Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex
Samson O. Obado , Marc Brillantes , Kunihiro Uryu , Wenzhu Zhang , Natalia E. Ketaren , Brian T. Chait , Mark C. Field , Michael P. Rout
Published: February 18, 2016
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.
Much of the core architecture of the eukaryotic cell was established over one billion years ago. Significantly, many cellular systems possess lineage-specific features, and architectural and compositional variation of complexes and pathways that are likely keyed to specific functional adaptations. The nuclear pore complex (NPC) contributes to many processes, including nucleocytoplasmic transport, interactions with the nuclear lamina, and mRNA processing. We exploited trypanosome parasites to investigate NPC evolution and conservation at the level of protein–protein interactions and composition. We unambiguously assigned NPC components to specific substructures and found that the NPC structural scaffold is generally conserved, albeit with lineage-specific elements. However, there is significant variation in pore membrane proteins and an absence of critical components involved in mRNA export in fungi and animals (opisthokonts). This is reflected by the completely symmetric localization of all trypanosome nucleoporins, with the exception of the nuclear basket. This architecture is highly distinct from opisthokonts. We also identify features that suggest a Ran-dependent system for mRNA export in trypanosomes, a system that may presage distinct mechanisms of protein and mRNA transport in animals and fungi. Our study highlights that shared composition of macromolecular assemblies does not necessarily equate to shared architecture. Identification of lineage-specific features within the trypanosome NPC significantly advances our understanding of mechanisms of nuclear transport, gene expression, and evolution of the nucleus.
Citation: Obado SO, Brillantes M, Uryu K, Zhang W, Ketaren NE, Chait BT, et al. (2016) Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex. PLoS Biol 14(2): e1002365. doi:10.1371/journal.pbio.1002365
Academic Editor: Thomas U. Schwartz, MIT, UNITED STATES
Received: September 28, 2015; Accepted: December 23, 2015; Published: February 18, 2016
Copyright: © 2016 Obado et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: This work is supported in whole or part by The National Institutes of Health grants: NIAID Exploratory/Developmental Research Grant 1R21AI096069 (to MPR), NIGMS GM103314 (to BTC), GM103511 and GM109824 (to MPR and BTC); and Wellcome Trust grant 082813/Z/07/Z (to MCF and MPR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: ALPS, amphipathic lipid-packing sensor; DAPI, 6-diamino-2-phenylindoledihidrochloride; FG, phenylalanine-glycine; GAP, GTPase Activating Protein; GFP, green fluorescent protein; iEM, immunoelectron microscopy; IP6, inositol hexakisphosphate; mRNP, messenger ribonucleoprotein; MS, mass spectrometry; NE, nuclear envelope; NPC, nuclear pore complex; Nups, nucleoporins; Pel, pellet; Poms, pore membrane proteins; PTU, polycistronic transcription units; RRM, RNA recognition motif; Sup, supernatant; TbNPC, T. brucei NPC; TbNups, T. brucei Nups; TM, trans-membrane domain
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