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Nuclear export of the pre-60S ribosomal subunit through single nuclear pores observed in real time. Nat Commun 2021; 12:6211. [PMID: 34707094 PMCID: PMC8551241 DOI: 10.1038/s41467-021-26323-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/02/2021] [Indexed: 11/08/2022] Open
Abstract
Ribosomal biogenesis has been studied by biochemical, genetic and electron microscopic approaches, but live cell data on the in vivo kinetics are still missing. Here we analyse the export kinetics of the large ribosomal subunit (pre-60S particle) through single NPCs in human cells. We established a stable cell line co-expressing Halo-tagged eIF6 and GFP-fused NTF2 to simultaneously label pre-60S particles and NPCs, respectively. By combining single molecule tracking and super resolution confocal microscopy we visualize the dynamics of single pre-60S particles during export through single NPCs. For export events, maximum particle accumulation is found in the centre of the pore, while unsuccessful export terminates within the nuclear basket. The export has a single rate limiting step and a duration of ∼24 milliseconds. Only about 1/3 of attempted export events are successful. Our results show that the mass flux through a single NPC can reach up to ~125 MDa·s-1 in vivo.
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2
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Ben-Yishay R, Mor A, Shraga A, Ashkenazy-Titelman A, Kinor N, Schwed-Gross A, Jacob A, Kozer N, Kumar P, Garini Y, Shav-Tal Y. Imaging within single NPCs reveals NXF1's role in mRNA export on the cytoplasmic side of the pore. J Cell Biol 2019; 218:2962-2981. [PMID: 31375530 PMCID: PMC6719458 DOI: 10.1083/jcb.201901127] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/21/2019] [Accepted: 07/03/2019] [Indexed: 12/12/2022] Open
Abstract
Translocation of mRNA through the nuclear pore complex (NPC) requires interactions with different NPC regions. To determine the interactions that are crucial for effective mRNA export in living cells, we examined mRNA export within individual pores by applying various types of mRNA export blocks that stalled mRNPs at different stages of transition. Focusing on the major mRNA export factor NXF1, we found that initial mRNP binding to the NPC did not require NXF1 in the NPC, whereas release into the cytoplasm did. NXF1 localization in the NPC did not require RNA or RNA binding. Superresolution microscopy showed that NXF1 consistently occupied positions on the cytoplasmic side of the NPC. Interactions with specific nucleoporins were pinpointed using FLIM-FRET for measuring protein-protein interactions inside single NPCs, showing that Dbp5 helicase activity of mRNA release is conserved in yeast and humans. Altogether, we find that specific interactions on the cytoplasmic side of the NPC are fundamental for the directional flow of mRNA export.
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Affiliation(s)
- Rakefet Ben-Yishay
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Amir Mor
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Amit Shraga
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Asaf Ashkenazy-Titelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Avital Schwed-Gross
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Avi Jacob
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Noga Kozer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Pramod Kumar
- Department of Physics, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yuval Garini
- Department of Physics, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel .,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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3
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Kubitscheck U, Siebrasse JP. Kinetics of transport through the nuclear pore complex. Semin Cell Dev Biol 2017; 68:18-26. [PMID: 28676422 DOI: 10.1016/j.semcdb.2017.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023]
Abstract
Single molecule microscopy techniques allow to visualize the translocation of single transport receptors and cargo molecules or particles through nuclear pore complexes. These data indicate that cargo molecule import into the nucleus takes less than 10ms and nuclear export of messenger RNA (mRNA) particles takes 50-350ms, up to several seconds for extremely bulky particles. This review summarizes and discusses experimental results on transport of nuclear transport factor 2 (NTF2), importin β and mRNA particles. Putative regulatory functions of importin β for the NPC transport mechanism and the RNA helicase Dbp5 for mRNA export kinetics are discussed.
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Affiliation(s)
- Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms-University Bonn, Wegeler Str. 12, D-53115 Bonn, Germany.
| | - Jan-Peter Siebrasse
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms-University Bonn, Wegeler Str. 12, D-53115 Bonn, Germany
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4
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Fišerová J, Efenberková M, Sieger T, Maninová M, Uhlířová J, Hozák P. Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data. J Cell Sci 2017; 130:2066-2077. [PMID: 28476938 DOI: 10.1242/jcs.198424] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/02/2017] [Indexed: 12/28/2022] Open
Abstract
The nuclear periphery (NP) plays a substantial role in chromatin organization. Heterochromatin at the NP is interspersed with active chromatin surrounding nuclear pore complexes (NPCs); however, details of the peripheral chromatin organization are missing. To discern the distribution of epigenetic marks at the NP of HeLa nuclei, we used structured illumination microscopy combined with a new MATLAB software tool for automatic NP and NPC detection, measurements of fluorescent intensity and statistical analysis of measured data. Our results show that marks for both active and non-active chromatin associate differentially with NPCs. The incidence of heterochromatin marks, such as H3K27me2 and H3K9me2, was significantly lower around NPCs. In contrast, the presence of marks of active chromatin such as H3K4me2 was only decreased very slightly around the NPCs or not at all (H3K9Ac). Interestingly, the histone demethylases LSD1 (also known as KDM1A) and KDM2A were enriched within the NPCs, suggesting that there was a chromatin-modifying mechanism at the NPCs. Inhibition of transcription resulted in a larger drop in the distribution of H1, H3K9me2 and H3K23me2, which implies that transcription has a role in the organization of heterochromatin at the NP.
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Affiliation(s)
- Jindřiška Fišerová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Prague 142 00, Czech Republic
| | - Michaela Efenberková
- Microscopy Centre - LM and EM, Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Prague 142 00, Czech Republic
| | - Tomáš Sieger
- Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, 121 35, Czech Republic
| | - Miloslava Maninová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Prague 142 00, Czech Republic
| | - Jana Uhlířová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Prague 142 00, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics CAS, v.v.i., Vídeňská 1083, Prague 142 00, Czech Republic.,Division BIOCEV, Institute of Molecular Genetics CAS, v.v.i., Průmyslová 595, Vestec, Prague 252 50, Czech Republic
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5
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Ben-Yishay R, Ashkenazy AJ, Shav-Tal Y. Dynamic Encounters of Genes and Transcripts with the Nuclear Pore. Trends Genet 2016; 32:419-431. [DOI: 10.1016/j.tig.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/20/2016] [Indexed: 01/04/2023]
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Abstract
The passage of mRNA molecules from the site of synthesis, through the nucleoplasm and the nuclear pore, en route to the cytoplasm, might appear straightforward. Nonetheless, several decades of detailed examination of this pathway, from high resolution electron microscopy in fixed specimens, through the development of immuno-detection techniques and fluorescence toolkits, to the current era of live-cell imaging, show this to be an eventful journey. In addition to mRNAs, several species of noncoding RNAs travel and function in the nucleus, some being retained within throughout their lifetime. This review will highlight the nucleoplasmic paths taken by mRNAs and noncoding RNAs in eukaryotic cells with special focus on live-cell data and in concurrence with the biophysical nature of the nucleus.
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Affiliation(s)
- Jonathan Sheinberger
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
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7
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Woodward CL, Chow SA. The nuclear pore complex: a new dynamic in HIV-1 replication. Nucleus 2012; 1:18-22. [PMID: 21327100 DOI: 10.4161/nucl.1.1.10571] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/07/2009] [Accepted: 11/10/2009] [Indexed: 01/08/2023] Open
Abstract
The ability to traverse an intact nuclear envelope and productively infect non-dividing cells is a salient feature of human immunodeficiency virus type 1 (HIV-1) and other lentiviruses, but the viral factors and mechanism of nuclear entry have not been defined. We have recently reported a functional role for the nucleoporin NUP153 in the nuclear import of the HIV-1 preintegration complex (PIC). Our findings suggest that HIV-1 sub-viral particles gain access to the nucleus by interacting directly with the nuclear pore complex (NPC) via the binding of PIC-associated integrase (IN) to the C-terminal domain of NUP153. This article discusses how NPC conformation and constitution might influence nuclear import of the PIC, and the subsequent integration of the viral cDNA into actively transcribed genes.
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Affiliation(s)
- Cora L Woodward
- Department of Molecular and Medical Pharmacology, and UCLA AIDS Institute, UCLA School of Medicine, Los Angeles, CA, USA
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8
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Prachař J. Structural features of transversal barrier in central channel of nuclear pore complex. Exp Cell Res 2012; 318:614-22. [PMID: 22285132 DOI: 10.1016/j.yexcr.2012.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 11/16/2022]
Abstract
The most important entity of the selective behavior of the nuclear pore complex (NPC) is considered to be the matter called "barrier," "meshwork" or "sieve." This part of NPC has not been well elucidated by using electron microscopy methods to date. In the present study, we demonstrated the presence of a coherent transversal barrier in the central channel of NPC, using high resolution transmission electron microscopy. It was found that the barrier is located in the middle of the central channel, i.e. at the level where the outer and inner nuclear membranes fuse. The thickness of this layer is evidently different in various NPCs and usually varies between 20 and 30 nm and its diameter is approximately 40 nm. The cytoplasmic and nuclear surfaces of the barrier are roughly parallel and plane. Moreover we suggest that the barrier may not be interrupted by any channel(s), at least not with a diameter above 10 nm. Further various appearances of the central channel with different particles were observed, presumably cargos and karyopherins captured in transit. A different type of central channel barrier with lipid bilayer membrane-like appearance is also discussed.
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Affiliation(s)
- Jarmil Prachař
- Laboratory of Electron Microscopy, Cancer Research Institute, Vlárska 7, 83391 Bratislava, Slovakia.
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Oeffinger M, Zenklusen D. To the pore and through the pore: a story of mRNA export kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:494-506. [PMID: 22387213 DOI: 10.1016/j.bbagrm.2012.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/07/2012] [Accepted: 02/09/2012] [Indexed: 12/26/2022]
Abstract
The evolutionary 'decision' to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transport mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Marlene Oeffinger
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec, Canada.
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10
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Grünwald D, Singer RH. Multiscale dynamics in nucleocytoplasmic transport. Curr Opin Cell Biol 2011; 24:100-6. [PMID: 22196930 DOI: 10.1016/j.ceb.2011.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 11/24/2011] [Indexed: 01/06/2023]
Abstract
The nuclear pore complex (NPC) has long been viewed as a point-like entry and exit channel between the nucleus and the cytoplasm. New data support a different view whereby the complex displays distinct spatial dynamics of variable duration ranging from milliseconds to events spanning the entire cell cycle. Discrete interaction sites outside the central channel become apparent, and transport regulation at these sites seems to be of greater importance than currently thought. Nuclear pore components are highly active outside the NPC or impact the fate of cargo transport away from the nuclear pore. The NPC is a highly dynamic, crowded environment-constantly loaded with cargo while providing selectivity based on unfolded proteins. Taken together, this comprises a new paradigm in how we view import/export dynamics and emphasizes the multiscale nature of NPC-mediated cellular transport.
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Affiliation(s)
- David Grünwald
- Delft University of Technology, Kavli Institute of Nanoscience, Department of Bionanoscience, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
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11
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Abstract
The central dogma of molecular biology - DNA makes RNA makes proteins - is a flow of information that in eukaryotes encounters a physical barrier: the nuclear envelope, which encapsulates, organizes and protects the genome. Nuclear-pore complexes, embedded in the nuclear envelope, regulate the passage of molecules to and from the nucleus, including the poorly understood process of the export of RNAs from the nucleus. Recent imaging approaches focusing on single molecules have provided unexpected insight into this crucial step in the information flow. This review addresses the latest studies of RNA export and presents some models for how this complex process may work.
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Landerer E, Villegas J, Burzio VA, Oliveira L, Villota C, Lopez C, Restovic F, Martinez R, Castillo O, Burzio LO. Nuclear localization of the mitochondrial ncRNAs in normal and cancer cells. Cell Oncol (Dordr) 2011; 34:297-305. [PMID: 21347712 DOI: 10.1007/s13402-011-0018-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2011] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND We have previously shown a differential expression of a family of mitochondrial ncRNAs in normal and cancer cells. Normal proliferating cells and cancer cells express the sense mitochondrial ncRNA (SncmtRNA). In addition, while normal proliferating cells express two antisense mitochondrial ncRNAs (ASncmtRNAs-1 and -2), these transcripts seem to be universally down-regulated in cancer cells. In situ hybridization (ISH) of some normal and cancer tissues reveals nuclear localization of these transcripts suggesting that they are exported from mitochondria. METHODS FISH and confocal microscopy, in situ digestion with RNase previous to ISH and electron microscopy ISH was employed to confirm the extra-mitochondrial localization of the SncmtRNA and the ASncmtRNAs in normal proliferating and cancer cells of human and mouse. RESULTS In normal human kidney and mouse testis the SncmtRNA and the ASncmtRNAs were found outside the organelle and especially localized in the nucleus associated to heterochromatin. In cancer cells, only the SncmtRNA was expressed and was found associated to heterochromatin and nucleoli. CONCLUSION The ubiquitous localization of these mitochondrial transcripts in the nucleus suggests that they are new players in the mitochondrial-nuclear communication pathway or retrograde signaling. Down regulation of the ASncmtRNAs seems to be an important step on neoplastic transformation and cancer progression.
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13
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Mor A, Shav-Tal Y. Dynamics and kinetics of nucleo-cytoplasmic mRNA export. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:388-401. [PMID: 21956938 DOI: 10.1002/wrna.41] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Activation of the gene expression pathway in eukaryotic cells results in the nuclear transcription of mRNA molecules, many of which are destined for translation into protein by cytoplasmic ribosomes. mRNA transcripts are exported from the nucleus to the cytoplasm via passage through nuclear pore complexes (NPCs), ∼125 MDa supramolecular complexes set in the double-membraned nuclear envelope. Understanding the kinetics of mRNA translocation, from the point of transcription through export, localization, translation, and degradation, is of fundamental interest since gene expression is regulated at all the different levels of this pathway. In this review, we delineate the steps taken by an mRNA molecule in transit to the nuclear envelope and during mRNA export, with specific focus on the dynamic aspects of nucleo-cytoplasmic mRNA transport as revealed by electron microscopy and live-cell imaging.
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Affiliation(s)
- Amir Mor
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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14
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Krull S, Dörries J, Boysen B, Reidenbach S, Magnius L, Norder H, Thyberg J, Cordes VC. Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion. EMBO J 2010; 29:1659-73. [PMID: 20407419 PMCID: PMC2876962 DOI: 10.1038/emboj.2010.54] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 03/09/2010] [Indexed: 12/21/2022] Open
Abstract
Amassments of heterochromatin in somatic cells occur in close contact with the nuclear envelope (NE) but are gapped by channel- and cone-like zones that appear largely free of heterochromatin and associated with the nuclear pore complexes (NPCs). To identify proteins involved in forming such heterochromatin exclusion zones (HEZs), we used a cell culture model in which chromatin condensation induced by poliovirus (PV) infection revealed HEZs resembling those in normal tissue cells. HEZ occurrence depended on the NPC-associated protein Tpr and its large coiled coil-forming domain. RNAi-mediated loss of Tpr allowed condensing chromatin to occur all along the NE's nuclear surface, resulting in HEZs no longer being established and NPCs covered by heterochromatin. These results assign a central function to Tpr as a determinant of perinuclear organization, with a direct role in forming a morphologically distinct nuclear sub-compartment and delimiting heterochromatin distribution.
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Affiliation(s)
- Sandra Krull
- Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Julia Dörries
- Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Björn Boysen
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Sonja Reidenbach
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Lars Magnius
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Helene Norder
- Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Johan Thyberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Volker C Cordes
- Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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15
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Mor A, Suliman S, Ben-Yishay R, Yunger S, Brody Y, Shav-Tal Y. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat Cell Biol 2010; 12:543-52. [PMID: 20453848 DOI: 10.1038/ncb2056] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 04/15/2010] [Indexed: 12/16/2022]
Abstract
The flow of genetic information in eukaryotic cells occurs through the nucleocytoplasmic translocation of mRNAs. Knowledge of in vivo messenger RNA export kinetics remains poor in comparison with that of protein transport. We have established a mammalian system that allowed the real-time visualization and quantification of large single mRNA-protein complexes (mRNPs) during export. The in vivo dynamics of bulk mRNP transport and export, from transcription to the nuclear pore complex (NPC), occurred within a 5-40 minute time frame, with no NPC pile-up. mRNP export was rapid (about 0.5 s) and kinetically faster than nucleoplasmic diffusion. Export inhibition demonstrated that mRNA-NPC interactions were independent of ongoing export. Nucleoplasmic transport dynamics of intron-containing and intronless mRNAs were similar, yet an intron did increase export efficiency. Here we provide visualization and analysis at the single mRNP level of the various steps in nuclear gene expression and the inter-chromatin tracks through which mRNPs diffuse, and demonstrate the kinetics of mRNP-NPC interactions and translocation.
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Affiliation(s)
- Amir Mor
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
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16
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Abstract
Eukaryotic cells have developed a series of highly controlled processes of transport between the nucleus and cytoplasm. The present review focuses on the latest advances in our understanding of nucleocytoplasmic exchange of molecules in yeast, a widely studied model organism in the field. It concentrates on the role of individual proteins such as nucleoporins and karyopherins in the translocation process and relates this to how the organization of the nuclear pore complex effectively facilitates the bidirectional transport between the two compartments.
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Arriagada G, Paredes R, van Wijnen AJ, Lian JB, van Zundert B, Stein GS, Stein JL, Montecino M. 1alpha,25-dihydroxy vitamin D(3) induces nuclear matrix association of the 1alpha,25-dihydroxy vitamin D(3) receptor in osteoblasts independently of its ability to bind DNA. J Cell Physiol 2009; 222:336-46. [PMID: 19885846 DOI: 10.1002/jcp.21958] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
1alpha,25-dihydroxy vitamin D(3) (vitamin D(3)) has an important role during osteoblast differentiation as it directly modulates the expression of key bone-related genes. Vitamin D(3) binds to the vitamin D(3) receptor (VDR), a member of the superfamily of nuclear receptors, which in turn interacts with transcriptional activators to target this regulatory complex to specific sequence elements within gene promoters. Increasing evidence demonstrates that the architectural organization of the genome and regulatory proteins within the eukaryotic nucleus support gene expression in a physiological manner. Previous reports indicated that the VDR exhibits a punctate nuclear distribution that is significantly enhanced in cells grown in the presence of vitamin D(3). Here, we demonstrate that in osteoblastic cells, the VDR binds to the nuclear matrix in a vitamin D(3)-dependent manner. This interaction of VDR with the nuclear matrix occurs rapidly after vitamin D(3) addition and does not require a functional VDR DNA-binding domain. Importantly, nuclear matrix-bound VDR colocalizes with its transcriptional coactivator DRIP205/TRAP220/MED1 which is also matrix bound. Together these results indicate that after ligand stimulation the VDR rapidly enters the nucleus and associates with the nuclear matrix preceding vitamin D(3)-transcriptional upregulation.
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Affiliation(s)
- Gloria Arriagada
- Facultad de Ciencias Biologicas, Departamento de Bioquimica y Biologia Molecular, Universidad de Concepcion, Concepcion, Chile
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18
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Eskiw CH, Rapp A, Carter DRF, Cook PR. RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci 2008; 121:1999-2007. [PMID: 18495842 DOI: 10.1242/jcs.027250] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We used electron spectroscopic imaging to map nucleoplasmic transcription sites in human cells at unprecedented resolution. HeLa cells were permeabilised, nascent transcripts were extended in BrUTP by approximately 40 nucleotides and the resulting BrRNA immunolabelled with gold particles before structures were viewed. Nascent RNA is almost invariably associated with polymorphic and nitrogen-rich (but phosphorus-poor) structures with a diameter of approximately 87 nm and mass of 10 MDa (calculated by reference to nucleosomes with known numbers of phosphorus and nitrogen atoms). Structures with similar atomic signatures and diameters were observed using correlative microscopy and in unpermeabilised cells. Our results are consistent with RNA synthesis occurring on the surface of these huge protein-rich transcription factories.
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19
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Heidecker B, Hare JM. The use of transcriptomic biomarkers for personalized medicine. Heart Fail Rev 2007; 12:1-11. [PMID: 17393305 DOI: 10.1007/s10741-007-9004-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 02/13/2007] [Indexed: 12/29/2022]
Abstract
Microarrays are a high throughput technology that allows the quantification of tens of thousands of RNA transcripts in a single reaction. This new technology offers the promise of comprehensive study of disease at a genomic level, potentially identifying novel molecular abnormalities, developing novel clinical biomarkers, and investigating drug efficacy. The ability to develop a molecular profile corresponding to a therapeutic effect is the basis for the concept of drug repositioning. With regard to prediction of clinical events, microarray technology has the potential to contribute to the development of sophisticated new biomarkers useful as predictors of disease etiology, outcome, and responsiveness to therapy-so-called personalized medicine. Currently progress in the field is hampered by a degree of skepticism about the reliability of microarray data and its relevance for clinical applications. Here we discuss possible pitfalls of transcriptomic analysis, review current developments in the cardiovascular area and address the use of transcriptomics for clinical applications.
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Affiliation(s)
- Bettina Heidecker
- Divison of Cardiology, Miller School of Medicine, University of Miami, Clinical Research Building, 1120 NW 14th Street, Suite 1112, Miami, FL 33136, USA
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20
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Montecino M, Stein GS, Cruzat F, Marcellini S, Stein JL, Lian JB, van Wijnen AJ, Arriagada G. An architectural perspective of vitamin D responsiveness. Arch Biochem Biophys 2007; 460:293-9. [PMID: 17288986 PMCID: PMC2715940 DOI: 10.1016/j.abb.2006.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 12/11/2006] [Accepted: 12/15/2006] [Indexed: 12/31/2022]
Abstract
Vitamin D serves as a principal modulator of skeletal gene transcription, thus necessitating an understanding of interfaces between the activity of this steroid hormone and regulatory cascades that are functionally linked to the regulation of skeletal genes. Physiological responsiveness requires combinatorial control where coregulatory proteins determine the specificity of biological responsiveness to physiological cues. It is becoming increasingly evident that the regulatory complexes containing the vitamin D receptor are dynamic rather than static. Temporal and spatial modifications in the composition of these complexes provide a mechanism for integrating regulatory signals to support positive or negative control through synergism and antagonism. Compartmentalization of components of vitamin D control in nuclear microenvironments supports the integration of regulatory activities, perhaps by establishing thresholds for protein activity in time frames that are consistent with the execution of regulatory signaling.
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Affiliation(s)
- Martin Montecino
- Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias Biologicas, Universidad de Concepcion, Concepcion, Chile.
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21
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Dimaano C, Ullman KS. Nucleocytoplasmic transport: integrating mRNA production and turnover with export through the nuclear pore. Mol Cell Biol 2004; 24:3069-76. [PMID: 15060131 PMCID: PMC381686 DOI: 10.1128/mcb.24.8.3069-3076.2004] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Christian Dimaano
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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22
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Galy V, Gadal O, Fromont-Racine M, Romano A, Jacquier A, Nehrbass U. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 2004; 116:63-73. [PMID: 14718167 DOI: 10.1016/s0092-8674(03)01026-2] [Citation(s) in RCA: 286] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The molecular mechanism underlying the retention of intron-containing mRNAs in the nucleus is not understood. Here, we show that retention of intron-containing mRNAs in yeast is mediated by perinuclearly located Mlp1. Deletion of MLP1 impairs retention while having no effect on mRNA splicing. The Mlp1-dependent leakage of intron-containing RNAs is increased in presence of ts-prp18 delta, a splicing mutant. When overall pre-mRNA levels are increased by deletion of RRP6, a nuclear exosome component, MLP1 deletion augments leakage of only the intron-containing portion of mRNAs. Our data suggest, moreover, that Mlp1-dependent retention is mediated via the 5' splice site. Intriguingly, we found Mlp-proteins to be present only on sections of the NE adjacent to chromatin. We propose that at this confined site the perinuclear Mlp1 implements a quality control step prior to export, physically retaining faulty pre-mRNAs.
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Affiliation(s)
- Vincent Galy
- Unité de Biologie Cellulaire du Noyau, CNRS URA 2582, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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23
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Stein GS, Lian JB, Stein JL, Wijnen AJV, Montecino M, Javed A, Pratap J, Choi J, Zaidi SK, Gutierrez S, Harrington K, Shen J, Young D. Intranuclear trafficking of transcription factors: Requirements for vitamin D-mediated biological control of gene expression. J Cell Biochem 2003; 88:340-55. [PMID: 12520536 DOI: 10.1002/jcb.10364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The architecturally associated subnuclear organization of nucleic acids and cognate regulatory factors suggest functional interrelationships between nuclear structure and gene expression. Mechanisms that contribute to the spatial distribution of transcription factors within the three-dimensional context of nuclear architecture control the sorting of regulatory information as well as the assembly and activities of sites within the nucleus that support gene expression. Vitamin D control of gene expression serves as a paradigm for experimentally addressing mechanisms that govern the intranuclear targeting of regulatory factors to nuclear domains where transcription of developmental and tissue-specific genes occur. We will present an overview of molecular, cellular, genetic, and biochemical approaches that provide insight into the trafficking of regulatory factors that mediate vitamin D control of gene expression to transcriptionally active subnuclear sites. Examples will be presented that suggest modifications in the intranuclear targeting of transcription factors abrogate competency for vitamin D control of skeletal gene expression during development and fidelity of gene expression in tumor cells.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, Massachusetts 01655, USA.
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24
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Fahrenkrog B, Aebi U. The vertebrate nuclear pore complex: from structure to function. Results Probl Cell Differ 2002; 35:25-48. [PMID: 11791407 DOI: 10.1007/978-3-540-44603-3_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Birthe Fahrenkrog
- M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
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25
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Rodríguez-López AM, Jackson DA, Iborra F, Cox LS. Asymmetry of DNA replication fork progression in Werner's syndrome. Aging Cell 2002; 1:30-9. [PMID: 12882351 DOI: 10.1046/j.1474-9728.2002.00002.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human aging is associated with accumulation of cells that have undergone replicative senescence. The rare premature aging Werner's syndrome (WS) provides a phenocopy of normal human aging and WS patient cells recapitulate the aging phenotype in culture as they rapidly lose the ability to proliferate or replicate their DNA. WS is associated with loss of functional WRN protein. Although the biochemical properties of WRN protein, which possesses both helicase and exonuclease activities, suggest an involvement in DNA metabolism, its action in cells is not clear. Here, we provide experimental evidence for a role of the WRN protein in DNA replication in normally proliferating cells. Most importantly, we demonstrate that in the absence of functional WRN protein, replication forks from origins of bidirectional replication fail to progress normally, resulting in marked asymmetry of bidirectional forks. We propose that WRN acts in normal DNA replication to prevent collapse of replication forks or to resolve DNA junctions at stalled replication forks, and that loss of this capacity may be a contributory factor in premature aging.
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Affiliation(s)
- Ana M Rodríguez-López
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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26
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Stewart M, Baker RP, Bayliss R, Clayton L, Grant RP, Littlewood T, Matsuura Y. Molecular mechanism of translocation through nuclear pore complexes during nuclear protein import. FEBS Lett 2001; 498:145-9. [PMID: 11412846 DOI: 10.1016/s0014-5793(01)02489-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The trafficking of macromolecules between cytoplasm and nucleus through nuclear pore complexes is mediated by specific carrier molecules such as members of the importin-beta family. Nuclear pore proteins (nucleoporins) frequently contain sequence repeats based on FG cores and carriers appear to move their cargo through the pores by hopping between successive FG cores. A major question is why some macromolecules are transported while others are not. This selectivity may be generated by the ability to bind FG repeats, a local concentration of carrier-cargo complexes near the entrance to the pore channel, and steric hindrance produced by high concentrations of nucleoporins in the channel.
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Affiliation(s)
- M Stewart
- MRC Laboratory of Molecular Biology, Hills Rd., CB2 2QH, Cambridge, UK.
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27
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Quimby BB, Lamitina T, L'Hernault SW, Corbett AH. The mechanism of ran import into the nucleus by nuclear transport factor 2. J Biol Chem 2000; 275:28575-82. [PMID: 10889207 DOI: 10.1074/jbc.m005055200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The small GTPase Ran is essential for virtually all nucleocytoplasmic transport events. It is hypothesized that Ran drives vectorial transport of macromolecules into and out of the nucleus via the establishment of a Ran gradient between the cytoplasm and nucleoplasm. Although Ran shuttles between the nucleus and cytoplasm, it is concentrated in the nucleus at steady state. We show that nuclear transport factor 2 (NTF2) is required to concentrate Ran in the nucleus in the budding yeast, Saccharomyces cerevisiae. To analyze the mechanism of Ran import into the nucleus by NTF2, we use mutants in a variety of nuclear transport factors along with biochemical analyses of NTF2 complexes. We find that Ran remains concentrated in the nucleus when importin-mediated protein import is disrupted and demonstrate that NTF2 does not form a stable complex with the transport receptor, importin-beta. Consistent with a critical role for NTF2 in establishing and maintaining the Ran gradient, we show that NTF2 is required for early embryogenesis in Caenorhabditis elegans. Our data distinguish between two possible mechanisms for Ran import by NTF2 and demonstrate that Ran import is independent from importin-beta-mediated protein import.
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Affiliation(s)
- B B Quimby
- Department of Biochemistry, Emory University School of Medicine and the Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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28
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Abstract
Significant progress has been made toward our understanding of the basic principle of nucleocytoplasmic transport, and the structure of transport factors, as well as the diversity of nucleocytoplasmic transport pathways. This review outlines the current knowledge of transport, and discusses the problems that remain as to how eukaryotic cells acquire additional levels for the regulation of gene expression from a diversity of nucleocytoplasmic transport pathways.
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Affiliation(s)
- N Imamoto
- Gene Network Laboratory, Structural Biology Center, National Institute of Genetics, Yata, Shizuoka, Japan.
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29
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Stewart M. Insights into the molecular mechanism of nuclear trafficking using nuclear transport factor 2 (NTF2). Cell Struct Funct 2000; 25:217-25. [PMID: 11129791 DOI: 10.1247/csf.25.217] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP. The simplicity and specialization of this system, combined with the availability of crystal structures of NTF2, RanGDP and their complex, has facilitated the investigation of the molecular mechanism of its trafficking. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. Mutants engineered on the basis of structural information together with determination of binding constants have been used to dissect the roles of these interactions in transport. Thus, NTF2 binds to RanGDP sufficiently strongly for the complex to remain intact during transport through NPCs, but the interaction between NTF2 and FxFG nucleoporins is much more transient, which would enable NTF2 to move through the NPC by hopping from one repeat to another. An analogous nucleoporin hopping mechanism may also be used by carrier molecules of the importin-beta family to move through NPCs.
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Affiliation(s)
- M Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England.
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30
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Stein GS, van Wijnen AJ, Stein JL, Lian JB, Montecino M, Choi J, Zaidi K, Javed A. Intranuclear trafficking of transcription factors: implications for biological control. J Cell Sci 2000; 113 ( Pt 14):2527-33. [PMID: 10862710 DOI: 10.1242/jcs.113.14.2527] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The subnuclear organization of nucleic acids and cognate regulatory factors suggests that there are functional interrelationships between nuclear structure and gene expression. Nuclear proteins that are localized in discrete domains within the nucleus include the leukemia-associated acute myelogenous leukemia (AML) and promyelocytic leukemia (PML) factors, the SC-35 RNA-processing factors, nucleolar proteins and components of both transcriptional and DNA replication complexes. Mechanisms that control the spatial distribution of transcription factors within the three-dimensional context of the nucleus may involve the sorting of regulatory information, as well as contribute to the assembly and activity of sites that support gene expression. Molecular, cellular, genetic and biochemical approaches have identified distinct protein segments, termed intranuclear-targeting signals, that are responsible for directing regulatory factors to specific subnuclear sites. Gene rearrangements that remove or alter intranuclear-targeting signals are prevalent in leukemias and have been linked to altered localization of regulatory factors within the nucleus. These modifications in the intranuclear targeting of transcription factors might abrogate fidelity of gene expression in tumor cells by influencing the spatial organization and/or assembly of machineries involved in the synthesis and processing of gene transcripts.
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Affiliation(s)
- G S Stein
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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31
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Bayliss R, Corbett AH, Stewart M. The molecular mechanism of transport of macromolecules through nuclear pore complexes. Traffic 2000; 1:448-56. [PMID: 11208130 DOI: 10.1034/j.1600-0854.2000.010602.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Trafficking of macromolecules between nuclear and cytoplasmic compartments takes place through the nuclear pore complexes (NPCs) of the nuclear envelope. Nuclear trafficking involves a complex series of interactions between cargo, soluble transport factors (carriers) and nuclear pore proteins (nucleoporins) that are orchestrated by the Ras-family GTPase Ran. The primary role of Ran is probably to establish directionality and to sort molecules to be transported by controlling the interaction between carriers and cargoes, so that they bind in one compartment but dissociate in the other. Translocation of carriers and cargo-carrier complexes through NPCs requires interactions between the carriers and nucleoporins that contain distinctive tandem sequence repeats based on cores rich in glycine and phenylalanine residues that are separated by hydrophilic linkers. Much recent work has focused on these interactions and, in particular, their specificity, regulation and function. Evidence is accumulating that carriers move through the NPC by distinct but overlapping routes using specific subsets of nucleoporins.
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Affiliation(s)
- R Bayliss
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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