Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor - PubMed (original) (raw)

Comparative Study

Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor

Nadja Neumann et al. PLoS One. 2010.

Abstract

Background: The Nuclear Pore Complex (NPC) facilitates molecular trafficking between nucleus and cytoplasm and is an integral feature of the eukaryote cell. It exhibits eight-fold rotational symmetry and is comprised of approximately 30 nucleoporins (Nups) in different stoichiometries. Nups are broadly conserved between yeast, vertebrates and plants, but few have been identified among other major eukaryotic groups.

Methodology/principal findings: We screened for Nups across 60 eukaryote genomes and report that 19 Nups (spanning all major protein subcomplexes) are found in all eukaryote supergroups represented in our study (Opisthokonts, Amoebozoa, Viridiplantae, Chromalveolates and Excavates). Based on parsimony, between 23 and 26 of 31 Nups can be placed in LECA. Notably, they include central components of the anchoring system (Ndc1 and Gp210) indicating that the anchoring system did not evolve by convergence, as has previously been suggested. These results significantly extend earlier results and, importantly, unambiguously place a fully-fledged NPC in LECA. We also test the proposal that transmembrane Pom proteins in vertebrates and yeasts may account for their variant forms of mitosis (open mitoses in vertebrates, closed among yeasts). The distribution of homologues of vertebrate Pom121 and yeast Pom152 is not consistent with this suggestion, but the distribution of fungal Pom34 fits a scenario wherein it was integral to the evolution of closed mitosis in ascomycetes. We also report an updated screen for vesicle coating complexes, which share a common evolutionary origin with Nups, and can be traced back to LECA. Surprisingly, we find only three supergroup-level differences (one gain and two losses) between the constituents of COPI, COPII and Clathrin complexes.

Conclusions/significance: Our results indicate that all major protein subcomplexes in the Nuclear Pore Complex are traceable to the Last Eukaryotic Common Ancestor (LECA). In contrast to previous screens, we demonstrate that our conclusions hold regardless of the position of the root of the eukaryote tree.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. NPC structure, composition and Nup conservation across eukaryotes.

a) Schematic section through the nuclear pore complex. Sub-complexes are indicated as boxes and marked in different colors to indicate their position in the pore. b) The table summarizes Nup distribution across eukaryotic super-groups. Color-coding matches that of the subcomplexes in (a). Nucleoporins indicated with bold letters are universally distributed across eukaryotes, as judged by presence in at least one genome from each of the five supergroups.

Figure 2

Figure 2. NPC components are traceable to LECA.

NPC pore composition in LECA based on two alternative rootings of the eukaryote tree. In the left hand tree, Excavates are the outgroup. The right hand tree is rooted on the basis of the unikont/bikont bifurcation. Gains (+) and losses (–) in different lineages are indicated under each scenario. Where gains and losses are equally probable, these are marked with (?).

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