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

Abstract

The core architecture of the eukaryotic cell was established well over one billion years ago, and is largely retained in all extant lineages. However, eukaryotic cells also possess lineagespecific features, frequently keyed to specific functional requirements. One quintessential core eukaryotic structure is the nuclear pore complex (NPC), responsible for regulating exchange of macromolecules between the nucleus and cytoplasm as well as acting as a nuclear organizational hub. NPC architecture has been best documented in one eukaryotic supergroup, the Opisthokonts (e.g. Saccharomyces cerevisiae and Homo sapiens), which although compositionally similar, have significant variations in certain NPC subcomplex structures. The variation of NPC structure across other taxa in the eukaryotic kingdom however, remains poorly understood. We explored trypanosomes, highly divergent organisms, and mapped and assigned their NPC proteins to specific substructures to reveal their NPC architecture. We showed that the NPC central structural scaffold is conserved, likely across all eukaryotes, but more peripheral elements can exhibit very significant lineage-specific losses, duplications or other alterations in their components. Amazingly, trypanosomes lack the major components of the mRNA export platform that are asymmetrically localized within yeast and vertebrate NPCs. Concomitant with this, the trypanosome NPC is ALMOST completely symmetric with the nuclear basket being the only major source of asymmetry. We suggest these features point toward a stepwise evolution of the NPC in which a coating scaffold first stabilized the pore after which selective gating emerged and expanded, leading to the addition of peripheral remodeling machineries on the nucleoplasmic and cytoplasmic sides of the pore.

Integrative structure and functional anatomy of a nuclear pore complex

“…10). In contrast, peripheral elements exhibit significant lineage-specific losses and duplications 38,39 . In yeast, each outer ring is formed by 8 copies of the Nup84 complex (Figs.…”

Pore timing: the evolutionary origins of the nucleus and nuclear pore complex

“…Trypanosomes have a simple peripheral organization and lack any obvious transport factor docking sites beyond the FG repeats 9 . In S. cerevisiae , docking sites are present on the NPC cytoplasmic side for several RNA remodeling proteins, including Gle1 and Dbp5; the lack of both of these docking sites and genes encoding the remodeling proteins in trypanosomes is likely a reflection of distinct mRNA splicing mechanisms, as previously discussed 3, 56 . In vertebrates, elaborate arrays of docking sites exist on the cytoplasmic platform, both for such RNA remodeling proteins and for nuclear transport accessory proteins such as Ran, RanGAP (Ran GTPase-activating protein), and Ubc9 (ubiquitin-conjugating gene product 9) 57, 58 .…”

Nuclear mRNA maturation and mRNA export control: from trypanosomes to opisthokonts

“…It is tempting to speculate, that the CCCH finger mediates mRNA binding of Mex67, perhaps even specific to the miniexon sequence that is present on every mRNA (Dostalova et al, 2013). Consistent with this hypothesis is the absence of a TREX-1 and TREX-2 complex in trypanosomes (see sections 'The TREX complex' and 'The TREX-2 or THSC complex') and the fact that no putative Mex67 adaptor protein co-purified with Mex67 (Dostalova et al, 2013;Obado et al, 2016). Two independent studies have analysed Mex67 interacting proteins (Table 6): The first study was a classical immunoprecipitation using TbMex67 with a C-terminal PTP tag as a bait (Dostalova et al, 2013).…”

“…Second, apparent orthologues to many NUPs with specific functions in mRNA export and export control are missing and this includes the entire ATP-dependent remodelling complex at the cytoplasmic site. Instead, mRNA export in trypanosomes is likely RanGTP dependent (Obado et al, 2016). Third, trypanosomes can initiate mRNA export co-transcriptionally, indicating that the completion of major processing steps such as polyadenylation and splicing is not required (Goos et al, 2019).…”