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The nuclear pore complex: bridging nuclear transport and gene regulation
Caterina Strambio-De-Castillia, Mario Niepel and Michael P. Rout
NATURE REVIEWS | Molecular ell Biology Vol. 1 1 . P. 490-501| july 2010 | 491 doi:10.1038/nrm2928

Abstract | Although the nuclear pore complex (NPC) is best known for its primary function as the key regulator of molecular traffic between the cytoplasm and the nucleus, a growing body of experimental evidence suggests that this structure participates in a considerably broader range of cellular activities on both sides of the nuclear envelope. Indeed, the NPC is emerging as an important regulator of gene expression through its influence on the internal architectural organization of the nucleus and its apparently extensive involvement in coordinating the seamless delivery of genetic information to the cytoplasmic protein synthesis machinery.

Nuclear periphery
The region of the nucleus comprised of the nuclear envelope and its associated structures, including the NPC and the nuclear components found in the neighbourhood.

β-Propeller
A compact structural protein domain of similarly sized β-sheets, which are stacked into a cylinder to resemble the blades of a propeller.

α-Solenoid
A structural protein domain composed of numerous pairs of antiparallel α helices that are stacked to form a solenoid.

LEM domain
(LAP2, emerin and MAN1 domain). A domain that is present in a family of evolutionarily conserved integral membrane proteins of the INM, which participate in chromatin organization, gene expression regulation and nuclear envelope biogenesis.

SUN domain
(sad1 and UNC84 domain). A conserved C?terminal aminoacid sequence found in integramembrane proteins of the INM. These proteins act with members of the KAsH domain?containing protein family to form a molecular velcro, which is thought to mediate several processes requiring nuclear repositioning,such as fertilization, establishment of polarity, division and differentiation.

Brownian motion
The seemingly random movement of particles suspended in a liquid or gas, which is driven by the kinetic energy of the particles in the system.

Heterochromatin
A highly condensed form of chromatin that is either genetically inactive or transcriptionally repressed. It is predominantly located near the nuclear envelope and includes centromeres, telomeres and silenced genes.

SUMO homeostasis
The overall level of proteins modified by the covalent attachment of sUMO. It is balanced through the regulated activities of sumoylating ligases and desumoylating proteases.

TRAMP complex
(Trf4 or Trf5, Air1 or Air2 and Mtr4 polyadenylation complex). A protein complex that functions in RNA processing, degradation and surveillance. It polyadenylates various aberrant nuclear RNAs and thus labels them for processing or degradation by the exosome complex.

Exosome complex
A complex of several exonucleases arranged in a ring structure that, assisted by RNA helicases, degrade RNAs in the nucleus and cytoplasm.

SAGA histone acetyltransferase complex
(spt, Ada, Gcn5 and acetyltransferase histone acetyltransferase complex). A large and highly conserved multiprotein complex required for the normal transcription of many genes.

TREX2 complex
(Transcriptionexport complex 2). TReX2 comprises Thp1, sac3, Cdc31 and the sus1 subunit of the sAGA complex involved in chromatin remodelling and transcriptional activation. TReX2 interacts with the NPC and is thought to have an important role in coupling sAGA?dependent gene expression to mRNA export.

THO complex
A multiprotein complex conserved among yeast and metazoans that is involved in mRNP biogenesis and export. In S. cerevisiae it consists of Hpr1, Mft1, Tho2 and Thp2. The human counterpart consists of the THO complex proteins THOC1THOC7.

TREX complex
(Transcriptionexport complex). A complex that consists of components of the THO complex together with Yra1 (homologous to human THOC4) and sub2 (homologous to human BAT1). The TReX complex interacts with the NPC through the non?Kap NTfs Mex67 and Mtr2, helping to anchor active genes to the nuclear periphery.

Gene gating hypothesis
The hypothesis in which the nuclear pore complexes are envisioned to serve as gene?gating organelles capable on interacting specifically with expanded (transcribable) portions of the genome

Spindle pole body (SPB)
The only microtubule organizing centre found in S. cerevisiae. sPBs are embedded in the nuclear envelope throughout the yeast life cycle and their functions include chromosome segregation during mitosis and meiosis, and intracellular trafficking.

Spindle assembly checkpoint (SAC)
The sAC monitors the correct attachment of kinetochores to spindle microtubules before anaphase. Unattached kinetochores activate this checkpoint and cause cell?cycle arrest through the inhibition of the anaphase-promoting complex.


.1.  |  Nuclear pore complex structure.


.2.  | The nuclear pore complex functions as a virtual gate .


.3.  |  The function of the nuclear pore complex peripheral structures .


.4.  |  The gene expression path traverses the NPc .

, (ER), (rev. Ref. 1). , , , , - . , , . , , , . , . nuclear pore complexes (NPCs).
NPCs, . ~50 mDa, ~30 , . nucleoporins (Nups). NPC : NPC , , NPC , NPC , (FIG. 1). NPC , (FIG. 2). NPC , NPC (FIG. 3). ( basket) NPC , . , (FIG.1).
NPC , . NPC, -, (RNPs) , "" (FIG. 3). basket , . NPCs, . , - (rev. Refs 2,3). , NPC , messenger RNP (mRNP) . - - , , (FIG. 3).

Structure of the NPC


NPC , 4. NPC ~125-nm , 8 . , (FIG. 1). ( ) NPC's , , (FIG. 1). NPC ~35 nm (rev. Refs 5,6).
NPC , , imaging 7,8. , (rev. Ref. 9) Nup NPC. Nups , .., 4 (FIG. 1): , ( ), Phe-Gly (FG). Nups ( lumenal ), NPC . Nups , NPC. NPC NPC , , -, NPC (., Saccharomyces cerevisiae Nup84 Nup170 . metazoan , the NUP170-NUP160 NUP35-NuP155 )10-12. FG Nups, . , Nups FG Nups.
Nups (fold) 9,13,14. NPC archi- tecture8 , NPC's consists of - , Nups β-propeller α-solenoid ( -- ) - , , , clathrin, coat protein I (COPI) COPII (rev. Ref. 15). "protocoatomer hypothesis", , , β-propeller α-solenoid , NPCs 8,14. protocoatomer ER, Golgi 1. , Nups, Nups NPC (rev. Ref. 9).


Mechanism of nucleocytoplasmic transport


NPC , , ; . , nuclear transport factors (NTFs) , " " (rev. Refs 16,17). NTFs, , karyopherin (Kap) (BOX 1).
NTFs , . NPC . . . . nuclear localization sequences (NLSs; ) nuclear export sequences (NESs; ). 18. -, NTFs. -, NTF- NPC FG Nups NPC. -, ( ), . , NLSs NESs NTFs NPC, NPC. Kap- , GTP- GDP- GTPase RAN, 19,20. RAN-GTP Kaps. RAN-GTP Kaps NES- . . NPC, GTP , . NTF RAN-GDP . NPC, .
FG Nups (rev. Ref. 21) NPC , .. docking NTF- NPC22,23. FG Nups Phe-Gly , 5-30 24. FG Nups : , NPC (., NUP62), , (., NuP153)8,25,26 (FIG. 1). , Phe-Gly , (strings), 27-29. . 160 FG Nups NPC8,25 . .., NPC , FG Nups, NTF- (fIG. 2). , ' NPC' - , Phe-Gly FG Nup - - , NTFs NTF-, FG Nups, , 30.
NPC . ( ) iris- , , NPC 31 , NTFs 32,33. . NPC , 25,26, FG Nups 25, NTF NPC34, ,



Box 1 | The karyopherin family of nuclear transport factors

The karyopherin (Kap) family of proteins in yeast is thought to comprise fourteen members (reviewed in Ref. 156). Some Kaps, known as importins, specialize in transporting cargoes into the nucleus, and others, known as exportins, ferry cargoes out of the nucleus (reviewed in Ref. 157). For example, in Saccharomyces cerevisiae, the nuclear transport factor (NTF) Kap123 is known to ferry ribosomal proteins into the nucleus, and one of the many jobs of chromosome region maintenance 1 (CRM1) is to help ferry pre"'60S ribosomal subunits out of the nucleus. In addition to ribosomal RNAs, other types of RNAs are transported by Kaps. For example, S. cerevisiae loss of suppression 1 (Los1) is recruited by tRNAs and promotes their nuclear export, whereas CRM1 is known to modulate the export of unspliced or partially spliced viral RNAs and might be involved with the regulated export of important mRNA species during specific developmental stages (reviewed in Ref. 158). Nevertheless, not all NTFs belong to the Kap family157. The most notable exceptions are nuclear RNA export factor 1 (NXF1) and NTF2"'like export factor 1 (NXT1) and their respective S. cerevisiae homologues, mRNA export factor of 67 kDa (Mex67) and mRNA transport protein 2 (Mtr2). These proteins are responsible for the nuclear export of mature messenger ribonucleoproteins and have no obvious structural resemblance to the Kap family (reviewed in Ref. 16).




RAN, 19, .
"virtual gating"25,53 , . " NPC . ."36. . NPC , , , (FIG. 2). , , NPC, , , FG Nups36. NPC Phe-Gly, , NPC. , Phe-Gly , . NPC. , FG Nups (gating) . FG Nups , 25, (collapse) , 28,37. , , FG Nups amyloid- 38-42, " - , "42; Phe-Gly , NTFs , . 36,43. 27,29,44,45. , -, , NTFs , "" ("bouncer s"), NPC 30,46,47.

Beyond transport: cytoplasmic functions


, NPC , . ., , NPC , - 48,49, , 50,51. . , NPC (FIG. 1; FIG. 3).
8 NPC, . , , , Phe-Gly Nups, NPC (., NuP214 NuP358 ( RANBP2) Nup42 Nup159 S. cerevisiae). 52. dynein (Dyn2), , Nup159 "pearls on a string, " , Phe-Gly Nup159 NPC. Nups, , , 53, NPC54,55 (FIG. 1; FIG. 3).
NUP214 ( CAN S. cerevisiae Nup159) Nup-like protein 2 (NUPL2; GC1 S. cerevisiae Nup42), mRNPs RNA helicase DEAD box protein 19B (DDX19B; DBP5) NPC RNA export mediator homologue GLE1, , NPC (rev. Ref. 53). Dbp5 Gle1, , , mRNP, nuclear polyadenylated RNA-binding protein 2 (Nab2) mex67, mRNPs, NPC . , , 56.
NuP358 , cyclophilin homology , zinc finger , small ubiquitin-related modifier (SUMO) ligase ubiquitin-conjugating protein 9 (UBC9; UBE2I) , GTP- GDP- RAN GTPase RAN GTPase-activating protein (GAP)57-59, , . ., NuP358, -, exportins 50, NPC55. HIV-1, regulator of virion expression (Rev) HIV-1 NUP358 NPC55. , NuP358, , sumoylation , NPC, 60. , NuP358 , NuP358 , . ( 61) 62 NPC63, NPC 'on track' 64,65.

Beyond transport: nuclear functions


1989, Hans Ris 66. , NPC 67,68. , , , NPC .
Nuclear basket: structure and potential roles. , , , 69-71. basket 8 , ~60-80 nm NPC 67-69,72 (FIG. 1; FIG. 3). , mRNPs, Chironomus basket's , , basket , NPC73-75. 8-10 nm - - , , , 68,69. , Triturus spp. Xenopus laevis, , . 69. 72, , basket . , , , NPC, , 49,76,77.
- , . , basket FG Nups, NUP153 Nup60 Nup1 S. cerevisiae. , translocated promoter region (TPR)78,79, Drosophila melanogaster Megator80,81 myosin-like protein 1 (Mlp1) Mlp2 S. cerevisiae82, basket, , 83,84. , TPR- , , , 81,82,85,86. , basket , basket . , , , SUMO , 75,76,81,87-101. , basket , , NPCs. basket (processing) , NPC, (FIG. 3).
Post-transcriptional control of gene expression. , - , NPC NPC (rev. Ref. 102). , basket 75,76,103. , basket, -, , , , (rev. Ref. 104). , mRNP, NPC, 105,106 (see next section and FIG. 4).
107. RNases. 108 , TRAMP , pre-mRNA downregulation protein 1 (Nrd1)-Nab3 ribosomal RNA-processing protein 6 (Rrp6). , - . , mRNPs NPC, establishes silent chromatin protein 1 (Esc1), pre-mRNA leakage protein 1 (Pml1), Pml39, PIN endonuclease Trex protein 1 (Swt1) Nab2 (Refs 87,92,93,98,109). , . , , -, desumoylating ubiquitin-like protein 1 (ulp1) . .. , ulp1 pre-mRNA , , ulp1- desumoylation , pre-mRNA, mRNPs ( - ) 92,94 .
Epigenetic control of gene expression. , , , . 110. , (rev. Ref. 2). , , , .. 111,112. 49 , 113. , NPCs , -, , , basket, 99-101,114-118.
114,116,119 . , inositol 1-phosphate synthase (INO1) galactokinase (GAL1), , , NPCs 89,116,120,121. , , , -, - - . basket, , Gal1, switching deficient-sucrose non-fermenting (SWI-SNF) - H2A.Z99,100,118,121,122.
(rev. Ref. 2). , , (FIG. 4). .., NPC NPC 3' 116,123. SAGA histone acetyltransferase , NPC TREX2 106,115,124-27. -NPC , -, THO TREX , - -mRNP106,115,128, 129-131. , TREX2 , Sac3 Sup1 cell division cycle protein 31 (Cdc31), 129. , Sac3 TREX2 SAGA- NPC, .. THO TREX, mex67-mtr2 (mRNA transport protein 2) mRNPs NPC. , 101,103,125,132,133. .., basket . NPC, 91,99-101,103,123 , (gating)49. . , , 106,121 'active barrier' 134 . basket , 75,76,82,103. , , NPC, -, Nups, , NPCs, 135,136.
Chromatin maintenance and repair. NPC , , (DSBs; rev.Ref. 3). , , Nup84 . . 137. , Mlp 88. , Mlps SUMO methyl methanesulphonate sensitivity protein 21 (Mms21), structural maintenance of chromosomes (SMC) , , 138 (. 3). , NPC, SUMO Ulp1 (Ref. 88), sumoylation , Ku protein of 80 kDa (yku80) 93. Ulp1 , SUMO, . NPC SUMO- 139, Nups, synthetic lethal of unknown function protein 5 (Slx5)-Slx8 SUMO- ubiquitin ligase 140. NPC DSBs140. , DSBs NPC-, SUMO- 'last resort' . (eroded) , NPC . , (uncapped) , checkpoint , radiation sensitive mutant 52 (Rad52), , , DSB. , NPC, .
, NPC ( BOX 2), , , . Nucleotide-excision repair (NER) , , , 143. NER , 144. , , SWI-SNF helicases 145. , RNA polymerase II 146. .., NPC, -, , (.., ; BOX 2).

Box 2 | NPC-associated microenvironments promote chromatin stability

Recent work links telomeres and unrepaired or slowly repaired double"'stranded DNA breaks to the SUN domain inner"'nuclear envelope integral membrane protein, monopolar spindle protein 3 (Mps3)141,159,160, which is required for spindle pole body (SPB) duplication, sister chromatid cohesion and meiotic bouquet formation161. This suggests that there is a specific perinuclear mechanism for handling unprotected DNA ends, in which Mps3"'dependent recruitment of wayward, broken chromosomal ends to the nuclear periphery might have an important regulatory role "" determining whether such ends are either recognized as telomeres to be capped by the telomerase machinery and stably anchored at inter"'nuclear pore complex (NPC) zones of the nuclear periphery162, or identified as damaged and shunted towards the basket to be repaired163. Interestingly, human SUN1 was found to have a role in NPC distribution in the plane of the nuclear envelope164, thus reinforcing the idea of a close inter"'talk between the NPC and other nuclear envelope components. The notion that this inter"'talk might contribute to the formation of a nuclear envelope"' and NPC"'associated functional microenvironment that promotes chromatin stability was recently reinforced by observations involving ribosomal DNA and nucleolar structure165, indicating that anchoring of the rDNA silencing machinery to the nuclear envelope by interactions with the spliced mRNA and cell cycle regulated protein 1 (Src1) LEM domain protein166 is required for peripheral localization and stabilization of highly repetitive yeast rDNA sequences. Interestingly, human SUN1 was found to have a role in NPC distribution in the plane of the nuclear envelope164, and Src1 was also found to participate in both the repression of sub"'telomeric gene expression and the close coordination between transcriptional regulation and messenger ribonucleoprotein export167, thus underscoring the existence of a functional interface between DNA repair, chromatin organization and the NPC. Further evidence of this connection comes from studies of the THO, TREX and TREX2 complexes. Lack of THO leads to a strong transcription"'associated hyper"'recombination phenotype and defects in nucleotide"'excision repair168,169, and several lines of evidence implicate the TREX and TREX2 complexes together with mRNA export factors and the NPC in preserving the integrity of actively transcribed DNA regions146,170,171.


Coordination of cell cycle progression. NPCs , ( , ) , (reviewed in Ref. 147). , 148. , S. cerevisiae , . S. cerevisiae, Mlps (spindle pole body (sPB)) 90. NPC spindle assembly checkpoint (sAC) mitotic arrest-deficient protein 1 (Mad1) Mad2 (Refs 149,150) (FIG. 3). Mad1 NPC Nup60 Mlps151, 152. , , D. melanogaster Aspergillus nidulans95-97,153,154 . TPR, , MAD1 MAD2 (Ref. 95), siRNA TPR MAD1 MAD2 NPC . D. melanogaster, Megator MAD1, MAD2 MPS1, SAC, 97. MAD1 MAD2 , Megator NPC. SAC , , TPR dynein154 . , TPR SAC, MAD1 MAD2 dynein, . TPR A. nidulans96, opisthokonts (.., ). NPC , , SACs 155.

Conclusions


Although it was initially seen as little more than a con- tainer for the genome, our view has evolved to recognize the nuclear envelope and its associated structures as key players in nuclear organization and gene regulation. Recent findings suggest that there is an extensive network of interactions, stretching out from the basket and interlinking neighbouring NPCs to establish a far-reaching molecular platform that ties together gene expression, nuclear division and genome stability (FIG. 3). At the same time, the NPC also coordinates the inter action of nuclear contents with the surrounding cytoskeleton by way of its cytoplasmic filaments. Why might the NPC be involved in such disparate nuclear functions? It is possible that active chromatin loops are recruited to the NPCs so that their transcripts can be efficiently exported by their physical proximity to the NPC transport channel. This seems less likely, however, as many active genes function efficiently away from the NPC and the rate of intra-nuclear transcript diffusion does not seem to be a rate-limiting factor in gene expression. However, given that the nucleus is so devoid of physical signposts that are not directly connected to chromatin, it could be that the baskets of NPCs are convenient markers where increased local concentrations of specific factors can induce the formation of highly dynamic microenvironments. Chromatin might converge onto such microenvironments by loop formation for efficient transcriptional regulation, post-transcriptional processing and the stabilization and repair of damage arising during transcription or replication. Indeed, the NPC, together with the nuclear envelope and the nuclear periphery, can be viewed as just one essential component of a large cellular machine that regulates the passage of information from DNA out of the nucleus to control and maintain the rest of the cell.
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