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Nucleocytoplasmic Transport and the
Nuclear Pore Complex |
Unlike their prokaryotic counterparts, eukaryotic cells
separate the nuclear synthesis of DNA and RNA from cytoplasmic protein synthesis with a barrier termed the nuclear envelope
(NE).1 The NE is perforated
by large proteinaceous assemblies, called nuclear pore complexes
(NPCs), which act as the sole gatekeepers controlling the exchange of
material between the two locales (reviewed in Ref. 1). NPCs are freely
permeable to small molecules (such as water and ions), but they
restrict the movement of larger molecules (such as proteins and RNAs)
across the NE. To overcome this barrier, macromolecules carry specific
signals that allow them to access the nucleocytoplasmic transport
machinery of the cell. In this way the cell ensures that only selected
macromolecules can travel between the nucleus and cytoplasm (reviewed
in Ref. 2).
Operationally, NPCs are composed of proteins called nucleoporins (or
Nups) forming the stationary phase for nucleocytoplasmic exchange,
whereas the mobile phase consists of soluble transport factors and
their cargoes. As nucleocytoplasmic transport is driven by a series of
specific interactions between components of both phases, it is
frequently difficult to determine which proteins are permanent
constituents of the NPC. Nevertheless, to understand how transport
occurs, we must characterize the players in both phases and understand
how their interplay leads to the coordinated vectorial exchange of
macromolecules across the NE. In this review we focus on recent results
that shed light on how some of these proteins interact to contribute to
the elaborate NPC architecture and its function as a transport machine.
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Architecture of the NPC |
NPCs from different organisms share a common fundamental
architecture (3). These similarities likely provide clues as to the key
features common to a functioning transport machine. The NPC is a large
octagonally symmetric cylindrical structure. In yeast it estimated to
be ~50 MDa, whereas in metazoans it is over twice this mass (3, 4).
Given that a ribosome at 4 MDa contains ~80 proteins, it might be
expected that the NPC would contain hundreds of different nucleoporins.
However, it has recently been shown that the yeast NPC contains only
~30 different proteins and the vertebrate NPC contains perhaps a few
more (5). This raises the question of how such a large complex can be
constructed from so few component parts. The answer appears to lie in
the symmetry of the structure (Figs.
1-3). The NPC is comprised of a cylindrical core from which numerous peripheral filaments project toward the nucleus and cytoplasm (reviewed in Ref. 6) (Figs. 1 and
2). The remarkable symmetry of the NPC is
most apparent in the central core. Not only is it composed of eight
identical spokes, but each spoke is also seemingly mirror symmetrical
both in a plane parallel to the NE and in a perpendicular plane running through the cylindrical axis. As predicted from this symmetry, all
nucleoporins examined thus far are present in multiple copies (apparently 1, 2, or 4 copies per spoke and hence 8, 16, or 32 copies
per NPC), and most are localized to both the nuclear and cytoplasmic
sides of the NE (5-7) (Fig. 3). By
combining this symmetry with the relatively large size of most known
nucleoporins (generally between 50 and 360 kDa), it becomes clear how
the massive NPC can actually be constructed from a comparatively small
number of proteins. Furthermore, the large size of nucleoporins
potentially allows them to span between more than one domain of the
NPC. However, for simplicity, we will begin by considering each major
morphological NPC domain in turn and examine how they may combine to
form the complete functional machine.

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Fig. 1.
Structure of the nuclear pore complex.
Each NPC is a large proteinaceous assembly embedded in the pore
membrane domain of the nuclear envelope, where the
inner and outer nuclear membranes fuse. The NPC
contains eight spokes, projecting radially from the wall of
the pore membrane and surrounding a central tube called the
central transporter. Each spoke is composed of numerous
struts and attached to its neighbors by four coaxial rings: an
outer spoke-ring in the lumen of the NE adjacent to the pore
membrane, a nucleoplasmic ring, a cytoplasmic
ring, and an inner spoke-ring surrounding the central
transporter. A considerable portion of each spoke traverses the pore
membrane and resides in the NE lumen. Together these structures
comprise the central core. Peripheral elements project from this core
toward the nucleoplasm and cytoplasm. These
include: numerous proximal filaments on both faces of the
cylindrical central core, whose presence (though not directly imaged)
is inferred from the large number of symmetrically disposed filamentous
nucleoporins; eight cytoplasmic filaments, attached at the
cytoplasmic ring; and nuclear filaments originating at the nuclear ring
and conjoining distally to form the nuclear basket, which
connects with elements of the nucleoskeleton (not shown).
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Fig. 2.
Visualization of NPC substructures.
Scanning electron microscopy (left) of a vertebrate
(Xenopus) NPC viewed en face from the cytoplasm
best reveals the cytoplasmic filaments (CF); an NPC viewed
similarly from the nucleoplasm shows the nuclear basket
(NB). The structures of the central core are revealed by
three-dimensional protein density maps generated by cryoelectron
microscopy and image processing (CryoEM, right)
of both vertebrate and yeast NPCs. The positions of the spoke
(SP) and central transporter (T) are indicated on
both the en face projection map (top
row) and longitudinal slice (bottom
row) of the vertebrate NPC. The positions of the cytoplasmic
ring (CR), nuclear ring (NR), outer spoke-ring
(OR), and inner spoke-ring (IR) are indicated on
a longitudinal slice. Diagrams at the left of the
micrographs show the corresponding orientation of the NPC.
Micrographs were kindly provided by Martin Goldberg and Terry
Allen (SEM) and Chris Akey (CryoEM).
Bar, 50 nm.
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Fig. 3.
Increasing resolution maps of the NPC
substructure. Immunoelectron microscopy (ImmunoEM) has
begun to map the position of the nucleoporins within the NPC, whereas
mass spectrometry (MS) is one of the new techniques
being used to map the direct interactions between individual
nucleoporins (5, 14).
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The Pore Membrane Domain and Formation of the Nuclear Pore |
The nuclear envelope is composed of three biochemically distinct
domains. The outer NE membrane is continuous with the endoplasmic reticulum and the inner membrane lies within the nucleus. Nuclear pores
are created by a fusion of these two membranes, thus defining the third
membrane domain, the pore membrane. The resulting channel connects the
nucleoplasm with the cytoplasm, and integral membrane proteins
localized to this domain are termed Poms (pore
membrane proteins). Although surprisingly little is known
about the function of each Pom, they likely play a central role in NPC
assembly by initiating the formation of the pore membrane domain,
stabilizing it, and serving as a membrane anchor site for the growing
NPC. Remarkably, little homology has been found so far between Poms from different organisms, but as the mechanism of pore formation is
probably conserved, it seems likely that such homologues exist and have
yet to be identified.
NPCs assemble continuously throughout interphase (8, 9); thus, the
formation of the pore membrane domain must be fast and coincide with
the insertion of the NPC, so that neither the nucleoplasm nor the ER
lumen leaks during this process. Early assembly intermediates clearly
have a pore membrane domain but apparently very little else and are
presumably stabilized by integral pore membrane proteins such as
Pom121p, which is recruited early in the reassembly process (10, 11).
Gp210, a pore membrane protein known to be a major constituent of the
lumenal ring, is apparently recruited later in NPC assembly (11). Gp210
is also hyperphosphorylated at the early stages of mitosis, and this
modification may be important to initiate the mitotic disassembly of
the NPC and nuclear envelope (12). Although Gp210 is a major
protein in metazoan NPCs, the lack of an orthologue in yeast further
suggests a possible role for Gp210 in NPC disassembly, as there is no
NE disassembly step during yeast mitosis.
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The Central Core: The Spoke-Ring Complex and Central
Transporter |
The core of the NPC is considered to be the compact, highly
symmetrical framework that underlies and stabilizes the central structure of the NPC. As might be expected, all the yeast nucleoporins that seem to fit within this category are relatively abundant components, localized to both faces of the NPC (5, 7). Surprisingly, only one-third of all the core nucleoporins is essential in yeast. This
is likely a result of the symmetry and compact organization of the
central core, such that proteins within this region make multiple
contacts with each other and contribute to an interwoven framework that
is stable to the loss of any individual component. This idea is
supported by various genetic and biochemical data. One of the best
examples for this connectivity is the well defined six-member Nup84p
subcomplex (Fig. 3) (13). Most proteins in this complex make
interactions with several of their neighbors, creating a network of
protein interactions stabilizing the overall structure (14). That only
two members of the complex are essential in yeast may reflect this
stability, such that the complex can suffer loss of components without
catastrophic consequences. When examined by electron microscopy, the
complex has a Y-shaped morphology and a mass of ~375 kDa. All the
members are symmetrically disposed within each NPC and present in an
estimated 16 copies (5, 13). Thus, this one subcomplex alone could
potentially account for ~6 MDa of the 50-MDa yeast NPC! How this
complex connects to the rest of the NPC still remains unclear, although
it has been suggested that the arms of the "Y" structure
interconnect to form one of the internal rings of the NPC (13).
A detailed comparison of the core structure in vertebrates and yeast
points to the presence of additional structures in vertebrates, including a radial arm and more elaborate nuclear and cytoplasmic rings
(Fig. 2) (3, 7, 15). However, the features of the central transporter
and spoke-ring complex are conserved between the two, as they are in
all eukaryotes studied. At the molecular level, for known core
components, there is also remarkable conservation. For example,
mammalian Nup155 can functionally replace its orthologue, the yeast
core protein Nup170p (16). The yeast Nup84p subcomplex also appears
conserved; sequence comparisons suggest that most members of this
subcomplex have metazoan orthologues, and a similar vertebrate complex
can be isolated containing at least some mammalian counterparts of the
yeast complex (17).
How does the core contribute to NPC function? As all
macromolecular transport across the NE occurs through the central
transporter, supported within the core of the NPC, the core is
obviously essential to transport. However, the core must also 1)
maintain the structural integrity of the NPC as a barrier to diffusion
while simultaneously being sufficiently flexible to withstand
morphological changes in the nuclear envelope, 2) support the stepwise
NPC assembly process, and 3) accommodate large transported cargo.
Indeed, the spoke-ring complex and the central transporter have been
observed in different morphological states by electron cryomicroscopy
(15, 18). These different conformations suggest a sequential dilation of the central transporter, progressing from a resting state permeable to only smaller molecules to the triggering of a fully dilated state by
the passage of the largest transport cargoes. Similar dramatic
conformational changes within the central transporter and nuclear
basket have been observed during the transport of large particles such
as ribonucleoprotein particles (RNPs) (19, 20).
Interestingly, in yeast, removal of the core components Nup170p and
Nup188p increases the nonselective macromolecular permeability of the
NPC (21). These results are the first to define nucleoporins involved
in controlling diffusion through the NPC and suggest that these
proteins are either part of the transporter itself or anchor proteins
that are.
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Nucleocytoplasmic Transport and the Peripheral
Nucleoporins |
The framework of the core also correctly positions the peripheral
nucleoporins. These nucleoporins are considered accessible to the
mobile phase of transport and thus play a more direct role in
interacting with carriers and their cargoes. Cargoes destined for the
nucleus carry a nuclear localization signal (NLS), whereas substrates
to be exported from the nucleus harbor nuclear export sequence
(reviewed in Ref. 2). The signals are, in turn, recognized by a
structurally related family of soluble transport receptor proteins
collectively termed karyopherins (kaps; also known as importins,
exportins, and transportins) (reviewed in Refs. 2 and 22). Transport
cargoes, such as nuclear proteins, messenger RNPs, tRNA, ribosomal
proteins, ribosomal subunits, and small nuclear RNPs, have distinct
NLSs or nuclear export sequences that are recognized by their own
particular cognate transport factors. This interaction is controlled by
the small GTPase Ran (see below and Refs. 23 and 24). Electron
microscopy studies suggest that the karyopherin-NLS-cargo complex docks
at multiple sites along the cytoplasmic filaments and through the NPC
(25, 26). Thus, it is proposed that nuclear import is facilitated by a
series of karyopherin docking and release steps, as the cargo-carrier complex moves along peripheral nucleoporins from the cytoplasmic filaments of the NPC through the central transporter, to the
nucleoplasmic face, where the complex is released to the nuclear
interior (27).
FG Nucleoporins Provide an Abundance of Transport Factor
Binding Sites at the NPC--
Of course, to fully understand how the
NPC might directly contribute to transport, it is necessary to first
characterize its components. The NPC is crammed with nucleoporins
characterized by the presence of the FG dipeptide (Phe-Gly) repeat
motifs. These repeats are present in nearly half the nucleoporins and
often take the form of GLFG or FXFG repeats, separated by
polar sequences of varying lengths. These so-called FG nucleoporins
appear to be built upon the core structure and are present throughout
the NPC, extending from the tips of the cytoplasmic filaments through the central transporter to the distal ring of the nuclear basket (Fig.
3) (5, 7). As the FG nucleoporins are strategically positioned to be
accessible to the mobile phase and interact directly with all of the
karyopherins studied (as well as other cargo-carrying transport
factors) (28), they are implicated directly in facilitating karyopherin/cargo movement across the NPC.
Analysis of the structure of an FG repeat region bound to a karyopherin
indicates that multiple FG repeats likely interact with numerous
conserved hydrophobic pockets running along the outside of the
karyopherin via phenylalanines in the FG repeat. Overall, the FG repeat
region adopts an extended conformation with little intrinsic secondary
structure. Furthermore, FG nucleoporins have been shown to form
filaments (30) and colocalize with the filamentous structures of the
NPC (reviewed in Refs. 6 and 7). This is consistent with these proteins
forming the majority of the filaments that emanate from the core and
extend into the nucleoplasm and cytoplasm, although other possible
conformational states cannot be excluded. As might be expected from
their projection from the core of the NPC, in many cases FG
nucleoporins are anchored to the core by one or the other of their ends
(31-34).
Different Transport Factors, Different Docking Sites--
Every
transport factor studied can bind FG nucleoporins that have also been
shown to bind other classes of transport factors (reviewed in Ref. 28).
This fact and the observations that saturated or irreversible binding
of some karyopherins to the NPC can be deleterious to other pathways
suggest that pathways through the NPC overlap in specificity. However,
considering the symmetry of the NPC and the abundance of FG
nucleoporins there may be ~160 transport factor binding sites per
NPC. Although this provides a multitude of possible binding sites for
each transport factor molecule, karyopherins have strong preferences
for a restricted subset of FG nucleoporins (reviewed in Ref. 28). This
could allow different karyopherins to simultaneously occupy different sites within a single NPC, while limiting the competitive interference between different pathways and increasing the potential transport flux
in both directions. Indeed, it has been shown that a single NPC is
capable of both exporting and importing different transport substrates
(35). The NPC could also use such docking specificity as a way to
globally regulate gene expression by simply modifying a nucleoporin
dedicated to a particular nuclear transport factor. One of the most
intriguing examples of this is the interaction between Kap121p and
Nup53p in yeast. Although in vitro binding studies and
in vivo fluorescence resonance energy transfer measurements demonstrate that Kap121p interacts with several different FG
nucleoporins while transiting the NPC, both studies suggest that Nup53p
is a specific docking site for Kap121p (36, 37). Thus, although not
absolute, it appears that Nup53p could confer control over the
Kap121p-mediated import pathway. Interestingly, Nup53p is phosphorylated at mitosis, and there is a concomitant decrease in the
binding of the karyopherin Kap121p to the NPC although it remains to be
determined if this results in a specific cell cycle-dependent change in nuclear import (36).
The Strategic Positioning of the Docking Sites: Efficient and
Directional Transport--
From studies mapping the relative position
of all the nucleoporins in yeast, it is striking that many FG
nucleoporins are symmetrically disposed closely surrounding the central
transporter, whereas FG nucleoporins localized exclusively to
either the nucleoplasmic or cytoplasmic sides are placed
further away from the core. This observation suggests that the
directionality of transport factors through the NPC is conferred by the
FG nucleoporins at the extremities of the NPC. It also likely that
there are more subtle arrangements of docking sites within the
symmetrical regions of the NPC in which precise order and distribution
helps correctly direct transport factors as they transit the pore.
Interestingly, like the core nucleoporins, complexes formed by the
peripheral nucleoporins are also well conserved. Thus both the yeast
Nsp1p nucleoporin subcomplex and the analogous vertebrate p62-p58-p54
complex are found on both sides of the NPC surrounding the central
transporter (5, 38-40). This together with the fact that there is only
minimum amino acid sequence conservation in the repeat motifs between presumed orthologues from different species (41) suggests that the
conservation lies in the functionality of the conserved binding sites
themselves and in their similar strategic positions within the NPCs of
different organisms.
The Energetics of Transport--
In addition to nucleoporins,
sustained karyopherin-mediated nucleocytoplasmic exchange requires
energy. The only known source of this energy is the small GTPase Ran
(reviewed in Refs. 23 and 24). However, as the translocation process
itself is not linked to GTP hydrolysis, it is likely that the energy
comes from a potential energy gradient across the NPC established by
the maintenance of distinct pools of Ran: GTP-Ran in the nucleus and GDP-Ran in the cytoplasm (Fig. 4). This
asymmetric distribution supports transport by triggering the assembly
and disassembly of transport complexes in the correct compartments.
Thus, importers release their cargoes when they interact with Ran-GTP
in the nucleus, whereas exporters utilize Ran-GTP to bind their
cargoes. Conversely, when the GTP on Ran is hydrolyzed (as is the case
in the cytoplasm) importers can bind their cargoes, but exporters will
release theirs.

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Fig. 4.
The Ran cycle. Ran cycles between its
GTP- and GDP-bound form dependent on its subcellular localization. The
different forms of Ran confer directionality to transport by dictating
where karyopherins bind and release their cargoes. See "The
Energetics of Transport" for details. D, Ran-GDP;
T, Ran-GTP.
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Although Ran is soluble in both the nucleoplasm and cytoplasm, it is
also directly tethered to the NPC through at least two different
protein motifs within nucleoporins. The first domain is homologous to
the cytoplasmic Ran-binding protein RanBP1. This domain binds both
Ran-GTP and Ran-GDP and has been found in the cytoplasmic FG
nucleoporin Nup358p (42). The second type of Ran binding domain,
characterized by a zinc finger motif, binds Ran-GDP and is present on
both Nup358p (43) and the nucleoplasmically disposed nucleoporin
Nup153p (44). Ran binding to these distal nuclear and cytoplasmic
components of the NPC may ensure a high concentration of Ran in the
vicinity of the nuclear pore, improving the efficiency of the transport
termination steps. This role may involve promoting the exchange of Ran
between transport factors and maintaining the Ran-GTP/Ran-GDP gradient
across the NPC. In addition, Nup358 tethers Ran-GAP (which activates
the GTPase activity of Ran) to the NPC (45, 46). Localizing karyopherin
docking sites, Ran binding sites, and Ran-GAP to the same nucleoporin may provide a means of ensuring highly efficient loading and unloading of transport factors and their cargoes during transport. This tethering
may be particularly important in the relatively large mammalian cells
where soluble factors have the potential to diffuse great distances
away from the pore. In this respect it is interesting that in the
smaller yeast cells, the only Ran-binding protein known to associate
with the NPC (Nup2p (47)) is dispensable, suggesting that the presence
of such domains at the NPC may not be an absolute requirement for transport.
The export of messenger ribonucleoprotein complexes seems to require
additional cofactors at the NPC with their cognate nucleoporin binding
sites. Thus, the RNA helicase Dbp5p is associated with both yeast
Nup159p and its vertebrate homologue Nup214; the RNP-binding protein
Gle2p is similarly bound to the NPC (reviewed in Ref. 28). These
proteins may aid in the quaternary structural changes in the RNP
necessary to wind it through the narrow central transporter and, in the
case of the ATP-driven helicase, provide additional energy for the
translocation of the comparatively huge RNP particles across the
NPC.
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The Mechanism of Transport |
Four major principles must be considered to develop a model for
transport through the NPC. First, the NPC provides a barrier to the
diffusion of macromolecules across the NE, but it must also be gated to
permit the rapid passage of macromolecules bearing the appropriate
signals. As there appears to be no NTP-driven mechanism to promote the
dilation of the channel, the apparent opening and closing of the
channel may not be actively gated by NPC components. The second
important principle is that the narrow diameter of the channel and the
Brownian motion of the flanking, closely spaced, filamentous
nucleoporins likely make macromolecular diffusion across the NPC
entropically unfavorable. Third, transport across the NPC is mediated
by a multitude of cargo-carrying transport factors that interact with
the large number of FG nucleoporins. One model proposes that the
entropic exclusion of the NPC can be overcome, in the case of transport
factor-cargo complexes, by the energy associated with their binding to
the FG nucleoporins themselves. As most of these FG nucleoporins are
equally distributed on both sides of the NE, transport factors could
then readily exchange between nucleoporins on both sides of the NE. The
NPC is therefore effectively a "virtual gate"; as proteins that can bind the NPC pass the diffusion barrier of the central channel much
more freely than those that do not, gating selectivity is achieved
without necessarily invoking a gate composed of any moving parts (in
the conventional sense) (5). The fourth principle is that asymmetric,
high affinity binding sites particularly at the extreme nuclear and
cytoplasmic faces of the NPC likely contribute (together with the Ran
GTP/GDP gradient) to determining the directionality of transport (5).
Indeed several lines of evidence indicate that a high affinity terminal
nucleoporin binding step contributes to the transport directionality of
karyopherin-cargo complexes (48-50).
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Summary and Perspectives |
The work discussed here still represents only a promising
beginning, and two major challenges remain. First, it remains necessary to determine the nature of the regulated interactions and connectivity of the mobile and stationary phase components and to test various models to understand in detail how these two phases interface to
regulate macromolecular transport across the nuclear envelope. Second,
we must establish what alterations and additions evolution has provided
to build nucleocytoplasmic transport systems capable of responding to
the various needs of cells found within the wide variety of eukaryotic organisms.