1
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Mars JC, Culjkovic-Kraljacic B, Borden KL. eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. Nucleus 2024; 15:2360196. [PMID: 38880976 PMCID: PMC11185188 DOI: 10.1080/19491034.2024.2360196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.
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Affiliation(s)
- Jean-Clément Mars
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
| | - Katherine L.B. Borden
- Institute of Research in Immunology and Cancer, Department of Pathology and Cell Biology, Université de Montréal, Montréal, QC, Canada
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2
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Gasser SM, Stutz F. SUMO in the regulation of DNA repair and transcription at nuclear pores. FEBS Lett 2023; 597:2833-2850. [PMID: 37805446 DOI: 10.1002/1873-3468.14751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023]
Abstract
Two related post-translational modifications, the covalent linkage of Ubiquitin and the Small Ubiquitin-related MOdifier (SUMO) to lysine residues, play key roles in the regulation of both DNA repair pathway choice and transcription. Whereas ubiquitination is generally associated with proteasome-mediated protein degradation, the impact of sumoylation has been more mysterious. In the cell nucleus, sumoylation effects are largely mediated by the relocalization of the modified targets, particularly in response to DNA damage. This is governed in part by the concentration of SUMO protease at nuclear pores [Melchior, F et al. (2003) Trends Biochem Sci 28, 612-618; Ptak, C and Wozniak, RW (2017) Adv Exp Med Biol 963, 111-126]. We review here the roles of sumoylation in determining genomic locus positioning relative to the nuclear envelope and to nuclear pores, to facilitate repair and regulate transcription.
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Affiliation(s)
- Susan M Gasser
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- ISREC Foundation, Agora Cancer Research Center, Lausanne, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Switzerland
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3
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Liang W, Hu C, Zhu Q, Cheng X, Gao S, Liu Z, Wang H, Li P, Gao Y, Qian R. Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma. Front Oncol 2023; 13:1007198. [PMID: 37284202 PMCID: PMC10240054 DOI: 10.3389/fonc.2023.1007198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/29/2023] [Indexed: 06/08/2023] Open
Abstract
Nuclear pore complex (NPC) is a major transport pivot for nucleocytoplasmic molecule exchange. Nucleoporin 205 (NUP205)-a main component of NPC-plays a key regulatory role in tumor cell proliferation; however, few reports document its effect on the pathological progression of lower-grade glioma (LGG). Therefore, we conducted an integrated analysis using 906 samples from multiple public databases to explore the effects of NUP205 on the prognosis, clinicopathological characteristics, regulatory mechanism, and tumor immune microenvironment (TIME) formation in LGG. First, multiple methods consistently showed that the mRNA and protein expression levels of NUP205 were higher in LGG tumor tissue than in normal brain tissue. This increased expression was mainly noted in the higher WHO Grade, IDH-wild type, and 1p19q non-codeleted type. Second, various survival analysis methods showed that the highly expressed NUP205 was an independent risk indicator that led to reduced survival time of patients with LGG. Third, GSEA analysis showed that NUP205 regulated the pathological progress of LGG via the cell cycle, notch signaling pathway, and aminoacyl-tRNA biosynthesis. Ultimately, immune correlation analysis suggested that high NUP205 expression was positively correlated with the infiltration of multiple immune cells, particularly M2 macrophages, and was positively correlated with eight immune checkpoints, particularly PD-L1. Collectively, this study documented the pathogenicity of NUP205 in LGG for the first time, expanding our understanding of its molecular function. Furthermore, this study highlighted the potential value of NUP205 as a target of anti-LGG immunotherapy.
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Affiliation(s)
- Wenjia Liang
- People’s Hospital of Henan University, Henan Provincial People’s Hospital, Microbiome Laboratory, Zhengzhou, Henan, China
| | - Chenchen Hu
- Intensive Care Unit, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qingyun Zhu
- People’s Hospital of Henan University, Henan Provincial People’s Hospital, Microbiome Laboratory, Zhengzhou, Henan, China
| | - Xingbo Cheng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Shanjun Gao
- Microbiome Laboratory, Henan Provincial People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Hongbo Wang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, Gansu, China
| | - Pengxu Li
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Yanzheng Gao
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, China
| | - Rongjun Qian
- Department of Neurosurgery, Henan Provincial People’s Hospital, People’s Hospital of Henan University, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
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4
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Zhang D, Zhang X. Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100495. [PMID: 34117705 DOI: 10.1002/smll.202100495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.
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Affiliation(s)
- Dan Zhang
- Cancer Centre and Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
| | - Xuanjun Zhang
- Cancer Centre and Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
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5
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Lautier O, Penzo A, Rouvière JO, Chevreux G, Collet L, Loïodice I, Taddei A, Devaux F, Collart MA, Palancade B. Co-translational assembly and localized translation of nucleoporins in nuclear pore complex biogenesis. Mol Cell 2021; 81:2417-2427.e5. [PMID: 33838103 DOI: 10.1016/j.molcel.2021.03.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
Abstract
mRNA translation is coupled to multiprotein complex assembly in the cytoplasm or to protein delivery into intracellular compartments. Here, by combining systematic RNA immunoprecipitation and single-molecule RNA imaging in yeast, we have provided a complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC). We report that binary interactions between NPC subunits can be established during translation, in the cytoplasm. Strikingly, the nucleoporins Nup1/Nup2, together with a number of nuclear proteins, are instead translated at nuclear pores, through a mechanism involving interactions between their nascent N-termini and nuclear transport receptors. Uncoupling this co-translational recruitment further triggers the formation of cytoplasmic foci of unassembled polypeptides. Altogether, our data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits and that localized translation can ensure the proper delivery of proteins to the pore and the nucleus.
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Affiliation(s)
- Ophélie Lautier
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Arianna Penzo
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Jérôme O Rouvière
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Guillaume Chevreux
- ProteoSeine@IJM, Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Louis Collet
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Isabelle Loïodice
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, UMR3664 Nuclear Dynamics, Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, UMR3664 Nuclear Dynamics, Paris, France
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de biologie Paris-Seine (IBPS), UMR 7238, Laboratoire de biologie computationnelle et quantitative, LCQB, 4 place Jussieu, 75005 Paris, France
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France.
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6
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The Nuclear Pore Complex and mRNA Export in Cancer. Cancers (Basel) 2020; 13:cancers13010042. [PMID: 33375634 PMCID: PMC7796397 DOI: 10.3390/cancers13010042] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Export of mRNAs from the nucleus to the cytoplasm is a key regulatory step in the expression of proteins. mRNAs are transported through the nuclear pore complex (NPC). Export of mRNAs responds to a variety of cellular stimuli and stresses. Revelations of the specific effects elicited by NPC components and associated co-factors provides a molecular basis for the export of selected RNAs, independent of bulk mRNA export. Aberrant RNA export has been observed in primary human cancer specimens. These cargo RNAs encode factors involved in nearly all facets of malignancy. Indeed, the NPC components involved in RNA export as well as the RNA export machinery can be found to be dysregulated, mutated, or impacted by chromosomal translocations in cancer. The basic mechanisms associated with RNA export with relation to export machinery and relevant NPC components are described. Therapeutic strategies targeting this machinery in clinical trials is also discussed. These findings firmly position RNA export as a targetable feature of cancer along with transcription and translation.
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7
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Niknam Hamidabad M, Asgari S, Haji Abdolvahab R. Nanoparticle-assisted polymer translocation through a nanopore. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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8
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Roy A, Narayan G. Oncogenic potential of nucleoporins in non-hematological cancers: recent update beyond chromosome translocation and gene fusion. J Cancer Res Clin Oncol 2019; 145:2901-2910. [DOI: 10.1007/s00432-019-03063-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022]
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9
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Soheilypour M, Mofrad MRK. Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system. Nucleus 2019; 9:202-211. [PMID: 29431587 PMCID: PMC5973141 DOI: 10.1080/19491034.2018.1439304] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Specifically, it is unclear how quality control proteins at the entry of the nuclear pore complex (NPC) distinguish normal and aberrant mRNAs. While some of the involved components are suggested to act as switches and recruit different factors to normal versus aberrant mRNAs, some experimental and computational evidence suggests that the combined effect of the regulated stochastic interactions between the involved components could potentially achieve an efficient quality control of mRNAs. In this review, we present a state-of-the-art portrait of the mRNA quality control research and discuss the current hypotheses proposed for dynamics of the cooperation between the involved components and how it leads to their shared goal: mRNA quality control prior to export into the cytoplasm.
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Affiliation(s)
- Mohammad Soheilypour
- a Molecular Cell Biomechanics Laboratory , Departments of Bioengineering and Mechanical Engineering, University of California , Berkeley
| | - Mohammad R K Mofrad
- a Molecular Cell Biomechanics Laboratory , Departments of Bioengineering and Mechanical Engineering, University of California , Berkeley
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10
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Zheleva A, Gómez-Orte E, Sáenz-Narciso B, Ezcurra B, Kassahun H, de Toro M, Miranda-Vizuete A, Schnabel R, Nilsen H, Cabello J. Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.
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Affiliation(s)
- Angelina Zheleva
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Eva Gómez-Orte
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | | | - Begoña Ezcurra
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Henok Kassahun
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María de Toro
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Juan Cabello
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
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11
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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: 22] [Impact Index Per Article: 4.4] [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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12
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Chumová J, Kourová H, Trögelová L, Halada P, Binarová P. Microtubular and Nuclear Functions of γ-Tubulin: Are They LINCed? Cells 2019; 8:cells8030259. [PMID: 30893853 PMCID: PMC6468392 DOI: 10.3390/cells8030259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 01/02/2023] Open
Abstract
γ-Tubulin is a conserved member of the tubulin superfamily with a function in microtubule nucleation. Proteins of γ-tubulin complexes serve as nucleation templates as well as a majority of other proteins contributing to centrosomal and non-centrosomal nucleation, conserved across eukaryotes. There is a growing amount of evidence of γ-tubulin functions besides microtubule nucleation in transcription, DNA damage response, chromatin remodeling, and on its interactions with tumor suppressors. However, the molecular mechanisms are not well understood. Furthermore, interactions with lamin and SUN proteins of the LINC complex suggest the role of γ-tubulin in the coupling of nuclear organization with cytoskeletons. γ-Tubulin that belongs to the clade of eukaryotic tubulins shows characteristics of both prokaryotic and eukaryotic tubulins. Both human and plant γ-tubulins preserve the ability of prokaryotic tubulins to assemble filaments and higher-order fibrillar networks. γ-Tubulin filaments, with bundling and aggregating capacity, are suggested to perform complex scaffolding and sequestration functions. In this review, we discuss a plethora of γ-tubulin molecular interactions and cellular functions, as well as recent advances in understanding the molecular mechanisms behind them.
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Affiliation(s)
- Jana Chumová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Hana Kourová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Lucie Trögelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavla Binarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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13
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Raich N, Mahmoudi S, Emre D, Karess RE. Mad1 influences interphase nucleoplasm organization and chromatin regulation in Drosophila. Open Biol 2018; 8:rsob.180166. [PMID: 30333236 PMCID: PMC6223205 DOI: 10.1098/rsob.180166] [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: 09/12/2018] [Accepted: 09/21/2018] [Indexed: 12/15/2022] Open
Abstract
The Drosophila Mad1 spindle checkpoint protein helps organize several nucleoplasmic components, and flies lacking Mad1 present changes in gene expression reflecting altered chromatin conformation. In interphase, checkpoint protein Mad1 is usually described as localizing to the inner nuclear envelope by binding the nucleoporin Tpr, an interaction believed to contribute to proper mitotic regulation. Whether Mad1 has other nuclear interphase functions is unknown. We found in Drosophila that Mad1 is present in nuclei of both mitotic and postmitotic tissues. Three proteins implicated in various aspects of chromatin organization co-immunoprecipitated with Mad1 from fly embryos: Mtor/Tpr, the SUMO peptidase Ulp1 and Raf2, a subunit of a Polycomb-like complex. In primary spermatocytes, all four proteins colocalized in a previously undescribed chromatin-associated structure called here a MINT (Mad1-containing IntraNuclear Territory). MINT integrity required all four proteins. In mad1 mutant spermatocytes, the other proteins were no longer confined to chromatin domains but instead dispersed throughout the nucleoplasm. mad1 flies also presented phenotypes indicative of excessive chromatin of heterochromatic character during development of somatic tissues. Together these results suggest that Drosophila Mad1, by helping organize its interphase protein partners in the nucleoplasm, contributes to proper chromatin regulation.
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Affiliation(s)
- Natacha Raich
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Souhir Mahmoudi
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Doruk Emre
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Roger E Karess
- CNRS, Institut Jacques Monod, UMR7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
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14
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García-Rubio M, Aguilera P, Lafuente-Barquero J, Ruiz JF, Simon MN, Geli V, Rondón AG, Aguilera A. Yra1-bound RNA-DNA hybrids cause orientation-independent transcription-replication collisions and telomere instability. Genes Dev 2018; 32:965-977. [PMID: 29954833 PMCID: PMC6075034 DOI: 10.1101/gad.311274.117] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/16/2018] [Indexed: 12/25/2022]
Abstract
R loops are an important source of genome instability, largely due to their negative impact on replication progression. Yra1/ALY is an abundant RNA-binding factor conserved from yeast to humans and required for mRNA export, but its excess causes lethality and genome instability. Here, we show that, in addition to ssDNA and ssRNA, Yra1 binds RNA-DNA hybrids in vitro and, when artificially overexpressed, can be recruited to chromatin in an RNA-DNA hybrid-dependent manner, stabilizing R loops and converting them into replication obstacles in vivo. Importantly, an excess of Yra1 increases R-loop-mediated genome instability caused by transcription-replication collisions regardless of whether they are codirectional or head-on. It also induces telomere shortening in telomerase-negative cells and accelerates senescence, consistent with a defect in telomere replication. Our results indicate that RNA-DNA hybrids form transiently in cells regardless of replication and, after stabilization by excess Yra1, compromise genome integrity, in agreement with a two-step model of R-loop-mediated genome instability. This work opens new perspectives to understand transcription-associated genome instability in repair-deficient cells, including tumoral cells.
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Affiliation(s)
- María García-Rubio
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Paula Aguilera
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 13273 Marseille, France
| | - Juan Lafuente-Barquero
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José F Ruiz
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Marie-Noelle Simon
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 13273 Marseille, France
| | - Vincent Geli
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labellisée Ligue, 13273 Marseille, France
| | - Ana G Rondón
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Andrés Aguilera
- Andalusian Center of Molecular Biology and Regenerative Medicine (CABIMER), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Pablo de Olavide, 41092 Seville, Spain
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15
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Li P, Stumpf M, Müller R, Eichinger L, Glöckner G, Noegel AA. The function of the inner nuclear envelope protein SUN1 in mRNA export is regulated by phosphorylation. Sci Rep 2017; 7:9157. [PMID: 28831067 PMCID: PMC5567243 DOI: 10.1038/s41598-017-08837-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/13/2017] [Indexed: 01/15/2023] Open
Abstract
SUN1, a component of the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex, functions in mammalian mRNA export through the NXF1-dependent pathway. It associates with mRNP complexes by direct interaction with NXF1. It also binds to the NPC through association with the nuclear pore component Nup153, which is involved in mRNA export. The SUN1-NXF1 association is at least partly regulated by a protein kinase C (PKC) which phosphorylates serine 113 (S113) in the N-terminal domain leading to reduced interaction. The phosphorylation appears to be important for the SUN1 function in nuclear mRNA export since GFP-SUN1 carrying a S113A mutation was less efficient in restoring mRNA export after SUN1 knockdown as compared to the wild type protein. By contrast, GFP-SUN1-S113D resembling the phosphorylated state allowed very efficient export of poly(A)+RNA. Furthermore, probing a possible role of the LINC complex component Nesprin-2 in this process we observed impaired mRNA export in Nesprin-2 knockdown cells. This effect might be independent of SUN1 as expression of a GFP tagged SUN-domain deficient SUN1, which no longer can interact with Nesprin-2, did not affect mRNA export.
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Affiliation(s)
- Ping Li
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Cologne, Germany.,Institutes of Biomedical Sciences, Shanxi University, 030006, Taiyuan, China
| | - Maria Stumpf
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Cologne, Germany
| | - Rolf Müller
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Cologne, Germany
| | - Ludwig Eichinger
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Cologne, Germany
| | - Gernot Glöckner
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Cologne, Germany.
| | - Angelika A Noegel
- Institute of Biochemistry I, Medical Faculty, University Hospital Cologne, Center for Molecular Medicine Cologne (CMMC) and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 52, 50931, Cologne, Germany.
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16
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Heinrich S, Derrer CP, Lari A, Weis K, Montpetit B. Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights. Bioessays 2017; 39. [PMID: 28052353 DOI: 10.1002/bies.201600124] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression.
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Affiliation(s)
| | | | - Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Karsten Weis
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, CA, USA
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17
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Soheilypour M, Mofrad MRK. Regulation of RNA-binding proteins affinity to export receptors enables the nuclear basket proteins to distinguish and retain aberrant mRNAs. Sci Rep 2016; 6:35380. [PMID: 27805000 PMCID: PMC5090210 DOI: 10.1038/srep35380] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/23/2016] [Indexed: 02/06/2023] Open
Abstract
Export of messenger ribonucleic acids (mRNAs) into the cytoplasm is a fundamental step in gene regulation processes, which is meticulously quality controlled by highly efficient mechanisms in eukaryotic cells. Yet, it remains unclear how the aberrant mRNAs are recognized and retained inside the nucleus. Using a new modelling approach for complex systems, namely the agent-based modelling (ABM) approach, we develop a minimal model of the mRNA quality control (QC) mechanism. Our results demonstrate that regulation of the affinity of RNA-binding proteins (RBPs) to export receptors along with the weak interaction between the nuclear basket protein (Mlp1 or Tpr) and RBPs are the minimum requirements to distinguish and retain aberrant mRNAs. Our results show that the affinity between Tpr and RBPs is optimized to maximize the retention of aberrant mRNAs. In addition, we demonstrate how the length of mRNA affects the QC process. Since longer mRNAs spend more time in the nuclear basket to form a compact conformation and initiate their export, nuclear basket proteins could more easily capture and retain them inside the nucleus.
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Affiliation(s)
- M. Soheilypour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, 94720, USA
| | - M. R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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18
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Paul B, Montpetit B. Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus. Mol Biol Cell 2016; 27:2742-56. [PMID: 27385342 PMCID: PMC5007094 DOI: 10.1091/mbc.e16-04-0244] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/29/2016] [Indexed: 01/17/2023] Open
Abstract
In a screen of >1000 essential gene mutants in Saccharomyces cerevisiae, 26 mutants are found that directly or indirectly affect mRNA processing and/or mRNA export. Single-molecule FISH data show that the majority of these mutants retain mRNAs at discrete locations within the nucleus, which include the nucleolus. Many protein factors are required for mRNA biogenesis and nuclear export, which are central to the eukaryotic gene expression program. It is unclear, however, whether all factors have been identified. Here we report on a screen of >1000 essential gene mutants in Saccharomyces cerevisiae for defects in mRNA processing and export, identifying 26 mutants with defects in this process. Single-molecule FISH data showed that the majority of these mutants accumulated mRNA within specific regions of the nucleus, which included 1) mRNAs within the nucleolus when nucleocytoplasmic transport, rRNA biogenesis, or RNA processing and surveillance was disrupted, 2) the buildup of mRNAs near transcription sites in 3′-end processing and chromosome segregation mutants, and 3) transcripts being enriched near nuclear pore complexes when components of the mRNA export machinery were mutated. These data show that alterations to various nuclear processes lead to the retention of mRNAs at discrete locations within the nucleus.
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Affiliation(s)
- Biplab Paul
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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19
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Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grunwald D, Montpetit B. In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol 2016; 211:1121-30. [PMID: 26694837 PMCID: PMC4687877 DOI: 10.1083/jcb.201503135] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Single-particle imaging in budding yeast demonstrates that mRNP export is fast (∼200 ms) and that mRNPs are retained at NPCs and undergo retrograde transport in a mex67-5 mutant, proving an essential role for Mex67p in directional mRNP transport. Many messenger RNA export proteins have been identified; yet the spatial and temporal activities of these proteins and how they determine directionality of messenger ribonucleoprotein (mRNP) complex export from the nucleus remain largely undefined. Here, the bacteriophage PP7 RNA-labeling system was used in Saccharomyces cerevisiae to follow single-particle mRNP export events with high spatial precision and temporal resolution. These data reveal that mRNP export, consisting of nuclear docking, transport, and cytoplasmic release from a nuclear pore complex (NPC), is fast (∼200 ms) and that upon arrival in the cytoplasm, mRNPs are frequently confined near the nuclear envelope. Mex67p functions as the principal mRNP export receptor in budding yeast. In a mex67-5 mutant, delayed cytoplasmic release from NPCs and retrograde transport of mRNPs was observed. This proves an essential role for Mex67p in cytoplasmic mRNP release and directionality of transport.
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Affiliation(s)
- Carlas Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Azra Lari
- Department of Cell Biology, University of Alberta, T6G 2H7 Edmonton, Alberta, Canada
| | | | - Anette Ouwehand
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Ammeret Rossouw
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Maximiliaan Huisman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Thomas Dange
- Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Mark Hopman
- Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Aviva Joseph
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daniel Zenklusen
- Departement de Biochimie et Medecine Moleculaire, Universite de Montreal, H3T 1J4 Montreal, Quebec, Canada
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland Department of Cell and Developmental Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, T6G 2H7 Edmonton, Alberta, Canada
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20
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Abstract
Nuclear pore complexes (NPCs) are indispensable for cell function and are at the center of several human diseases. NPCs provide access to the nucleus and regulate the transport of proteins and RNA across the nuclear envelope. They are aqueous channels generated from a complex network of evolutionarily conserved proteins known as nucleporins. In this Cell Science at a Glance article and the accompanying poster, we discuss how transport between the nucleoplasm and the cytoplasm is regulated, what we currently know about the structure of individual nucleoporins and the assembled NPC, and how the cell regulates assembly and disassembly of such a massive structure. Our aim is to provide a general overview on what we currently know about the nuclear pore and point out directions of research this area is heading to.
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21
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Schwartz TU. The Structure Inventory of the Nuclear Pore Complex. J Mol Biol 2016; 428:1986-2000. [PMID: 27016207 DOI: 10.1016/j.jmb.2016.03.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/18/2022]
Abstract
The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.
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Affiliation(s)
- Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
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22
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Abstract
Nuclear pore complexes (NPCs) have been shown to regulate distinct steps of the gene expression process, from transcription to mRNA export. In particular, mRNAs expressed from intron-containing genes are surveyed by a specific NPC-dependent quality control pathway ensuring that unspliced mRNAs are retained within the nucleus. In this Extra View, we summarize the different approaches that have been developed to evaluate the contribution of various NPC components to the expression of intron-containing genes. We further present the mechanistic models that could account for pre-mRNA retention at the nuclear side of NPCs. Finally, we discuss the possibility that other stages of intron-containing gene expression could be regulated by nuclear pores, in particular through the regulation of mRNA biogenesis factors by the NPC-associated SUMO protease Ulp1.
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Affiliation(s)
- Amandine Bonnet
- a Institut Jacques Monod; CNRS; UMR 7592; Univ Paris Diderot ; Sorbonne Paris Cité; Paris , France
| | - Benoit Palancade
- a Institut Jacques Monod; CNRS; UMR 7592; Univ Paris Diderot ; Sorbonne Paris Cité; Paris , France
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23
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Keller A, Bader SL, Kusebauch U, Shteynberg D, Hood L, Moritz RL. Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides. Mol Cell Proteomics 2015; 15:1151-63. [PMID: 26704149 DOI: 10.1074/mcp.m115.054478] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Indexed: 11/06/2022] Open
Abstract
Posttranslational modifications of proteins play an important role in biology. For example, phosphorylation is a key component in signal transduction in all three domains of life, and histones can be modified in such a variety of ways that a histone code for gene regulation has been proposed. Shotgun proteomics is commonly used to identify posttranslational modifications as well as chemical modifications from sample processing. However, it favors the detection of abundant peptides over the repertoire presented, and the data analysis usually requires advance specification of modification masses and target amino acids, their number constrained by available computational resources. Recent advances in data independent acquisition mass spectrometry technologies such as SWATH-MS enable a deeper recording of the peptide contents of samples, including peptides with modifications. Here, we present a novel approach that applies the power of SWATH-MS analysis to the automated pursuit of modified peptides. With the new SWATHProphet(PTM) functionality added to the open source SWATHProphet software, precursor ions consistent with a modification are identified along with the mass and localization of the modification in the peptide sequence in a sensitive and unrestricted manner without the need to anticipate the modifications in advance. Using this method, we demonstrate the detection of a wide assortment of modified peptides, many unanticipated, in samples containing unpurified synthetic peptides and human urine, as well as in phospho-enriched human tissue culture cell samples.
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Affiliation(s)
- Andrew Keller
- From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
| | - Samuel L Bader
- From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
| | - Ulrike Kusebauch
- From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
| | - David Shteynberg
- From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
| | - Leroy Hood
- From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
| | - Robert L Moritz
- From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109
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24
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Sloan KE, Gleizes PE, Bohnsack MT. Nucleocytoplasmic Transport of RNAs and RNA-Protein Complexes. J Mol Biol 2015; 428:2040-59. [PMID: 26434509 DOI: 10.1016/j.jmb.2015.09.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022]
Abstract
RNAs and ribonucleoprotein complexes (RNPs) play key roles in mediating and regulating gene expression. In eukaryotes, most RNAs are transcribed, processed and assembled with proteins in the nucleus and then either function in the cytoplasm or also undergo a cytoplasmic phase in their biogenesis. This compartmentalization ensures that sequential steps in gene expression and RNP production are performed in the correct order and it allows important quality control mechanisms that prevent the involvement of aberrant RNAs/RNPs in these cellular pathways. The selective exchange of RNAs/RNPs between the nucleus and cytoplasm is enabled by nuclear pore complexes, which function as gateways between these compartments. RNA/RNP transport is facilitated by a range of nuclear transport receptors and adaptors, which are specifically recruited to their cargos and mediate interactions with nucleoporins to allow directional translocation through nuclear pore complexes. While some transport factors are only responsible for the export/import of a certain class of RNA/RNP, others are multifunctional and, in the case of large RNPs, several export factors appear to work together to bring about export. Recent structural studies have revealed aspects of the mechanisms employed by transport receptors to enable specific cargo recognition, and genome-wide approaches have provided the first insights into the diverse composition of pre-mRNPs during export. Furthermore, the regulation of RNA/RNP export is emerging as an important means to modulate gene expression under stress conditions and in disease.
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Affiliation(s)
- Katherine E Sloan
- Institute for Molecular Biology, Goettingen University Medical Department, 37073 Goettingen, Germany
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099, Université de Toulouse-Paul Sabatier, CNRS, Toulouse, France
| | - Markus T Bohnsack
- Institute for Molecular Biology, Goettingen University Medical Department, 37073 Goettingen, Germany; Goettingen Centre for Molecular Biosciences, Georg-August-University, 37075 Goettingen, Germany.
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25
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GGGGCC repeat expansion in C9orf72 compromises nucleocytoplasmic transport. Nature 2015; 525:129-33. [PMID: 26308899 DOI: 10.1038/nature14974] [Citation(s) in RCA: 604] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 07/24/2015] [Indexed: 12/30/2022]
Abstract
The GGGGCC (G4C2) repeat expansion in a noncoding region of C9orf72 is the most common cause of sporadic and familial forms of amyotrophic lateral sclerosis and frontotemporal dementia. The basis for pathogenesis is unknown. To elucidate the consequences of G4C2 repeat expansion in a tractable genetic system, we generated transgenic fly lines expressing 8, 28 or 58 G4C2-repeat-containing transcripts that do not have a translation start site (AUG) but contain an open-reading frame for green fluorescent protein to detect repeat-associated non-AUG (RAN) translation. We show that these transgenic animals display dosage-dependent, repeat-length-dependent degeneration in neuronal tissues and RAN translation of dipeptide repeat (DPR) proteins, as observed in patients with C9orf72-related disease. This model was used in a large-scale, unbiased genetic screen, ultimately leading to the identification of 18 genetic modifiers that encode components of the nuclear pore complex (NPC), as well as the machinery that coordinates the export of nuclear RNA and the import of nuclear proteins. Consistent with these results, we found morphological abnormalities in the architecture of the nuclear envelope in cells expressing expanded G4C2 repeats in vitro and in vivo. Moreover, we identified a substantial defect in RNA export resulting in retention of RNA in the nuclei of Drosophila cells expressing expanded G4C2 repeats and also in mammalian cells, including aged induced pluripotent stem-cell-derived neurons from patients with C9orf72-related disease. These studies show that a primary consequence of G4C2 repeat expansion is the compromise of nucleocytoplasmic transport through the nuclear pore, revealing a novel mechanism of neurodegeneration.
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26
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Wickramasinghe VO, Laskey RA. Control of mammalian gene expression by selective mRNA export. Nat Rev Mol Cell Biol 2015; 16:431-42. [PMID: 26081607 DOI: 10.1038/nrm4010] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear export of mRNAs is a crucial step in the regulation of gene expression, linking transcription in the nucleus to translation in the cytoplasm. Although important components of the mRNA export machinery are well characterized, such as transcription-export complexes TREX and TREX-2, recent work has shown that, in some instances, mammalian mRNA export can be selective and can regulate crucial biological processes such as DNA repair, gene expression, maintenance of pluripotency, haematopoiesis, proliferation and cell survival. Such findings show that mRNA export is an unexpected, yet potentially important, mechanism for the control of gene expression and of the mammalian transcriptome.
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Affiliation(s)
- Vihandha O Wickramasinghe
- Medical Research Centre (MRC) Cancer Unit, Hutchison/MRC Research Centre, Box 197, Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Ronald A Laskey
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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27
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Oeffinger M, Montpetit B. Emerging properties of nuclear RNP biogenesis and export. Curr Opin Cell Biol 2015; 34:46-53. [PMID: 25938908 DOI: 10.1016/j.ceb.2015.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/23/2015] [Accepted: 04/14/2015] [Indexed: 01/02/2023]
Abstract
RNA biology has recently seen an explosion of data due to advances in RNA sequencing, proteomic, and RNA imaging technologies. In this review, we highlight progress that has been made using these approaches in the area of nuclear RNP biogenesis and export. Excitingly, the ability to collect quantitative data at the 'omics' scale combined with measurements of transcription, decay, and transport kinetics is providing the information needed to address RNP biogenesis at a systems level. We believe this to be a necessary and critical next step that will lead to a better understanding of how RNP quality, diversity, and fate emerge from a defined set of nuclear RNP assembly and maturation steps.
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Affiliation(s)
- Marlene Oeffinger
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec, Canada H2W 1R7; Département de biochimie et médicine moléculaire, Université de Montréal, Montréal, Québec, Canada H3T 1J4; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada H3A 1A3.
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, 5-14 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7.
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Bonnet A, Bretes H, Palancade B. Nuclear pore components affect distinct stages of intron-containing gene expression. Nucleic Acids Res 2015; 43:4249-61. [PMID: 25845599 PMCID: PMC4417180 DOI: 10.1093/nar/gkv280] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/20/2015] [Indexed: 12/20/2022] Open
Abstract
Several nuclear pore-associated factors, including the SUMO-protease Ulp1, have been proposed to prevent the export of intron-containing messenger ribonucleoparticles (mRNPs) in yeast. However, the molecular mechanisms of this nuclear pore-dependent mRNA quality control, including the sumoylated targets of Ulp1, have remained unidentified. Here, we demonstrate that the apparent 'pre-mRNA leakage' phenotype arising upon ULP1 inactivation is shared by sumoylation mutants of the THO complex, an early mRNP biogenesis factor. Importantly, we establish that alteration of THO complex activity differentially impairs the expression of intronless and intron-containing reporter genes, rather than triggering bona fide 'pre-mRNA leakage'. Indeed, we show that the presence of introns within THO target genes attenuates the effect of THO inactivation on their transcription. Epistasis analyses further clarify that different nuclear pore components influence intron-containing gene expression at distinct stages. Ulp1, whose maintenance at nuclear pores depends on the Nup84 complex, impacts on THO-dependent gene expression, whereas the nuclear basket-associated Mlp1/Pml39 proteins prevent pre-mRNA export at a later stage, contributing to mRNA quality control. Our study thus highlights the multiplicity of mechanisms by which nuclear pores contribute to gene expression, and further provides the first evidence that intronic sequences can alleviate early mRNP biogenesis defects.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Hugo Bretes
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ecole Doctorale Gènes Génomes Cellules, Université Paris Sud-11, 91400 Orsay, France
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
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Abstract
Understanding of the roles that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 1 (HOS1) plays in the plant's ability to sense and respond to environmental signals has grown dramatically. Mechanisms through which HOS1 affects plant development have been uncovered, and the broader consequences of hos1 on the plant's ability to perceive and respond to its environment have been investigated. As such, it has been possible to place HOS1 as a key integrator of temperature information in response to both acute signals and cues that indicate time of year into developmental processes that are essential for plant survival. This review summarizes knowledge of HOS1's form and function, and contextualizes this information so that it is relevant for better understanding the processes of cold signalling, flowering time, and nuclear pore complex function more broadly.
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Affiliation(s)
- Dana R MacGregor
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Colney Lane, Norwich, Norfolk NR4 7UH, UK
| | - Steven Penfield
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Colney Lane, Norwich, Norfolk NR4 7UH, UK
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