Intrinsic protein disorder reveals divergent signaling architectures and lifestyle adaptation in Entamoeba species

Intrinsic protein disorder plays a central role in cellular regulation and host-pathogen interactions, yet its proteome-wide distribution and functional organization in amoebozoan parasites remain poorly understood. Here, we present the first comparative analysis of intrinsic disorder across the proteomes of Entamoeba histolytica , which causes amoebic dysentery, and two related species, E. dispar , and E. invadens . For comparison, we analyzed intrinsic protein disorder in two phylogenetically distant parasites, Plasmodium falciparum and Trypanosoma brucei . Overall, Entamoeba species exhibited significantly lower levels of intrinsic disorder than P. falciparum and T. brucei . Despite this, all organisms displayed a conserved functional trend in which increasing disorder was associated with a shift from metabolic and catalytic processes toward gene expression-related functions. However, notable organism-specific differences emerged. P. falciparum showed persistent enrichment of gene expression functions across all disorder levels, while T. brucei maintained metabolic, redox, and transport processes throughout the disorder spectrum. In contrast, Entamoeba species uniquely retained GTPase- and phosphorylation-associated signaling across all levels of disorder, with the strongest enrichment observed in the pathogenic species, E. histolytica and E. invadens . This pattern likely reflects a reliance on rapid environmental sensing, cytoskeletal remodeling, and vesicle trafficking, necessary for successful infection. Consistent with this, there was reduced enrichment of G-protein signaling in the non-pathogenic commensal, E. dispar , especially in highly disordered proteins. Secretome analysis further revealed that, unlike P. falciparum , E. histolytica possesses a more structurally ordered secretome, suggesting selection for stable catalytic proteins in the host intestinal environment. Finally, no consistent relationship was identified between intrinsic disorder and vaccine efficacy for several key antigenic targets. Together, these findings demonstrate that intrinsic disorder is differentially deployed across parasites, and utilization of disordered proteins has diverged in accordance with each organism’s lifecycle and host interaction strategy. These findings highlight the role of intrinsic disorder in shaping parasitism.