101
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Blasius TL, Takao D, Verhey KJ. NPHP proteins are binding partners of nucleoporins at the base of the primary cilium. PLoS One 2019; 14:e0222924. [PMID: 31553752 PMCID: PMC6760808 DOI: 10.1371/journal.pone.0222924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Cilia are microtubule-based organelles that protrude from the surface of eukaryotic cells to generate motility and to sense and respond to environmental cues. In order to carry out these functions, the complement of proteins in the cilium must be specific for the organelle. Regulation of protein entry into primary cilia has been shown to utilize mechanisms and components of nuclear gating, including nucleoporins of the nuclear pore complex (NPC). We show that nucleoporins also localize to the base of motile cilia on the surface of trachea epithelial cells. How nucleoporins are anchored at the cilium base has been unclear as transmembrane nucleoporins, which anchor nucleoporins at the nuclear envelope, have not been found to localize at the cilium. Here we use the directed yeast two-hybrid assay to identify direct interactions between nucleoporins and nephronophthisis proteins (NPHPs) which localize to the cilium base and contribute to cilium assembly and identity. We validate NPHP-nucleoporin interactions in mammalian cells using the knocksideways assay and demonstrate that the interactions occur at the base of the primary cilium using bimolecular fluorescence complementation. We propose that NPHP proteins anchor nucleoporins at the base of primary cilia to regulate protein entry into the organelle.
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Affiliation(s)
- T. Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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102
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Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R. Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT. Angew Chem Int Ed Engl 2019; 58:13004-13008. [PMID: 31314157 PMCID: PMC6771475 DOI: 10.1002/anie.201905685] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/26/2019] [Indexed: 11/07/2022]
Abstract
The nuclear pore complex (NPC) is one of the largest and most complex protein assemblies in the cell and, among other functions, serves as the gatekeeper of nucleocytoplasmic transport. Unraveling its molecular architecture and functioning has been an active research topic for decades with recent cryogenic electron microscopy and super-resolution studies advancing our understanding of the architecture of the NPC complex. However, the specific and direct visualization of single copies of NPC proteins is thus far elusive. Herein, we combine genetically-encoded self-labeling enzymes such as SNAP-tag and HaloTag with DNA-PAINT microscopy. We resolve single copies of nucleoporins in the human Y-complex in three dimensions with a precision of circa 3 nm, enabling studies of multicomponent complexes on the level of single proteins in cells using optical fluorescence microscopy.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for NanoscienceLMU MunichGeschwister-Scholl-Platz 180539MunichGermany
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Maximilian T. Strauss
- Faculty of Physics and Center for NanoscienceLMU MunichGeschwister-Scholl-Platz 180539MunichGermany
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Florian Schueder
- Faculty of Physics and Center for NanoscienceLMU MunichGeschwister-Scholl-Platz 180539MunichGermany
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Alexander Auer
- Faculty of Physics and Center for NanoscienceLMU MunichGeschwister-Scholl-Platz 180539MunichGermany
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)Meyerhofstraße 169117HeidelbergGermany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)Meyerhofstraße 169117HeidelbergGermany
| | - Vilma Jimenez Sabinina
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)Meyerhofstraße 169117HeidelbergGermany
| | - Jervis V. Thevathasan
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)Meyerhofstraße 169117HeidelbergGermany
| | - Jonas Ries
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)Meyerhofstraße 169117HeidelbergGermany
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology Laboratory (EMBL)Meyerhofstraße 169117HeidelbergGermany
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoscienceLMU MunichGeschwister-Scholl-Platz 180539MunichGermany
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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103
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Infante E, Stannard A, Board SJ, Rico-Lastres P, Panagaki F, Beedle AE, Rajan VS, Rostkova E, Lezamiz A, Wang YJ, Breen SG, Shanahan C, Roca-Cusachs P, Garcia-Manyes S. The mechanical stability of proteins regulates their translocation rate into the cell nucleus. NATURE PHYSICS 2019; 15:973-981. [PMID: 37484710 PMCID: PMC7614795 DOI: 10.1038/s41567-019-0551-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/10/2019] [Indexed: 07/25/2023]
Abstract
The translocation of mechanosensitive transcription factors (TFs) across the nuclear envelope is a crucial step in cellular mechanotransduction. Yet the molecular mechanisms by which external mechanical cues control the nuclear shuttling dynamics of TFs through the nuclear pore complex (NPC) to activate gene expression are poorly understood. Here, we show that the nuclear import rate of myocardin-related transcription factor A (MRTFA) - a protein that regulates cytoskeletal dynamics via the activation of the TF serum response factor (SRF) - inversely correlates with the protein's nanomechanical stability and does not relate to its thermodynamic stability. Tagging MRTFA with mechanically resistant proteins results in the downregulation of SRF-mediated myosin light-chain 9 (MYL9) gene expression and subsequent slowing down of cell migration. We conclude that the mechanical unfolding of proteins regulates their nuclear translocation rate through the NPC, and highlight the role of the NPC as a selective mechanosensor able to discriminate forces as low as ~10 pN. The modulation of the mechanical stability of TFs may represent a new strategy for the control of gene expression.
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Affiliation(s)
- Elvira Infante
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Stephanie J. Board
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Palma Rico-Lastres
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Fani Panagaki
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Amy E.M. Beedle
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Vinoth Sundar Rajan
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Elena Rostkova
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Ainhoa Lezamiz
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Yong Jian Wang
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Samuel Gulaidi Breen
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
| | - Catherine Shanahan
- Cardiovascular Division, James Black Centre, King’s College London, London SE5 9NU, UK Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and
| | - Pere Roca-Cusachs
- Technology (BIST) and University of Barcelona, 08028 Barcelona, Spain
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King’s College London, WC2R 2LS, London, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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104
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Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R. Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically‐Encoded Probes for DNA‐PAINT. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Maximilian T. Strauss
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Alexander Auer
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Vilma Jimenez Sabinina
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Jervis V. Thevathasan
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience LMU Munich Geschwister-Scholl-Platz 1 80539 Munich Germany
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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105
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Abstract
During my postdoc interview in June of 1998, I asked Günter why he was moving more towards the nucleus in his latest studies. He said, "Well Joe, that's where everything starts." By the end of the interview, I accepted the postdoc. He had a way of making everything sound so cool. Günter's progression was natural, since the endoplasmic reticulum and the nucleus are the only organelles that share the same membrane. The nuclear envelope extends into a double membrane system with nuclear pore complexes embedded in the pore membrane openings. Even while writing this review, I remember Günter stressing; it is the nuclear pore complex. Just saying nuclear pore doesn't encompass the full magnitude of its significance. The nuclear pore complex is one of the largest collection of proteins that fit together for an overall function: transport. This review will cover the Blobel lab contributions in the quest for the blueprint of the nuclear pore complex from isolation of the nuclear envelope and nuclear lamin to the ring structures.
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106
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Sun J, Shi Y, Yildirim E. The Nuclear Pore Complex in Cell Type-Specific Chromatin Structure and Gene Regulation. Trends Genet 2019; 35:579-588. [PMID: 31213386 DOI: 10.1016/j.tig.2019.05.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022]
Abstract
Nuclear pore complex (NPC)-mediated nucleocytoplasmic trafficking is essential for key cellular processes, such as cell growth, cell differentiation, and gene regulation. The NPC has also been viewed as a nuclear architectural platform that impacts genome function and gene expression by mediating spatial and temporal coordination between transcription factors, chromatin regulatory proteins, and transcription machinery. Recent findings have uncovered differential and cell type-specific expression and distinct chromatin-binding patterns of individual NPC components known as nucleoporins (Nups). Here, we examine recent studies that investigate the functional roles of NPCs and Nups in transcription, chromatin organization, and epigenetic gene regulation in the context of development and disease.
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Affiliation(s)
- Jiayu Sun
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Durham, NC 27710, USA
| | - Yuming Shi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Durham, NC 27710, USA
| | - Eda Yildirim
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Cancer Institute, Durham, NC 27710, USA.
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107
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Vallotton P, Rajoo S, Wojtynek M, Onischenko E, Kralt A, Derrer CP, Weis K. Mapping the native organization of the yeast nuclear pore complex using nuclear radial intensity measurements. Proc Natl Acad Sci U S A 2019; 116:14606-14613. [PMID: 31262825 PMCID: PMC6642398 DOI: 10.1073/pnas.1903764116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective transport across the nuclear envelope (NE) is mediated by the nuclear pore complex (NPC), a massive ∼100-MDa assembly composed of multiple copies of ∼30 nuclear pore proteins (Nups). Recent advances have shed light on the composition and structure of NPCs, but approaches that could map their organization in live cells are still lacking. Here, we introduce an in vivo method to perform nuclear radial intensity measurements (NuRIM) using fluorescence microscopy to determine the average position of NE-localized proteins along the nucleocytoplasmic transport axis. We apply NuRIM to study the organization of the NPC and the mobile transport machinery in budding yeast. This reveals a unique snapshot of the intact yeast NPC and identifies distinct steady-state localizations for various NE-associated proteins and nuclear transport factors. We find that the NPC architecture is robust against compositional changes and could also confirm that in contrast to Chlamydomonas reinhardtii, the scaffold Y complex is arranged symmetrically in the yeast NPC. Furthermore, NuRIM was applied to probe the orientation of intrinsically disordered FG-repeat segments, providing insight into their roles in selective NPC permeability and structure.
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Affiliation(s)
- Pascal Vallotton
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland;
| | - Sasikumar Rajoo
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Evgeny Onischenko
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Annemarie Kralt
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Carina Patrizia Derrer
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, Swiss Federal Institute of Technology Zürich (ETH Zürich), 8093 Zürich, Switzerland;
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108
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Asymmetrical localization of Nup107-160 subcomplex components within the nuclear pore complex in fission yeast. PLoS Genet 2019; 15:e1008061. [PMID: 31170156 PMCID: PMC6553703 DOI: 10.1371/journal.pgen.1008061] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/01/2019] [Indexed: 01/05/2023] Open
Abstract
The nuclear pore complex (NPC) forms a gateway for nucleocytoplasmic transport. The outer ring protein complex of the NPC (the Nup107-160 subcomplex in humans) is a key component for building the NPC. Nup107-160 subcomplexes are believed to be symmetrically localized on the nuclear and cytoplasmic sides of the NPC. However, in S. pombe immunoelectron and fluorescence microscopic analyses revealed that the homologous components of the human Nup107-160 subcomplex had an asymmetrical localization: constituent proteins spNup132 and spNup107 were present only on the nuclear side (designated the spNup132 subcomplex), while spNup131, spNup120, spNup85, spNup96, spNup37, spEly5 and spSeh1 were localized only on the cytoplasmic side (designated the spNup120 subcomplex), suggesting the complex was split into two pieces at the interface between spNup96 and spNup107. This contrasts with the symmetrical localization reported in other organisms. Fusion of spNup96 (cytoplasmic localization) with spNup107 (nuclear localization) caused cytoplasmic relocalization of spNup107. In this strain, half of the spNup132 proteins, which interact with spNup107, changed their localization to the cytoplasmic side of the NPC, leading to defects in mitotic and meiotic progression similar to an spNup132 deletion strain. These observations suggest the asymmetrical localization of the outer ring spNup132 and spNup120 subcomplexes of the NPC is necessary for normal cell cycle progression in fission yeast. The nuclear pore complexes (NPCs) form gateways to transport intracellular molecules between the nucleus and the cytoplasm across the nuclear envelope. The Nup107-160 subcomplex, that forms nuclear and cytoplasmic outer rings, is a key complex responsible for building the NPC by symmetrical localization on the nuclear and cytoplasmic sides of the nuclear pore. This structural characteristic was found in various organisms including humans and budding yeasts, and therefore believed to be common among “all” eukaryotes. However, in this paper, we revealed an asymmetrical localization of the homologous components of the human Nup107-160 subcomplex in fission yeast by immunoelectron and fluorescence microscopic analyses: in this organism, the Nup107-160 subcomplex is split into two pieces, and each of the split pieces is differentially distributed to the nuclear and cytoplasmic side of the NPC: one piece is only in the nuclear side while the other piece is only in the cytoplasmic side. This contrasts with the symmetrical localization reported in other organisms. In addition, we confirmed that the asymmetrical configuration of the outer ring structure is necessary for cell cycle progression in fission yeast. This study provides notions of diverse structures and functions of NPCs evolved in eukaryotes.
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109
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Molecular assay for an intronic variant in NUP93 that causes steroid resistant nephrotic syndrome. J Hum Genet 2019; 64:673-679. [PMID: 31015583 DOI: 10.1038/s10038-019-0606-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 01/09/2023]
Abstract
Advances in molecular genetics have revealed that approximately 30% of cases with steroid-resistant nephrotic syndrome (SRNS) are caused by single-gene mutations. More than 50 genes are responsible for SRNS. One such gene is the nucleoporin, 93-KD (NUP93). Thus far, few studies have reported mutations of NUP93 in SRNS. Here, we describe an NUP93 biallelic mutation in a 9-year-old boy with focal segmental glomerular sclerosis (FSGS). Notably, one mutation comprised an intronic variant; we conducted in vivo and in vitro analysis to characterize this variant. We found two heterozygous mutations in NUP93: c.2137-18G>A in intron 19 and a novel nonsense mutation c.727A>T (p.Lys243*) in exon 8. We conducted RNA sequencing and in vitro splicing assays by using minigene construction, combined with protein expression analysis to determine the pathogenicity of the intronic variant. Both RNA sequencing and in vitro splicing assay showed exon 20-skipping by the intronic variant. In protein expression analysis, aberrant subcellular localization with small punctate vesicles in the cytoplasm was observed for the intronic variant. Taken together, we concluded that c.2137-18G>A was linked to pathogenicity due to aberrant splicing. NUP93 variants are quite rare; however, we have shown that even intronic variants in NUP93 can cause SRNS. This study provides a fundamental approach to validate the intronic variant, as well as new insights regarding the clinical spectrum of SRNS caused by rare gene variants.
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110
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Abstract
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.
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Affiliation(s)
- Bernhard Hampoelz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , ,
| | - Amparo Andres-Pons
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Current affiliation: Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
| | - Panagiotis Kastritis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Current affiliation: ZIK HALOmem, Martin Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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111
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Abstract
The name “eukaryote” is derived from Greek, meaning “true kernel”, and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all—at least not in a form we would recognize today—and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor.
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Affiliation(s)
- Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK.,Biology Centre, Institute of Parasitology, Faculty of Sciences, University of South Bohemia, Ceske Budejovice, Czech Republic
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112
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Bilir Ş, Kojidani T, Mori C, Osakada H, Kobayashi S, Koujin T, Hiraoka Y, Haraguchi T. Roles of Nup133, Nup153 and membrane fenestrations in assembly of the nuclear pore complex at the end of mitosis. Genes Cells 2019; 24:338-353. [PMID: 30821042 DOI: 10.1111/gtc.12677] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/15/2019] [Accepted: 02/24/2019] [Indexed: 12/25/2022]
Abstract
Reassembly of the nuclear pore complex (NPC) at the end of mitosis is an important event for eukaryotic nuclear function. In this study, we examined the dynamic behaviors of the endoplasmic reticulum (ER) by "Live CLEM" imaging. In metaphase, numerous fenestrations on the ER membrane were observed around chromosomes. In telophase, these fenestrations became filled at the region attached to chromosomes, whereas they remained open at the region unattached to chromosomes, suggesting that NPC assembly takes place at fenestrations on the membrane. To determine the roles of nucleoporins in postmitotic NPC formation, we used artificial beads conjugated with anti-GFP antibody, which captures GFP-fused proteins on the beads when incorporated into cells. Live CLEM imaging of telophase cells containing Nup133-coated beads or Nup153-coated beads showed that Nup133 and Nup153, as the sole effector molecules, assembled the NPC-like structure on the membrane fenestrations. Indirect immunofluorescence staining of the Nup133-coated beads showed that Nup133 effectively assembled Nup107 and ELYS, whereas minimal assembly of Nup98 and Nup62 was observed; the Nup153-coated bead effectively assembled Nup98, Nup62 and Pom121, but assembled neither Nup107 nor ELYS. Our results suggest that Nup133 and Nup153 play different roles in assembling the NPC on membrane fenestrations.
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Affiliation(s)
- Şükriye Bilir
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Tomoko Kojidani
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan.,Japan Women's University, Tokyo, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Shouhei Kobayashi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
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113
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Frey S, Rees R, Schünemann J, Ng SC, Fünfgeld K, Huyton T, Görlich D. Surface Properties Determining Passage Rates of Proteins through Nuclear Pores. Cell 2019; 174:202-217.e9. [PMID: 29958108 DOI: 10.1016/j.cell.2018.05.045] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 02/18/2018] [Accepted: 05/21/2018] [Indexed: 10/28/2022]
Abstract
Nuclear pore complexes (NPCs) conduct nucleocytoplasmic transport through an FG domain-controlled barrier. We now explore how surface-features of a mobile species determine its NPC passage rate. Negative charges and lysines impede passage. Hydrophobic residues, certain polar residues (Cys, His), and, surprisingly, charged arginines have striking translocation-promoting effects. Favorable cation-π interactions between arginines and FG-phenylalanines may explain this apparent paradox. Application of these principles to redesign the surface of GFP resulted in variants that show a wide span of transit rates, ranging from 35-fold slower than wild-type to ∼500 times faster, with the latter outpacing even naturally occurring nuclear transport receptors (NTRs). The structure of a fast and particularly FG-specific GFPNTR variant illustrates how NTRs can expose multiple regions for binding hydrophobic FG motifs while evading non-specific aggregation. Finally, we document that even for NTR-mediated transport, the surface-properties of the "passively carried" cargo can strikingly affect the translocation rate.
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Affiliation(s)
- Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Renate Rees
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kevser Fünfgeld
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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114
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Abstract
The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo-electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
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Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
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115
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Padavannil A, Sarkar P, Kim SJ, Cagatay T, Jiou J, Brautigam CA, Tomchick DR, Sali A, D'Arcy S, Chook YM. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 2019; 8:e43630. [PMID: 30855230 PMCID: PMC6453568 DOI: 10.7554/elife.43630] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/09/2019] [Indexed: 01/29/2023] Open
Abstract
We report the crystal structure of nuclear import receptor Importin-9 bound to its cargo, the histones H2A-H2B. Importin-9 wraps around the core, globular region of H2A-H2B to form an extensive interface. The nature of this interface coupled with quantitative analysis of deletion mutants of H2A-H2B suggests that the NLS-like sequences in the H2A-H2B tails play a minor role in import. Importin-9•H2A-H2B is reminiscent of interactions between histones and histone chaperones in that it precludes H2A-H2B interactions with DNA and H3-H4 as seen in the nucleosome. Like many histone chaperones, which prevent inappropriate non-nucleosomal interactions, Importin-9 also sequesters H2A-H2B from DNA. Importin-9 appears to act as a storage chaperone for H2A-H2B while escorting it to the nucleus. Surprisingly, RanGTP does not dissociate Importin-9•H2A-H2B but assembles into a RanGTP•Importin-9•H2A-H2B complex. The presence of Ran in the complex, however, modulates Imp9-H2A-H2B interactions to facilitate its dissociation by DNA and assembly into a nucleosome.
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Affiliation(s)
- Abhilash Padavannil
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Prithwijit Sarkar
- Department of Biological SciencesUniversity of Texas at DallasRichardsonUnited States
| | - Seung Joong Kim
- Department of PhysicsKorea Advanced Institute of Science and Technology (KAIST)DaejeonKorea
| | - Tolga Cagatay
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Jenny Jiou
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Chad A Brautigam
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Diana R Tomchick
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, California Institute for Quantitative BiosciencesUniversity of California, San FranciscoSan FranciscoUnited states
| | - Sheena D'Arcy
- Department of Chemistry and BiochemistryUniversity of Texas at DallasRichardsonUnited States
| | - Yuh Min Chook
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasUnited States
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116
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Gu C, Vovk A, Zheng T, Coalson RD, Zilman A. The Role of Cohesiveness in the Permeability of the Spatial Assemblies of FG Nucleoporins. Biophys J 2019; 116:1204-1215. [PMID: 30902367 DOI: 10.1016/j.bpj.2019.02.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/02/2018] [Accepted: 02/26/2019] [Indexed: 12/31/2022] Open
Abstract
Nuclear pore complexes (NPCs) conduct selective, bidirectional transport across the nuclear envelope. The NPC passageway is lined by intrinsically disordered proteins that contain hydrophobic phenylalanine-glycine (FG) motifs, known as FG nucleoporins (FG nups), that play the key role in the NPC transport mechanism. Cohesive interactions among the FG nups, which arise from the combination of hydrophobic, electrostatic, and other forces, have been hypothesized to control the morphology of the assemblies of FG nups in the NPC, as well as their permeability with respect to the transport proteins. However, the role of FG nup cohesiveness is still vigorously debated. Using coarse-grained polymer theory and numerical simulations, we study the effects of cohesiveness on the selective permeability of in vitro FG nup assemblies in different geometries that have served as proxies for the morphological and transport properties of the NPC. We show that in high-density FG nup assemblies, increase in cohesiveness leads to the decrease in their permeability, in accordance with the accepted view. On the other hand, the permeability of low-density assemblies is a nonmonotonic function of the cohesiveness, and a moderate increase in cohesiveness can enhance permeability. The density- and cohesiveness-dependent effects on permeability are explained by considering the free-energy cost associated with penetrating the FG nup assemblies. We discuss the implications of these findings for the organization and function of the NPC.
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Affiliation(s)
- Chad Gu
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Andrei Vovk
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Rob D Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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117
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Chopra K, Bawaria S, Chauhan R. Evolutionary divergence of the nuclear pore complex from fungi to metazoans. Protein Sci 2018; 28:571-586. [PMID: 30488506 PMCID: PMC6371224 DOI: 10.1002/pro.3558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 12/19/2022]
Abstract
Nuclear pore complex (NPC) is the largest multimeric protein assembly of the eukaryotic cell, which mediates the nucleocytoplasmic transport. The constituent proteins of this assembly (nucleoporins) are present in varying copy numbers to give a size from ~ 60 MDa (yeast) to 112 MDa (human) and share common ancestry with other membrane‐associated complexes such as COPI/COPII and thus share the same structural folds. However, the nucleoporins across species exhibit very low percentage sequence similarity and this reflects in their distinct secondary structure and domain organization. We employed thorough sequence and phylogenetic analysis guided from structure‐based alignments of all the nucleoporins from fungi to metazoans to understand the evolution of NPC. Through evolutionary pressure analysis on various nucleoporins, we deduced that these proteins are under differential selection pressure and hence the homologous interacting partners do not complement each other in the in vitro pull‐down assay. The super tree analysis of all nucleoporins taken together illustrates divergent evolution of nucleoporins and notably, the degree of divergence is more apparent in higher order organisms as compared to lower species. Overall, our results support the hypothesis that the protein–protein interactions in such large multimeric assemblies are species specific in nature and hence their structure and function should also be studied in an organism‐specific manner.
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Affiliation(s)
- Kriti Chopra
- National Center for Cell Science, S.P. Pune University, Pune, 411007, Maharashtra, India
| | - Shrankhla Bawaria
- National Center for Cell Science, S.P. Pune University, Pune, 411007, Maharashtra, India
| | - Radha Chauhan
- National Center for Cell Science, S.P. Pune University, Pune, 411007, Maharashtra, India
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118
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Biallelic mutations in nucleoporin NUP88 cause lethal fetal akinesia deformation sequence. PLoS Genet 2018; 14:e1007845. [PMID: 30543681 PMCID: PMC6307818 DOI: 10.1371/journal.pgen.1007845] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/27/2018] [Accepted: 11/20/2018] [Indexed: 12/20/2022] Open
Abstract
Nucleoporins build the nuclear pore complex (NPC), which, as sole gate for nuclear-cytoplasmic exchange, is of outmost importance for normal cell function. Defects in the process of nucleocytoplasmic transport or in its machinery have been frequently described in human diseases, such as cancer and neurodegenerative disorders, but only in a few cases of developmental disorders. Here we report biallelic mutations in the nucleoporin NUP88 as a novel cause of lethal fetal akinesia deformation sequence (FADS) in two families. FADS comprises a spectrum of clinically and genetically heterogeneous disorders with congenital malformations related to impaired fetal movement. We show that genetic disruption of nup88 in zebrafish results in pleiotropic developmental defects reminiscent of those seen in affected human fetuses, including locomotor defects as well as defects at neuromuscular junctions. Phenotypic alterations become visible at distinct developmental stages, both in affected human fetuses and in zebrafish, whereas early stages of development are apparently normal. The zebrafish phenotypes caused by nup88 deficiency are rescued by expressing wild-type Nup88 but not the disease-linked mutant forms of Nup88. Furthermore, using human and mouse cell lines as well as immunohistochemistry on fetal muscle tissue, we demonstrate that NUP88 depletion affects rapsyn, a key regulator of the muscle nicotinic acetylcholine receptor at the neuromuscular junction. Together, our studies provide the first characterization of NUP88 in vertebrate development, expand our understanding of the molecular events causing FADS, and suggest that variants in NUP88 should be investigated in cases of FADS. Fetal movement is a prerequisite for normal fetal development and growth. Fetal akinesia deformation sequence (FADS) is the result of decreased fetal movement coinciding with congenital malformations related to impaired fetal movement. FADS may be caused by heterogenous defects at any point along the motor system pathway and genes encoding components critical to the neuromuscular junction and acetylcholine receptor clustering represent a major class of FADS disease genes. We report here biallelic, loss-of-function mutations in the nucleoporin NUP88 that result in lethal FADS and with this the first lethal human developmental disorder due to mutations in a nucleoporin gene. We show that loss of Nup88 in zebrafish results in defects reminiscent of those seen in affected human fetuses and loss of NUP88 affects distinct developmental stages, both during human and zebrafish development. Consistent with the notion that a primary cause for FADS is impaired formation of the neuromuscular junction, loss of Nup88 in zebrafish coincides with abnormalities in acetylcholine receptor clustering, suggesting that defective NUP88 function in FADS impairs neuromuscular junction formation.
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119
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Guan Y, Gao X, Tang Q, Huang L, Gao S, Yu S, Huang J, Li J, Zhou D, Zhang Y, Shi D, Liang D, Liu Y, Li L, Cui Y, Xu L, Chen YH. Nucleoporin 107 facilitates the nuclear export of Scn5a mRNA to regulate cardiac bioelectricity. J Cell Mol Med 2018; 23:1448-1457. [PMID: 30506890 PMCID: PMC6349201 DOI: 10.1111/jcmm.14051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/13/2018] [Accepted: 11/05/2018] [Indexed: 01/02/2023] Open
Abstract
Nucleoporins (Nups) are known to be functional in nucleo‐cytoplasmic transport, but the roles of nucleoporins in nonproliferating cells, such as cardiac myocytes, are still poorly understood. In this study, we report that Nup107 regulates cardiac bioelectricity by controlling the nucleo‐cytoplasmic trafficking of Scn5a mRNA. Overexpression of Nup107 induced the protein expression of Scn5a rather than that of other ion channels, with no effects of their mRNA levels. The analysis for the protein production demonstrated Nup107‐facilitated transport of Scn5a mRNA. Using RIP‐PCR and luciferase assay, we found that the 5′‐UTR of Scn5a mRNA was not involved in the interaction, whereas the spatial interaction between Nup107 protein and Scn5a mRNA was formed when Scn5a mRNA passing through the nuclear pore. Functionally, Nup107 overexpression in neonatal rat ventricle myocytes significantly increased the currents of Scn5a‐encoded INa channel. Moreover, the close correlation between Nup107 and Nav1.5 protein expression was observed in cardiomycytes and heart tissues subjected to hypoxia and ischaemic insults, suggesting a fast regulation of Nup107 on Nav1.5 channel in cardiac myocytes in a posttranscriptional manner. These findings may provide insights into the emergent control of cardiac electrophysiology through Nup‐mediated modulation of ion channels.
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Affiliation(s)
- Yi Guan
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Xueting Gao
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Qiuyu Tang
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Lin Huang
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Siyun Gao
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Shuai Yu
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China
| | - Jiale Huang
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Li
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Daizhan Zhou
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yangyang Zhang
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dan Shi
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dandan Liang
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Liu
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li Li
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Yingyu Cui
- Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Liang Xu
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi-Han Chen
- Heart Health Center, East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
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120
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Zilman A. Aggregation, Phase Separation and Spatial Morphologies of the Assemblies of FG Nucleoporins. J Mol Biol 2018; 430:4730-4740. [DOI: 10.1016/j.jmb.2018.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022]
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121
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Kane M, Rebensburg SV, Takata MA, Zang TM, Yamashita M, Kvaratskhelia M, Bieniasz PD. Nuclear pore heterogeneity influences HIV-1 infection and the antiviral activity of MX2. eLife 2018; 7:e35738. [PMID: 30084827 PMCID: PMC6101944 DOI: 10.7554/elife.35738] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
HIV-1 accesses the nuclear DNA of interphase cells via a poorly defined process involving functional interactions between the capsid protein (CA) and nucleoporins (Nups). Here, we show that HIV-1 CA can bind multiple Nups, and that both natural and manipulated variation in Nup levels impacts HIV-1 infection in a manner that is strikingly dependent on cell-type, cell-cycle, and cyclophilin A (CypA). We also show that Nups mediate the function of the antiviral protein MX2, and that MX2 can variably inhibit non-viral NLS function. Remarkably, both enhancing and inhibiting effects of cyclophilin A and MX2 on various HIV-1 CA mutants could be induced or abolished by manipulating levels of the Nup93 subcomplex, the Nup62 subcomplex, NUP88, NUP214, RANBP2, or NUP153. Our findings suggest that several Nup-dependent 'pathways' are variably exploited by HIV-1 to target host DNA in a cell-type, cell-cycle, CypA and CA-sequence dependent manner, and are differentially inhibited by MX2.
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Affiliation(s)
- Melissa Kane
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Stephanie V Rebensburg
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Matthew A Takata
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
| | - Trinity M Zang
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | | | - Mamuka Kvaratskhelia
- Division of Infectious DiseasesUniversity of Colorado School of MedicineAuroraUnited States
| | - Paul D Bieniasz
- Laboratory of RetrovirologyThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
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122
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Shav-Tal Y, Tripathi T. Yeast and Human Nuclear Pore Complexes: Not So Similar After All. Trends Cell Biol 2018; 28:589-591. [PMID: 29941187 DOI: 10.1016/j.tcb.2018.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 11/17/2022]
Abstract
Nucleoporin subunits that generate the nuclear pore complex (NPC) are highly conserved in evolution. High-resolution structures of the NPC are available, but the actual NPC composition in yeast has only been quantified recently. Two studies reveal major differences between species, suggesting high flexibility in NPC structures during evolution.
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Affiliation(s)
- Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong 793022, Meghalaya, India.
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123
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Dörrbaum AR, Kochen L, Langer JD, Schuman EM. Local and global influences on protein turnover in neurons and glia. eLife 2018; 7:34202. [PMID: 29914620 PMCID: PMC6008053 DOI: 10.7554/elife.34202] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/19/2018] [Indexed: 12/31/2022] Open
Abstract
Regulation of protein turnover allows cells to react to their environment and maintain homeostasis. Proteins can show different turnover rates in different tissue, but little is known about protein turnover in different brain cell types. We used dynamic SILAC to determine half-lives of over 5100 proteins in rat primary hippocampal cultures as well as in neuron-enriched and glia-enriched cultures ranging from <1 to >20 days. In contrast to synaptic proteins, membrane proteins were relatively shorter-lived and mitochondrial proteins were longer-lived compared to the population. Half-lives also correlate with protein functions and the dynamics of the complexes they are incorporated in. Proteins in glia possessed shorter half-lives than the same proteins in neurons. The presence of glia sped up or slowed down the turnover of neuronal proteins. Our results demonstrate that both the cell-type of origin as well as the nature of the extracellular environment have potent influences on protein turnover.
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Affiliation(s)
- Aline R Dörrbaum
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lisa Kochen
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany
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124
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Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M. In situ architecture of the algal nuclear pore complex. Nat Commun 2018; 9:2361. [PMID: 29915221 PMCID: PMC6006428 DOI: 10.1038/s41467-018-04739-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.
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Affiliation(s)
- Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Center for Structural Systems Biology (CSSB), Notkestrasse 85, 22607, Hamburg, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Daniela Strenkert
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Patrice A Salomé
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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125
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Lin DH, Correia AR, Cai SW, Huber FM, Jette CA, Hoelz A. Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat Commun 2018; 9:2319. [PMID: 29899397 PMCID: PMC5998080 DOI: 10.1038/s41467-018-04459-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 04/27/2018] [Indexed: 11/25/2022] Open
Abstract
The nuclear pore complex (NPC) controls the passage of macromolecules between the nucleus and cytoplasm, but how the NPC directly participates in macromolecular transport remains poorly understood. In the final step of mRNA export, the DEAD-box helicase DDX19 is activated by the nucleoporins Gle1, Nup214, and Nup42 to remove Nxf1•Nxt1 from mRNAs. Here, we report crystal structures of Gle1•Nup42 from three organisms that reveal an evolutionarily conserved binding mode. Biochemical reconstitution of the DDX19 ATPase cycle establishes that human DDX19 activation does not require IP6, unlike its fungal homologs, and that Gle1 stability affects DDX19 activation. Mutations linked to motor neuron diseases cause decreased Gle1 thermostability, implicating nucleoporin misfolding as a disease determinant. Crystal structures of human Gle1•Nup42•DDX19 reveal the structural rearrangements in DDX19 from an auto-inhibited to an RNA-binding competent state. Together, our results provide the foundation for further mechanistic analyses of mRNA export in humans. The export of mRNA to the cytosol depends on the nuclear pore complex (NPC) and the activation of the helicase DDX19, but their interplay in humans remains poorly understood. Here, the authors present a structural and functional analysis of DDX19 activation, revealing how the human NPC regulates mRNA export.
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Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ana R Correia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Sarah W Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Claudia A Jette
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
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126
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Gillon A, Nielsen K, Steel C, Cornwall J, Sheard P. Exercise attenuates age-associated changes in motoneuron number, nucleocytoplasmic transport proteins and neuromuscular health. GeroScience 2018; 40:177-192. [PMID: 29736782 DOI: 10.1007/s11357-018-0020-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/17/2018] [Indexed: 12/31/2022] Open
Abstract
Life expectancy continues to extend, although frailty caused by loss of skeletal muscle mass continues unimpeded. Muscle atrophy caused by withdrawal of motor nerves is a feature of old age, as it is in amyotrophic lateral sclerosis (ALS) in which skeletal muscle denervation results from motoneuron death. In ALS, direct links have been established between motoneuron death and altered nucleocytoplasmic transport, so we ask whether similar defects accompany motoneuron death in normal ageing. We used immunohistochemistry on mouse tissues to explore potential links between neuromuscular junction (NMJ) degeneration, motoneuron death and nucleocytoplasmic transport regulatory proteins. Old age brought neuromuscular degeneration, motoneuron loss and reductions in immunodetectable levels of key nucleocytoplasmic transport proteins in lumbar motoneurons. We then asked whether exercise inhibited these changes and found that active elderly mice experienced less motoneuron death, improved neuromuscular junction morphology and retention of key nucleocytoplasmic transport proteins in lumbar motoneurons. Our results suggest that emergent defects in nucleocytoplasmic transport may contribute to motoneuron death and age-related loss of skeletal muscle mass, and that these defects may be reduced by exercise.
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Affiliation(s)
- Ashley Gillon
- Department of Physiology, School of Biomedical Sciences, University of Otago, P.O. Box 913, Dunedin, New Zealand.
| | - Kathrine Nielsen
- Department of Physiology, School of Biomedical Sciences, University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Charlotte Steel
- Department of Physiology, School of Biomedical Sciences, University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Jon Cornwall
- Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Philip Sheard
- Department of Physiology, School of Biomedical Sciences, University of Otago, P.O. Box 913, Dunedin, New Zealand
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127
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Endicott SJ, Brueckner M. NUP98 Sets the Size-Exclusion Diffusion Limit through the Ciliary Base. Curr Biol 2018; 28:1643-1650.e3. [PMID: 29731308 DOI: 10.1016/j.cub.2018.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/14/2018] [Accepted: 04/04/2018] [Indexed: 12/16/2022]
Abstract
The primary cilium maintains a well-regulated complement of soluble and membrane proteins, allowing it to mediate a variety of signaling pathways that are essential for development and tissue homeostasis [1-3]. Entry into the cilium is regulated at the base, where a complex containing nucleoporins, referred to as the "ciliary pore complex" (CPC), has been proposed to set a size-exclusion limit for soluble molecule diffusion into the cilium [4-6]. Here, using a fluorescence-based diffusion trap system, we demonstrate that NUP98, a component of the phenylalanine-glycine (FG) hydrogel permeability barrier at the nuclear pore complex [7, 8], limits the diffusion of soluble molecules >70 kDa into the cilium in cultured mammalian cells. Small interfering RNA (siRNA)-mediated knockdown of NUP98 increases the rate of diffusion of molecules >100 kDa into the cilium. The tubulin heterodimer, the building block of the axoneme [9, 10], is approximately 100 kDa in size. After knockdown of NUP98, cilia become shorter, and their length is more sensitive to changes in cytoplasmic soluble tubulin levels. These data indicate a novel function of the ciliary pore complex, limiting diffusion of soluble tubulin between the ciliary matrix and the cytosol, allowing the cilium to regulate its length independently of cytosolic microtubule dynamics.
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Affiliation(s)
- S Joseph Endicott
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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128
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Burns JR, Howorka S. Defined Bilayer Interactions of DNA Nanopores Revealed with a Nuclease-Based Nanoprobe Strategy. ACS NANO 2018; 12:3263-3271. [PMID: 29493216 DOI: 10.1021/acsnano.7b07835] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA nanopores are a recent class of bilayer-puncturing nanodevices that can help advance biosensing, synthetic biology, and nanofluidics. Here, we create archetypal lipid-anchored DNA nanopores and characterize them with a nanoprobe-based approach to gain essential information about their interactions with bilayers. The strategy determines the molecular accessibility of DNA pores with a nuclease and can thus distinguish between the nanopores' membrane-adhering and membrane-spanning states. The analysis reveals, for example, that pores interact with bilayers in two steps whereby fast initial membrane tethering is followed by slower reorientation to the puncturing state. Tethering occurs for pores with one anchor, while puncturing requires multiple anchors. Both low and high-curvature membranes are good substrates for tethering, but efficient insertion proceeds only for high-curvature bilayers of the examined lipid composition. This is likely due to the localized lipid misalignments and the associated lower energetic barrier for pore permeation. Our study advances the fields of DNA nanotechnology and nanopores by overcoming the considerable experimental hurdle of efficient membrane insertion. It also provides mechanistic insights to aid the design of advanced nanopores, and offers a useful route to probe bilayer orientation of DNA nanostructures.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
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129
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Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy. Proc Natl Acad Sci U S A 2018; 115:E3969-E3977. [PMID: 29632211 DOI: 10.1073/pnas.1719398115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.
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130
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Rowley PA, Patterson K, Sandmeyer SB, Sawyer SL. Control of yeast retrotransposons mediated through nucleoporin evolution. PLoS Genet 2018; 14:e1007325. [PMID: 29694349 PMCID: PMC5918913 DOI: 10.1371/journal.pgen.1007325] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Yeasts serve as hosts to several types of genetic parasites. Few studies have addressed the evolutionary trajectory of yeast genes that control the stable co-existence of these parasites with their host cell. In Saccharomyces yeasts, the retrovirus-like Ty retrotransposons must access the nucleus. We show that several genes encoding components of the yeast nuclear pore complex have experienced natural selection for substitutions that change the encoded protein sequence. By replacing these S. cerevisiae genes with orthologs from other Saccharomyces species, we discovered that natural sequence changes have affected the mobility of Ty retrotransposons. Specifically, changing the genetic sequence of NUP84 or NUP82 to match that of other Saccharomyces species alters the mobility of S. cerevisiae Ty1 and Ty3. Importantly, all tested housekeeping functions of NUP84 and NUP82 remained equivalent across species. Signatures of natural selection, resulting in altered interactions with viruses and parasitic genetic elements, are common in host defense proteins. Yet, few instances have been documented in essential housekeeping proteins. The nuclear pore complex is the gatekeeper of the nucleus. This study shows how the evolution of this large, ubiquitous eukaryotic complex can alter the replication of a molecular parasite, but concurrently maintain essential host functionalities regarding nucleocytoplasmic trafficking.
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Affiliation(s)
- Paul A. Rowley
- BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States of America
| | - Suzanne B. Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
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131
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Abstract
Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.
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132
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Popp D, Koh F, Scipion CPM, Ghoshdastider U, Narita A, Holmes KC, Robinson RC. Advances in Structural Biology and the Application to Biological Filament Systems. Bioessays 2018; 40:e1700213. [PMID: 29484695 DOI: 10.1002/bies.201700213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Fujiet Koh
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Clement P M Scipion
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Akihiro Narita
- Nagoya University Graduate School of Science Structural Biology Research Center and Division of Biological Sciences, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kenneth C Holmes
- Max Planck Institute for Medical Research, D69120 Heidelberg, Germany
| | - Robert C Robinson
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore.,Research Institute for Interdisciplinary Science Okayama University, Okayama 700-8530, Japan
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133
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Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS NANO 2018; 12:1508-1518. [PMID: 29350911 PMCID: PMC5834394 DOI: 10.1021/acsnano.7b08044] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.
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Affiliation(s)
- Patrick D. Ellis Fisher
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - Luke K. Davis
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
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134
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Abstract
A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h. We identified 4000-6000 proteins in several non-dividing cell types, corresponding to 9699 unique protein identifications over the entire data set. We observed similar protein half-lives in B-cells, natural killer cells and monocytes, whereas hepatocytes and mouse embryonic neurons show substantial differences. Our data set extends and statistically validates the previous observation that subunits of protein complexes tend to have coherent turnover. Moreover, analysis of different proteasome and nuclear pore complex assemblies suggests that their turnover rate is architecture dependent. These results illustrate that our approach allows investigating protein turnover and its implications in various cell types.
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135
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Otsuka S, Ellenberg J. Mechanisms of nuclear pore complex assembly - two different ways of building one molecular machine. FEBS Lett 2018; 592:475-488. [PMID: 29119545 PMCID: PMC6220763 DOI: 10.1002/1873-3468.12905] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 12/16/2022]
Abstract
The nuclear pore complex (NPC) mediates all macromolecular transport across the nuclear envelope. In higher eukaryotes that have an open mitosis, NPCs assemble at two points in the cell cycle: during nuclear assembly in late mitosis and during nuclear growth in interphase. How the NPC, the largest nonpolymeric protein complex in eukaryotic cells, self-assembles inside cells remained unclear. Recent studies have started to uncover the assembly process, and evidence has been accumulating that postmitotic and interphase NPC assembly use fundamentally different mechanisms; the duration, structural intermediates, and regulation by molecular players are different and different types of membrane deformation are involved. In this Review, we summarize the current understanding of these two modes of NPC assembly and discuss the structural and regulatory steps that might drive the assembly processes. We furthermore integrate understanding of NPC assembly with the mechanisms for rapid nuclear growth in embryos and, finally, speculate on the evolutionary origin of the NPC implied by the presence of two distinct assembly mechanisms.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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136
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IDPs in macromolecular complexes: the roles of multivalent interactions in diverse assemblies. Curr Opin Struct Biol 2018; 49:36-43. [PMID: 29306779 DOI: 10.1016/j.sbi.2017.12.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 01/21/2023]
Abstract
Intrinsically disordered proteins (IDPs) have critical roles in a diverse array of cellular functions. Of relevance here is that they are components of macromolecular complexes, where their conformational flexibility helps mediate interactions with binding partners. IDPs often interact with their binding partners through short sequence motifs, commonly repeated within the disordered regions. As such, multivalent interactions are common for IDPs and their binding partners within macromolecular complexes. Here we discuss the importance of IDP multivalency in three very different macromolecular assemblies: biomolecular condensates, the nuclear pore, and the cytoskeleton.
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137
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De Magistris P, Tatarek-Nossol M, Dewor M, Antonin W. A self-inhibitory interaction within Nup155 and membrane binding are required for nuclear pore complex formation. J Cell Sci 2018; 131:jcs.208538. [PMID: 29150488 DOI: 10.1242/jcs.208538] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/13/2017] [Indexed: 01/02/2023] Open
Abstract
Nuclear pore complexes (NPCs) are gateways through the nuclear envelope. How they form into a structure containing three rings and integrate into the nuclear envelope remains a challenging paradigm for coordinated assembly of macro-complexes. In vertebrates, the cytoplasmic and nucleoplasmic rings of NPCs are mostly formed by multiple copies of the Nup107-Nup160 complex, whereas the central, or inner ring is composed of Nup53, Nup93, Nup155 and the two paralogues Nup188 and Nup205. Inner ring assembly is only partially understood. Using in vitro nuclear assembly reactions, we show that direct pore membrane binding of Nup155 is crucial for NPC formation. Replacing full-length Nup155 with its N-terminal β-propeller allows assembly of the outer ring components to the NPC backbone that also contains Nup53. However, further assembly, especially recruitment of the Nup93 and Nup62 complexes, is blocked. Self-interaction between the N- and C-terminal domains of Nup155 has an auto-inhibitory function that prevents interaction between the N-terminus of Nup155 and the C-terminal region of Nup53. Nup93 can overcome this block by binding to Nup53, thereby promoting formation of the inner ring and the NPC.
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Affiliation(s)
- Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany.,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Manfred Dewor
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany .,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
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138
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Tan PS, Lemke EA. Probing Differential Binding Mechanisms of Phenylalanine-Glycine-Rich Nucleoporins by Single-Molecule FRET. Methods Enzymol 2018; 611:327-346. [PMID: 30471692 PMCID: PMC7611734 DOI: 10.1016/bs.mie.2018.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Phenylalanine-glycine-rich nucleoporins (FG-Nups) are intrinsically disordered proteins, constituting the selective barrier of the nuclear pore complex. They are highly dynamic under physiological conditions and studying their interaction with nuclear transport receptors (NTRs) is key to understanding the molecular mechanism of nucleocytoplasmic transport. Distinct conformational features of FG-Nups interacting with diverse NTRs can be detected by multiparameter single-molecule fluorescence energy transfer (smFRET), which is a powerful technique for studying the dynamics and interactions of biomolecules in solution. Here we provide a detailed protocol utilizing smFRET to reveal differential binding mechanisms of FG-Nups to NTRs, with a focus on practical considerations on sample preparation of unglycosylated and glycosylated FG-Nups, site-specific dual-labeling, smFRET measurements, and data analysis.
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Affiliation(s)
- Piau Siong Tan
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Edward A. Lemke
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany,Biocenter, Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Mainz, Germany,Institute of Molecular Biology (IMB), Mainz, Germany,Corresponding author:
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139
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Majumder S, Willey PT, DeNies MS, Liu AP, Luxton GWG. A synthetic biology platform for the reconstitution and mechanistic dissection of LINC complex assembly. J Cell Sci 2018; 132:jcs.219451. [DOI: 10.1242/jcs.219451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/19/2018] [Indexed: 11/20/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) is a conserved nuclear envelope-spanning molecular bridge that is responsible for the mechanical integration of the nucleus with the cytoskeleton. LINC complexes are formed by a transluminal interaction between the outer and inner nuclear membrane KASH and SUN proteins, respectively. Despite recent structural insights, our mechanistic understanding of LINC complex assembly remains limited by the lack of an experimental system for its in vitro reconstitution and manipulation. Here, we describe artificial nuclear membranes (ANMs) as a synthetic biology platform based on mammalian cell-free expression for the rapid reconstitution of SUN proteins in supported lipid bilayers. We demonstrate that SUN1 and SUN2 are oriented in ANMs with solvent-exposed C-terminal KASH-binding SUN domains. We also find that SUN2 possesses a single transmembrane domain, while SUN1 possesses three. Finally, SUN protein-containing ANMs bind synthetic KASH peptides, thereby reconstituting the LINC complex core. This work represents the first in vitro reconstitution of KASH-binding SUN proteins in supported lipid bilayers using cell-free expression, which will be invaluable for testing proposed models of LINC complex assembly and its regulation.
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Affiliation(s)
- Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48019, USA
| | - Patrick T. Willey
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maxwell S. DeNies
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48019, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48019, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48019, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48019, USA
- Biophysics Program, University of Michigan, Ann Arbor, MI, 48019, USA
| | - G. W. Gant Luxton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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140
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Teimer R, Kosinski J, von Appen A, Beck M, Hurt E. A short linear motif in scaffold Nup145C connects Y-complex with pre-assembled outer ring Nup82 complex. Nat Commun 2017; 8:1107. [PMID: 29062044 PMCID: PMC5653651 DOI: 10.1038/s41467-017-01160-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023] Open
Abstract
Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs), which are formed from multiple copies of ~30 different nucleoporins (Nups) and inserted into the double nuclear membrane. Many of these Nups are organized into subcomplexes, of which the Y-shaped Nup84 complex is the major constituent of the nuclear and cytoplasmic rings. The Nup82–Nup159–Nsp1 complex is another module that, however, is only assembled into the cytoplasmic ring. By means of crosslinking mass spectrometry, biochemical reconstitution, and molecular modeling, we identified a short linear motif in the unstructured N-terminal region of Chaetomium thermophilum Nup145C, a subunit of the Y-complex, that is sufficient to recruit the Nup82 complex, but only in its assembled state. This finding points to a more general mechanism that short linear motifs in structural Nups can act as sensors to cooperatively connect pre-assembled NPC modules, thereby facilitating the formation and regulation of the higher-order NPC assembly. The Nup82–Nup159–Nsp1 complex, which plays a key role in mRNA export, is recruited late during the process of nuclear pore complex (NPC) assembly. Here the authors combine crosslinking mass spectrometry, biochemical reconstitution and molecular modeling to gain insights into the mechanism of Nup82 recruitment to the NPC.
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Affiliation(s)
- Roman Teimer
- Biochemistry Center of Heidelberg University (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Alexander von Appen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Ed Hurt
- Biochemistry Center of Heidelberg University (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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141
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Linder MI, Köhler M, Boersema P, Weberruss M, Wandke C, Marino J, Ashiono C, Picotti P, Antonin W, Kutay U. Mitotic Disassembly of Nuclear Pore Complexes Involves CDK1- and PLK1-Mediated Phosphorylation of Key Interconnecting Nucleoporins. Dev Cell 2017; 43:141-156.e7. [PMID: 29065306 PMCID: PMC5654724 DOI: 10.1016/j.devcel.2017.08.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 07/04/2017] [Accepted: 08/25/2017] [Indexed: 01/09/2023]
Abstract
During interphase, the nuclear envelope (NE) serves as a selective barrier between cytosol and nucleoplasm. When vertebrate cells enter mitosis, the NE is dismantled in the process of nuclear envelope breakdown (NEBD). Disassembly of nuclear pore complexes (NPCs) is a key aspect of NEBD, required for NE permeabilization and formation of a cytoplasmic mitotic spindle. Here, we show that both CDK1 and polo-like kinase 1 (PLK1) support mitotic NPC disintegration by hyperphosphorylation of Nup98, the gatekeeper nucleoporin, and Nup53, a central nucleoporin linking the inner NPC scaffold to the pore membrane. Multisite phosphorylation of Nup53 critically contributes to its liberation from its partner nucleoporins, including the pore membrane protein NDC1. Initial steps of NPC disassembly in semi-permeabilized cells can be reconstituted by a cocktail of mitotic kinases including cyclinB-CDK1, NIMA, and PLK1, suggesting that the unzipping of nucleoporin interactions by protein phosphorylation is an important principle underlying mitotic NE permeabilization.
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Affiliation(s)
- Monika I Linder
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Mario Köhler
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Paul Boersema
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Cornelia Wandke
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Joseph Marino
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.
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142
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Onischenko E, Tang JH, Andersen KR, Knockenhauer KE, Vallotton P, Derrer CP, Kralt A, Mugler CF, Chan LY, Schwartz TU, Weis K. Natively Unfolded FG Repeats Stabilize the Structure of the Nuclear Pore Complex. Cell 2017; 171:904-917.e19. [PMID: 29033133 DOI: 10.1016/j.cell.2017.09.033] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/25/2017] [Accepted: 09/19/2017] [Indexed: 12/30/2022]
Abstract
Nuclear pore complexes (NPCs) are ∼100 MDa transport channels assembled from multiple copies of ∼30 nucleoporins (Nups). One-third of these Nups contain phenylalanine-glycine (FG)-rich repeats, forming a diffusion barrier, which is selectively permeable for nuclear transport receptors that interact with these repeats. Here, we identify an additional function of FG repeats in the structure and biogenesis of the yeast NPC. We demonstrate that GLFG-containing FG repeats directly bind to multiple scaffold Nups in vitro and act as NPC-targeting determinants in vivo. Furthermore, we show that the GLFG repeats of Nup116 function in a redundant manner with Nup188, a nonessential scaffold Nup, to stabilize critical interactions within the NPC scaffold needed for late steps of NPC assembly. Our results reveal a previously unanticipated structural role for natively unfolded GLFG repeats as Velcro to link NPC subcomplexes and thus add a new layer of connections to current models of the NPC architecture.
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Affiliation(s)
- Evgeny Onischenko
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Jeffrey H Tang
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Kasper R Andersen
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kevin E Knockenhauer
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Pascal Vallotton
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Carina P Derrer
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Annemarie Kralt
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Christopher F Mugler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Leon Y Chan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland.
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143
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Fu G, Tu LC, Zilman A, Musser SM. Investigating molecular crowding within nuclear pores using polarization-PALM. eLife 2017; 6:e28716. [PMID: 28949296 PMCID: PMC5693140 DOI: 10.7554/elife.28716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
The key component of the nuclear pore complex (NPC) controlling permeability, selectivity, and the speed of nucleocytoplasmic transport is an assembly of natively unfolded polypeptides, which contain phenylalanine-glycine (FG) binding sites for nuclear transport receptors. The architecture and dynamics of the FG-network have been refractory to characterization due to the paucity of experimental methods able to probe the mobility and density of the FG-polypeptides and embedded macromolecules within intact NPCs. Combining fluorescence polarization, super-resolution microscopy, and mathematical analyses, we examined the rotational mobility of fluorescent probes at various locations within the FG-network under different conditions. We demonstrate that polarization PALM (p-PALM) provides a rich source of information about low rotational mobilities that are inaccessible with bulk fluorescence anisotropy approaches, and anticipate that p-PALM is well-suited to explore numerous crowded cellular environments. In total, our findings indicate that the NPC's internal organization consists of multiple dynamic environments with different local properties.
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Affiliation(s)
- Guo Fu
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
| | - Li-Chun Tu
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
| | - Anton Zilman
- Department of PhysicsUniversity of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoCanada
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
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144
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Abstract
Infected cells can undergo apoptosis as a protective response to viral infection, thereby limiting viral infection. As viruses require a viable cell for replication, the death of the cell limits cellular functions that are required for virus replication and propagation. Picornaviruses are single-stranded RNA viruses that modify the host cell apoptotic response, probably in order to promote viral replication, largely as a function of the viral proteases 2A, 3C, and 3CD. These proteases are essential for viral polyprotein processing and also cleave cellular proteins. Picornavirus proteases cleave proapoptotic adaptor proteins, resulting in downregulation of apoptosis. Picornavirus proteases also cleave nucleoporins, disrupting the orchestrated manner in which signaling pathways use active nucleocytoplasmic trafficking, including those involved in apoptosis. In addition to viral proteases, the transmembrane 2B protein alters intracellular ion signaling, which may also modulate apoptosis. Overall, picornaviruses, via the action of virally encoded proteins, exercise intricate control over and subvert cell death pathways, specifically apoptosis, thereby allowing viral replication to continue.
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145
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Pulupa J, Rachh M, Tomasini MD, Mincer JS, Simon SM. A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics. J Gen Physiol 2017; 149:951-966. [PMID: 28887410 PMCID: PMC5694938 DOI: 10.1085/jgp.201711769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/27/2017] [Accepted: 08/10/2017] [Indexed: 11/25/2022] Open
Abstract
The phenylalanine-glycine–repeat nucleoporins are essential for transport through the nuclear pore complex. Pulupa et al. observe reptation of these nucleoporins on a physiological timescale in coarse-grained computational simulations. The phenylalanine-glycine–repeat nucleoporins (FG-Nups), which occupy the lumen of the nuclear pore complex (NPC), are critical for transport between the nucleus and cytosol. Although NPCs differ in composition across species, they are largely conserved in organization and function. Transport through the pore is on the millisecond timescale. Here, to explore the dynamics of nucleoporins on this timescale, we use coarse-grained computational simulations. These simulations generate predictions that can be experimentally tested to distinguish between proposed mechanisms of transport. Our model reflects the conserved structure of the NPC, in which FG-Nup filaments extend into the lumen and anchor along the interior of the channel. The lengths of the filaments in our model are based on the known characteristics of yeast FG-Nups. The FG-repeat sites also bind to each other, and we vary this association over several orders of magnitude and run 100-ms simulations for each value. The autocorrelation functions of the orientation of the simulated FG-Nups are compared with in vivo anisotropy data. We observe that FG-Nups reptate back and forth through the NPC at timescales commensurate with experimental measurements of the speed of cargo transport through the NPC. Our results are consistent with models of transport where FG-Nup filaments are free to move across the central channel of the NPC, possibly informing how cargo might transverse the NPC.
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Affiliation(s)
- Joan Pulupa
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY
| | - Manas Rachh
- Courant Institute of Mathematical Sciences, New York, NY
| | - Michael D Tomasini
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY
| | - Joshua S Mincer
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY .,Department of Anesthesiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY
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146
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Lapetina DL, Ptak C, Roesner UK, Wozniak RW. Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes. J Cell Biol 2017; 216:3145-3159. [PMID: 28883038 PMCID: PMC5626528 DOI: 10.1083/jcb.201609049] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 05/26/2017] [Accepted: 07/31/2017] [Indexed: 11/22/2022] Open
Abstract
Lapetina et al. identify a protein interaction network involved in the association of chromatin with the nuclear envelope. This network includes a telomere tether, a silencing factor, a SUMO E3 ligase, and an array of nucleoporins that together form a complex distinct from nuclear pore complexes. Interactions occurring at the nuclear envelope (NE)–chromatin interface influence both NE structure and chromatin organization. Insights into the functions of NE–chromatin interactions have come from the study of yeast subtelomeric chromatin and its association with the NE, including the identification of various proteins necessary for tethering subtelomeric chromatin to the NE and the silencing of resident genes. Here we show that four of these proteins—the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170—physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups). Importantly, this group of Nups is largely restricted to members of the inner and outer NPC rings, but it lacks numerous others including cytoplasmically and nucleoplasmically positioned Nups. We propose that this Sir4-associated Nup complex is distinct from holo-NPCs and that it plays a role in subtelomeric chromatin organization and NE tethering.
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Affiliation(s)
- Diego L Lapetina
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Ulyss K Roesner
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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147
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Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol Syst Biol 2017; 13:936. [PMID: 28743795 PMCID: PMC5527848 DOI: 10.15252/msb.20167412] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions, and structure of a third of the C. thermophilum proteome within these extracts. We identified 27 distinct protein communities that include 108 interconnected complexes, which dynamically associate with each other and functionally benefit from being in close proximity in the cell. Furthermore, we investigated the structure of fatty acid synthase within these extracts by cryoEM and this revealed multiple, flexible states of the enzyme in adaptation to its association with other complexes, thus exemplifying the need for in situ studies. As the components of the captured protein communities are known—at both the protein and complex levels—this study constitutes another step forward toward a molecular understanding of subcellular organization.
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Affiliation(s)
- Panagiotis L Kastritis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Thomas Bock
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Yuanyue Li
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matt Z Rogon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Katarzyna Buczak
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Natalie Romanov
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Matthew J Betts
- Cell Networks, Bioquant & Biochemie Zentrum Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Khanh Huy Bui
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Wim J Hagen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marco L Hennrich
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marie-Therese Mackmull
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Robert B Russell
- Cell Networks, Bioquant & Biochemie Zentrum Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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148
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Zilkenat S, Grin I, Wagner S. Stoichiometry determination of macromolecular membrane protein complexes. Biol Chem 2017; 398:155-164. [PMID: 27664774 DOI: 10.1515/hsz-2016-0251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/20/2016] [Indexed: 01/01/2023]
Abstract
Gaining knowledge of the structural makeup of protein complexes is critical to advance our understanding of their formation and functions. This task is particularly challenging for transmembrane protein complexes, and grows ever more imposing with increasing size of these large macromolecular structures. The last 10 years have seen a steep increase in solved high-resolution membrane protein structures due to both new and improved methods in the field, but still most structures of large transmembrane complexes remain elusive. An important first step towards the structure elucidation of these difficult complexes is the determination of their stoichiometry, which we discuss in this review. Knowing the stoichiometry of complex components not only answers unresolved structural questions and is relevant for understanding the molecular mechanisms of macromolecular machines but also supports further attempts to obtain high-resolution structures by providing constraints for structure calculations.
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149
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Hayama R, Rout MP, Fernandez-Martinez J. The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. Curr Opin Cell Biol 2017. [PMID: 28624666 DOI: 10.1016/j.ceb.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The study of the nuclear pore complex (NPC) is a fascinating endeavor, as it not only implies uncovering the 'engineering marvel' of its architecture and function, but also provides a key window into a significant evolutionary event: the origin of the eukaryotic cell. The combined efforts of many groups in the field, with the help of novel methodologies and new model organisms, are facilitating a much deeper understanding of this complex assembly. Here we cover recent advances on the characterization of the structure of the NPC scaffold and of the biophysical mechanisms that define the permeability barrier. We identify common architectural and functional principles between those two NPC compartments, expanding the previous protocoatomer hypothesis to suggest possible evolutionary origins for the FG nucleoporins and the NPC permeability barrier.
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Affiliation(s)
- Ryo Hayama
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
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150
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Zhang J, Roggero VR, Allison LA. Nuclear Import and Export of the Thyroid Hormone Receptor. VITAMINS AND HORMONES 2017; 106:45-66. [PMID: 29407444 DOI: 10.1016/bs.vh.2017.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The thyroid hormone receptors, TRα1 and TRβ1, are members of the nuclear receptor superfamily that forms one of the most abundant classes of transcription factors in multicellular organisms. Although primarily localized to the nucleus, TRα1 and TRβ1 shuttle rapidly between the nucleus and cytoplasm. The fine balance between nuclear import and export of TRs has emerged as a critical control point for modulating thyroid hormone-responsive gene expression. Mutagenesis studies have defined two nuclear localization signal (NLS) motifs that direct nuclear import of TRα1: NLS-1 in the hinge domain and NLS-2 in the N-terminal A/B domain. Three nuclear export signal (NES) motifs reside in the ligand-binding domain. A combined approach of shRNA-mediated knockdown and coimmunoprecipitation assays revealed that nuclear entry of TRα1 is facilitated by importin 7, likely through interactions with NLS-2, and importin β1 and the adapter importin α1 interacting with both NLS-1 and NLS-2. Interestingly, TRβ1 lacks NLS-2 and nuclear import depends solely on the importin α1/β1 heterodimer. Heterokaryon and fluorescence recovery after photobleaching shuttling assays identified multiple exportins that play a role in nuclear export of TRα1, including CRM1 (exportin 1), and exportins 4, 5, and 7. Even single amino acid changes in TRs dramatically alter their intracellular distribution patterns. We conclude that mutations within NLS and NES motifs affect nuclear shuttling activity, and propose that TR mislocalization contributes to the development of some types of cancer and Resistance to Thyroid Hormone syndrome.
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Affiliation(s)
- Jibo Zhang
- College of William and Mary, Williamsburg, VA, United States
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