Structure and Assembly of the Nuclear Pore Complex

2019 ◽  
Vol 48 (1) ◽  
pp. 515-536 ◽  
Author(s):  
Bernhard Hampoelz ◽  
Amparo Andres-Pons ◽  
Panagiotis Kastritis ◽  
Martin Beck
Keyword(s):  
Posttranslational Modifications ◽  
Current Knowledge ◽  
Protein Complexes ◽  
Hierarchical Organization ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Multiple Copies ◽  
Architectural Principles ◽  
Protein Components ◽  
Pore Complexes

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange. They are exceptionally large protein complexes that fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. About 30 different protein components, termed nucleoporins, assemble in multiple copies into an intricate cylindrical architecture. Here, we review our current knowledge of the structure of nucleoporins and how those come together in situ. We delineate architectural principles on several hierarchical organization levels, including isoforms, posttranslational modifications, nucleoporins, and higher-order oligomerization of nucleoporin subcomplexes. We discuss how cells exploit this modularity to faithfully assemble NPCs.

scholarly journals MINFLUX nanoscopy delivers multicolor nanometer 3D-resolution in (living) cells

2019 ◽  
Author(s):  
Klaus C. Gwosch ◽  
Jasmin K. Pape ◽  
Francisco Balzarotti ◽  
Philipp Hoess ◽  
Jan Ellenberg ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Three Dimensional ◽  
Living Cells ◽  
Three Dimensions ◽  
Nanometer Scale ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Fluorescent Marker ◽  
Excitation Beam ◽  
Pore Complexes

The ultimate goal of biological superresolution fluorescence microscopy is to provide three-dimensional resolution at the size scale of a fluorescent marker. Here, we show that, by localizing individual switchable fluorophores with a probing doughnut-shaped excitation beam, MINFLUX nanoscopy provides 1–3 nanometer resolution in fixed and living cells. This progress has been facilitated by approaching each fluorophore iteratively with the probing doughnut minimum, making the resolution essentially uniform and isotropic over scalable fields of view. MINFLUX imaging of nuclear pore complexes of a mammalian cell shows that this true nanometer scale resolution is obtained in three dimensions and in two color channels. Relying on fewer detected photons than popular camera-based localization, MINFLUX nanoscopy is poised to open a new chapter in the imaging of protein complexes and distributions in fixed and living cells.

scholarly journals Dunking into the Lipid Bilayer: How Direct Membrane Binding of Nucleoporins Can Contribute to Nuclear Pore Complex Structure and Assembly

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3601
Author(s):  
Mohamed Hamed ◽  
Wolfram Antonin
Keyword(s):  
Nuclear Envelope ◽  
Current Knowledge ◽  
Complex Structure ◽  
Transmembrane Proteins ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Membrane Spanning ◽  
Pore Complexes ◽  
And Function ◽  
Membrane Spanning Domains

Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins are an integral part of NPCs and thought to anchor these complexes in the nuclear envelope. In addition, a number of nucleoporins without membrane spanning domains interact with the pore membrane. Here we review our current knowledge of how these proteins interact with the membrane and how this interaction can contribute to NPC assembly, stability and function as well as shaping of the pore membrane.

scholarly journals A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009889
Author(s):  
Amandine Bonnet ◽  
Carole Chaput ◽  
Noé Palmic ◽  
Benoit Palancade ◽  
Pascale Lesage
Keyword(s):  
Transcriptional Control ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Ltr Retrotransposons ◽  
Loss Of Function ◽  
Protein Coding ◽  
Multiple Copies ◽  
Ty1 Retrotransposition ◽  
Pore Complexes ◽  
The Impact

Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposon under tight transcriptional control.

scholarly journals The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study

2019 ◽  
Vol 20 (3) ◽  
pp. 596 ◽  
Author(s):  
Ankur Mishra ◽  
Wouter Sipma ◽  
Liesbeth Veenhoff ◽  
Erik Van der Giessen ◽  
Patrick Onck
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Intrinsically Disordered Proteins ◽  
Protein Complexes ◽  
Disordered Proteins ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Pore Complexes

Nuclear pore complexes (NPCs) are large protein complexes embedded in the nuclear envelope separating the cytoplasm from the nucleoplasm in eukaryotic cells. They function as selective gates for the transport of molecules in and out of the nucleus. The inner wall of the NPC is coated with intrinsically disordered proteins rich in phenylalanine-glycine repeats (FG-repeats), which are responsible for the intriguing selectivity of NPCs. The phosphorylation state of the FG-Nups is controlled by kinases and phosphatases. In the current study, we extended our one-bead-per-amino-acid (1BPA) model for intrinsically disordered proteins to account for phosphorylation. With this, we performed molecular dynamics simulations to probe the effect of phosphorylation on the Stokes radius of isolated FG-Nups, and on the structure and transport properties of the NPC. Our results indicate that phosphorylation causes a reduced attraction between the residues, leading to an extension of the FG-Nups and the formation of a significantly less dense FG-network inside the NPC. Furthermore, our simulations show that upon phosphorylation, the transport rate of inert molecules increases, while that of nuclear transport receptors decreases, which can be rationalized in terms of modified hydrophobic, electrostatic, and steric interactions. Altogether, our models provide a molecular framework to explain how extensive phosphorylation of FG-Nups decreases the selectivity of the NPC.

scholarly journals Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex

2012 ◽  
Vol 109 (38) ◽  
pp. 15241-15246 ◽  
Author(s):  
Silvija Bilokapic ◽  
Thomas U. Schwartz
Keyword(s):  
Nucleocytoplasmic Transport ◽  
Biological Data ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Multiple Copies ◽  
Critical Unit ◽  
Species Specific ◽  
Pore Complexes

Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs), enormous assemblies composed of multiple copies of ∼30 different proteins called nucleoporins. To unravel the basic scaffold underlying the NPC, we have characterized the species-specific scaffold nucleoporin Nup37 and ELY5/ELYS. Both proteins integrate directly via Nup120/160 into the universally conserved heptameric Y-complex, the critical unit for the assembly and functionality of the NPC. We present the crystal structure of Schizosaccharomyces pombe Nup37 in complex with Nup120, a 174-kDa subassembly that forms one of the two short arms of the Y-complex. Nup37 binds near the bend of the L-shaped Nup120 protein, potentially stabilizing the relative orientation of its two domains. By means of reconstitution assays, we pinpoint residues crucial for this interaction. In vivo and in vitro results show that ELY5 binds near an interface of the Nup120–Nup37 complex. Complementary biochemical and cell biological data refine and consolidate the interactions of Nup120 within the current Y-model. Finally, we propose an orientation of the Y-complex relative to the pore membrane, consistent with the lattice model.

High resolution analysis of mammalian nuclear structure throughout the cell cycle: implications for nuclear pore complex assembly during interphase and mitosisThis paper is one of a selection of papers published in this Special Issue, entitled The Nucleus: A Cell Within A Cell.

2006 ◽  
Vol 84 (3-4) ◽  
pp. 423-430 ◽  
Author(s):  
Sheona P. Drummond ◽  
Sandra A. Rutherford ◽  
Helen S. Sanderson ◽  
Terry D. Allen
Keyword(s):  
Cell Cycle ◽  
Mammalian Cells ◽  
Molecular Transport ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
High Resolution Analysis ◽  
Multiple Copies ◽  
A Cell ◽  
Specific Proteins ◽  
Pore Complexes

Nuclear pore complexes (NPCs) are the gateways for both active and passive bidirectional molecular transport between the nucleoplasm and cytoplasm. These mega-dalton assemblies are composed of multiple copies of approximately 30 distinct proteins termed nucleoporins. Higher eukaryotes display an “open” mitosis in which the NPCs, nuclear envelope, and lamina disassemble. During mitosis several nucleoporins are redistributed to kinetochores until they are recruited back to the periphery of chromatin as the NPCs are reassembled. Within this study we have developed and optimized the visualization of mammalian cells and their chromosome profiles throughout the cell-cycle. Close attention has been paid to the preservation of chromatin, membranes, and NPC structure to investigate the ultrastructural locations of specific proteins in both interphase and mitosis.

scholarly journals The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control

2005 ◽  
Vol 171 (6) ◽  
pp. 955-965 ◽  
Author(s):  
David J. Dilworth ◽  
Alan J. Tackett ◽  
Richard S. Rogers ◽  
Eugene C. Yi ◽  
Rowan H. Christmas ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Transcriptional Control ◽  
Active Role ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Nucleotide Exchange ◽  
Control Of Gene Expression ◽  
Macromolecular Transport ◽  
Protein Components ◽  
Pore Complexes

Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus. Several protein components of yeast NPCs have been implicated in the epigenetic control of gene expression. Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity. To understand this function of Nup2p, we investigated the interactions of Nup2p with other proteins and with DNA using immunopurifications coupled with mass spectrometry and microarray analyses. These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

scholarly journals Ubiquitylation of the nuclear pore complex controls nuclear migration during mitosis in S. cerevisiae

2012 ◽  
Vol 196 (1) ◽  
pp. 19-27 ◽  
Author(s):  
Akira Hayakawa ◽  
Anna Babour ◽  
Lucie Sengmanivong ◽  
Catherine Dargemont
Keyword(s):  
Posttranslational Modifications ◽  
Systematic Approach ◽  
Protein Transport ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Molecular Architecture ◽  
Dynein Light Chain ◽  
Large Protein ◽  
Pore Complexes ◽  
Cytoplasmic Side

Nuclear pore complexes (NPCs) correspond to large protein transport complexes responsible for selective nucleocytoplasmic exchange. Although research has revealed much about the molecular architecture and roles of the NPC subcomplexes, little is known about the regulation of NPC functions by posttranslational modifications. We used a systematic approach to show that more than half of NPC proteins were conjugated to ubiquitin. In particular, Nup159, a nucleoporin exclusively located on the cytoplasmic side of the NPC, was monoubiquitylated by the Cdc34/SCF (Skp1–Cdc53–F-box E3 ligase) enzymes. Preventing this modification had no consequences on nuclear transport or NPC organization but strongly affected the ability of Nup159 to target the dynein light chain to the NPC. This led to defects in nuclear segregation at the onset of mitosis. Thus, defining ubiquitylation of the yeast NPC highlights yet-unexplored functions of this essential organelle in cell division.

scholarly journals Nup53 Is Required for Nuclear Envelope and Nuclear Pore Complex Assembly

2008 ◽  
Vol 19 (4) ◽  
pp. 1753-1762 ◽  
Author(s):  
Lisa A. Hawryluk-Gara ◽  
Melpomeni Platani ◽  
Rachel Santarella ◽  
Richard W. Wozniak ◽  
Iain W. Mattaj
Keyword(s):  
Nuclear Envelope ◽  
Critical Role ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Egg Extracts ◽  
Multiple Copies ◽  
Xenopus Egg ◽  
Pore Complexes ◽  
Xenopus Egg Extracts

Transport across the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs). These structures are composed of various subcomplexes of proteins that are each present in multiple copies and together establish the eightfold symmetry of the NPC. One evolutionarily conserved subcomplex of the NPC contains the nucleoporins Nup53 and Nup155. Using truncation analysis, we have defined regions of Nup53 that bind to neighboring nucleoporins as well as those domains that target Nup53 to the NPC in vivo. Using this information, we investigated the role of Nup53 in NE and NPC assembly using Xenopus egg extracts. We show that both events require Nup53. Importantly, the analysis of Nup53 fragments revealed that the assembly activity of Nup53 depleted extracts could be reconstituted using a region of Nup53 that binds specifically to its interacting partner Nup155. On the basis of these results, we propose that the formation of a Nup53–Nup155 complex plays a critical role in the processes of NPC and NE assembly.

scholarly journals The SUMO proteases SENP1 and SENP2 play a critical role in nucleoporin homeostasis and nuclear pore complex function

2014 ◽  
Vol 25 (1) ◽  
pp. 160-168 ◽  
Author(s):  
Kin-Hoe Chow ◽  
Suzanne Elgort ◽  
Mary Dasso ◽  
Maureen A. Powers ◽  
Katharine S. Ullman
Keyword(s):  
Nuclear Pore Complex ◽  
Posttranslational Modifications ◽  
Critical Role ◽  
Complex Function ◽  
Building Blocks ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Sumo Proteases ◽  
Specific Protease ◽  
Pore Complexes

Nuclear pore complexes are composed of ∼30 different proteins, each present at the pore in multiple copies. Together these proteins create specialized channels that convey cargo between the cytoplasm and the nuclear interior. With the building blocks of nuclear pores identified, one challenge is to decipher how these proteins are coordinately produced and assembled into macromolecular pore structures with each cell division. Specific individual pore proteins and protein cofactors have been probed for their role in the assembly process, as well as certain kinases that add a layer of regulation via the phosphorylation status of nucleoporins. Other posttranslational modifications are candidates for coordinating events of pore assembly as well. In this study of two pore-associated small ubiquitin-like modifier (SUMO) proteases, sentrin/SUMO-specific protease 1 (SENP1) and SENP2, we observe that many nucleoporins are mislocalized and, in some cases, reduced in level when SENP1 and SENP2 are codepleted. The pore complexes present under these conditions are still capable of transport, although the kinetics of specific cargo is altered. These results reveal a new role for the pore-associated SENPs in nucleoporin homeostasis and in achieving proper configuration of the nuclear pore complex.

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