Evolutionary diversification of the nuclear pore complex in Entamoeba histolytica reveals conserved and lineage-specific nucleoporins

Nuclear pore complexes (NPCs) are the gateways for macromolecular exchange between the nucleus and cytoplasm. Although NPC architecture is broadly conserved across eukaryotes, substantial lineage-specific diversification has emerged, particularly among divergent protists. Here, we investigated the NPC of Entamoeba histolytica, an evolutionarily divergent amoebozoan and the causative agent of amebiasis. Using the FG-repeat nucleoporin EhNup98-like as bait in affinity purification coupled with mass spectrometry, we identified various associated proteins, including a previously uncharacterized candidate nucleoporin with similarity to Nup53/Nup35. Reciprocal proteomic analysis of EhNup53-like further recovered a broader repertoire of candidate NPC components, including proteins corresponding to conserved nucleoporins as well as several uncharacterized nuclear pore-associated proteins. Structural analyses indicated that this EhNup53-like protein retains a conserved RNA recognition motif (RRM)-like fold despite extensive primary-sequence divergence, while displaying lineage-specific features, including an expanded repeat-rich region and truncation of the C-terminal region typically associated with Nup155 binding. Together, these findings expand the known candidate nucleoporins in E. histolytica and reveal NPC-associated networks that combines recognizable conserved components with extensively remodeled and poorly characterized proteins. Our study highlights the evolutionary plasticity of the NPC and provides a framework for understanding how nuclear pore architecture has diversified across deeply divergent eukaryotic lineages.