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 lineage-specific 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.

Keywords: Trypanosoma brucei; eukaryogenesis; mRNA export; molecular evolution; nuclear pore complex.

Figure 1.

Schematic of opisthokont NPCs. A schematic of textbook NPCs highlighting each distinct nuclear pore subcomplex. The approximate location messenger ribonucleprotein (mRNP) remodeling factors required for mRNA export out of the NPC is also shown.

Figure 2.

(A) comparison between Excavate and Opisthokont NPCs and transport through them. Trypanosomes (Excavates) have a symmetric NPC with the exception of the nuclear basket unlike in opisthokonts (yeast and humans). Furthermore, trypanosomes lack the cytoplasmic mRNA platform including mRNP (ribonucleoproteins) remodeling factors such as the ATP-dependent DEAD box helicase Dbp5 and Gle1 that are crucial for mRNA export in opisthokonts. Instead, mRNA export in trypanosomes appears to rely on the RanGDP/GTP gradient similar to protein export, as opposed to ATP in opisthokonts. This may be related to the unusual mechanisms trypanosomes use for controlling gene expression. Trypanosome protein-coding genes are intronless and each gene lacks an individual polymerase II promoter. Thus, trypanosome genes (green boxes) are transcribed into long multigene (polycistronic) transcripts that are resolved into single mRNAs by trans-splicing of a mini exon, also known as the spliced leader sequence (purple box) at the 5′ end of each gene, splicing out of intergenic (orange lines) sequences and polyadenylated (AAA). Processed and export competent mRNA are exported through the NPC by the Mex67/Mtr2 heterodimer (pink ovals). Protein coding genes in opisthokonts (and most other eukaryotes) have introns (orange boxes) and individual promoters (flags) and are transcribed as singly (monocistronic). Transcribed mRNAs are co-transcriptionally 5′-capped (gray circles), and introns spliced (orange lines) before export by Mex67/Mtr2 in conjunction with the actions of the ATP dependent helicase Dbp5.

Figure 3.

Evolution of the NPC. We propose a model in which the NPC evolved gating functions in a stepwise manner starting with a simple coat that acquired complexity through a series of duplications as observed in endomembrane trafficking. This then led to the evolution of FG-Nups and then further diversification into the current metazoan type NPC with a nuclear basket and cytoplasmic filaments.