce cytopathic effects in the host or that have been implicated in manipulating the immune response. Here, we expand the scope to other amoebae, including less-pathogenic Entamoeba species and highly pathogenic free-living amoebae. In this paper, proteases that affect mucin, extracellular matrix, immune system components, and diverse tissues and cells are included, based on studies in amoebic cultures and animal models. We also include proteases used by amoebae to degrade iron-containing proteins because iron scavenger capacity is currently considered a virulence factor for pathogens. In addition, proteases that have a role in adhesion and encystation, which are essential for establishing and transmitting infection, are discussed. The study of proteases and their specific inhibitors is relevant to the search for new therapeutic targets and to increase the power of drugs used to treat the diseases caused by these complex microorganisms. 1. Introduction Amoeba is a general name that is used for protists that form a large and diverse assemblage of eukaryotes that are characterized by various types of pseudopodia [1, 2]. Some amoebae are pathogenic and even parasitic to human and other vertebrate hosts. The four amoebae that are dealt with in this paper have been classified under two Super Groups, Amoebozoa and Excavata, as follows: (a) Entamoeba, Acanthamoeba, and Balamuthia are classified under the Super Group Amoebozoa; (b) Naegleria fowleri is classified under Super Group Excavata [1, 2]. The genus Entamoeba includes several species, such as E. histolytica, which causes amoebiasis, an infection in the gut characterized by invasion of the intestinal mucosa that occasionally spreads to other organs, mainly the liver, and E. dispar and E. moshkovskii, which are morphologically similar to E. histolytica and have been recently recognized as separate species. Although E. dispar and E. moshkovskii have no apparent invasive potential, they exhibit some pathogenicity [3, 4]. Molecular phylogeny analysis places the genus Entamoeba on one of the lowermost branches of the eukaryotic tree, closest to Dictyostelium [5]. Although Entamoeba, originally thought to lack mitochondria, nuclear-encoded mitochondrial genes and a remnant organelle have now been identified. The
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