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

Nuclear pore complexes (NPCs) serve as gateways for macromolecular exchange between the nucleus and cytoplasm across eukaryotes. While NPCs maintain a broadly conserved architecture, significant lineage-specific diversification has occurred, especially among divergent protists. This study delves into the NPC of Entamoeba histolytica, a divergent amoebozoan responsible for amebiasis.

Through affinity purification coupled with mass spectrometry using EhNup98-like as bait, researchers identified numerous associated proteins, including a novel candidate nucleoporin with resemblance to Nup53/Nup35. Subsequent reciprocal proteomic analysis of EhNup53-like unearthed a wider array of candidate NPC components, encompassing both conserved nucleoporins and several uncharacterized nuclear pore-associated proteins.

Structural analyses unveiled that the EhNup53-like protein harbors a conserved RNA recognition motif (RRM)-like fold, despite extensive primary-sequence divergence. Additionally, it exhibits lineage-specific features, such as an expanded repeat-rich region and truncation of the C-terminal region typically associated with Nup155 binding.

These findings augment the known candidate nucleoporins in E. histolytica and unveil NPC-associated networks that amalgamate recognizable conserved components with extensively remodeled and poorly characterized proteins. The study underscores the evolutionary flexibility of the NPC and offers a framework for comprehending the diversification of nuclear pore architecture across deeply divergent eukaryotic lineages.