INTRODUCTION

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The defining characteristic of eukaryotic cells is the segregation of nucleic acid synthesis and processing into a membrane-bound compartment, the nucleus. The nuclear envelope is a double membrane contiguous with, and presumably evolved from, the endoplasmic reticulum (ER). One might speculate that the binding of ER vesicles to chromatin during mitosis perhaps helped ensure a balanced division of the ER to the two daughter cells and that during early evolution the vesicles began to fuse on and therefore enclose the surface of the chromatin. However, complete enclosure would be lethal, and proteins were therefore needed to maintain holes in the envelope, holes of sufficient size to permit the passage of ribosomes and mRNA molecules. Although these holes may originally have been no more than open passageways to allow diffusion, they ultimately became the nuclear pore complexes (NPCs)arguably the largest protein structures in the eukaryotic cell (200).

Compartmentalization provides opportunity for regulation, and the import and export of proteins and nucleic acids through the pores of modern eukaryotes is tightly controlled. This nucleocytoplasmic traffic has also become functionally and mechanistically diversified, serving not only to permit operation of the basal replication, transcription, and processing machinery but also to regulate the cell cycle, transcriptional activation and repression, circadian rhythms, and a host of other processes.

Diversification of nucleocytoplasmic transport has evolved by a different route from that taken for the translocation of ions and small molecules across membranes. For these species, cells have evolved numerous channels and carriers that span the membrane bilayer. However, the NPCs appear on the basis of electron microscopy, yeast genetics, and biochemistry to be identical and to permit passage of all of the various types of cargo that need to cross between the nuclear and cytoplasmic compartments (55, 215, 280).

The selectivity of nucleocytoplasmic transport rests in part on the structure of the NPCs but additionally depends on a variety of soluble carriers. These carrier proteins are designed to recognize cargo destined for translocation and to shuttle back and forth efficiently through the nuclear pores. Rapid progress has been made within the past few years in the identification and analysis of these soluble carriers and of accessory factors that aid their work, and this review will focus mainly on this aspect of nucleocytoplasmic transport. Our understanding of the structure and function of the NPCs has been hindered by their great complexity, but is beginning to yield to new imaging methods and yeast genetics (47, 60, 215, 248, 280). These advances, together with the development of technologies to observe the movement of single protein molecules through NPCs (118), will ultimately allow a detailed molecular understanding of the process of nucleocytoplasmic transport.

During interphase, the only means of access to the nucleoplasm is through the NPCs. These are octagonally symmetric structures composed of a cylindrical channel that is attached to an outer rim by eight spokes (for reviews, see references 48, 58, 183, 215, 247, and 270). Viewed in cross section, the central channel, spokes, and rim are sandwiched between two rings. From the ring that faces the cytoplasm there extend eight fibrils, while from the nuclear ring extend eight long filaments that are linked at their extremities to another ring, so as to form a structure like a basket or fishing net. The basket ring appears to be able to open and close, like an iris, in response to changes in calcium ion concentration, but the function of this conformational change is not known (248).

The yeast NPC is rather smaller than that found in higher eukaryotes, but, weighing in at 30 to 60 MDa, it is still about 15 times the size of a ribosome. It was surprising, therefore, when exhaustive analysis of purified yeast NPCs revealed an upper limit of only about 30 distinct protein components (60, 215). Ribosomes, by comparison, contain ~75 different proteins. Localization of the NPC components by electron microscopy also unexpectedly revealed that most are symmetrically localized on the nucleoplasmic and cytoplasmic faces of the NPC. Only the peripheral, filamentous structures appear to have distinct compositions. The small number of components may be related to the high degree of symmetry of the NPC and to the fact that the average polypeptide size (~100 kDa) is much larger than that of ribosomal proteins. NPC symmetry may be fundamental to the transport mechanism, a topic discussed below.

The proteins of the NPC are called nucleoporins. Their synthesis, association into subcomplexes and assembly into NPCs, structural features, and functions are all the focus of intensive studies but will not be reviewed exhaustively here. Briefly, the nucleoporins can be divided into three groups: those that span the nuclear membrane, nonmembrane proteins that contain multiple repeats of a Phe-Gly motif, and nonmembrane proteins that do not. Associated with the NPC there are also shared-function, peripheral, or other proteins that may be transport cofactors or assembly factors rather than bona fide structural components (60, 215, 249, 280).

The number of NPCs per nucleus varies widely with the organism, cell type, and growth conditions, but mammalian cells typically contain ~3,000 to 5,000 NPCs (153, 216). The structure is consistent with there being a single channel per NPC through which all transport proceeds, and passive diffusion of small molecules is consistent with a channel of about 9 nm in diameter and 45 nm long (117). Only proteins with a diameter of less than ~5 nm, however, can diffuse across the nuclear boundary within a period of a few minutes. However, ribosomal subunits that are 25 nm in diameter, giant ribonuclear protein particles such as the Balbiani ring, and 26-nm gold particles can all be accommodated by the pores (61). The fundamental question, then, in understanding NPC function is how such a remarkable degree of flexibility and discrimination is provided. The answer must account for the lack of any motor proteins, ATPases, or GTPases among the components of the NPC.

The concept of specific nuclear transport signals arose from the observation that certain proteins, larger than the passive diffusion limit (~50 kDa) for the NPC, can accumulate within the nucleus. A classic series of experiments on nucleoplasmin provided the first proof of the existence of such signals, and the first signal sequence for nuclear import was identified in the simian virus 40 (SV40) large-T antigen (53, 112). This sequence, PKKKRK, and that found in nucleoplasmin, KRPAATKKAGQAKKKKLD (210), are the prototypes for the monopartite and bipartite nuclear-localization signals (NLS) now known to be present in manyprobably thousandsof different proteins (Table 1). A useful Web server (PSORTII) for identifying potential NLS sequences in protein sequences is available at http://psort.nibb.ac.jp:8800/.

One could imagine two likely mechanisms by which such signals might operate. Either they would bind directly to components of the NPC and be translocated through the pores like passengers on a moving walkway, or they could be recognized by soluble receptors that would carry them through the pores, like cargo carried on a truck. The development of an in vitro assay for nuclear import, using digitonin-permeabilized cells, provided the critical advance that demonstrated the second mechanism to be correct (3). Accumulation of a fluorescently tagged protein containing an NLS into the nuclei of permeabilized cells did not occur in the absence of cytosol. Fractionation of the cytosol led to the discovery of four soluble transport factors that could, together with ATP, reconstitute nuclear import (2, 160). One of these factors, importin (also called karyopherin, Kap, and PTAC58), was shown to bind directly to an NLS, confirming the soluble receptor-carrier hypothesis (1, 2, 81, 164).

The other transport factors that were isolated from cytosol using the in vitro assay were Ran, a small GTPase (also called TC4) (154, 160), NTF2 (also called p10 or pp15) (161, 189), and importin (also called karyopherin, p97, and PTAC97) (35, 78, 198). The functions of each of these factors will be discussed in more detail below. For the present, it is sufficient to note that importin itself does not interact with the NPC but instead functions as an adapter that binds to importin and that importin is the carrier that allows translocation through the pore.

These studies revolutionized the field, but it became apparent that many nuclear proteins do not contain classical mono- or bipartite NLSs and must either use alternate entry mechanisms or piggyback on cargo that does contain a classical NLS. One example is hnRNPA1. This abundant protein shuttles efficiently between the nuclear and cytoplasmic compartments, but the sequence responsible for shuttling, called M9, is glycine and asparagine rich and does not bind to importin (Table 1) (155). Rather, M9 was shown to be recognized by a novel protein, named transportin (karyopherin2), that is related to importin (196). A similar protein, Kap104, was also found in budding yeast (5) (Table 1). Each protein from this family that has been studied to date functions as a carrier in nucleocytoplasmic transport.

A priori, one might have expected that the carriers would be capable of transporting cargo in both directions through the pores, but to date this property has been demonstrated for only two family members, the yeast Kap142/Msn5 and mammalian importin13(157, 285). All of the other carriers appear to function exclusively either as importins or as exportins. Kap142 can import the yeast trimeric replication protein A (RPA) to the nucleus. As an exportin, it carries various proteinsPho4, Mig1, Far1, and Ste5to the cytoplasm (52, 110, 150, 236). It is unusual in that it exports only phosphorylated cargoes, but the consensus sequence context that allows recognition of specific phosphoserines by this carrier has not yet been defined.

Crm1 (exportin1, or Xpo1 in budding yeast) was the first export carrier to be identified (69, 72, 179, 241). It recognizes a short motif rich in leucine or related hydrophobic residues, which is found in the protein kinase A inhibitor PKI, in the human immunodeficiency virus (HIV) protein Rev, in RanBP1, and in dozens of other proteins (65, 73, 166, 208, 269). LxxxLxxLxL is the prototypical nuclear export signal (NES) sequence (Table 1), but other hydrophobic residues can substitute for several of the Leu residues, the number of intervening residues is somewhat variable, and prolines situated between the hydrophobic residues disrupt function (25). There are also efficient NESs that do not conform even to this rather vague consensus. The NES in the NFAT transcription factor, IVAAINALTT, is one example (123). Additionally, motifs that exactly match the PKI/Rev pattern sometimes have no export function, for instance in Ste5 (unpublished observation), perhaps because they are not exposed on the protein surface. The unambiguous definition of an NES is confounded by the high frequency of hydrophobic residues in protein sequences.

Many other import or export signal sequences must exist, but so far they have not been carefully dissected and are often much larger than the classical NLS and NES motifs. The import signal for uridine-rich small nuclear ribonucleoproteins (U snRNPs) comprises both the m3G cap on the RNA of the U snRNP and sequences within the Sm core protein of the RNP, which are recognized by an adapter protein called snurportin that, like importin, binds to importin (100, 181). Similarly, the export signal for snurportin, which is recognized by Crm1, is a large domain that encompasses most of the protein rather than a short hydrophobic sequence (185).

Most known import signals, except for M9, do have a basic character, however. For example, the NLSs present in ribosomal proteins such as L25 and L23a are highly basic (105, 224). Some viral cargoes bind directly to importin rather than through an importin adapter, and they also possess highly basic, arginine-rich NLSs (88, 182, 258). Additionally, certain cargoes with short basic sequences are able to bind to a distinct site on importin and be transported simultaneously with proteins possessing a monopartite NLS (K. Plafker and I. G. Macara, unpublished data). This common theme may reflect the evolutionary relationship between the importin family and the signals they recognize. On the other hand, it is just as likely to be a quirk that reflects the biased nature of the very small group of NLSs that have been characterized to date.

To add to this complexity, there are transport factors that are unrelated to the importin family and proteins that can translocate through the NPCs in the absence of other soluble factors. In the first category are the yeast protein Mex67 and its mammalian homologue TAP, which most probably bind directly to mRNA sequences (84, 101, 114); cytoplasmic calreticulin is an export carrier for steroid receptors (96) (see next section). In the second category there are proteins such as hnRNPK and -catenin, both of which most probably interact with the NPCs directly (59, 156, 282).

Clearly, we have not yet exhausted the repertoire of nuclear import and export signals. Nor have we identified all of the diverse mechanisms by which these signals can be regulated. Numerous proteins possess classical NLSs that are exposed or hidden or show altered import rates when nearby serine or threonine residues are phosphorylated (for a review, see reference 109). For example, phosphorylation of Pho4 not only permits recognition by Msn5 but also inhibits binding to the importin for this protein, Pse1 (Kap121) (110, 127). Phosphorylation by the PKB/Akt protein kinase within an NLS in the forkhead transcription factor, AFX, blocks nuclear import and results in a rapid shift of the protein to the cytoplasm (29, 30, 253). Masking of the NLS in NF-B by IB maintains the NF-B in the cytoplasm until IB is phosphorylated and degraded. This story is complicated, however, by the discovery that IB itself shuttles in and out of the nucleus (219, 261). Another example of masking involves the 14-3-3 family of proteins, which recognize phosphorylated serine residues within the sequence context RSxS*xP (where the asterisk indicates the phosphorylated residue). Cdc25, a protein tyrosine phosphatase that regulates the cell cycle, becomes associated with 14-3-3 when phosphorylated by a checkpoint kinase. Cdc25 possesses both an NES and a dominant NLS, but when bound to 14-3-3 the NLS is masked and Cdc25 accumulates in the cytoplasm (167). A similar mechanism may be involved in the cytoplasmic retention of forkhead transcription factors.

NESs can also be masked. One example is provided by telomerase reverse transcriptase, to which 14-3-3 can bind in a non-phosphoserine-dependent manner and block an NES (231). Another case is the transcription factor NFAT, which, in the presence of calcium ions, interacts with calcineurin. NFAT contains both an NES and one or two NLSs (depending on the isoform) and shuttles constitutively, so that masking of the NES by calcineurin permits nuclear accumulation (288). A twist on this story is that NFAT can also be negatively regulated by protein kinase A, which creates 14-3-3 binding sites on NFAT that may mask the NLS (167).

A reverse of this type of situation occurs when NLS or NES function is not masked but requires the formation of a complex. As an illustration, the import of a fission yeast protein called Mei2, which is necessary for meiosis, has to associate with a small RNA (mei-RNA) before it can accumulate in the nucleus (278). A different mechanism controls the localization of yAP1, a transcription factor that responds to oxidative stress. Cysteine residues within the NES of yAP1 are sensitive to the redox state of the cell, and their oxidation blocks interaction with the exportin, Crm1 (279).

Only during the last few years has the extraordinary range of processes that are controlled at the level of nucleocytoplasmic transport been recognized. Everything from apoptosis to circadian rhythms and from signal transduction to the cell cycle is regulated, at least in part, by switching NLSs and NESs on or off. Nuclear transport is the one common link between these diverse processes.

Most of the proteins that carry cargo through the NPCs are members of the importin/karyopherin family (Table 2). For consistency, we will refer to this family as the karyopherins, defining those that are involved in nuclear import as importins and those involved in export as exportins. Other, structurally unrelated carriers include TAP/Mex67 and calreticulin.

One feature common to the karyopherins is their ability to bind to nucleoporins. Where tested, most appear able to interact with regions of these proteins that are rich in FxFG repeats, but there are also distinct specificities (47, 70, 102, 199, 203, 228, 276). Another common feature is that karyopherins can form a complex with the GTP-bound state of the Ran GTPase. In some cases this interaction is of low affinity and is hard to detect; in others the K_d for Ran is in the low nanomolar range (76, 195, 233) (Table 2). The purpose of the interaction is to regulate the binding of cargo. Ran is the most abundant member of the Ras superfamily of GTPases, constituting about 0.4% of the total cell protein (21). Like other members of the superfamily, Ran functions as a molecular switch and undergoes a conformational change between the GDP- and GTP-bound states. Conversion between these forms is regulated by a guanine nucleotide exchange factor (RanGEF) and a GTPase-activating protein (RanGAP) (14, 18, 20). Another feature, common to most members of the superfamily but lacking in Ran, is a posttranslational modification at the C terminus by a prenyl group. Instead, Ran possesses an acidic C-terminal domain that is integral to its switch function (209).

A key to understanding the role of Ran in nucleocytoplasmic transport was the discovery that RanGEF is restricted to the nucleus and RanGAP is localized to the cytoplasmic compartment(99, 176). This asymmetry creates a steep Ran-GTP gradient across the NPC, and it is this gradient that provides the vectorial information for nuclear import and export (80). As will be discussed in detail below, Ran-GTP triggers the disassembly of import carriers from their cargoes but promotes the assembly of exportin-cargo complexes.

We will discuss transportin1 (Kap2) first, as a relatively simple example of an importin; then importin, which can use various adapters; and then Crm1, as an example of an exportin.

Transportin1 (Kap2). The crystal structure of a complex between transportin1 and Ran:GppNHp has been solved. (39). The GppNHp is a slowly hydrolyzing analog of GTP. Transportin1 has a mass of about 101 kDa and is entirely -helical. It has a remarkable structure, consisting of 18 HEAT/Armadillo (Arm) domains that are twisted in a superhelix like an S in which the bottom arch has been rotated forward, out of the plane of the page, by 90° (Fig. 1A). (HEAT domains are named after the proteins in which similar sequences were first identified: huntingtin, elongation factor 3, the A subunit of protein phosphatase 2A, and the Tor1 kinase. They also resemble the HEAT/Arm repeats of -catenin and importin.) Each HEAT domain is made up of two -helices (A and B) that are joined by a sharp turn to form a hairpin structure. Individual HEAT domains are linked either by loops or by additional short helices. The B helices form the concave surfaces of the arches. Ran is nestled in the N-terminal arch. The binding site for the M9 NLS sequence has been roughly mapped to the C-terminal arch.

View larger version (54K): [in this window] [in a new window]   FIG. 1.   Structures of carrier complexes with Ran (A), the N-terminal domain of importin (IBB domain) (B), and a bipartite NLS (C). H1 to H18 identify the HEAT motifs of transportin1 and importin. L7 is the loop within HEAT motif7. Ran (bound to GppNHp, a nonhydrolyzable analogue of GTP), the IBB domain, and the NLS are shown in white. Note how the HEAT motifs H11 to H18 are twisted up and around the IBB domain, compared to their positions in panel A (39, 263). A1 to A10 identify the ARM motifs, which are closely related to HEAT motifs. Note that the superhelical twist is in the same direction in all three structures and that the ligands all interact with the concave inner surface of the carriers.

View larger version (22K): [in this window] [in a new window]   FIG. 2.   Mechanism of cargo import by direct interaction with an importin carrier protein. RanGTP is present at high concentrations only in the nucleus, where it disassembles the cargo-importin complex. The importin-RanGTP complex returns to the cytoplasm, where the GTP is hydrolyzed, releasing the RanGDP from the importin.

Importin. Importin is a more complex type of carrier, because it can carry cargo either directly (at distinct sites) or via an adapter protein (Fig. 2 and 3). The best known adapter is importin, a 55-kDa protein that binds to classical, basic NLS sequences. There is only one gene encoding an importin in budding yeast, but six isoforms, which differ from one another mainly at their C termini, are known in mammals (151). Although each recognizes the monopartite SV40 NLS with similar affinity, they differ in their affinities for other NLSs (125, 126, 159, 168, 260, 268). The structural basis for these distinctions is not yet known. In addition, the C termini of the importin isoforms can form binding sites for distinct cargo proteins, such as Stat1 and Nup50, which may be carried into the nucleus simultaneously with other cargo containing monopartite NLSs (232; K. Plafker and I. G. Macara, submitted for publication). Other adapters for importin include snurportin, which binds to m⁷G-capped Usn RNAs; the frog protein XRIP, which binds to RPA; and importin-7, which facilitates histone H1 import (81, 104, 107, 182, 258, 259, 266). XRIP is of particular interest as an example of divergent evolution, because no homologue of this protein exists in budding yeast and because its cargo, RPA, is instead imported by the karyopherin Kap142/Msn5 (285).

View larger version (42K): [in this window] [in a new window]   FIG. 3.   Mechanism of cargo import by the importin-importin pathway. In this mechanism, the cargo binds to an adapter, importin, rather than directly to the carrier. The cargo-importin-importin complex is disassembled in the nucleus by RanGTP. Importin returns to the cytosol, as shown in Fig. 2. The importin requires a carrier for export, called CAS (CseI in budding yeast). Assembly of the export complex requires RanGTP. The ternary importin-CAS-RanGTP complex is disassembled in the cytoplasm by hydrolysis of the GTP.

View larger version (105K): [in this window] [in a new window]   FIG. 4.   Comparison of the Ran-GTP interacting surfaces between importin- and transportin1. (A) Alignment of the Ran binding domains of importin and transportin1. Residues in importin that bind Ran are shown in yellow. Residues in transportin1 that bind Ran are shown in blue. Loop7 is indicated in pink. (B) Amino acid sequence of Ran showing the Switch 1 and Switch 2 regions that undergo a conformational switch between the GTP and GDP binding states, and the basic patch. Residues that bind importin are shown in yellow; residues that bind transportin1 are shown in blue (39, 263).

Importin. The structure of the adapter protein, importin, has also been solved, and it bears a striking resemblance to that of importin and transportin1 (45, 124). The NLS binding domain consists of 10 Armadillo motifs stacked into a right-handed superhelix, and repeats 2 to 5 can be superimposed well onto HEAT repeats 9 to 12 of importin (Fig. 1C). This similarity supports the proposal that all HEAT and Arm repeat proteins are related evolutionarily. The NLS sits in the concave inner groove of importin, which is lined with conserved tryptophan and asparagine residues. There are two binding pockets, a major one formed by Arm 2 to 4, occupied by monopartite NLSs, and a second, closer to the C terminus (Arm 7 to 8), that can be occupied by the N-terminal portion of bipartite NLSs (44).

Other importins. There are 10 known members of the yeast karyopherin family that function as importins (276). An 11th, Lph2, remains to be characterized but probably also functions in nuclear import, because the mammalian ortholog is importin-11, which mediates the nuclear accumulation of a ubiquitin ligase E2 subunit, UbcM2 (195). The number of mammalian importins is likely to be at least double that of yeast importins (79). Remarkably, many of the yeast importins are not essential for survival, although their deletion sometimes leads to growth defects. Why is this? First, there are many types of import cargo whose size is below the free diffusion limit for the NPC. Examples are ribosomal proteins and histones. Free diffusion of such proteins will be slow but may be sufficient to maintain life. Second, there is redundancy of function between importins, which reduces the reliance on any single carrier. For example, Kap123 (Yrb4) and Kap121 (Pse1) both import ribosomal proteins and Kap121 and Kap123 can import histones H2A/H2B (165, 191, 217, 227). In mammalian cells, at least one ribosomal protein, rpL23a, can also be imported by multiple carriers, including importin and transportin (105). The purpose underlying such redundancy is unclear but may be related to the sheer volume of proteins that need to be imported in order to build ribosomes and maintain protein synthesis at optimal levels.

Crm1/Xpo1. Isolated Crm1 has only a very low affinity for Ran-GTP and a similarly low affinity for most NES cargoes. Together, however, they can form a relatively stable ternary complex (9, 10, 69). This complex can exit the nucleus through the NPCs and is dissociated by hydrolysis of the Ran-GTP (Fig. 5). The empty Crm1 then returns to the nucleus. Studies of Crm1-mediated export were helped enormously by the discovery that an antifungal agent, leptomycinB, is a highly specific and potent inhibitor of Crm1 function (69, 72, 131, 179, 274). LeptomycinB reacts irreversibly with a Cys residue (Cys 529) near or within the cargo binding domain of the protein (130). Interestingly, this Cys is lacking in the homologous gene product from budding yeast (Xpo1), which, consequently, is resistant to the agent.

View larger version (21K): [in this window] [in a new window]   FIG. 5.   Mechanism of cargo export. Cargo binds weakly to the export carrier in the absence of RanGTP but tightly in its presence. The ternary cargo-exportin-RanGTP complex is disassembled in the cytoplasm by GTP hydrolysis on Ran. The exportin is presumed to return empty to the nucleus.

Cofactors. There are several problems with the simple model that has been proposed for Ran-dependent NES cargo loading and disassembly. First, the concentration of Ran-GTP in the nucleus is calculated to be in the 10 to 15 µM range, so that a significant amount of Crm1 may be bound to Ran-GTP even in the absence of cargo. This Crm1/Ran-GTP complex could move through the NPCs to the cytosol, where the Ran-GTP would be hydrolyzed. Such a futile cycling of Crm1 would deplete the Ran gradient. Second, the affinities of NESs for Crm1 are often in the 100 nM to 1.0 µM range even in the presence of Ran-GTP (with the exception of snurportin, which has a much higher affinity). This can present a problem if the nuclear concentrations of these cargoes are low. Futile cycling of empty carrier is reduced by the low affinity of Crm1 for nucleoporins in the absence of Ran-GTP (67, 116). In addition, Crm1 recently has been found to use cofactors, namely, RanBP3, Nxt1, RanBP1, and possibly eIF-5A, that together potentiate NES binding, help Crm1 that is loaded with cargo to bind to nucleoporins in the NPC, and stimulate cargo unloading in the cytoplasm (22, 95, 142). RanBP3 can associate directly with Crm1, and the complex possesses an enhanced affinity for Ran-GTP and NES-cargo (142). In an in vitro assay using a limiting Crm1 concentration, RanBP3 stimulates export. Additionally, it inhibits the binding of unloaded Crm1 to the NPC. One potential mechanism for the effect on NPC binding is through a Ran-mediated conformational change in the "F domain" of RanBP3, which contains two nucleoporin-like FxFG motifs and which can bind constitutively to Crm1. We have proposed that in the absence of Ran, the F domain blocks the nucleoporin interaction site on Crm1, but that on binding Ran, the F domain is released, thus permitting the Crm1 to associate with the NPC. RanBP3 also stimulates the Ran exchange factor, RanGEF, and permits the formation of a Crm1-Ran-RanBP3-RCC1 complex (M. Nemergut and M. Lindsay, unpublished data). Therefore, RanBP3 may also facilitate export by directly stimulating the production of Crm1/Ran-GTP.

Other exportins. Budding yeast possesses four known exportins in the karyopherin family, including Crm1 and Kap142/Msn5. These proteins all have mammalian homologs. At least one additional mammalian carrier, exportin4, has no yeast equivalent (144). Exportin4 can carry eIF-5A out of the nucleus. Interestingly, binding by exportin4 depends on a hypusine modification of eIF-5A. Crm1 has been reported to bind and export unmodified eIF-5A, although this is disputed (95, 144). Cse1 (equivalent to the mammalian Cas) is responsible for recycling importin back to the cytosol (Fig. 3A) (134, 135, 239). It recognizes conserved sequences within Arm repeats 8 to 10 and must displace NLS cargo in order to bind (90). This latter property ensures that the cargo remains in the nucleus when the importin returns to the cytosol.

OTHER CARRIERS

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Tap/Mex67

Other classes of RNA, such as rRNA and mRNA, do not compete with tRNA for export when microinjected into Xenopus oocyte nuclei, indicating that they use a mechanism distinct from that used by exportin-t (106). Nor do they compete with each other. Most mRNAs are produced as large precursors that must be spliced, modified, and assembled into RNP complexes before they can be exported. Different types of mRNA recruit different RNP proteins, some of which may need to be removed prior to export while others remain bound during translocation and must be reimported from the nucleus after disassembly from the mRNA in the cytoplasm. These complications make analysis of mRNA export more difficult than that of single proteins.

One approach to simplify such analysis is to study individual retroviral genomic RNAs that are exported as unspliced or incompletely spliced species. Simian type D retroviruses contain a unique RNA sequence that functions as a constitutive transport element (CTE) (190). The CTE recruits a cellular factor called TAP that overcomes nuclear retention by the splicing machinery and drives export of the viral RNA (28, 84, 113). TAP (also named NXF1) is therefore a nuclear export factor. But is it specific for viral RNAs, or does it normally function in the export of endogenous RNAs? High concentrations of the CTE RNA can cause nuclear accumulation of mammalian endogenous mRNA, suggesting that the RNAs are competing for a common factor (190, 218). Moreover, TAP is weakly related to a yeast protein, Mex67, that is required for the exit of multiple classes of yeast mRNAs, and TAP can complement a MEX67 disruption (101, 114, 221, 230). Taken together, these data imply that TAP may play an important role in the cellular pathway for mRNA export. However, it remains to be proven that TAP is the major export carrier for endogenous mRNAs, and the recent identification of a family of TAP/NXF genes suggests that there may be complications to this story (89).

Exactly how TAP works in export remains unclear. It bears no structural resemblance to the karyopherins. Rather, it contains an unusual RNP binding domain and a leucine-rich repeat domain in its N-terminal half, unexpectedly similar to a heterodimer involved in RNA splicing, although the significance of this relationship remains unclear (141). Both domains are required for specific CTE binding. However, most cellular mRNAs do not contain the stem-loop structure found in the CTE, and CTE export is not promoted by the yeast homologue, Mex67, or by other members of the TAP family; therefore, the issue of direct mRNA binding to TAP remains to be addressed.

Mex67 binds with high affinity to a second essential mRNA export factor, called Mtr2, which appears to help dock the complex at the NPC (221, 250). Remarkably, TAP binds a functionally related factor, but one with no sequence similarity to the yeast Mtr2 (114). This small protein, p15 or NXT1, is closely allied to NTF2 but has been reported to bind Ran-GTP rather than Ran-GDP, although this property has been disputed (23, 114). RNA export assays suggest that NXT1 is an essential cofactor for TAP function, and TAP/NXT1 can partially rescue the viability of a Mex67 Mtr2 double deletion (114, 178). Surprisingly, TAP itself possesses an NTF2-like domain in the C-terminal half of the protein, which is the region involved in binding NXT1 (252). We know that NTF2 forms homodimers, so NXT1 perhaps heterodimerizes with the NTF2-like domain of TAP. NXT1 has been reported to facilitate the export of multiple classes of RNA in an in vitro export assay (178), and mutations that disrupt Ran-GTP binding are inactive. However, other studies indicate that the export of spliced mRNAs is completely independent of Ran (42).

Another factor that binds Mex67 is Yra1, a nuclear protein that can associate with RNA and possesses RNA-RNA annealing activity (251). A mouse homologue, ALY, can bind either Mex67 or TAP and partially complement a YRA1 deletion. Temperature-sensitive mutants of YRA1 are defective in mRNA export. Yra1 may recruit and facilitate the interaction of Mex67 or TAP/NXF proteins with mRNA, but it is not yet clear whether the RNA-RNA annealing function has physiological relevance.

Many other factors are involved in one way or another with RNA export. After pre-mRNA splicing, the molecules must be packaged into an exportable configuration and then unpackaged in the cytoplasm prior to translation. In yeast, Rip1, Pab1, Np13, Nab2, Hrp1, Dbp5, Gle1, and Gle2 are all required for efficient mRNA export (43). Some of these proteins (Np13, Nab2, and Hrp1) are mRNA binding proteins, others (such as Rip1) are nucleoporins, others (Gle1, Gle2, and Dbp5) bind the NPC, and one (Dbp5) is a DEAD-box protein that may be involved in unpackaging the RNA on the cytoplasmic side of the NPC. However, the mechanistic role of most of these proteins remains unresolved. To complicate matters further, recent studies suggest an unexpected linkage between phosphoinositide metabolism and mRNA export, through inositol hexakisphosphate (284). Finally, there are indications that nuclear actin may somehow influence RNA export, although the mechanism remains entirely obscure (95). Much of the confusion in the field is generated by the plethora of RNA species; the multiple transcription, processing, and splicing steps that precede and may be tightly coupled to RNA export; the large number of factors involved; and the problems associated with reconstituting in vitro export assays. It is encouraging that in the face of such complexities, so much progress has been made.

Functional assays can often turn up new and quite unexpected discoveries. The development of an in vitro nuclear protein export assay (97) led recently to the isolation of a new factor that can promote the export both of NES cargo and of steroid receptors (96). This factor was identified as calreticulin, a protein commonly thought to reside exclusively in the ER. Clearly, however, preconceptions can be misleading, and there is evidence of a distinct, soluble pool of calreticulin in cells. This protein can bind directly to the glucocorticoid receptor and to other members of the nuclear receptor superfamily. The glucocorticoid receptor is cytoplasmic in the absence of its ligand (cortisol), but binding of the ligand exposes at least two classical NLSs, which permit its accumulation in the nucleus (208, 223). There it activates gene expression. On withdrawal of ligand, the receptor slowly returns to the cytoplasm by a mechanism that most investigators find to be independent of Crm1 (145). Knockout mice that lack calreticulin accumulate the glucocorticoid receptors in their nuclei constitutively, and the reintroduction of calreticulin into cells derived from these mice rescues the ability of the receptor to recycle back to the cytoplasm. Most interestingly, the binding site for calreticulin on these receptors lies within the DNA binding domain, and calreticulin inhibits association with the promoter elements of receptor-responsive genes (50). Therefore, calreticulin may help switch off gene expression after ligand dissociation both by blocking the rebinding to DNA and by promoting export from the nucleus. However, we do not know if calreticulin is a true carrier or is instead a chaperone that promotes the loading of cargoes onto a karyopherin. Critically, it will be essential to determine whether it can bind directly to nucleoporinsa defining characteristic of bona fide nuclear transport carriers. Important questions also remain concerning the mechanisms for loading and unloading of calreticulin binding to steroid receptors.

There are no motors in the nuclear pores. Rather, carriers appear to translocate from one side to the other by a process of facilitated diffusion. This process does not require energy and is nondirectional (57, 205). How, then, are macromolecules moved against a concentration gradient into or out of the nucleus?

First, a binding protein resident in only one compartment could sequester the transport cargo. The free cargo concentration would remain equal on both sides of the nuclear envelope, of course, but the total concentration would be higher in the compartment in which it was sequestered. One example of this mechanism may be the 14-3-3 proteins, which may function as cytoplasmic retention factors for certain phosphorylated proteins (167). Another example is -catenin, which can bind and be retained by specific transcription factors in the nucleus (59, 282).

Second, the cargo could be covalently modified in one compartment, for example by phosphorylation, such that it no longer interacts with the carrier. This modification would reduce the free concentration of cargo available to the carrier in that compartment and drive accumulation by mass action. An example of this type of mechanism may be the nuclear accumulation of cyclin B (254).

Third, the binding of cargo to the carrier may be regulated by a second factor, such that assembly occurs in only one compartment and disassembly occurs in the other. As discussed above, Ran-GTP fulfills this regulatory function by promoting the assembly of export complexes or the disassembly of import complexes. It has the advantage of flexibility, because chemical modifications to the cargo are avoided, and it probably accounts for the bulk of all nucleocytoplasmic transport through the NPCs. Any such system involves work, however, because, directly or indirectly, the negative free energy of loading the cargo onto the carrier must be paid for during unloading, to complete the thermodynamic cycle.

The Ran GTPase system depends on the maintenance of a high nuclear concentration of Ran-GTP, and the cost of the transport cycle is paid for by the hydrolysis of the Ran-GTP to Ran-GDP in the cytoplasm. The requirement for a Ran-GTP gradient across the nuclear envelope has been demonstrated experimentally, for both nuclear import and export (103, 207). A simple example of the role of Ran in nuclear transport is provided by transportin, which imports the mRNA binding protein hnRNPA1. Binding of cargo in the cytosol is spontaneous. Release in the nucleus is driven by the free energy of binding Ran-GTP (G  51 kJ mol¹). On returning to the cytoplasm, the transportin/Ran-GTP complex must be disassembled. This step requires hydrolysis of the Ran-GTP (G  33 kJ mol¹) and is the only functionally irreversible reaction in the transport cycle. One Ran-GTP molecule is consumed per cycle. The hydrolysis of the GTP throws a conformational switch in Ran that prevents transportin binding.

A mechanism of this type has two important consequences. First, Ran is required only for accumulation of the cargo against a concentration gradient and not for the actual translocation of the carrier or cargo through the NPC. Second, each complete transport cycle involves the transport of one Ran-GTP molecule out of the nucleus. The first consequence has been demonstrated experimentally, using permeabilized cells and stoichiometric amounts of transportin with an M9 fusion protein as cargo (57, 128, 170, 171, 205). The second consequence has been demonstrated for importin-, for which case the export of a carrier/Ran-GTP complex has been observed.

How is the Ran gradient maintained? This question has two parts. The first concerns the way in which Ran-GTP is produced in the nucleus and hydrolyzed in the cytoplasm, while the second concerns the mechanism by which Ran is returned to the nucleus after it has been released from transportin or any of the other karyopherins. The endogenous GTPase activity and guanine nucleotide off-rates for Ran are extremely low (k_cat  1.5 × 10⁵ s¹; k_off  1.8 × 10⁵ s¹), and, as with other small GTPases, there are regulatory factors that catalyze these processes (120). GTP hydrolysis on Ran is catalyzed by a cytoplasmic GTPase-activating protein called RanGAP, and guanine nucleotide exchange is catalyzed by a nuclear RanGEF that in mammals is called RCC1 (Prp20 in budding yeast). Both are potent factors that can accelerate the basal rates by as much as 500,000-fold. The low intrinsic GTPase and exchange rates for Ran are essential to prevent dissipation of the gradient between the nucleus and cytoplasm; the high catalytic rate constants of the regulatory factors ensure efficient gradient generation.

The Ran exchange factor was initially identified in mammalian cells from a temperature-sensitive allele that caused premature chromosome condensation at the nonpermissive temperature (hence the name RCC1, for "regulator of chromosome condensation") (176, 262). In yeast it is an essential gene, temperature-sensitive alleles of which have pleiotropic effects related to RNA transport and cell cycle defects (7, 71, 108). Like the exchange factors for other small GTPases, RanGEF stimulates the release of guanine nucleotides from Ran by stabilizing the nucleotide-free, or apo-Ran, state (120, 122).

RanGEF is a constitutively nuclear protein, associated with chromatin (176). The crystal structure reveals a donut shape, created from seven "propeller blades" equally distributed around a central hole (Fig. 6A) (202). Several other proteins appear to contain RCC1-like motifs, but there is no evidence to date that they catalyze nucleotide exchange on Ran (86, 158, 212). Extensive mutagenesis and docking experiments have suggested that Ran binds to one face of the donut while the other face is responsible for binding to chromatin (11). The structure of the Ran-RanGEF complex has recently been solved, confirming the predicted binding surfaces and suggesting that an acidic residue in RanGEF plays a critical role in the exchange reaction by interacting with a lysine in the phosphate binding loop of Ran (201).

View larger version (39K): [in this window] [in a new window]   FIG. 6.   Structures of the RanGEF RCC1 (A) and of RanGAP (B). (A) The first 20 amino acids, containing the NLS, are absent. (B) The arginine finger residue is indicated. This residue is required for catalytic activity (93, 202).

The N terminus forms an extended chain, hanging off the donut core, and contains a monopartite NLS. The mammalian RanGEF, RCC1, requires this NLS for nuclear import via the importin-importin system, with a preference for the importin3 isoform. However, deletion of this NLS does not prevent nuclear import, suggesting that a second, Ran-independent mechanism exists, perhaps to guard against accumulation in the cytoplasm, which would probably be toxic to the cell (126, 172, 255).

RanGEF binds directly to nucleosomes, an interaction that is mediated preferentially by histones H2A and H2B, to which RanGEF binds with high affinity (173). The N-terminal tails of the histones appear to be dispensable for binding, and an interesting speculation is that the RanGEF binds to the exposed internucleosome faces, like hubcaps on a car wheel. Intriguingly, the histones can activate exchange activity by about twofold, presumably by inducing a conformational change in the RanGEF. RanBP3 also binds to and activates RCC1 (M. E. Nemergut, M. Lindsay, and I. G. Macara unpublished data). The effect is additive with the histone stimulation, and these data, together with computational modeling of Ran import, suggest that the modulation of RCC1 exchange activity may provide the cell with a mechanism for the global control of nuclear transport.

Frog sperm chromatin is very highly compacted and contains little or no RanGEF. It also lacks histones H2A and H2B. Decondensation of sperm chromatin can be induced in vitro, either by addition of an egg cytosolic extract or by addition of the acidic nuclear protein, nucleoplasmin, plus exogenous histones H2A and H2B. During this process, the exogenous histones become incorporated into the decondensed chromatin and RanGEF associates with the chromatin. We think that this process is key to the regulated formation of a nuclear envelope around the chromatin. Nuclear envelope formation occurs by the fusion of vesicles on or near the chromatin surface (26, 75, 271), and the trigger for this event was found recently to be the formation and/or turnover of Ran-GTP (91, 286). Remarkably, nuclear envelopes can even be formed in oocyte extracts around Sepharose beads to which glutathione S-transferase-Ran-GTP has been attached, demonstrating that no other chromatin components are required for this process. The staged association of RanGEF with sperm chromatin after its initial decondensation will produce a Ran-GTP "atmosphere" close to the chromatin surface, which may then induce vesicle fusion and nuclear envelope formation (91, 286).

The fission yeast RanGAP (rna1) has remarkably symmetric structure, composed of 11 leucine-rich repeats that together form a crescent (93). Each repeat forms a - hairpin, with the -helices on the convex face of the crescent (Fig. 6B). Many GAPs appear to use a common "arginine finger" mechanism for the stimulation of small GTPases, in which a key Arg residue inserts into the nucleotide binding pocket of the GTPase and stabilizes the transition state (4, 226). An Arg residue in the third leucine-rich repeat may fulfill this function for RanGAP. The structures of several small GTPase-GAP complexes have been solved, and in each case the GAPs bind to the so-called Switch 1 and Switch 2 regions of the GTPases. These are the key regions that undergo a conformational rearrangement triggered by the change in state of the guanine nucleotide, and it is likely that the corresponding sequences in Ran are involved in binding RanGAP.

RanGAP is cytoplasmic. Mammalian RanGAP behaves in solution as a dimer and is larger than the diffusion limit for passive movement through the NPCs (18). However, the fission yeast rna1 is smaller and does not appear to behave as a dimer. In budding yeast, RanGAP contains both an NLS and several NES sequences, indicating that it may shuttle into and out of the nucleus, and its cytoplasmic localization is dependent on the exportin activity of Crm1 (62). Why RanGAP should shuttle is unclear. Moreover, in the fission yeast RanGAP, the hydrophobic residues that correspond to the NES sequences are not exposed but are mostly buried beneath the concave inner surface of the crescent. Given the close relatedness between RanGAP orthologs, the budding yeast protein most probably has a very similar structure to that of the fission yeast protein and the putative NES is unlikely to be functional in the context of the full-length protein.

In mammalian cells a substantial fraction of RanGAP is posttranslationally modified. Antibodies detect a form of the protein with lower mobility in sodium dodecyl sulfate-polyacrylamide gel electropheresis than would be predicted from its molecular mass, and analysis by mass spectrometry revealed that this form comprised an adduct of RanGAP with a novel, 8-kDa, ubiquitin-related polypeptide that was named GMP1, or SUMO-1 (149, 152). A growing number of other proteins have since been found to be SUMO modified, including Mdm2 and p53, and in several cases SUMOylation plays a regulatory role, inhibiting ubiquitination and protein degradation (32, 211). In RanGAP, it appears that the SUMO modification targets the protein to Nup358/RanBP2 in the cytoplasmic fibrils of the NPC (149, 152, 220). This localization may increase the efficiency with which the RanGAP can hydrolyze Ran-GTP that is exported with karyopherins from the nucleus. However, Nup358/RanBP2, and a closely related gene product, RanBP2L1, are not expressed ubiquitously, so it remains to be established that targeting is the only function of the SUMO modification (63, 174). Clearly it is not essential in budding yeast, which does not SUMO modify its RanGAP. Neither yeast nor Drosophila contains a homologue of Nup358/RanBP2.

An important limitation to RanGAP function is that its activity is blocked by karyopherins (66, 80). The Switch 2 region of Ran-GTP is buried in complexes with karyopherin-2 or importin and is inaccessible to RanGAP (39, 263). Therefore, a second factor must interact with the complex and permit RanGAP function. This factor is a Ran binding protein called RanBP1.

RanBP1 consists principally of a Ran binding domain (RanBD) (15, 46, 180). The mammalian version possesses a nuclear export signal in a C-terminal extension and may dimerize through a short N-terminal extension (208, 289). In budding yeast the export signal appears to be contained within the RanBD (133). The export signals are not merely a safety mechanism in case of leakage of RanBP1 into the nucleus. RanBP1 shuttles rapidly in and out through the nuclear pores. The import mechanism is not fully understood but appears to be carrier independent (133, 194). The RanBD is conserved in all eukaryotes, although, oddly, the nematode Caenorhabditis elegans possesses a Ran binding protein that more closely resembles RanBP2 than RanBP1, and contains two RanBDs (15).

The affinity of the RanBD for Ran-GTP is very high (132). The crystal structure of Ran in a complex with a RanBD reveals an unusually close embrace between the two polypeptides, in which an acidic "hand" at the C terminus of Ran wraps around to a basic patch on the RanBD while an acidic "hand" at the N terminus of the RanBD is stretched across to bind a basic patch on Ran (Fig. 7B) (264). The body of the RanBD, which forms a so-called -barrel, is held closely against the Switch 1 region and against other residues in the C-terminal half of the Ran protein. Comparison of the conformation of Ran-GDP with that of Ran in complex with the RanBD explains why the interaction is specific for the GTP-bound state. Like other small GTPases, the orientation of the Switch 1 loop is very different between the two states. In addition, and uniquely to Ran, the C terminus possesses a highly acidic sequence that may be attached, when Ran is in the GDP-bound state, to a basic patch between residues 139 to 142 (Fig. 7A). This conformation stabilizes the association with the nucleotide. Interaction of Ran with GTP triggers reorientation of Switch 1 and displacement of the C-terminal arm, which, when Ran binds the RanBD, then swings out through an angle of nearly 180° (Fig. 7B).

View larger version (59K): [in this window] [in a new window]   FIG. 7.   Structures of RanGDP-NTF2 (A) and RanGTP-RanBD (B). NTF2 forms a dimer, and each subunit associates with one molecule of RanGDP. Ran is shown in green, the nucleotide is shown in blue, and the NTF2 subunits are shown in red and yellow. Note the location of the Ran C-terminal arm (blue-green) in close juxtaposition to the basic patch on the RanGDP. When bound to a RanBD, the C-terminal arm (blue-green) of RanGTP is extended away from the body of the Ran (green) and embraces the RanBD (red). The N terminus of the RanBD (orange) loops around the Ran and contacts the basic patch (246, 264).

A RanBD can stimulate RanGAP activity by about 10-fold, although it has no effect on GTP hydrolysis on its own (15, 19). How does it work? One possibility is that in the absence of a RanBD, the acidic -DEDDDL sequence remains tethered to Ran-GTP, although the upstream part of the C-terminal arm must have moved to accommodate the reorientation of the Switch 1 region that occurs on binding GTP. This conformation may reduce the affinity for RanGAP. Binding of a RanBD then pulls the C terminus of Ran aside, to facilitate RanGAP binding. Consistent with this hypothesis, deletion of the -DEDDDL sequence potentiates Ran-GTP hydrolysis by RanGAP but destroys responsiveness to RanBP1 (209).

In the Ran-importin complexes, the C-terminal arm is also released from its basic patch on Ran but remains exposed (92). The Switch 2 region is almost entirely buried, and RanGAP is ineffective in catalyzing GTP hydrolysis How does the RanBD overcome the blockade of RanGAP activity? The interfaces between Ran-GTP and the RanBD do not overlap substantially with those of Ran and the importins, and the three proteins can form a stable ternary complex (37, 147). Whether RanGAP can interact with RanGTP in a quarternary complex with RanBD and importins, however, or whether the importins must first be released remains unclear. Competition between the RanBD and importin for interaction with Ran residues N154 and E158 could increase the off-rate of Ran-GTP from the importin. Additionally, the attachment of the C-terminal tail of Ran to the RanBD may play an important role. Deletion of the -DEDDDL sequence significantly increases the affinity of Ran for importin, most probably because the C terminus no longer has to be displaced from its basic pocket. One would expect that either deletion of the -DEDDDL or displacement by a RanBD would increase the on-rate for importin binding to a similar extent. We therefore suggest that in the ternary complex of Ran-GTP-importin-RanBD, both the on- and off-rates are substantially increased compared to those in the Ran-GTP-importin binary complex. This increase enables RanGAP to access the Ran-GTP and terminate the transport cycle by hydrolyzing the nucleotide to GDP.

The termination step for importin is rather more complicated, however, because the off-rate of Ran-GTP is too slow, even in the presence of a RanBD, to be useful. Addition of importin can facilitate the process, probably by competing with Ran-GTP and blocking its rebinding to importin (17, 146). The association of importin with nucleoporins may also increase the off-rate of Ran-GTP from importin (68)

A further complication is presented by the ability of RanBDs, together with importins, to form stable ternary complexes with Ran-GDP, even though the affinity of either protein alone for Ran-GDP is extremely low (~10⁷-fold lower than that for Ran-GTP) (36). The displacement of the C terminus again probably plays a critical role in the formation of this ternary complex. The physiological role of the complex remains, however, completely obscure.