The nuclear pore complex: A comprehensive review of structure and function

Stanislaw P Stawicki; Joseph M Steffen

doi:10.4103/IJAM.IJAM_26_17

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Year : 2017 | Volume : 3 | Issue : 3 | Page : 24-38

The nuclear pore complex: A comprehensive review of structure and function

Stanislaw P Stawicki, Joseph M Steffen
Department of Biology, College of Arts and Sciences, University of Louisville, Louisville, KY, USA

Date of Web Publication

21-Apr-2017

Correspondence Address:
Stanislaw P Stawicki
Department of Research and Innovation, St. Luke's University Health Network, EW2 Research Administration, 801, Ostrum Street, Bethlehem, PA 18015
USA

Source of Support: None, Conflict of Interest: None

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DOI: 10.4103/IJAM.IJAM_26_17

Abstract

The nuclear pore complex (NPC) is an important functional entity of every eukaryotic cell's nuclear membrane. It enables selective transport of materials across the nuclear membrane in an organized and orderly fashion. Substances carried in and out of the nucleus by the NPC include three major groups of molecules: (a) Messenger ribonucleic acid molecules, (b) proteins, and (c) ribonucleoproteins (RNPs). The transport across the nuclear membrane involves adenosine triphosphate hydrolysis in the great majority of cases even though certain guanosine triphosphate-hydrolyzing mechanisms have also been identified. The understanding of the NPC appears crucial to our understanding of certain pathological processes. For example, it has been found that certain human viruses can “trick” our cells into transporting their RNPs into the nucleus using signal peptides similar to the human nuclear-localizing signals. The major challenge of today's research on the NPC resides in identification of over one hundred of its distinct polypeptide units and in determining their functions and interactions. To date, many of the structural proteins involved in the NPC have been identified, but the mechanism of their interactions still remains largely hypothetical. This project discusses the structure and function of the NPC.
The following core competencies are addressed in this article: Medical knowledge.
Republished with permission from: Stawicki SP, Steffen JM. The nuclear pore complex: A comprehensive review of structure and function. OPUS 12 Scientist 2007;1(2):39-87.

Keywords: Nuclear pore complex, review, structure and function

How to cite this article:
Stawicki SP, Steffen JM. The nuclear pore complex: A comprehensive review of structure and function. Int J Acad Med 2017;3, Suppl S1:24-38

How to cite this URL:
Stawicki SP, Steffen JM. The nuclear pore complex: A comprehensive review of structure and function. Int J Acad Med [serial online] 2017 [cited 2023 Mar 28];3, Suppl S1:24-38. Available from: https://www.ijam-web.org/text.asp?2017/3/3/24/204954

Introduction

The nucleus is the most prominent, and arguably the most important, organelle in eukaryotic cells. It acts as the main repository of genetic information, the deoxyribonucleic acid (DNA). This fact, in a broader sense, establishes the nucleus as the “control center” of the cell. It is in the nucleus that DNA, ribonucleic acids (RNAs), and ribonucleoproteins (RNPs) are synthesized. These macromolecules are responsible for directing transcriptional and translational activity, which ultimately results in protein production and cell propagation.

The nucleus is surrounded by a nuclear envelope. The nuclear envelope is a double phospholipid bilayer, its external surface continuous with the endoplasmic reticulum, and its inner surface facing the nucleoplasm. The structure of the nuclear envelope was elucidated using freeze-fracture transmission electron microscopy.^[1] The only known passageway that allows macromolecules to enter into and exit from the nucleus during interphase is the extremely complex macromolecular assembly of numerous protein subunits called the nuclear pore complex (NPC).^[2] Each NPC is a wheel-shaped structure of about 120 nm in external diameter [Figure 1] and [Figure 2]. It exhibits an eight sided or octagonal symmetry. The hub of the NPC consists of a cylindrical structure, the so-called central transporter.^[3] The approximate dimensions of an inactive NPC channel are 9–10 nm in diameter and 15 nm in length.^[4],[3]

Figure 1: A diagram showing the nuclear pore complex based on data obtained using high-voltage transmission electron microscopy and low-voltage scanning electron microscopy. N indicates nucleoplasm, C indicates cytoplasm. (1) One can see the hourglass-shaped central component (red) inserted into the nuclear pore and limited by a 120 nm diameter rings on both the nucleoplasmic and the cytoplasmic side (brown). (2) There are eight short filaments projecting out of the nucleoplasmic 120 nm ring and into the interspace between nucleus and cytoplasm (dark blue). (3) There are eight short, twisted filaments on the cytoplasmic side (yellow). (4) Projecting on the nuclear side is eight long thin filaments which connect with the nucleoplasmic 120 nm ring (green endings) (drawing modified from Spector, 1993)

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Figure 2: A diagram showing the interrelationships of the major components of the nuclear envelope: the inner and the outer membranes joined in regions where they are penetrated by nuclear pore complexes (a). Four major elements of the nuclear pore complex can be observed in this diagram: the cytoplasmic filaments, the central plug (channel complex), the nuclear basket, and the ring-spoke complex. The isolated ring-spoke complex is pictured in (b) to show that it contains structures extending into the perinuclear space (Figure modified from Bastos et al., 1995)

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There is no consensus on how NPCs evolved. Likewise, little is known about NPC biogenesis. Formation of the NPC is an intricate process involving membrane fusion and the orderly assembly of over 100 distinct polypeptides present in different stoichiometric ratios. NPC assembly requires the involvement of many nuclear and cytoplasmic proteins. One of the few studies describing this process demonstrated that the NPC assembly is both a time- and temperature-dependent process. Meier et al.^[5] showed that annulate lamellae, a cytoplasmic organelle consisting of stacks of flattened membrane cisternae perforated by numerous pore complexes, form spontaneously in a reconstituted system derived from Xenopus egg extracts. The nucleoporins (a generic name used for individual NPC subunits) present in a disassembled state in the cytoplasm became associated with membranes and were pelletable with them. The nucleoporins found in these complexes included NUP58, NUP60, NUP97, NUP153, and NUP200. Upon further analysis, the complexes were also found to contain gp210, an integral membrane pore protein. Guanosine triphosphate (GTP)-gamma-S (an unhydrolyzable analog of GTP, which poisons energy-requiring processes) prevented incorporation of the soluble pore proteins into membranes.^[5] Recently, a novel protein named Sec13, in conjunction with NUP84p (nucleoporin 84p), has been determined to be necessary for normal NPC formation.^[6] gp210, an essential NPC protein, has been found to be abundant in the cytoplasm in Drosophila early in embryogenesis.^[7] This cytoplasmic gp210 was found mainly in association with membrane vesicles. It is thought that the cytoplasmic gp210 fuels rapid assembly of new nuclei and NPCs. The cytoplasmic levels of gp210 are maximal early during embryonic development, after which they steadily drop. Failure of NPC formation is catastrophic and will result in cellular death.

The number of pores in the nuclear membrane can vary from anywhere between 2 and 4 pores/mm² (mammalian lymphocytes) to over 60 pores/mm² (mature Xenopus oocyte). This provides an estimate of 2000–4000 pores per nucleus.^[8] The apparent molecular weight of an individual NPC [Table 1] is thought to be approximately 120–125 MDa (MDa = 1,000,000 Daltons) in a variety of vertebrate cells.^[8],[9] The yeast NPC, in contrast to that of higher eukaryotes, is considerably smaller and has an approximate molecular weight of 60 MDa.^[10]

Table 1: Mass of the intact nuclear pore complex and its major structural components (from Panté N, Aebi U. Toward a molecular understanding of the structure and function of the nuclear pore complex. International Review of Cytology. 1996;162:225-55)

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The NPC is a crucial component of the nuclear membrane of each eukaryotic cell. It is of paramount importance because of its function in selective transport of macromolecules between the nucleoplasm and the cytoplasm. In the past several years, our knowledge concerning the NPC has considerably expanded thanks to widespread application of in vitro systems such as Xenopus oocytes and yeast genetic systems.^[11] However, Bastos et al.^[8] reported that, by mid-1995, only about 20 of the NPC proteins had been identified. The function of many of these subunits is unknown though many have been localized to specific positions within the pore complex.

Compared to the animal NPC, the plant NPC has not received as much attention from the biological community. This is partially because the NPC in plants is thought to be similar to that of animals. One can speculate that, like certain histone proteins, the NPC protein subunits would very likely be structurally and functionally conserved throughout eukaryotic cells. This would make plant NPCs likely to closely resemble animal NPCs in structure and function. However, one of the few studies regarding the NPC in plants demonstrated a unique posttranslational modification of NPC proteins with oligosaccharides. Heese-Peck et al.^[12] found that certain plant NPC proteins are chemically modified by the addition of N-acetylglucosamine (GlcNAc), which binds to proteins mainly through a hydroxyl group. Subsequent sugar analyses revealed that the plant glycans with terminal GlcNAc differ from the single O-linked GlcNAc of vertebrate NPC proteins in that they are built of oligosaccharides that are greater in size than five GlcNAc residues. The authors suggest that this modification may convey properties to the plant NPCs that are different from those of other eukaryotes.^[12]

The nucleus is the control center of the eukaryotic cell. The NPC is the main gateway between the cytoplasm and the nucleoplasm during the interphase. Even though the evolutionary origin of the NPC is unknown and its size varies from species to species, there is a great deal of homology between organisms. This homology allows comparisons between different species' NPC, leading to better understanding of that structure. Several transport mechanisms have recently been postulated for nucleocytoplasmic transport. In the following sections, I will describe the history of NPC research, our current understanding of NPC structure and function, as well as the implications of NPC research in the field of virology.

Brief History of the Nuclear Pore Complex Research

In his 1995 review article, Agutter describes the early developments leading to the discovery of NPCs.^[13] According to Agutter, one of the earliest attempts to explain the cell's translocation and transport mechanisms was put forth by Peters in 1930, who postulated that cells have a compartmentalized structure with transport mechanisms specific for a given substrate and location. Early NPC research was limited by inadequate technical capabilities and instrumentation. This situation changed in the 1950s. During that period, many new analytical techniques became available, which enabled scientists to both assess intracellular functions more specifically and to better visualize macromolecular structures. Electron microscopy, in particular, gave a substantial boost to the development of NPC research during this period.

In the early 1950s, Coons et al.^[14] injected three nonrat proteins into rats and then determined the intracellular distribution of the injected material by a fluorescent antibody technique. They found that the injected proteins had entered the nuclei of various tissues, often appearing in the nucleus in high concentration, resulting in greater chemiluminescence than in the cytoplasm.

At approximately the same time, Holtfreter ^[15] reported penetration of hemoglobin (MW ~64 kDa) into isolated amphibian oocyte nuclei suspended in a hemoglobin solution. Even though this experiment was not conclusive, it indicated that materials of a considerable molecular weight could move into the nucleus. This suggested that some kind of channel might exist between the nucleoplasm and the cytoplasm.

Feldherr ^[16] reported that polyvinylpyrrolidone-coated gold particles of 100 angstroms (approximately the size of a small monosaccharide) in diameter or more can penetrate the nuclear membrane. In some cases, these particles were found at higher concentration inside the nucleus than outside. The author, based on electron microscopic observations, suggested that this movement proceeded through specialized channels, termed nuclear pores.

The first detailed observations regarding the structure of the NPC were concerned with its physical size. These initial direct observations utilized high-resolution electron microscopy. Feldherr (1965) noted that nuclear pores measured about 640 angstroms in longitudinal section in Amoeba proteus.^[17] He subsequently reported the NPC of the multinucleated ameba Chaos chaos to be approximately 615 angstroms.^[18] Wooding and O'Donnell ^[19] noted that they were approximately 1000 angstroms in bull. Both research groups also noted the annular structure of pores, with a central density plugging the lumen of the NPC [Figure 1] and [Figure 2].^[19]

During the late 1970s and the 1980s, the NPC received much more attention. This was partially due to more refined analytical techniques developed during the 1970s. The first protein components of the NPC were identified during that period. In the 1980s, NPC research increased in both quantity and quality. Researchers from many countries began to coordinate their efforts. The first list of NPC proteins was being constructed at a modest pace. In the late 1980s, NPC researchers began to decipher not only the structure but also the mechanisms of transport through the NPC as well as the import and export factors involved in translocation.

By the mid-1990s, the protein import mechanism of the NPC was elucidated in some detail. Nuclear localization signals (NLSs), which direct proteins to the pore complex, were described. Furthermore, studies of RNA and RNP export began to yield important clues though more slowly than protein import studies.

As of today, relatively few of the NPC subunits have been assigned both structural and functional roles. The extensive use of genetic analyses and cross-species homology between the highly conserved proteins of the NPC allowed molecular dissection of many of the NPC proteins and brought us closer to understanding its structure and function.^[20] Understanding of the functioning of the NPC and its three-dimensional structure allows us to look into the operational details of this elaborate structure. As the growth of the field accelerates in the near future, the NPC structure and function will ultimately be completely “deciphered.”

General Description of Nuclear Pore Transport

The NPC has several transport functions. It can function as a passive diffusion channel, an ion channel, or as a macromolecule shuttle channel, transporting substances bidirectionally between the nucleoplasm and the cytoplasm. On the one hand, the NPC contains a passive diffusion channel for transport of small (<10 nm, MW <300) molecules. On the other hand, energy is used to facilitate the transport of larger molecules.^[3] In the latter instance, one has to keep in mind that molecules being moved are not only just physically large but also, in some instances, moved against their concentration gradient.

It is not unreasonable to hypothesize that the more metabolically active the nucleus of a given cell is, the more NPCs it might contain. For example, a DNA-synthesizing cell needs to import about one million histone molecules from the cytosol every 3 min.^[4] If an average cell nucleus contains 2000-4000 NPCs, then the workload on each NPC in transporting the histones alone is over 100/s. What about other proteins, messenger ribonucleic acid (mRNA) transcripts, ribosomal subunits, and transfer RNAs, all of which are transported continuously as well? The amazing efficiency of nuclear pore translocation is difficult to comprehend.

The NPC is a cylindrical channel about 9–10 nm in diameter and 15 nm long. This poses a problem: How can molecules of a diameter larger than 9–10 nm get into and out of the nucleus? According to Alberts et al.,^[4] the NPC can expand (or “stretch”) in diameter to approximately 26 nm. This would explain how molecules as massive as a large ribosomal subunit (MW ~1590 kDa) can be exported out of the nucleus. One could also hypothesize that these molecules are transported in an at least partially unfolded state, perhaps with the assistance of chaperone proteins.

The processes of nuclear import and export are temperature dependent. Panté and Aebi ^[9] injected cells with 14-nm nucleoplasmin-gold labeled particles. These particles were found predominantly at the cytoplasmic side of the NPC at low temperatures, but when the temperature was raised, the same gold particles had been imported into the nucleus.^[9]

The import of protein molecules into the nucleus is a two-step process. The first stage of this process consists of a protein docking at the cytoplasmic side of the NPC. The second stage is an adenosine triphosphate (ATP)-dependent translocation through the central transporter. This process also requires GTP hydrolysis and GTP/guanosine diphosphate (GDP) exchange in one of the nucleocytoplasmic shuttle factors (shown in NUCLEAR PORE COMPLEX: PROTEIN TRANSPORT).

Proteins Imported Into Nucleus Contain Nuclear Localization Sequences

Many proteins, endogenous transcription factors, tumor suppressor proteins, steroid hormone receptors, as well as nuclear lamins contain a nuclear localization sequence (or signal) or NLS.^[21] Most of the NLSs are short amino acid sequences, which are incorporated into nascent polypeptide chains. These sequences are rich in positively charged amino acids, especially lysine and arginine.^[4] Proteins bearing the NLS sequence are called karyophiles or nucleus-seekers. It can be inferred that NLS sequences would show at least some homology between different groups of karyophiles. In fact, using an SV40 viral particle (Vp) 3 model, Dean and Kasamatsu ^[22] determined viral NLS sequences to be highly homologous with those of the specific host.

It is generally agreed that there are at least two types of NLSs. In addition to the short, basic NLS sequence [Table 2] consisting of the basic peptide PKKKRKV,^[8] Simos and Hurt ^[11] described another form of NLS consisting of two clusters of basic amino acid residues separated by an ill-defined spacer sequence of about ten amino acids. This distinct new form of NLS was termed the bipartite NLS ^[11] and can be described ^[8] by the following sequence: KRX10KKKK (X representing an unspecified amino acid). It is now known that this bipartite NLS is more common than any other NLS sequence.^[8] One of the karyophilic proteins, nucleoplasmin, used widely as a model for protein import studies contains this classic bipartite NLS sequence.^[8]

Table 2: Nuclear import/export sequences (including their amino acid composition)

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Vancurova et al.^[21] examined the NLS using variants of the SV40 large T-antigen's nuclear localization sequence region linked to beta-galactosidase.^[21] They found a cdc2 kinase site (threonine residue 124) on the amino flank of the NLS. They also discovered that the presence of a casein kinase II site (serine residue 122) enhanced subsequent nuclear pore binding of transportable proteins. The casein kinase site is likely to be a general phosphorylation site, necessary for the docking, and translocation processes.

The presence of the cdc2 kinase site at the threonine residue 124 points to a possibility that there could be a correlation between the cell cycle and levels of NPC activity. Macaulay et al.^[23] reported that several NPC proteins were highly phosphorylated at mitosis, making them potential candidates for cdc2 kinase activity. Whether phosphorylation of these proteins is in anyway connected to the phosphorylation of NLS sequences is unclear. A possible connection can be proposed between phosphorylation of nuclear pore subunits and disassembly of the nucleus during the prophase of the mitosis.

Guiochon-Mantel et al.^[24] suggested that NLS sequences are not only responsible for nuclear import of polypeptides but also facilitate nuclear export of these substances. Throughout the literature, one can encounter both nuclear import signals (NISs) as well as nuclear export signals (NESs). Whereas the NISs seem to be fairly conserved, NESs display much more variety.

Structural Components of the Nuclear Pore Complex

As an entity, the NPC contains over a hundred distinct types of polypeptide chains, which interact with one another. The ultimate effect of this interaction is the orderly translocation of materials into and out of the nucleus. The known elements of the NPC constitute a family of proteins ranging in molecular weight from 25 kDa to at least 357 kDa. Many of the NPC proteins from animal cells are glycosylated with O-linked GlcNAc.^[25] In fact, the absence of N-acetylglucosaminylated pore proteins alters the appearance of the assembled complexes.^[5] Another common characteristic of many NPC proteins is that they often contain multiple inexact repeats of Gly-Leu-Phe-Gly (GLFG), Phe-Gly (FG), and Phe-XXX-Phe-Gly (FXFG) sequences.^[26] These repeats have been shown to be involved in binding of transportable substrates.

Spector ^[2] reported that the NPC consists of four major structural supercomplexes, which interact with each other. The first is an hourglass-shaped central component [shown in red in [Figure 1] inserted into the nuclear pore and limited by a ring of 120 nm in diameter on both intranuclear and cytoplasmic sides. The second component [shown in dark blue in [Figure 1] is a ring of eight particles, arranged octahedrally, connected by spokes to the nucleoplasmic ring, and located around the hourglass-shaped central component. The third major structural feature of the NPC consists of eight short, twisted filaments on the cytoplasmic side of the pore [shown in yellow in [Figure 1]. Finally, there are eight long thin filaments, which project from the 120 nm ring into the nucleoplasm. Their ends are attached to a smaller ring [shown in green in [Figure 1]. The overall structure gives it an appearance of a fish trap. Approximate molecular weights of known NPC components can be found in [Table 3] and [Table 4]. A large class of proteins called nucleoporins is involved in physical translocation of substances across the nuclear envelope. The great majority of nucleoporins facilitate protein and RNP transport in a process requiring ATP and GTP hydrolysis.

Table 3: Structural elements of the nuclear pore complex and their function

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Table 4: Nuclear import/export factors, inhibitors, and their function

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Akey ^[27] has shown that the architecture of the central spoke [Figure 2] responds to changes in the turgor pressure of the nuclear envelope. Thus, the NPC seems to be a flexible structure. This observation supports the general model of the NPC being a flexible, adjustable molecular assembly.

It was shown by Iovine et al.^[28] that a GLFG repetitive region present on numerous nucleoporins interacts with the Kap95p nuclear protein import factor. These nucleoporins include NUP116, NUP98, and NUP100. Deletion of the GLFG repeats, or reduction in their number, decreased the NPC's ability to import proteins. Yokoyama et al.^[29] further proposed that the XXX-Phe-XXX-Phe-Gly (XFXFG) pentapeptide motif is highly characteristic of NPC proteins. Thus, it might be inferred that proteins with this type of repeat are very likely to be considered NPC proteins.

The nuclear pore protein NUP98 was shown to be asymmetrically distributed to the cytoplasmic side of the NPC.^[26] NUP98 has been proposed to act as one of several docking site nucleoporins involved in the cytosolic docking of substrates. The docking site on NUP98 was mapped to its N-terminal half, which contains all of the GLFG, FG, and FXFG peptide repeats. Radu et al.^[26] suggested that NUP98, together with peptide repeat domains of other nucleoporins, forms an array of sites for cytoplasmic docking of transportable substrates and that the bidirectional transport across the NPC proceeds by repeated docking and undocking reactions.

Wu et al.^[30] localized the cytoplasmically exposed nucleoporin NUP358 at or near the tip of the cytoplasmic filaments of the NPC. This nucleoporin contains Ran-GTP binding sites, zinc fingers, a cyclophilin A homologous domain, and leucine-rich regions. NUP358 is the first nucleoporin shown to contain binding sites for two of the three soluble nuclear transport factors (NTFs) so far isolated, karyopherin and Ran-GTP. This fact strongly suggests that NUP358 is involved in nuclear protein import.^[30] It is not known whether NUP358 is implicated in anyway with RNA and/or RNP export.

There is nearly universal agreement that one of the most important components in the NPC transport mechanism is the large (234 kDa) protein complex called p62, thought to consist of four distinct polypeptides (p45, p54, p58, and p62). Bastos et al.^[8] described the p62 complex as essential for NPC function. The p62 subunit of the p62 complex has been found to be associated with mRNA nuclear export ^[31] as well as protein import ^[32],[33] by several research groups. D'Onofrio et al.^[25] have deduced part of the complementary DNA (cDNA) sequence coding for the p62 subunit of the p62 supercomplex. Based on the CNBr analysis of the polypeptide sequence of p62, they have engineered fusion products of LacZ and p62 and isolated the corresponding mRNA. D'Onofrio et al., having determined the amino acid sequence of p62, predicted the secondary structure of p62 and determined its homology to other known protein sequences. Only limited homology was found between p62 and other proteins. Regions of amino acid sequence similarity were found between the alpha-helical regions of p62 and those of myosin heavy chain (MHC), tropomyosin, alpha-actinin, and actin. Berrios et al.^[34] reported localization of a MHC-like polypeptide to Drosophila NPCs, suggesting that it was a nonmuscle isoform of MHC. According to Clever et al.,^[35] p62 is located in the central transporter apparatus of the NPC. If the above speculations are correct, p62 could be involved in ATP hydrolysis, comparable to that of the muscle MHC ATPase domain.

Wesierska-Gadek et al.^[36] reported that autoantibodies from patients with primary biliary cirrhosis preferentially react with the amino-terminal domain of the gp210 NPC glycoprotein. They reported that gp210, an integral protein of the NPC, contains a large glycosylated cis-terminal domain, a single transmembrane segment, and a short cytoplasmic tail. It is the cytoplasmic tail to which the autoantibodies appeared to bind in these patients. In addition to confirming the approximate location of gp210, Wesierska-Gadek et al.^[36] proposed that autoantibody for gp210 be used as a screening test for biliary cirrhosis. Bastos et al.^[8] postulated that gp210 likely functions in anchoring the NPC to the nuclear membranes. In agreement with this hypothesis, Clever et al.^[35] reported that gp210 spans the lumen of the nuclear envelope. The importance of gp210 is best exemplified by the fact that the progression of a cell from G2 phase into M phase was inhibited when monoclonal antibodies against gp210 were used,^[37] suggesting that gp210 might be relevant to the nuclear disassembly process (just as it was implicated with nuclear formation in an embryo).^[7]

Several proteins were recently localized to specific sites within the NPC itself. An essential yeast nucleoporin, NUP159, has been localized to the cytoplasmic side of the NPC.^[38] It contains a coiled-coil domain as well as a domain of repeated motifs.^[38] Kraemer et al.^[38] used Escherichia coli to express five separate segments of NUP159. They found that the segment containing the repeat motif was directly involved in binding a transportable nuclear substrate in the presence of vertebrate cytosolic extract containing NTFs. Karyopherin-beta, a transport factor mediating the docking of substrates to the NPC, demonstrated high affinity for this repeat motif as well.^[38]

NUP153 and p250 were recently localized to specific sites within the NPC by Pante.^[39] NUP153 was found to be a constituent of the nuclear pore basket [shown in green in [Figure 1], whereas p250 was found to be present in the cytoplasmic filaments [shown in yellow in [Figure 1]. The cytoplasmically exposed filaments were recently found to be involved in binding of cytoplasmic nuclear import factors by Pante and Aebi.^[9]

NUP180 has been reported by Bastos et al.^[8] to be present in the cytoplasmic ring and cytoplasmic filaments. The function of NUP180 has not yet been elucidated. The paramount importance of this nucleoporin in either the structure and/or function of the NPC can be assumed from the fact that it is highly conserved in all vertebrates studied to date.

A summary of nuclear import/export factors, inhibitors, including their known or suspected function, is provided in [Table 4].

Nuclear Pore Complex: Protein Transport

Docking of cytoplasmic proteins destined for the nucleus requires a 56 kDa NLS receptor (also known as alpha-karyopherin, importin-alpha, or SRP1alpha) and a 97-kDa protein (also known as beta-karyopherin or importin-beta). Besides these two karyopherins, other components known to be necessary for successful translocation of proteins through the NPC include the Ran/TC4 GTPase and NTF2/B-2.

Görlich et al.^[40] have determined that there are distinct functions for soluble factors, namely, importin-alpha, importin-beta, and Ran in nucleocytoplasmic import. Importin-alpha has been found to be primarily responsible for NLS recognition. Along with importin-beta, importin-alpha binds the import substrate in the cytosol and the complex docks as a single entity to the NPC through importin-beta. The translocation process itself is mediated by the energy-dependent Ran, which ultimately results in accumulation of the imported substrate and importin-alpha inside the nucleus. In contrast to Ran and importin-alpha, importin-beta accumulates at the nuclear envelope but not in the nucleoplasm. Using immunoelectron microscopy, the presence of importin-beta was detected on both sides of the nuclear pore, which suggests that the nuclear pore-targeting protein complex is likely to move as a single entity from its initial docking NPC site, through the central part of the nuclear pore, and is then disassembled on the nucleoplasmic side, with the importin-beta subunit being returned to the cytoplasm.^[40],[41] Similar conclusions were reported by Adam.^[42]

Simos and Hurt ^[11] described in detail how Ran/GTPmediated protein transport takes place [Figure 3]. The first two events necessary for translocation are (a) binding of importin-alpha and importin-beta to the protein that is to be translocated and (b) interaction of Ran/GTP with the dimer form of a small, 15 kDa protein called Ranip. The importin-karyophile complex then (c) binds to the cytoplasmic filaments on the surface of the NPC. This event is termed docking. Once bound, the complex is then translocated (d) utilizing the Ranip-Ran/GTP complex as a mediator. GTP hydrolysis is necessary for the translocation to occur. Following the translocation, the complex dissociates inside the nucleus.^[4] A similar general description of the necessary steps was provided by Imamoto.^[43] Following translocation and release of Ran/GDP from the NPC, it is restored to Ran/GTP by a nuclear chromatin-associated factor (RCC1), which catalyzes the exchange of GDP for GTP.^[44] Thus, the entire cycle can be repeated, literally “recycling” all of its components. If, on the other hand, RCC1 is deactivated or absent, or if the Ran/GTP complex does not enter the nucleus, the cycle cannot repeat itself and nuclear import stalls.^[11],[29]

Figure 3: A diagram of the nuclear protein import mechanism. The two subunits of the nuclear localization signal receptor (alpha and beta) are responsible for binding a nuclear localization signal-containing protein (dark gray) in the cytosol and for docking it to the cytoplasmic side of the nuclear pore complex. The docking process is mediated through interactions with the repeat domains of nucleoporins (zigzagged heavy lines). Ran-guanosine triphosphate and Ranip are also recruited to the nuclear pore complex by Ran-binding nucleoporins and p62, respectively. One of the requirements for the translocation of karyophile/nuclear localization signal receptor complex into the nucleoplasm is hydrolysis of guanosine triphosphate by Ran. This hydrolysis is assisted by Ran GTPase-activating protein. It is unclear whether alpha or beta importin, or both, follows the karyophile into the nucleus. Ran-GDP can be reactivated in the nucleus by nucleotide exchange catalyzed by RCC1. Ran-guanosine triphosphate then returns to cytoplasm (modified from Simos and Hurt, 1995)

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It is still unclear whether the Ran/RCC1 cycle is required for both nuclear import and nuclear export or whether Ran participates in different cellular pathways (i.e., in RNA/RNP nuclear export) utilizing different effectors. Likely, protein effector candidates include: Ran-binding protein 1 (RanBP1), Ran GTPase-activating protein (RanGAP1), and RanBPX.^[11] RanGAP1 is the product of the RNA1 gene, mutations of which result in deficiencies of transfer RNA (tRNA) and ribosomal (rRNA) processing and mRNA export. The fact that two antagonistic Ran regulators, RCC1 (responsible for GDP/GTP exchange) and RanGAP1 (responsible for activation of GTP hydrolysis), are separated by the nuclear envelope suggests that Ran may shuttle between the nucleus and the cytoplasm.

It is interesting to note that lack of RCC1 can be partially compensated for by overexpression of a related protein, Ran/TC4,^[29] which suggests that Ran/TC4 functions downstream of RCC1 in the above pathway.

Yokoyama et al.^[29] purified a large novel protein containing a 700-residue leucine-rich amino-terminal, four RanBP1-homologous domains, eight zinc-finger motifs similar to those of NUP153, and a carboxy-terminal with high resemblance to cyclophilin. This novel protein, named RanBP2, contains an XFXFG pentapeptide motif characteristic of NPC proteins. Immunolocalization suggests that RanBP2 is a constituent of the NPC, and the fact that NLS-mediated nuclear import can be inhibited by an antibody directed against RanBP2 supports a functional role of RanBP2 in protein import.

Wilken et al.^[45] reported that a partial cDNA clone coding for the mouse homolog of the human Ran-GTP binding protein (RanBP2) was obtained by screening a murine expression library with antibodies to NUP180. The 3795-bp open reading frame of the cDNA encoded a polypeptide consisting of 1265 amino acids and containing three Ran-GTP binding domains. These domains are almost identical to the previously published partial amino acid sequence of human RanBP2. Further analysis revealed that murine RanBP contains tandemly repeated zinc fingers of the Cys2-Cys2 type and multiple copies of the FXFG nucleoporin-characteristic motif clustered in regions preceding the Ran-binding domains. Subsequent use of antibodies directed against a synthetic peptide matching the derived amino acid sequence showed binding to the cytoplasmic rings of the NPC. Thus, Wilken et al.^[45] provided strong evidence that RanBP2 provides docking sites for import of substrate-receptor complexes. At the same time, they reaffirmed the view that the repeat motifs are involved in docking of transportable substrates. Furthermore, they suggested that the affinity of the RanBP2 for the transport substrate is modulated in a Ran-dependent fashion, further strengthening the existing protein import model.

NUP1p is an NPC protein containing many degenerate repeat sequences of the Phe-Ser-Phe-Gly type in their central domains. This protein has been shown to be required for efficient nucleocytoplasmic transport reactions by Schlaich and Hurt.^[46] Cells with a deleted NUP1p gene were viable in terms of vegetative survival, but their growth was impaired. NSP1p, structurally related to NUP1p, has been found to perform NUP1p's tasks but with decreased efficiency. This was especially pronounced at higher temperatures. At 37°C, the cellular growth rate was seriously inhibited in delta-NUP1p (deleted NUP1p gene) cells, whereas at 23°C, it was relatively normal.

Chi et al.^[47] sequenced and characterized the nuclear protein import factor p97 (importin-beta) and reported that it contains 23 cysteine residues and binds zinc. Subsequent analysis demonstrated that there are at least three other cytosolic proteins that interact with p97. Chi et al.^[47] also found that a bound metal ion is necessary for the nuclear envelope binding activity of p97.

Paschal and Gerace ^[48] described the NTF2, which is apparently a dimer of 14 kDa subunits and is present at 6-10 copies per cell. It was shown to interact with the NPC glycoprotein p62.^[48] Since Paschal and Gerace ^[48] also mention that NTF2 is likely to interact with other cytoplasmic and nucleoplasmic factors, it might be argued that NTF2 is an importin homolog. The authors speculate that NTF2 is a part of a larger complex that assembles at the NPC during nuclear import, which further strengthens the current nucleocytoplasmic import model. The fact that only 6–10 copies of NTF2 were present per cell presents a quantitative problem, considering that an average nuclear envelope contains 2000–4000 pores.

An interesting case study of nucleocytoplasmic protein import was described by Bustamante et al.,^[49] who demonstrated that TATA-binding protein (TBP; a transcription factor which binds to DNA in order to assist initiation of transcription) is translocated through the NPC in an ATP-dependent fashion. The TBP translocation process could be detected as a transient plugging of the NPC channels. At the same time, a transient reduction in single NPC channel conductance occurred. Bustamante et al. also discovered that TBP was able to modify the NPC structure and function at concentrations above 250 pM, which is based on an observation that the NPC unplugging following TBP transport was accompanied by permanent channel opening.^[49] From these results, it was proposed that there might be three novel functions for TBP: (a) Stabilization of the NPC; (b) forcing NPC channels into an open state; and (c) increasing the number of functional channels. Since TBP is a protein necessary for gene transcription, these observations are potentially relevant to the understanding of gene expression mechanisms underlying normal cell function and pathology.

Nuclear Pore Complex: Ribonucleic Acid and Ribonucleoprotein Transport

Although RNA and RNP nucleocytoplasmic transport mechanisms are as yet largely unknown, several clues point toward the possibility that they are regulated by both nuclear and cytoplasmic factors. Several major proteins involved in this process have been characterized during the last decade.^[50] Three major types of RNAs and RNPs are actively exported from the nucleus through the NPC. These RNAs include small nuclear RNAs (snRNAs), mRNAs, and tRNAs. Because these RNA molecules are usually packaged with proteins into RNP complexes, they are probably exported as RNPs. This is consistent with the evidence provided by Mehlin et al.,^[51] who used electron microscopy to visualize nucleocytoplasmic export of Balbiani ring granules, premessenger RNP particles in the salivary glands of Chironomus.

Feldherr et al.^[52] have reported the results of an experiment in which they coated 20 nm gold spheres with small RNA molecules (tRNA and 5S RNA). These spheres were microinjected into (a) the nuclei of frog oocytes or (b) into the cytoplasm. Spheres initially injected into the nuclear compartment were rapidly exported from the nucleus while spheres placed in the cytosol remained there. This experiment suggests that certain RNA sequences could serve as NESs.

In view of NPC selectivity for transportable substrates, the export of RNA molecules from the nucleus could be much like nuclear protein import, i.e., a signal-dependent, receptor-mediated process. The nuclear export of RNA also seems to be carrier mediated and energy dependent, taking place in at least two steps: (a) The RNPs move from their transcription and assembly site to the nuclear envelope before (b) translocation into the cytoplasm.^[53],[54] A specific “common” targeting signal, equivalent to a protein NLS, has not been found for RNA. It appears that different classes of RNA depend for their export on specific signals which could either lie in the RNA itself or be provided by the protein component of the RNPs. Experiments with microinjections into Xenopus oocytes demonstrate that the export of different types of RNA is mediated by different saturable factors;^[11] for example, the transport of an snRNA molecule, present at a low concentration, can be inhibited by another snRNA, present at a higher concentration but is not inhibited by mRNA, rRNA, or tRNA. Homopolymeric RNA (RNA containing multiple repeats of the same ribonucleotide) seems to be an exception to this rule since it inhibits the export of more than one class of RNA,^[11] suggesting that some common factors required for export of RNAs/RNPs exist.

Another, apparently general, determinant for RNA export is the dissociation of RNAs from common intranuclear retention sites that may represent a rate-limiting step for the export process. Analysis of mutations affecting the export capability of a specific RNA molecule has led to the identification of features that constitute cis-acting signals important for export. Some of these signals include the 5' cap structure of U snRNAs and mRNAs, the 3' ends of histone mRNA, and sequence-specific determinants within tRNAs and 5S rRNAs.^[11] Any protein that selectively recognizes these features would be a good candidate for a nuclear export factor. In fact, a protein complex consisting of two cap-binding proteins (CBP80 and CBP20) has been found to be a required element for U snRNA export.^[55]

Schlaich and Hurt ^[46] have shown that cells defective in the NUP1p gene product were not able to export poly (A) + mRNA. This was true despite the fact that NSP1p, a NUP1p-related protein, which can carry some of the protein import functions of NUP1p, was present in the system. Therefore, it seems quite likely that NUP1p is a potential candidate for a poly(A) + nuclear export mediator.

Michael et al.^[56] were able to demonstrate that a so-called M9 domain within a protein component of hnRNP A1 was used as a nuclear transport signal (NTS). The 38-amino acid M9 domain was found to bear no resemblance to other examples of NLS protein import sequences. The M9 domain, which has no single-stranded nucleic acid-binding activity (i.e., RNA) in vitro, shows both NES and NIS activity.

The fact that histone molecules labeled with poly(A) + RNA particles have successfully been used to block nuclear pores to export strongly suggests that poly-A sequences are by themselves NESs.^[57] Nuclear pore protein NUP133p has been implicated in export of poly(A) + RNA particles. Cells with defective NUP133p display accumulation of poly(A) + RNA inside their nuclei.^[58] It may be possible that NUP133p interacts with p62 during poly(A) + RNA transport out of the nucleus as both have been found to play a role in RNA and RNP export. Dargemont et al.^[31] determined that nucleoporin p62 directly interacts with mRNA during nuclear export. They also suggested that mRNA transport is competitive and mRNA-specific. They showed that export of one mRNA molecule can be inhibited by introducing another mRNA molecule into the system but was not inhibited when snRNA, tRNA, or rRNA was added to the same system.^[31] They also determined that wheat-germ agglutinin (WGA) was able to inhibit mRNA transport. The inhibitory action of WGA is not clearly understood, but seems to be broader than just inhibition of mRNA export, as it was also able to inhibit ribosomal subunit export. Dargemont et al.^[31] also concluded that WGA may inhibit protein translocation by binding to N-acetylglucosaminylated nucleoporins, p62 being the most prominent. WGA binding to an GlcNAc residue on p62 has been reported previously.^[59]

Nucleoporin NUP120p, according to Aitchison et al.,^[60] is involved in transport of polyadenylated mRNA from the nucleus. Mutant cells with defective NUP120 were found to accumulate large quantities of poly(A) + mRNA in their nuclei, displayed extensive fragmentation of the nucleolus, spindle defects, and cellular death.^[60] Similar but less severe defects were reported by Hurwitz and Blobel ^[10] during studies of another nucleoporin, NUP82.

Simos and Hurt ^[11] report that RCC1 might not only be necessary for translocation of proteins (as described in a previous section) but also for nuclear export of U snRNA molecules. Similar conclusions were drawn by Yokoyama et al.,^[29] who reported that loss of RCC1 caused malfunctioning of nuclear RNA export as well as defects in cell cycle progression and nuclear protein import.

Visa et al.^[55] found that a cap-binding complex (CBC) formed by two cap-binding proteins, CBP20 and CBP80, is involved in RNA metabolism, including nuclear export of certain RNA polymerase II-transcribed U snRNA complexes. The CBC binds to the nascent pre-mRNA shortly after initiation of transcription, stays in the RNP after pre-mRNA splicing is completed, and remains attached to the 5' end during translocation of the resulting RNP through the NPC ^[55] [Figure 4]. Moreover, the CBC was found to be so highly conserved that antibodies against human CBP20 cross-reacted with the CBP20 from the dipteran Chironomus tentans.

Figure 4: Nucleocytoplasmic export of U small nuclear ribonucleic acids, messenger ribonucleic acids, and sequence-specific determinants within transfer ribonucleic acids and 5S ribosomal ribonucleic acids utilizing cap-binding complex. The cap-binding complex consists of two subunits: Cap-binding complex 20 and cap-binding complex 80. These subunits complex with the 5' cap structure on the ribonucleic acid molecule and facilitate the transport of that molecule into the cytoplasm, where the complex dissociates (modified from Visa NE et al., 1996)

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Nuclear Pore Complex and Virology

Viral infection of eukaryotic cells also depends on the NPC. Thus, our knowledge of the NPC has possible implications in therapies directed at viral infections. Certainly, as in each case of a successful infection, the viral DNA, RNA, RNP, or protein has to pass through the NPC if its ultimate goal, the replication of the virus itself, is to take place. As the only gateway between the cytoplasm and the nucleoplasm, the NPC is one of the crucial factors in the viral propagation process. As viruses evolved, they developed effective ways of “tricking” NPCs to allow them into the nucleus. Most viral proteins have NLS sequences that resemble those of their host cells.

Simian virus 40 (SV40) has become one of the most studied models for investigation of NPC function in viral protein and DNP (protein-coated DNA) translocation into the nucleus. SV40 is a convenient target for investigation because it only contains about 5000 bases in its total genome.^[61] Dean and Kasamatsu ^[22] examined signal- and energy-dependent nuclear transport of SV40 DNA and proteins. Based on the assumption that NTS-containing proteins are transported into the nucleus through the NPC, they established an in vitro system composed of simian nuclei and nuclear pores. Isolated nuclei accumulated either fluorescently labeled SV40 Vp3-NTS peptide-BSA conjugates (NTS-wt-BSA), as assayed cytochemically, or 125I-NTS-wt-BSA, as assayed by filtration, in both a signal- and an ATP-dependent manner. The process was inhibited by the lectin germ agglutinin but not by concanavalin A (Con-A). Mutations in NTS or complete lack of the NTS also inhibited the process. This system accurately reproduced processes that occur in vivo and confirmed that a functional NTS is necessary for the process to occur. It seems that the SV40 nuclear DNA transport is facilitated by the viral coat proteins, which protect the genome until it is safely brought into the nucleoplasm.^[35]

Clever et al.^[35] determined that SV40 protein particles were karyophilic. The nuclear accumulation of Vp1 was seen within 2 h of microinjection of SV40 into cells. The nuclear entry of virion was blocked by WGA and mAb 414 (monoclonal antibody 414), both of which bind to p62, strongly suggesting involvement of that protein in nuclear virion transport. Con-A, which binds to gp210, does not inhibit virion transport, suggesting that the karyopherin-mediated pathway is not utilized in this sequence of events.

Kemler et al.^[62] found that nuclear import of influenza virus vRNPs required energy and was inhibited by antibodies to NPC proteins, suggesting that the NPC requires energy to facilitate RNA and RNP transport.

Fischer et al.^[63] found evidence that the HIV-1 Rev activation domain is a NES. Its mode of function seems to exploit nuclear export pathways used for specific cellular RNAs. Perhaps, one of the therapies against HIV will use the strategy of selectively blocking the virus-specific pathways in infected cells.

Conclusions

The NPC is one of the most important elements of the eukaryotic cell. Whenever a defect occurs in the formation of NPCs, cellular death follows. The NPC regulates the flow of macromolecules between the cytoplasm and the nucleoplasm. It is responsible, to a large degree, for posttranscriptional/pretranslational control of the distribution of RNPs as well as co-transcriptional control of certain other snRNA molecules. There are numerous associated protein and RNA transport factors, along with over a hundred distinct polypeptides involved in the functioning of the NPC.^[8]

Many NPC components have been identified, and functionalities of the most important of them have also been described. No doubt, there are many more proteins and transport factors involved in translocation through the NPC. As we learn more about it, the entire “NPC puzzle” will gradually become just another part of the newest cell biology texts. Besides describing the NPC components, we have also been able to elucidate the karyopherin-dependent nucleocytoplasmic protein import. The Ranip-Ran/GTP protein import cycle offers us the best explanation of how the NPC works. Many of the cellular signals, which direct macromolecules to the nucleus, have been identified. The energy dependence and temperature dependence of the translocation have also been firmly established.

The study of NPCs has come a long way since the first experiments involving nucleocytoplasmic transport. It is hard to believe that, beginning only 40 years ago, scientists were able to learn so much about this intricate structure and its function. Improved analytical techniques as well as novel equipment will allow discovery of new aspects of the NPC and application of this knowledge outside the laboratory. For example, the knowledge of NPC structure and function might improve existing cancer treatments. The fact that the product of the oncogene-activating gene Tpr is a phosphorylated form of a protein of the NPC ^[64] might advance the knowledge of carcinogenesis. Virology and oncology seem currently to be the most direct beneficiaries of the new NPC developments.

The NPC is very complex and will require a great deal of scientific investigation before its structure and function can be fully understood. New subunits of the NPC are being elucidated almost daily, adding to the array of known nuclear import and export factors and sequences. Numerous nuclear import and export factors have been characterized thus far, and more are being identified at the present time. Once biologists have more insight into NPC structure, they will be able to deduce much more about its function. Likewise, the knowledge of both structure and function of the NPC will allow the scientists to understand evolutionary origins of this elaborate and vital structure of every eukaryotic cell.

Acknowledgments

Justifications for re-publishing this scholarly content include: (a) The phasing out of the original publication – the OPUS 12 Scientist and (b) Wider dissemination of the research outcome(s) and the associated scientific knowledge.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.

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Figures

[Figure 1], [Figure 2], [Figure 3], [Figure 4]

Tables

[Table 1], [Table 2], [Table 3], [Table 4]

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