Nucleocytoplasmic Transport.

Structural and functional characterization of the p62 complex, a subcomplex of the nuclear pore complex

Nuclear transport pathways use soluble receptors to mediate the translocation of protein and cargo through the nuclear pore complex (NPC). In October 2005, investigators from around the globe braved the threat of hurricane Wilma and presented their latest findings at the Nucleocytoplasmic Transport Meeting at Jekyll Island, GA, USA. The meeting was organized by Drs Maureen Powers, Chuck Cole, and Douglass Forbes. Major themes within the meeting included architecture of the NPC, structural analysis of receptors, regulation of nuclear transport, models for translocation, and emerging roles for the NPC and lamina in gene expression. The transport of proteins and RNAs between the cytoplasm and nucleus is mediated by nuclear pore complexes (NPCs), large proteinaceous structures embedded in the double membrane of the nuclear envelope (NE) (1–4). The NPC structure is conserved in all eukaryotes and is composed of approximately 30 separate proteins termed nucleoporins (Nups), most of which are present in multiple copies per NPC. Nups provide docking sites for soluble transport receptors that mediate the translocation of protein and RNA cargoes through the NPC. The karyopherin family is composed of receptors for import (importins) and export (exportins). These receptors mediate most protein import and export pathways in the cell, as well as the export of some RNAs. Transport receptors recognize specific sequences termed nuclear localization signals (NLSs) or nuclear export signals (NESs) contained in the cargo protein. mRNAs are exported by a class of transport receptors that are distinct from the karyopherin family. An important regulator of nuclear transport is the small GTPase Ran, and its GTPase activating protein (RanGAP) and guanine nucleotide exchange factor (RanGEF or RCC1). Previous models of the NPC have been based primarily on low-resolution cryo-electron microscopy (EM) studies and the immuno-EM localization of a handful of NPC proteins (Figure 1A) (4). More recently, proteomic approaches have established the identities of virtually all the protein constituents of the NPC, setting the stage for a more complete picture of the NPC (5,6). Michael Rout (The Rockefeller University, New York, NY, USA) and colleagues used a computational approach to reconstruct the arrangement of 30 different Nups in the NPC. The model combined EM immunolocalization data with protein–protein interaction data obtained by immunoprecipitation of tagged Nups. This exciting model gives us the first glimpse of an integrated view of the locations of individual Nups and various subcomplexes of the NPC. Of course, solving the atomic structure of the NPC is one of the ‘holy grails’ of the field, and Thomas Schwartz (Massachusetts Institute of Technology, Boston, MA, USA) updated the meeting on his progress toward solving the structure of the p62 complex, a subcomplex located in the central channel of the NPC. Given its enormous size (>100 MDa), it might be necessary to piece together subcomplexes to solve the complete NPC structure. Antibody studies have allowed the localization of a small number of Nups that are asymmetrically positioned on either the nuclear or cytoplasmic sides of the NPC, and Nups with biased locations are good candidates for specialized transport functions. Two nucleoplasmic Nups in vertebrates are the large nucleoporins Nup153 and TPR. Volker Cordes (ZMBH, Heidelberg, Germany) used domain-specific antibodies to analyze the structural arrangement of TPR at the NPC by scanning and transmission EM. He found that different TPR domains correspond to distinct segments of the nuclear basket, with TPR homodimers forming a central loop to contact Nup153 at the NPC nuclear ring, while both N- and C-terminus of TPR project toward the nucleoplasm. Volker's antibody data provide strong evidence that TPR is the key component of the nuclear basket. Gallery of images illustrating some diverse aspects of nuclear structure and function.(A) NPCs on the surface of the NE membrane of Xenopus oocytes visualized by field emission scanning electron microscopy. Cytoplasmic filaments of the NPC appear as globular structures that line the perimeter of the pore. The image is courtesy of Dr Terry Allen. (B) Mitotic embryo fibroblast from a rae1+/–nup98+/– mouse imaged during anaphase B. While most of the chromosomes (green) have moved to the spindle poles, lagging chromosomes (red arrow) are visible and give rise to aneuploidy. Image is courtesy of Dr Jan van Duersen. (C) Model of transmembrane linkages between proteins in the cytoplasm and nucleus. Nesprins bind actin filaments in the cytoplasm and contact SUN domain proteins in the NE lumen. SUN domain proteins also contact lamins; these interactions are thought to provide a continuous linkage between the cytoskeleton and the nucleoskeleton. The image is courtesy of Dr Brian Burke and is reproduced from Crisp et al. (26) with permission from Rockefeller University Press. A subset of Nups contain repeats of the amino acids phenylalanine-glycine, and many studies have established that these FG repeats are binding sites for the karyopherins moving through the central channel of the NPC (1,2,7). It is estimated that the central channel of the NPC contains several hundred FG repeats. There is much debate within the field as to what this channel looks like and how it mediates a selective gating mechanism. Models include a central tube lined with FG repeats that acts as an affinity gate (also called virtual gating), or a sieve-like channel where disordered FG repeats mediate hydrophobic interactions between Nups creating a gel-like phase that generates a permeability barrier within the NPC (also called the selective phase model) (1,2). Michael Rexach (University of California, Santa Cruz, CA, USA) used a new bead-based, real-time equilibrium-binding assay to test for low-affinity interactions between FG regions of Nups. Binding required phenylalanine residues in FG motifs and was disrupted by hexanediol, an alcohol known to weaken the NPC permeability barrier in transport assays. He concluded that FG regions of Nups interact with each other, supporting the ‘selective phase’ model for NPC gating. Dirk Gorlich (ZMBH, Heidelberg, Germany) reported on efforts by his group to address the properties of the central channel envisioned to be important for the selective phase model. He surprised the meeting by showing that a single FG nucleoporin, Nsp1p, can assemble into a three-dimensional ‘hydrogel’ with molecular sieve-like properties. Dirk also showed that a mutant version of Nsp1p where the >50 FG repeats had been mutated fails to form the ‘hydrogel’. These results were consistent with the idea that interactions between hydrophobic repeats in Nups could play structural and functional roles in the permeability barrier. Future experiments will determine whether this ‘hydrogel’ displays other properties of the central channel and help address longstanding questions regarding the central channel, including how gating of the NPC is achieved. Earlier studies by several groups have indicated that different karyopherins display distinct binding specificities for FG Nups in vitro. An extensive collection of FG-domain deletion strains created by the Wente laboratory is being used to probe the interactions between different karyopherins and the central channel in Saccharomyces cerevisiae (8). It has been shown that Kap104p-mediated translocation is more sensitive than Kap95p/Kap60p-mediated translocation to certain FG-domain deletions (8). David Goldfarb (University of Rochester, Rochester, NY, USA) presented recent experiments that are most consistent with the notion that Kap95p/Kap60p does better than Kap104p in these FG-domain deletion strains, because it competes better for remaining FG-binding sites. This advantage may normally occur under stress, because elevated levels of Hsp70 favor the translocation of Kap95p/Kap60p over Kap104p. The karyopherin family comprises the major family of transport receptors. In yeast, there are 14 members of this family, and in human cells, there are more than 20 members (1,2). Although the amino acid sequence identities are low, each Kap has similar large size (approximately 100 kDa) and are all predicted to consist of multiple (approximately 20) HEAT motifs. The HEAT motif is a helix-loop-helix structure that owes its name to the proteins in which it was originally identified (9). Kaps contain an N-terminal domain that interacts with RanGTP and nucleoporins. Kaps also bind directly (or via adapters) to the NLSs or NESs of their cargoes. The crystal structures of several karyopherins, empty, with cargo, and with RanGTP, have all been solved. At the meeting, several groups focused on further analysis of karyopherins at the atomic level. The overall theme in these talks was that karyopherins have great conformational flexibility and that members of this family can have different conformations despite the fact that they all are composed of tandem HEAT repeats. Murray Stewart (Medical Research Council, Cambridge, UK) discussed the crystal structure of Kap95p. He proposed that this importin is flexible when binding to cargoes, but the interaction with RanGTP, which precludes cargo binding, introduces inflexibility into the protein. Murray continued this theme in discussing his structure of the Cse1p, the receptor that mediates nuclear export of importin-α (10). Elena Conti's laboratory (EMBL, Heidelberg, Germany) has solved the structure of unliganded Cse1p and found it to form a relatively rigid ring-like structure. In this closed conformation, the binding sites for either importin-α or RanGTP are distorted. Indeed, Cse1p binds either importin-α or Ran with micromolar affinity, while the simultaneous interaction of Cse1p with importin-α and RanGTP occurs with nanomolar affinity and is correlated with the open conformation of Cse1p observed in Murray's structure. This conformational regulation provides a rationale for why Cse1p fails to interact with importin-α in the cytosol, in the absence of RanGTP. Reporting on a low-resolution study of conformations of different transport factors, Elena dismissed the idea of a general importin-like or exportin-like structure. For example, the exportin Xpo-t is more similar in overall structure to importin-β than it is to the exportin Cse1 (11). It appears that the most common feature of karyopherins is their flexibility in acquiring distinct conformations depending on whether they are empty or interacting with RanGTP or cargo. Conformational differences were to be expected due to acidic loops and insertions found between HEAT repeats in assorted family members. Lucy Pemberton (University of Virginia, Charlottesville, VA, USA) reported that a single karyopherin, Kap114p, can bind multiple cargoes simultaneously in vitro, and hopefully future structures will address how these 7interactions take place at the atomic level. Collectively, these studies suggest that we still have a lot to learn about the complexity of karyopherin–cargo interactions. There was a very lively session describing efforts to analyze the mechanism of nuclear transport at the single-molecule level, as well as efforts to model nuclear transport. Although much is known about individual components of the transport machinery, and many important binding interactions have been characterized, tracking individual cargoes as they transit through the NPC should provide clues about the transport mechanism. Ulrich Kubitschek (University of Bonn, Bonn, Germany) used single-molecule far-field fluorescence microscopy to visualize nuclear transport through NPCs of both permeabilized and living cells. Intracellular single-molecule detection in the nanometer range is feasible using this technique. Binding of cargo reduced the dwell times of the transport receptors in the NPC, suggesting that cargo has an important influence on karyopherin interactions with Nups. Seigfried Musser (Texas A&M, College Station, TX, USA) presented his measurements of import efficiency, which is the number of molecules that are transported divided by the number of molecules that interact with an NPC. In the permeabilized cell system, he found that both import efficiency and translocation time were dependent on the concentration of the importin-β, as import efficiency was higher and the translocation time was faster with increasing importin-β concentrations. Seigfried speculated that the cargo-free importin-β concentration within the NPC may regulate nucleocytoplasmic transport rates. Ruti Kapon (Weizmann Institute of Science, Rehovot, Israel) examined receptor-mediated import through the NPC using a non-equilibrium statistical mechanics model where all reactions are modeled using kinetic rates. Her model suggested that the selectivity of the channel against receptor-free cargo, in itself, leads to accumulation of the cargo in the destination compartment even if the translocation process itself is unbiased. A major question in the field is how the NPC coordinates import and export through the same channel. Ruti suggested that synchronization of import and export is based on stochastic fluctuations in the NPC. She posited the NPC is unidirectional for a characteristic time, but it can spontaneously change its directionality. Thus, for given periods, an individual NPC can be dedicated to either import or export. Experimental analysis is required to establish the validity of these models. Ian Macara (University of Virginia, Charlottesville, VA, USA) presented his ongoing studies that combine computer simulation and microinjection assays to monitor fluorescent cargoes and recombinant receptors in real time. Ian discussed his previous observation that in living cells, high levels of importin-β or RanGEF inhibit import of an NLS-cargo (12). Excess RanGEF probably sequesters Ran in the nucleus, whereas excess importin-β may deplete Ran from the nucleus by co-opting it for futile nucleoplasmic shuttling cycles. In his new studies, Ian used a shuttling NES-NLS cargo that can reach steady-state localization in the cell. Excess importin-β and Crm1 decreased the N:C ratio of the reporter, whereas importin-α increased the N:C ratio. Components of the Ran system had little effect most likely because the reporter reflected both import and export function. There was an interesting discussion regarding how importin-α-dependent transport is less efficient and energetically more costly given the need to recycle importin-α to the cytoplasm, but importin-α proteins endow the cell with greater flexibility in terms of binding diverse cargoes (13). Nuclear export of mRNA is mediated principally by Mex67p/TAP/NXF1, a highly conserved receptor family that is unrelated to the karyopherin family of import and export receptors (14). Functional coupling between mRNA export and upstream reactions (transcription and mRNA processing) is mediated by several multiprotein complexes. The TREX complex consists of proteins involved in transcription elongation and mRNA export and includes the THO protein complex as well as the mRNA export factors Yra1p/Aly and Sub2p/Uap56 (14). There were several talks that addressed the links between mRNA transcription, processing and nuclear export. Andres Aguilera (University of Seville, Spain) showed that the THO protein complex functions in co-transcriptional mRNP formation, and he described a new component of the THO complex, Tho1p. Tho1p is a conserved RNA-binding protein that interacts with transcribed chromatin in a THO- and RNA-dependent manner. These results suggested that Tho1p, similar to Sub2p, assembles onto nascent mRNA during transcription and participates in mRNP biogenesis and nuclear export. Nuclear export of mRNA is also coordinated with mRNA splicing and 5′ capping. Robin Reed (Harvard Medical School, Boston, MA, USA) showed that the human TREX complex is recruited to the 5′-end of mRNA in a splicing- and cap-dependent manner. The TREX complex binds to the 5′-methyl cap-binding protein, CBP80, an interaction that provides a plausible mechanism for TREX recruitment to the 5′-end of mRNA. The findings presented by Robin suggest a model of mRNA export that differs from models from Melissa Moore's laboratory, which were based on coupling the export machinery to the exon junction complex (15). Francoise Stutz (University of Geneva, Geneva, Switzerland) continued the theme of coupled reactions by describing links between the RNA export factor Yra1p/Aly, and Mlp1p and Mlp2p, yeast homologs of TPR that face the nucleoplasm. Previously, Francoise identified genetic interactions between the MLP1/2 and YRA1 that suggested that the Mlp1/2p proteins provide a scaffold at the NPC for Yra1p-dependent docking of mRNPs (16). Yra1p appears to directly regulate transcription, as recruitment of TBP to an induced promoter is decreased in a yra1 mutant. Francoise found that this effect could be reversed in a yra1/mlp2 double mutant, suggesting that Mlp1/2p negatively regulates the transcriptional function of Yra1p. Collectively, these talks emphasized the close links between nuclear export, transcription and RNA processing and suggested that the NPC may regulate transcription by several mechanisms. John Aitchison (Institute for Systems Biology, Seattle, WA, USA) focused on the role of nucleoporin Nup2p, which displays dynamic associations with the NPC. John investigated the previous observation that Nup2p has boundary activity when tethered to chromatin (17). John and colleagues used a variety of assays, including chromatin immunoprecipitation and gene arrays, to show that Nup2p regulates gene expression and gene silencing. Another component of the nuclear transport machinery, the RanGEF Prp20p, was found to have similar chromatin-related functions. The human homolog of Prp20p is known to interact with core histones, and as Nup2p interacts with both the NPC and Prp20p, these data argue for linkage between the NPC and chromatin. As the association of Nup2p with the NPC is transient, the data suggest that the NPC might play an anchoring role and help direct the partitioning of chromatin into inactive and active regions. The mRNA export events downstream of TREX and TAP/Nxf1/Mex67p are poorly defined. Some exported hnRNPs are enormous, suggesting that this must be an energy-requiring process. RanGTP does not appear to regulate this process, suggesting that other important regulatory mechanisms might exist. Three talks discussed Dbp5p, an RNA helicase that plays a role in mRNA export and transiently associates with the cytoplasmic side of the NPC. Karsten Weis (University of California, Berkeley, CA, USA) showed that the DExD/H-box protein Dbp5p has intrinsically low ATPase activity and is unable to associate stably with RNA in the absence of ATP, suggesting that Dbp5p alone is an inactive enzyme. He also showed that the NPC-associated protein Gle1p the ATPase activity of Dbp5p and presented a model in which these proteins as a complex to mRNA export. Wente University, USA) reported a similar that Gle1p and Dbp5p but in was to show that the the activity of Dbp5p by in the of the This is interesting in of analysis of the role of in nuclear transport, where showed that cytoplasmic is required for mRNA export Collectively, these findings to how small molecules may regulate mRNA export. Chuck Medical School, USA) focused on the role of Dbp5p in mRNA processing at distinct from export through the NPC. mRNA is increased in a mutant, and a of Dbp5p with He described new between Dbp5p and which are cytoplasmic structures that are to be necessary for mRNA and these data the model that Dbp5p may play important roles in mRNA export and processing both at the NPC and in the factors that play important roles in mRNA export have been and (University of California, CA, USA) described analysis of the yeast mRNA export factor This protein is an membrane protein that to the Although is not thought to be a of the NPC, it interacts with several which is consistent with a role in transport. She showed that interacts with mRNPs in and is required for the NE localization of the mRNA export factor She proposed a model where this membrane protein provides binding sites to the NPC to help mRNPs and in the for export. these studies suggest that mRNA export is a process a of factors that appear to regulate this process from transcription to talks addressed nucleocytoplasmic transport of components required for protein Medical USA) discussed the import and export of which are one of the most of In previous showed that in the nucleus in the exportin mutant can be into the nucleus in a mechanism that is dependent on Ran and the importin that of might be of an mRNA or it could be of a mechanism for given that in the nucleus in to (University of TX, USA) focused on nuclear export of the which on as an for export. of the from the cytoplasmic GTPase and the protein In in the nucleus, and accumulation in the These suggest a mechanism of the export complex can occur in the focused on the nuclear export and cytoplasmic processing of RNA component of the He showed that processing of the of the in occurs in the cytoplasm nuclear export. This is a of models that show that processing is in the nucleus. This is necessary for the activity of the in and might be important for interaction with in the nucleus. consist of core proteins and an RNA and are for biogenesis and mRNA It is not known how these but University, New York, NY, USA) the role of the protein in the process. between nucleus and cytoplasm and one of the core to the nascent is by core protein, to in and transcription factors of import and export as a of cytoplasmic signals with nuclear import export can have a influence on the nuclear concentration of transcription factors The receptor and (University of Virginia, Charlottesville, VA, USA) presented showing that export is by of a to the export (University of Germany) described his molecular analysis of nuclear export of nuclear factor of of nucleoporins or export of RNA export or protein and are on the cytoplasmic side of the NPC these Nups may be the sites where export complexes are and into the nucleoporins a that has on a number of transcription factors and The of the that this has the stage for how regulates protein USA) reported that reduced levels of in the in the nuclear transport of a transcription factor that is a downstream of transcription factors to on nuclear import mediated by karyopherins, but the of the protein can an that direct interaction with John USA) presented findings from and yeast that a model nuclear localization of high group transcription factors as than the observation that nuclear transport can be correlated with the in cells, the of whether there are in the nuclear transport machinery during in is University, used in and to show that there are in the expression of importin-α and importin-β receptors during This that nuclear transport might be at the of receptor during links between cell the import receptor and the RNA-binding protein were reported by University, of the import was shown to accumulation in the cytoplasm of in As can bind and factors and the effect of cytoplasmic was to and protein cell The study of and their regulatory mechanisms has many aspects of cell and the field of nuclear transport has been of the first export signals to be is by the human protein and to be a cargo for cell nuclear export. an RNA export function that is for the it is a David (University of Virginia, Charlottesville, VA, USA) presented his new results from a to of the small molecules in the display micromolar of function in cells. David an that to one of the small of that function can be identified in this of of regulation in has to a based on signals that nuclear export of RNA to the The transport in which this is by the export receptor The is to be to higher but the for RNA export signals in mRNAs has been by the in these signals at the sequence level. have for the of RNA export (University of Virginia, Charlottesville, VA, USA) used a system to for and identified in the human The have sequence to the with one the for a which that mediates nuclear export of its mRNA. In previous USA) had identified a nucleotide RNA transport and showed that its activity is to the from used a to in in the mouse RNA export, like RNA export, on the appears to contact with the structural between and should provide into the important of of mRNAs by direct mechanisms. Two talks presented at the meeting addressed how to the nucleus. In the of proteins are and the is through the NPC into the cell nucleus. (The Research CA, USA) has to the import mechanism and has identified a key role for protein which contains NLSs and the interaction between and cell import

Just as the great explorations revealed a world far more diverse and rich than had been imagined before, a mass of fast accumulating data is disclosing a much more complex and sophisticated picture of the nucleus than hitherto assumed. The nucleus has long been thought of as some sort of enclosure circumscribed by a double membrane and containing the genetic material of the cell. The inner and outer nuclear membranes join periodically at the nuclear pores, forming complexes supposed to create large channels for the free diffusion of ions and small macromolecules. In this view, the flow of calcium between nucleus and cytoplasm would appear unrestricted, with nuclear Ca2+ signals originating from cytosolic Ca2+ waves merely by passive transmission through the nuclear pore complex (NPC). However, recent evidence has changed the mappa mundi of the cell. It has been shown that nuclear Ca2+ can be regulated independently of cytosolic Ca2+ changes. And, just as the Terra Incognita discovered beyond the Ocean Sea proved a fabulous New World, the nuclear envelope (NE) between the cytoplasm and nucleoplasm appears to play an essential role in the regulation of Ca2+ signals inside the nucleus. It contains proteins that regulate and respond to changes in nucleosolic Ca2+ concentration ([Ca2+]nucleosol). Furthermore, several specific Ca2+‐dependent nuclear functions have been described and the list is growing. The regulation of nuclear Ca2+ signals, and the role of nuclear Ca2+ as a specific regulator of nuclear events through Ca2+‐binding proteins, were the main themes of the recent EMBO workshop entitled ‘Calcium signals in the cell nucleus’, organized by A.N.Malviya and coworkers in Strasbourg, France. The existence of Ca2+ signals at the level of the nucleoplasm has never been a real issue, as the …

The nuclear pore complex: a jack of all trades?

MEL-28 Is Downstream of the Ran Cycle and Is Required for Nuclear-Envelope Function and Chromatin Maintenance

Importin-β: Structural and Dynamic Determinants of a Molecular Spring

Nuclear pore complexes (NPCs) are supramolecular nanomachines that mediate the exchange of macromolecules and inorganic ions between the nucleus and the cytosol. Although there is no doubt that large cargo is transported through the centrally located channel, the route of ions and small molecules remains debatable. We thus tested the hypothesis that there are two separate pathways by imaging NPCs using atomic force microscopy, NPC electrical conductivity measurements, and macromolecule permeability assays. Our data indicate a spatial separation between the active transport of macromolecules through the central channel and the passive transport of ions and small macromolecules through the pore periphery.

How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using a high-throughput imaging RNAi screen, we identify and mechanistically characterize ELYS, a nucleoporin required for post-mitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. ELYS knockdown results in small nuclei, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β-mediated nuclear import decreases nuclear size. Conversely, ELYS overexpression increases nuclear size, enriches nuclear lamin B2 at the nuclear periphery, and elevates NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. Thus, we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.

Nuclear pore complexes (NPCs) are large supramolecular assemblies that perforate the double-membraned nuclear envelope and serve as the sole gateways of molecular exchange between the cytoplasm and the nucleus in interphase cells. Combining novel specimen preparation regimes with innovative use of high-resolution scanning electron microscopy, Hans Ris produced in the late eighties stereo images of the NPC with unparalleled clarity and structural detail, thereby setting new standards in the field. Since that time, efforts undertaken to resolve the molecular structure and architecture, and the numerous interactions that occur between NPC proteins (nucleoporins), soluble transport receptors, and the small GTPase Ran, have led to a deeper understanding of the functional role of NPCs in nucleocytoplasmic transport. In spite of these breakthroughs, getting to the bottom of the actual cargo translocation mechanism through the NPC remains elusive and controversial. Here, we review recent insights into NPC function by correlating structural findings with biochemical data. By introducing new experimental and computational results, we reexamine how NPCs can discriminate between receptor-mediated and passive cargo to promote vectorial translocation in a highly regulated manner. Moreover, we comment on the importance and potential benefits of identifying and experimenting with individual key components implicated in the translocation mechanism. We conclude by dwelling on questions that we feel are pertinent to a more rational understanding of the physical aspects governing NPC mechanics. Last but not least, we substantiate these uncertainties by boldly suggesting a new direction in NPC research as a means to verify such novel concepts, for example, a de novo designed 'minimalist' NPC.

To fulfil their function, nuclear pore complexes (NPCs) must discriminate between inert proteins and nuclear transport receptors (NTRs), admitting only the latter. This specific permeation is thought to depend on interactions between hydrophobic patches on NTRs and phenylalanine-glycine (FG) or related repeats that line the NPC. Here, we tested this premise directly by conjugating different hydrophobic amino-acid analogues to the surface of an inert protein and examining its ability to cross NPCs unassisted by NTRs. Conjugation of as few as four hydrophobic moieties was sufficient to enable passage of the protein through NPCs. Transport of the modified protein proceeded with rates comparable to those measured for the innate protein when bound to an NTR and was relatively insensitive both to the nature and density of the amino acids used to confer hydrophobicity. The latter observation suggests a non-specific, small, and plant interaction network between cargo and FG repeats.

Now that it is likely that all yeast nucleoporins are known, one of the ultimate goals is the in vitro assembly of the entire nuclear pore complex from its approximately 30 individual components. Here, we report the reconstitution of seven proteins (Nup133p, Nup145p-C, Nup120p, Nup85p, Nup84p, Seh1p and Sec13p) into a heptameric 0.5 MDa nuclear pore subcomplex. We found that double plasmid transformation combined with bi-cistronic mRNA translation allow the expression and assembly of distinct subcomplexes of up to five nucleoporins in a single Escherichia coli cell. During the sequential reconstitution of the Nup84p complex, smaller assembly intermediates can be isolated, which exhibit modular structures determined by electron microscopy that finally make up the whole Y-shaped Nup84p complex. Importantly, a seventh subunit, Nup133p, was incorporated into the complex through its interaction with Nup84p, thereby elongating one arm of the Y-shaped assembly to an approximately 40 nm long stalk. Taken together, our data document that the Nup84p-Nup133p complex self-assembles in a modular concept from distinct smaller nucleoporin construction sets.

One of the remarkable features of eukaryotes is the nucleus, delimited by the nuclear envelope (NE), a complex structure and home to the nuclear lamina and nuclear pore complex (NPC). For decades, these structures were believed to be mainly architectural elements and, in the case of the NPC, simply facilitating nucleocytoplasmic trafficking. More recently, the critical roles of the lamina, NPC and other NE constituents in genome organisation, maintaining chromosomal domains and regulating gene expression have been recognised. Importantly, mutations in genes encoding lamina and NPC components lead to pathogenesis in humans, while pathogenic protozoa disrupt the progression of normal development and expression of pathogenesis-related genes. Here, we review features of the lamina and NPC across eukaryotes and discuss how these elements are structured in trypanosomes, protozoa of high medical and veterinary importance, highlighting lineage-specific and conserved aspects of nuclear organisation.

Nucleocytoplasmic transport occurs through the nuclear pore complex (NPC), which in yeast is a ~50 MDa complex consisting of ~30 different proteins. Small molecules can freely exchange through the NPC, but macromolecules larger than ~40 kDa must be aided across by transport factors, most of which belong to a related family of proteins termed karyopherins (Kaps). These transport factors bind to the disordered phenylalanine-glycine (FG) repeat domains in a family of NPC proteins termed FG nups, and this specific binding allows the transport factors to cross the NPC. However, we still know little in terms of the molecular and kinetic details regarding how this binding translates to selective passage of transport factors across the NPC. Here we show that the specific interactions between Kaps and FG nups are strongly modulated by the presence of a cellular milieu whose proteins appear to act as very weak competitors that nevertheless collectively can reduce Kap/FG nup affinities by several orders of magnitude. Without such modulation, the avidities between Kaps and FG nups measured in vitro are too tight to be compatible with the rapid transport kinetics observed in vivo. We modeled the multivalent interactions between the disordered repeat binding sites in the FG nups and multiple cognate binding sites on Kap, showing that they should indeed be sensitive to even weakly binding competitors; the introduction of such competition reduces the availability of these binding sites, dramatically lowering the avidity of their specific interactions and allowing rapid nuclear transport.

Nucleoporins Directly Stimulate Expression of Developmental and Cell-Cycle Genes Inside the Nucleoplasm

The cell nucleus is surrounded by a double membrane system, the nuclear envelope (NE), with the outer nuclear membrane being continuous with the endoplasmic reticulum. Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes, forming aqueous channels that allow free diffusion of small molecules but that also mediate the energy-dependent transport of large macromolecules. The NPC represents the largest known molecular complex and is composed of about 30 different proteins, termed nucleoporins (Nups). Here, we review recent studies that provide novel insight into the structural and functional organization of nucleocytoplasmic transport. In addition, prospects towards a high resolution model of the nuclear pore are discussed.