Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

Abstract

The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes.

Integrative structure and functional anatomy of a nuclear pore complex

“…10). Overall, the inner ring architecture is similar in both yeast and vertebrates, in agreement with it being the most conserved part of the NPC 142 .…”

“…Generally, the inner ring appears most conserved 37,38 , as seen in a comparison of our yeast structure with the human scaffold 6 , although the latter is more expanded (Extended Data Fig. 10).…”

Comparative interactomics provides evidence for functional specialization of the nuclear pore complex

“…Until recently, detailed compositional, structural and functional information of the NPC was only available for Saccharomyces cerevisiae (Sc) and Homo sapiens (Hs), both members of the Opisthokont supergroup, and thus relatively, closely related. [2][3][4] In the last 7 years, NPC components have been well cataloged in 2 further supergroups, Excavata (Trypanosoma brucei (Tb)) by us, 4,5 and Archaeplastida (Arabidopsis thaliana (At)), 6,7 resulting in remarkable initial insights into the structure, evolution and species-specific adaptations of the NPC.…”

“…1). [3][4][5][6][7][8][9][10][11] Poms and the core scaffold form the major structural framework while FG-Nups establish the permeability barrier of the NPC and facilitate nucleocytoplasmic transport through interactions with soluble transport factors (karyopherins), with directionality dependent on a Ran GTP/GDP gradient. 12 There is extremely low sequence similarity between excavate and opisthokont Nups.…”

“…4 Despite this, trypanosome Nups share a remarkable architectural and domain organization with opisthokonts and plants, highlighting that structural considerations such as detailed fold arrangements are key to the function of these proteins (Table 1). 4,5 The core scaffold of the NPC comprises the inner and outer rings that are composed almost exclusively of proteins comprised of b-propellers, a-solenoids, or an N-terminal b-propeller and C-terminal a-solenoid (b-a). 13,14 These characteristics are shared with major classes of membrane interacting proteins, such as vesicle coat proteins (COPI, COPII, clathrin and tethering complexes) and intraflagellar complexes, suggestive of a common ancestry between the endomembrane trafficking system and the NPC, a theory known as the "protocoatomer hypothesis".…”