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Odell J, Lammerding J. Lamins as structural nuclear elements through evolution. Curr Opin Cell Biol 2023; 85:102267. [PMID: 37871500 PMCID: PMC10841731 DOI: 10.1016/j.ceb.2023.102267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023]
Abstract
Lamins are nuclear intermediate filament proteins with important, well-established roles in humans and other vertebrates. Lamins interact with DNA and numerous proteins at the nuclear envelope to determine the mechanical properties of the nucleus, coordinate chromatin organization, and modulate gene expression. Many of these functions are conserved in the lamin homologs found in basal metazoan organisms, including Drosophila and Caenorhabditis elegans. Lamin homologs have also been recently identified in non-metazoans, like the amoeba Dictyostelium discoideum, yet how these proteins compare functionally to the metazoan isoforms is only beginning to emerge. A better understanding of these distantly related lamins is not only valuable for a more complete picture of eukaryotic evolution, but may also provide new insights into the function of vertebrate lamins.
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Affiliation(s)
- Jacob Odell
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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2
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Strachan J, Leidecker O, Spanos C, Le Coz C, Chapman E, Arsenijevic A, Zhang H, Zhao N, Spoel SH, Bayne EH. SUMOylation regulates Lem2 function in centromere clustering and silencing. J Cell Sci 2023; 136:jcs260868. [PMID: 37970674 PMCID: PMC10730020 DOI: 10.1242/jcs.260868] [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: 12/02/2022] [Accepted: 11/07/2023] [Indexed: 11/17/2023] Open
Abstract
Regulation by the small modifier SUMO is heavily dependent on spatial control of enzymes that mediate the attachment and removal of SUMO on substrate proteins. Here, we show that in the fission yeast Schizosaccharomyces pombe, delocalisation of the SUMO protease Ulp1 from the nuclear envelope results in centromeric defects that can be attributed to hyper-SUMOylation at the nuclear periphery. Unexpectedly, we find that although this localised hyper-SUMOylation impairs centromeric silencing, it can also enhance centromere clustering. Moreover, both effects are at least partially dependent on SUMOylation of the inner nuclear membrane protein Lem2. Lem2 has previously been implicated in diverse biological processes, including the promotion of both centromere clustering and silencing, but how these distinct activities are coordinated was unclear; our observations suggest a model whereby SUMOylation serves as a regulatory switch, modulating Lem2 interactions with competing partner proteins to balance its roles in alternative pathways. Our findings also reveal a previously unappreciated role for SUMOylation in promoting centromere clustering.
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Affiliation(s)
- Joanna Strachan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Orsolya Leidecker
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany
| | - Christos Spanos
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Clementine Le Coz
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Elliott Chapman
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Ana Arsenijevic
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Haidao Zhang
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Ning Zhao
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Steven H. Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Elizabeth H. Bayne
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
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3
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London N, Medina-Pritchard B, Spanos C, Rappsilber J, Jeyaprakash AA, Allshire RC. Direct recruitment of Mis18 to interphase spindle pole bodies promotes CENP-A chromatin assembly. Curr Biol 2023; 33:4187-4201.e6. [PMID: 37714149 DOI: 10.1016/j.cub.2023.08.063] [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: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
CENP-A chromatin specifies mammalian centromere identity, and its chaperone HJURP replenishes CENP-A when recruited by the Mis18 complex (Mis18C) via M18BP1/KNL2 to CENP-C at kinetochores during interphase. However, the Mis18C recruitment mechanism remains unresolved in species lacking M18BP1, such as fission yeast. Fission yeast centromeres cluster at G2 spindle pole bodies (SPBs) when CENP-ACnp1 is replenished and where Mis18C also localizes. We show that SPBs play an unexpected role in concentrating Mis18C near centromeres through the recruitment of Mis18 by direct binding to the major SPB linker of nucleoskeleton and cytoskeleton (LINC) component Sad1. Mis18C recruitment by Sad1 is important for CENP-ACnp1 chromatin establishment and acts in parallel with a CENP-C-mediated Mis18C recruitment pathway to maintain centromeric CENP-ACnp1 but operates independently of Sad1-mediated centromere clustering. SPBs therefore provide a non-chromosomal scaffold for both Mis18C recruitment and centromere clustering during G2. This centromere-independent Mis18-SPB recruitment provides a mechanism that governs de novo CENP-ACnp1 chromatin assembly by the proximity of appropriate sequences to SPBs and highlights how nuclear spatial organization influences centromere identity.
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Affiliation(s)
- Nitobe London
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Bethan Medina-Pritchard
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK; Institute of Biotechnology, Technische Universität, 13355 Berlin, Germany
| | - A Arockia Jeyaprakash
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK; Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK.
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4
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Le TK, Hirano Y, Asakawa H, Okamoto K, Fukagawa T, Haraguchi T, Hiraoka Y. A ubiquitin-proteasome pathway degrades the inner nuclear membrane protein Bqt4 to maintain nuclear membrane homeostasis. J Cell Sci 2023; 136:jcs260930. [PMID: 37694715 DOI: 10.1242/jcs.260930] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
Aberrant accumulation of inner nuclear membrane (INM) proteins is associated with deformed nuclear morphology and mammalian diseases. However, the mechanisms underlying the maintenance of INM homeostasis remain poorly understood. In this study, we explored the degradation mechanisms of the INM protein Bqt4 in the fission yeast Schizosaccharomyces pombe. We have previously shown that Bqt4 interacts with the transmembrane protein Bqt3 at the INM and is degraded in the absence of Bqt3. Here, we reveal that excess Bqt4, unassociated with Bqt3, is targeted for degradation by the ubiquitin-proteasome system localized in the nucleus and Bqt3 antagonizes this process. The degradation process involves the Doa10 E3 ligase complex at the INM. Bqt4 is a tail-anchored protein and the Cdc48 complex is required for its degradation. The C-terminal transmembrane domain of Bqt4 was necessary and sufficient for proteasome-dependent protein degradation. Accumulation of Bqt4 at the INM impaired cell viability with nuclear envelope deformation, suggesting that quantity control of Bqt4 plays an important role in nuclear membrane homeostasis.
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Affiliation(s)
- Toan Khanh Le
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasuhiro Hirano
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Haruhiko Asakawa
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Koji Okamoto
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tatsuo Fukagawa
- Laboratory of Chromosome Biology, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tokuko Haraguchi
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
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5
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Fukuda T, Saigusa T, Furukawa K, Inoue K, Yamashita SI, Kanki T. Hva22, a REEP family protein in fission yeast, promotes reticulophagy in collaboration with a receptor protein. Autophagy 2023; 19:2657-2667. [PMID: 37191320 PMCID: PMC10472877 DOI: 10.1080/15548627.2023.2214029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
The endoplasmic reticulum (ER) undergoes selective autophagy called reticulophagy or ER-phagy. Multiple reticulon- and receptor expression enhancing protein (REEP)-like ER-shaping proteins, including budding yeast Atg40, serve as reticulophagy receptors that stabilize the phagophore on the ER by interacting with phagophore-conjugated Atg8. Additionally, they facilitate phagophore engulfment of the ER by remodeling ER morphology. We reveal that Hva22, a REEP family protein in fission yeast, promotes reticulophagy without Atg8-binding capacity. The role of Hva22 in reticulophagy can be replaced by expressing Atg40 independently of its Atg8-binding ability. Conversely, adding an Atg8-binding sequence to Hva22 enables it to substitute for Atg40 in budding yeast. Thus, the phagophore-stabilizing and ER-shaping activities, both of which Atg40 solely contains, are divided between two separate factors, receptors and Hva22, respectively, in fission yeast.Abbreviations: AIM: Atg8-family interacting motif; Atg: autophagy related; DTT: dithiothreitol; ER: endoplasmic reticulum GFP: green fluorescent protein; NAA: 1-naphthaleneacetic acid; REEP: receptor expression enhancing protein; RFP: red fluorescent protein; UPR: unfolded protein response.
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Affiliation(s)
- Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tetsu Saigusa
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kentaro Furukawa
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiichi Inoue
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shun-ichi Yamashita
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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6
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Panstruga R, Antonin W, Lichius A. Looking outside the box: a comparative cross-kingdom view on the cell biology of the three major lineages of eukaryotic multicellular life. Cell Mol Life Sci 2023; 80:198. [PMID: 37418047 PMCID: PMC10329083 DOI: 10.1007/s00018-023-04843-3] [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: 02/22/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/08/2023]
Abstract
Many cell biological facts that can be found in dedicated scientific textbooks are based on findings originally made in humans and/or other mammals, including respective tissue culture systems. They are often presented as if they were universally valid, neglecting that many aspects differ-in part considerably-between the three major kingdoms of multicellular eukaryotic life, comprising animals, plants and fungi. Here, we provide a comparative cross-kingdom view on the basic cell biology across these lineages, highlighting in particular essential differences in cellular structures and processes between phyla. We focus on key dissimilarities in cellular organization, e.g. regarding cell size and shape, the composition of the extracellular matrix, the types of cell-cell junctions, the presence of specific membrane-bound organelles and the organization of the cytoskeleton. We further highlight essential disparities in important cellular processes such as signal transduction, intracellular transport, cell cycle regulation, apoptosis and cytokinesis. Our comprehensive cross-kingdom comparison emphasizes overlaps but also marked differences between the major lineages of the three kingdoms and, thus, adds to a more holistic view of multicellular eukaryotic cell biology.
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Affiliation(s)
- Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074, Aachen, Germany
| | - Alexander Lichius
- inncellys GmbH, Dorfstrasse 20/3, 6082, Patsch, Austria
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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7
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Chen R, Buchmann S, Kroth A, Arias-Loza AP, Kohlhaas M, Wagner N, Grüner G, Nickel A, Cirnu A, Williams T, Maack C, Ergün S, Frantz S, Gerull B. Mechanistic Insights of the LEMD2 p.L13R Mutation and Its Role in Cardiomyopathy. Circ Res 2023; 132:e43-e58. [PMID: 36656972 DOI: 10.1161/circresaha.122.321929] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Nuclear envelope proteins play an important role in the pathogenesis of hereditary cardiomyopathies. Recently, a new form of arrhythmic cardiomyopathy caused by a homozygous mutation (p.L13R) in the inner nuclear membrane protein LEMD2 was discovered. The aim was to unravel the molecular mechanisms of mutant LEMD2 in the pathogenesis of cardiomyopathy. METHODS We generated a Lemd2 p.L13R knock-in mouse model and a corresponding cell model via CRISPR/Cas9 technology and investigated the cardiac phenotype as well as cellular and subcellular mechanisms of nuclear membrane rupture and repair. RESULTS Knock-in mice developed a cardiomyopathy with predominantly endocardial fibrosis, left ventricular dilatation, and systolic dysfunction. Electrocardiograms displayed pronounced ventricular arrhythmias and conduction disease. A key finding of knock-in cardiomyocytes on ultrastructural level was a significant increase in nuclear membrane invaginations and decreased nuclear circularity. Furthermore, increased DNA damage and premature senescence were detected as the underlying cause of fibrotic and inflammatory remodeling. As the p.L13R mutation is located in the Lap2/Emerin/Man1 (LEM)-domain, we observed a disrupted interaction between mutant LEMD2 and BAF (barrier-to-autointegration factor), which is required to initiate the nuclear envelope rupture repair process. To mimic increased mechanical stress with subsequent nuclear envelope ruptures, we investigated mutant HeLa-cells upon electrical stimulation and increased stiffness. Here, we demonstrated impaired nuclear envelope rupture repair capacity, subsequent cytoplasmic leakage of the DNA repair factor KU80 along with increased DNA damage, and recruitment of the cGAS (cyclic GMP-AMP synthase) to the nuclear membrane and micronuclei. CONCLUSIONS We show for the first time that the Lemd2 p.L13R mutation in mice recapitulates human dilated cardiomyopathy with fibrosis and severe ventricular arrhythmias. Impaired nuclear envelope rupture repair capacity resulted in increased DNA damage and activation of the cGAS/STING/IFN pathway, promoting premature senescence. Hence, LEMD2 is a new player inthe disease group of laminopathies.
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Affiliation(s)
- Ruping Chen
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
- Department of Medicine I (R.C., T.W., C.M., S.F., B.G.), University Hospital Würzburg, Germany
| | - Simone Buchmann
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
| | - Amos Kroth
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
| | - Anahi-Paula Arias-Loza
- Department of Nuclear Medicine, Comprehensive Heart Failure Center (A.-P.A.-L.), University Hospital Würzburg, Germany
| | - Michael Kohlhaas
- Department of Translational Research, Comprehensive Heart Failure Center (M.K., A.N., C.M.), University Hospital Würzburg, Germany
| | - Nicole Wagner
- Institute of Anatomy and Cell Biology, University of Würzburg, Germany (N.W., S.E.)
| | - Gianna Grüner
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
| | - Alexander Nickel
- Department of Translational Research, Comprehensive Heart Failure Center (M.K., A.N., C.M.), University Hospital Würzburg, Germany
| | - Alexandra Cirnu
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
| | - Tatjana Williams
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
- Department of Medicine I (R.C., T.W., C.M., S.F., B.G.), University Hospital Würzburg, Germany
| | - Christoph Maack
- Department of Medicine I (R.C., T.W., C.M., S.F., B.G.), University Hospital Würzburg, Germany
- Department of Translational Research, Comprehensive Heart Failure Center (M.K., A.N., C.M.), University Hospital Würzburg, Germany
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, University of Würzburg, Germany (N.W., S.E.)
| | - Stefan Frantz
- Department of Medicine I (R.C., T.W., C.M., S.F., B.G.), University Hospital Würzburg, Germany
- Comprehensive Heart Failure Center (S.F.), University Hospital Würzburg, Germany
| | - Brenda Gerull
- Department of Cardiovascular Genetics, Comprehensive Heart Failure Center (R.C., S.B., A.K., G.G., A.C., T.W., B.G.), University Hospital Würzburg, Germany
- Department of Medicine I (R.C., T.W., C.M., S.F., B.G.), University Hospital Würzburg, Germany
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8
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Borah S, Dhanasekaran K, Kumar S. The LEM-ESCRT toolkit: Repair and maintenance of the nucleus. Front Cell Dev Biol 2022; 10:989217. [PMID: 36172278 PMCID: PMC9512039 DOI: 10.3389/fcell.2022.989217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/24/2022] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic genome is enclosed in a nuclear envelope that protects it from potentially damaging cellular activities and physically segregates transcription and translation.Transport across the NE is highly regulated and occurs primarily via the macromolecular nuclear pore complexes.Loss of nuclear compartmentalization due to defects in NPC function and NE integrity are tied to neurological and ageing disorders like Alzheimer’s, viral pathogenesis, immune disorders, and cancer progression.Recent work implicates inner-nuclear membrane proteins of the conserved LEM domain family and the ESCRT machinery in NE reformation during cell division and NE repair upon rupture in migrating cancer cells, and generating seals over defective NPCs. In this review, we discuss the recent in-roads made into defining the molecular mechanisms and biochemical networks engaged by LEM and many other integral inner nuclear membrane proteins to preserve the nuclear barrier.
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Affiliation(s)
- Sapan Borah
- National Institute of Immunohaematology, Mumbai, Maharashtra, India
- *Correspondence: Sapan Borah, ; Karthigeyan Dhanasekaran, ; Santosh Kumar,
| | - Karthigeyan Dhanasekaran
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
- *Correspondence: Sapan Borah, ; Karthigeyan Dhanasekaran, ; Santosh Kumar,
| | - Santosh Kumar
- National Centre for Cell Science, Pune, Maharashtra, India
- *Correspondence: Sapan Borah, ; Karthigeyan Dhanasekaran, ; Santosh Kumar,
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9
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Varberg JM, Unruh JR, Bestul AJ, Khan AA, Jaspersen SL. Quantitative analysis of nuclear pore complex organization in Schizosaccharomyces pombe. Life Sci Alliance 2022; 5:e202201423. [PMID: 35354597 PMCID: PMC8967992 DOI: 10.26508/lsa.202201423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/06/2023] Open
Abstract
The number, distribution, and composition of nuclear pore complexes (NPCs) in the nuclear envelope varies between cell types and changes during cellular differentiation and in disease. To understand how NPC density and organization are controlled, we analyzed the NPC number and distribution in the fission yeast Schizosaccharomyces pombe using structured illumination microscopy. The small size of yeast nuclei, genetic features of fungi, and our robust image analysis pipeline allowed us to study NPCs in intact nuclei under multiple conditions. Our data revealed that NPC density is maintained across a wide range of nuclear sizes. Regions of reduced NPC density are observed over the nucleolus and surrounding the spindle pole body (SPB). Lem2-mediated tethering of the centromeres to the SPB is required to maintain NPC exclusion near SPBs. These findings provide a quantitative understanding of NPC number and distribution in S. pombe and show that interactions between the centromere and the nuclear envelope influences local NPC distribution.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Andrew J Bestul
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Azqa A Khan
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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10
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Emami P, Ueno M. 3,3'-Diindolylmethane induces apoptosis and autophagy in fission yeast. PLoS One 2021; 16:e0255758. [PMID: 34890395 PMCID: PMC8664220 DOI: 10.1371/journal.pone.0255758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/25/2021] [Indexed: 01/26/2023] Open
Abstract
3,3'-Diindolylmethane (DIM) is a compound derived from the digestion of indole-3-carbinol, found in the broccoli family. It induces apoptosis and autophagy in some types of human cancer. DIM extends lifespan in the fission yeast Schizosaccharomyces pombe. The mechanisms by which DIM induces apoptosis and autophagy in humans and expands lifespan in fission yeasts are not fully understood. Here, we show that DIM induces apoptosis and autophagy in log-phase cells, which is dose-dependent in fission yeast. A high concentration of DIM disrupted the nuclear envelope (NE) structure and induced chromosome condensation at an early time point. In contrast, a low concentration of DIM induced autophagy but did not disrupt NE structure. The mutant defective in autophagy was more sensitive to a low concentration of DIM, demonstrating that the autophagic pathway contributes to the survival of cells against DIM. Moreover, our results showed that the lem2 mutant is more sensitive to DIM. NE in the lem2 mutant was disrupted even at the low concentration of DIM. Our results demonstrate that the autophagic pathway and NE integrity are important to maintain viability in the presence of a low concentration of DIM. The mechanism of apoptosis and autophagy induction by DIM might be conserved in fission yeast and humans. Further studies will contribute to the understanding of the mechanism of apoptosis and autophagy by DIM in fission yeast and humans.
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Affiliation(s)
- Parvaneh Emami
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Masaru Ueno
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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11
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Padilla-Mejia NE, Makarov AA, Barlow LD, Butterfield ER, Field MC. Evolution and diversification of the nuclear envelope. Nucleus 2021; 12:21-41. [PMID: 33435791 PMCID: PMC7889174 DOI: 10.1080/19491034.2021.1874135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.
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Affiliation(s)
- Norma E. Padilla-Mejia
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexandr A. Makarov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lael D. Barlow
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Erin R. Butterfield
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České, Czech Republic
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12
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The Role of Emerin in Cancer Progression and Metastasis. Int J Mol Sci 2021; 22:ijms222011289. [PMID: 34681951 PMCID: PMC8537873 DOI: 10.3390/ijms222011289] [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: 09/28/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly recognized in the field that cancer cells exhibit changes in the size and shape of their nuclei. These features often serve as important biomarkers in the diagnosis and prognosis of cancer patients. Nuclear size can significantly impact cell migration due to its incredibly large size. Nuclear structural changes are predicted to regulate cancer cell migration. Nuclear abnormalities are common across a vast spectrum of cancer types, regardless of tissue source, mutational spectrum, and signaling dependencies. The pervasiveness of nuclear alterations suggests that changes in nuclear structure may be crucially linked to the transformation process. The factors driving these nuclear abnormalities, and the functional consequences, are not completely understood. Nuclear envelope proteins play an important role in regulating nuclear size and structure in cancer. Altered expression of nuclear lamina proteins, including emerin, is found in many cancers and this expression is correlated with better clinical outcomes. A model is emerging whereby emerin, as well as other nuclear lamina proteins, binding to the nucleoskeleton regulates the nuclear structure to impact metastasis. In this model, emerin and lamins play a central role in metastatic transformation, since decreased emerin expression during transformation causes the nuclear structural defects required for increased cell migration, intravasation, and extravasation. Herein, we discuss the cellular functions of nuclear lamina proteins, with a particular focus on emerin, and how these functions impact cancer progression and metastasis.
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13
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Pawar S, Kutay U. The Diverse Cellular Functions of Inner Nuclear Membrane Proteins. Cold Spring Harb Perspect Biol 2021; 13:a040477. [PMID: 33753404 PMCID: PMC8411953 DOI: 10.1101/cshperspect.a040477] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nuclear compartment is delimited by a specialized expanded sheet of the endoplasmic reticulum (ER) known as the nuclear envelope (NE). Compared to the outer nuclear membrane and the contiguous peripheral ER, the inner nuclear membrane (INM) houses a unique set of transmembrane proteins that serve a staggering range of functions. Many of these functions reflect the exceptional position of INM proteins at the membrane-chromatin interface. Recent research revealed that numerous INM proteins perform crucial roles in chromatin organization, regulation of gene expression, genome stability, and mediation of signaling pathways into the nucleus. Other INM proteins establish mechanical links between chromatin and the cytoskeleton, help NE remodeling, or contribute to the surveillance of NE integrity and homeostasis. As INM proteins continue to gain prominence, we review these advancements and give an overview on the functional versatility of the INM proteome.
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Affiliation(s)
- Sumit Pawar
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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14
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Modelling Nuclear Morphology and Shape Transformation: A Review. MEMBRANES 2021; 11:membranes11070540. [PMID: 34357190 PMCID: PMC8304582 DOI: 10.3390/membranes11070540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
As one of the most important cellular compartments, the nucleus contains genetic materials and separates them from the cytoplasm with the nuclear envelope (NE), a thin membrane that is susceptible to deformations caused by intracellular forces. Interestingly, accumulating evidence has also indicated that the morphology change of NE is tightly related to nuclear mechanotransduction and the pathogenesis of diseases such as cancer and Hutchinson–Gilford Progeria Syndrome. Theoretically, with the help of well-designed experiments, significant progress has been made in understanding the physical mechanisms behind nuclear shape transformation in different cellular processes as well as its biological implications. Here, we review different continuum-level (i.e., energy minimization, boundary integral and finite element-based) approaches that have been developed to predict the morphology and shape change of the cell nucleus. Essential gradients, relative advantages and limitations of each model will be discussed in detail, with the hope of sparking a greater research interest in this important topic in the future.
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15
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Deolal P, Mishra K. Regulation of diverse nuclear shapes: pathways working independently, together. Commun Integr Biol 2021; 14:158-175. [PMID: 34262635 PMCID: PMC8259725 DOI: 10.1080/19420889.2021.1939942] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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16
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Borah S, Thaller DJ, Hakhverdyan Z, Rodriguez EC, Isenhour AW, Rout MP, King MC, Lusk CP. Heh2/Man1 may be an evolutionarily conserved sensor of NPC assembly state. Mol Biol Cell 2021; 32:1359-1373. [PMID: 34010011 PMCID: PMC8694041 DOI: 10.1091/mbc.e20-09-0584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Integral membrane proteins of the Lap2-emerin-MAN1 (LEM) family have emerged as important components of the inner nuclear membrane (INM) required for the functional and physical integrity of the nuclear envelope. However, like many INM proteins, there is limited understanding of the biochemical interaction networks that enable LEM protein function. Here, we show that Heh2/Man1 can interact with major scaffold components of the nuclear pore complex (NPC), specifically the inner ring complex (IRC), in evolutionarily distant yeasts. Although an N-terminal domain is required for Heh2 targeting to the INM, we demonstrate that more stable interactions with the NPC are mediated by a C-terminal winged helix (WH) domain, thus decoupling INM targeting and NPC binding. Inhibiting Heh2's interactions with the NPC by deletion of the Heh2 WH domain leads to NPC clustering. Interestingly, Heh2's association with NPCs can also be disrupted by knocking out several outer ring nucleoporins. Thus, Heh2's interaction with NPCs depends on the structural integrity of both major NPC scaffold complexes. We propose a model in which Heh2 acts as a sensor of NPC assembly state, which may be important for NPC quality control mechanisms and the segregation of NPCs during cell division.
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Affiliation(s)
- Sapan Borah
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - David J Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | | | - Elisa C Rodriguez
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - Anthony W Isenhour
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | | | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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17
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Lu MS, Drubin DG. Cdc42 GTPase regulates ESCRTs in nuclear envelope sealing and ER remodeling. J Cell Biol 2021; 219:151867. [PMID: 32556066 PMCID: PMC7401818 DOI: 10.1083/jcb.201910119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/11/2020] [Accepted: 05/01/2020] [Indexed: 12/21/2022] Open
Abstract
Small GTPases of the Rho family are binary molecular switches that regulate a variety of processes including cell migration and oriented cell divisions. Known Cdc42 effectors include proteins involved in cytoskeletal remodeling and kinase-dependent transcription induction, but none are involved in the maintenance of nuclear envelope integrity or ER morphology. Maintenance of nuclear envelope integrity requires the EndoSomal Complexes Required for Transport (ESCRT) proteins, but how they are regulated in this process remains unknown. Here, we show by live-cell imaging a novel Cdc42 localization with ESCRT proteins at sites of nuclear envelope and ER fission and, by genetic analysis of cdc42 mutant yeast, uncover a unique Cdc42 function in regulation of ESCRT proteins at the nuclear envelope and sites of ER tubule fission. Our findings implicate Cdc42 in nuclear envelope sealing and ER remodeling, where it regulates ESCRT disassembly to maintain nuclear envelope integrity and proper ER architecture.
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Affiliation(s)
- Michelle Seiko Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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18
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High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library. G3-GENES GENOMES GENETICS 2020; 10:4649-4663. [PMID: 33109728 PMCID: PMC7718735 DOI: 10.1534/g3.120.401880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nuclear envelope (NE) contains a specialized set of integral membrane proteins that maintain nuclear shape and integrity and influence chromatin organization and gene expression. Advances in proteomics techniques and studies in model organisms have identified hundreds of proteins that localize to the NE. However, the function of many of these proteins at the NE remains unclear, in part due to a lack of understanding of the interactions that these proteins participate in at the NE membrane. To assist in the characterization of NE transmembrane protein interactions we developed an arrayed library of integral and peripheral membrane proteins from the fission yeast Schizosaccharomyces pombe for high-throughput screening using the split-ubiquitin based membrane yeast two -hybrid system. We used this approach to characterize protein interactions for three conserved proteins that localize to the inner nuclear membrane: Cut11/Ndc1, Lem2 and Ima1/Samp1/Net5. Additionally, we determined how the interaction network for Cut11 is altered in canonical temperature-sensitive cut11-ts mutants. This library and screening approach is readily applicable to characterizing the interactomes of integral membrane proteins localizing to various subcellular compartments.
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19
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Burla R, La Torre M, Maccaroni K, Verni F, Giunta S, Saggio I. Interplay of the nuclear envelope with chromatin in physiology and pathology. Nucleus 2020; 11:205-218. [PMID: 32835589 PMCID: PMC7529417 DOI: 10.1080/19491034.2020.1806661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
The nuclear envelope compartmentalizes chromatin in eukaryotic cells. The main nuclear envelope components are lamins that associate with a panoply of factors, including the LEM domain proteins. The nuclear envelope of mammalian cells opens up during cell division. It is reassembled and associated with chromatin at the end of mitosis when telomeres tether to the nuclear periphery. Lamins, LEM domain proteins, and DNA binding factors, as BAF, contribute to the reorganization of chromatin. In this context, an emerging role is that of the ESCRT complex, a machinery operating in multiple membrane assembly pathways, including nuclear envelope reformation. Research in this area is unraveling how, mechanistically, ESCRTs link to nuclear envelope associated factors as LEM domain proteins. Importantly, ESCRTs work also during interphase for repairing nuclear envelope ruptures. Altogether the advances in this field are giving new clues for the interpretation of diseases implicating nuclear envelope fragility, as laminopathies and cancer. ABBREVIATIONS na, not analyzed; ko, knockout; kd, knockdown; NE, nuclear envelope; LEM, LAP2-emerin-MAN1 (LEM)-domain containing proteins; LINC, linker of nucleoskeleton and cytoskeleton complexes; Cyt, cytoplasm; Chr, chromatin; MB, midbody; End, endosomes; Tel, telomeres; INM, inner nuclear membrane; NP, nucleoplasm; NPC, Nuclear Pore Complex; ER, Endoplasmic Reticulum; SPB, spindle pole body.
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Affiliation(s)
- Romina Burla
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Fiammetta Verni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Giunta
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- Rockefeller University, New York, NY, USA
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
- Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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20
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ESCRT-III controls nuclear envelope deformation induced by progerin. Sci Rep 2020; 10:18877. [PMID: 33139753 PMCID: PMC7606583 DOI: 10.1038/s41598-020-75852-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/21/2020] [Indexed: 01/29/2023] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging disorder, caused by mutation in the gene encoding lamin A/C, which produces a truncated protein called progerin. In cells from HGPS patients, progerin accumulates at the nuclear membrane (NM), where it causes NM deformations. In this study, we investigated whether progerin-induced NM deformation involved ESCRT-III, a protein complex that remodels nuclear and cytoplasmic membranes. The ESCRT-III protein CHMP4B was recruited to sites of aberrant NM proliferation in human cells ectopically expressing progerin and in patient-derived HGPS fibroblasts. Derepression of NM deformation in these cells was observed following depletion of CHMP4B or an ESCRT-III adaptor, ALIX. Treatment with rapamycin (which induce autophagic clearance of progerin and reverse progerin-induced cellular phenotypes) down-regulated progerin-induced NM deformation, whereas treatment with bafilomycin A1 (an inhibitor of autophagy and lysosome-based degradation) or CHMP4B depletion antagonized the effects of rapamycin. These results indicate that the ALIX-mediated ESCRT-III pathway plays a suppressive role in progerin-induced NM deformation and suggest that autophagy down-regulates progerin-induced NM deformation in a manner dependent on ESCRT-III machinery.
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21
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Capella M, Braun S. ESCRTing Heterochromatin Out of the Nuclear Periphery. Dev Cell 2020; 53:3-5. [PMID: 32259492 DOI: 10.1016/j.devcel.2020.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
ESCRT proteins fulfill an important function in membrane remodeling and scission. In this issue of Developmental Cell, Pieper et al. reveal that the ESCRT machinery releases the inner nuclear membrane protein Lem2 from heterochromatin, thus ensuring its function in nuclear envelope resealing after mitosis.
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Affiliation(s)
- Matías Capella
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Sigurd Braun
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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22
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Abstract
The fission yeast silent mating-type region provides an excellent system to ask how chromatic domains with opposite effects on gene expression coexist side by side along chromosomes and to investigate roles played by DNA elements and architectural proteins in the phenomenon. By showing that the IR-L and IR-R chromatin boundaries favor heterochromatin formation in the domain that separates them, dependent on each other and on binding sites for the architectural factor TFIIIC, our work brings to light an important function of these elements and supports the notion that similar types of interactions between boundaries might in other organisms as well stimulate heterochromatin formation in intervening chromosomal loops to actively shape gene expression landscapes. In fission yeast, the inverted repeats IR-L and IR-R function as boundary elements at the edges of a 20-kb silent heterochromatic domain where nucleosomes are methylated at histone H3K9. Each repeat contains a series of B-box motifs physically associated with the architectural TFIIIC complex and with other factors including the replication regulator Sap1 and the Rix1 complex (RIXC). We demonstrate here the activity of these repeats in heterochromatin formation and maintenance. Deletion of the entire IR-R repeat or, to a lesser degree, deletion of just the B boxes impaired the de novo establishment of the heterochromatic domain. Nucleation proceeded normally at the RNA interference (RNAi)-dependent element cenH but subsequent propagation to the rest of the region occurred at reduced rates in the mutants. Once established, heterochromatin was unstable in the mutants. These defects resulted in bistable populations of cells occupying alternate “on” and “off” epigenetic states. Deleting IR-L in combination with IR-R synergistically tipped the balance toward the derepressed state, revealing a concerted action of the two boundaries at a distance. The nuclear rim protein Amo1 has been proposed to tether the mating-type region and its boundaries to the nuclear envelope, where Amo1 mutants displayed milder phenotypes than boundary mutants. Thus, the boundaries might facilitate heterochromatin propagation and maintenance in ways other than just through Amo1, perhaps by constraining a looped domain through pairing.
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23
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Nuclear Envelope Proteins Modulating the Heterochromatin Formation and Functions in Fission Yeast. Cells 2020; 9:cells9081908. [PMID: 32824370 PMCID: PMC7464478 DOI: 10.3390/cells9081908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
The nuclear envelope (NE) consists of the inner and outer nuclear membranes (INM and ONM), and the nuclear pore complex (NPC), which penetrates the double membrane. ONM continues with the endoplasmic reticulum (ER). INM and NPC can interact with chromatin to regulate the genetic activities of the chromosome. Studies in the fission yeast Schizosaccharomyces pombe have contributed to understanding the molecular mechanisms underlying heterochromatin formation by the RNAi-mediated and histone deacetylase machineries. Recent studies have demonstrated that NE proteins modulate heterochromatin formation and functions through interactions with heterochromatic regions, including the pericentromeric and the sub-telomeric regions. In this review, we first introduce the molecular mechanisms underlying the heterochromatin formation and functions in fission yeast, and then summarize the NE proteins that play a role in anchoring heterochromatic regions and in modulating heterochromatin formation and functions, highlighting roles for a conserved INM protein, Lem2.
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24
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Almendáriz-Palacios C, Gillespie ZE, Janzen M, Martinez V, Bridger JM, Harkness TAA, Mousseau DD, Eskiw CH. The Nuclear Lamina: Protein Accumulation and Disease. Biomedicines 2020; 8:E188. [PMID: 32630170 PMCID: PMC7400325 DOI: 10.3390/biomedicines8070188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023] Open
Abstract
Cellular health is reliant on proteostasis-the maintenance of protein levels regulated through multiple pathways modulating protein synthesis, degradation and clearance. Loss of proteostasis results in serious disease and is associated with aging. One proteinaceous structure underlying the nuclear envelope-the nuclear lamina-coordinates essential processes including DNA repair, genome organization and epigenetic and transcriptional regulation. Loss of proteostasis within the nuclear lamina results in the accumulation of proteins, disrupting these essential functions, either via direct interactions of protein aggregates within the lamina or by altering systems that maintain lamina structure. Here we discuss the links between proteostasis and disease of the nuclear lamina, as well as how manipulating specific proteostatic pathways involved in protein clearance could improve cellular health and prevent/reverse disease.
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Affiliation(s)
- Carla Almendáriz-Palacios
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (C.A.-P.); (V.M.)
| | - Zoe E. Gillespie
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (Z.E.G.); (M.J.); (T.A.A.H.)
| | - Matthew Janzen
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (Z.E.G.); (M.J.); (T.A.A.H.)
| | - Valeria Martinez
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (C.A.-P.); (V.M.)
| | - Joanna M. Bridger
- Centre for Genome Engineering and Maintenance, College of Health, Life and Medical Sciences, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK;
| | - Troy A. A. Harkness
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (Z.E.G.); (M.J.); (T.A.A.H.)
| | - Darrell D. Mousseau
- Cell Signalling Laboratory, Department of Psychiatry, University of Saskatchewan, Saskatoon, SK S7N 5A5, Canada;
| | - Christopher H. Eskiw
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (C.A.-P.); (V.M.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada; (Z.E.G.); (M.J.); (T.A.A.H.)
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25
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Lusk CP, Ader NR. CHMPions of repair: Emerging perspectives on sensing and repairing the nuclear envelope barrier. Curr Opin Cell Biol 2020; 64:25-33. [PMID: 32105978 PMCID: PMC7371540 DOI: 10.1016/j.ceb.2020.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
Understanding how the integrity of the nuclear membranes is protected against internal and external stresses is an emergent challenge. Work reviewed here investigated the mechanisms by which losses of nuclear-cytoplasmic compartmentalization are sensed and ameliorated. Fundamental to these is spatial control over interactions between the endosomal sorting complexes required for transport machinery and LAP2-emerin-MAN1 family inner nuclear membrane proteins, which together promote nuclear envelope sealing in interphase and at the end of mitosis. We suggest that the size of the nuclear envelope hole dictates the mechanism of its repair, with larger holes requiring barrier-to-autointegration factor and the potential triggering of a postmitotic nuclear envelope reassembly pathway in interphase. We also consider why these mechanisms fail at ruptured micronuclei. Together, this work re-emphasizes the need to understand how membrane flow and local lipid metabolism help ensure that the nuclear envelope is refractory to mechanical rupture yet fluid enough to allow its essential dynamics.
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Affiliation(s)
- C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06520, USA.
| | - Nicholas R Ader
- Department of Cell Biology, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06520, USA
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26
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Bossone KA, Ellis JA, Holaska JM. Histone acetyltransferase inhibition rescues differentiation of emerin-deficient myogenic progenitors. Muscle Nerve 2020; 62:128-136. [PMID: 32304242 DOI: 10.1002/mus.26892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 03/05/2020] [Accepted: 04/07/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Emery-Dreifuss muscular dystrophy (EDMD) is a disease characterized by skeletal muscle wasting, major tendon contractures, and cardiac conduction defects. Mutations in the gene encoding emerin cause EDMD1. Our previous studies suggested that emerin activation of histone deacetylase 3 (HDAC3) to reduce histone 4-lysine 5 (H4K5) acetylation (ac) is important for myogenic differentiation. METHODS Pharmacological inhibitors (Nu9056, L002) of histone acetyltransferases targeting acetylated H4K5 were used to test whether increased acetylated H4K5 was responsible for the impaired differentiation seen in emerin-deficient myogenic progenitors. RESULTS Nu9056 and L002 rescued impaired differentiation in emerin deficiency. SRT1720, which inhibits the nicotinamide adenine dinucleotide (NAD)+ -dependent deacetylase sirtuin 1 (SIRT1), failed to rescue myotube formation. DISCUSSION We conclude that emerin regulation of HDAC3 activity to affect H4K5 acetylation dynamics is important for myogenic differentiation. Targeting H4K5ac dynamics represents a potential new strategy for ameliorating the skeletal muscle wasting seen in EDMD1.
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Affiliation(s)
- Katherine A Bossone
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States.,Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States
| | - Joseph A Ellis
- Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States
| | - James M Holaska
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, United States.,Department of Pharmaceutical Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States
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27
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Stephens AD. Chromatin rigidity provides mechanical and genome protection. Mutat Res 2020; 821:111712. [PMID: 32590202 PMCID: PMC8186544 DOI: 10.1016/j.mrfmmm.2020.111712] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
The nucleus is the organelle in the cell that contains the genome and its associate proteins which is collectively called chromatin. New work has shown that chromatin and its compaction level, dictated largely through histone modification state, provides rigidity to protect and stabilize the nucleus. Alterations in chromatin, its mechanics, and downstream loss of nuclear shape and stability are hallmarks of human disease. Weakened nuclear mechanics and abnormal morphology have been shown to cause rupturing of the nucleus which results in nuclear dysfunction including DNA damage. Thus, the rigidity provided by chromatin to maintain nuclear mechanical stability also provides its own protection from DNA damage via compartmentalization maintenance.
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Affiliation(s)
- Andrew D Stephens
- Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, United States.
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28
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Pieper GH, Sprenger S, Teis D, Oliferenko S. ESCRT-III/Vps4 Controls Heterochromatin-Nuclear Envelope Attachments. Dev Cell 2020; 53:27-41.e6. [PMID: 32109380 PMCID: PMC7139201 DOI: 10.1016/j.devcel.2020.01.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 12/05/2019] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
Abstract
Eukaryotic genomes are organized within the nucleus through interactions with inner nuclear membrane (INM) proteins. How chromatin tethering to the INM is controlled in interphase and how this process contributes to subsequent mitotic nuclear envelope (NE) remodeling remains unclear. We have probed these fundamental questions using the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis. We show that attachments between heterochromatin and the transmembrane Lem2-Nur1 complex at the INM are remodeled in interphase by the ESCRT-III/Vps4 machinery. Failure of ESCRT-III/Vps4 to release Lem2-Nur1 from heterochromatin leads to persistent association of chromosomes with the INM throughout mitosis. At mitotic exit, such trapping of Lem2-Nur1 on heterochromatin prevents it from re-establishing nucleocytoplasmic compartmentalization. Our work identifies the Lem2-Nur1 complex as a substrate for the nuclear ESCRT machinery and explains how the dynamic tethering of chromosomes to the INM is linked to the establishment of nuclear compartmentalization.
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Affiliation(s)
- Gerard H Pieper
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Simon Sprenger
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80/82, A-6020, Innsbruck, Austria.
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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29
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Holla S, Dhakshnamoorthy J, Folco HD, Balachandran V, Xiao H, Sun LL, Wheeler D, Zofall M, Grewal SIS. Positioning Heterochromatin at the Nuclear Periphery Suppresses Histone Turnover to Promote Epigenetic Inheritance. Cell 2019; 180:150-164.e15. [PMID: 31883795 DOI: 10.1016/j.cell.2019.12.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/29/2019] [Accepted: 12/04/2019] [Indexed: 01/09/2023]
Abstract
In eukaryotes, heterochromatin is generally located at the nuclear periphery. This study investigates the biological significance of perinuclear positioning for heterochromatin maintenance and gene silencing. We identify the nuclear rim protein Amo1NUPL2 as a factor required for the propagation of heterochromatin at endogenous and ectopic sites in the fission yeast genome. Amo1 associates with the Rix1PELP1-containing RNA processing complex RIXC and with the histone chaperone complex FACT. RIXC, which binds to heterochromatin protein Swi6HP1 across silenced chromosomal domains and to surrounding boundary elements, connects heterochromatin with Amo1 at the nuclear periphery. In turn, the Amo1-enriched subdomain is critical for Swi6 association with FACT that precludes histone turnover to promote gene silencing and preserve epigenetic stability of heterochromatin. In addition to uncovering conserved factors required for perinuclear positioning of heterochromatin, these analyses elucidate a mechanism by which a peripheral subdomain enforces stable gene repression and maintains heterochromatin in a heritable manner.
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Affiliation(s)
- Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ling-Ling Sun
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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30
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Gallardo P, Barrales RR, Daga RR, Salas-Pino S. Nuclear Mechanics in the Fission Yeast. Cells 2019; 8:cells8101285. [PMID: 31635174 PMCID: PMC6829894 DOI: 10.3390/cells8101285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022] Open
Abstract
In eukaryotic cells, the organization of the genome within the nucleus requires the nuclear envelope (NE) and its associated proteins. The nucleus is subjected to mechanical forces produced by the cytoskeleton. The physical properties of the NE and the linkage of chromatin in compacted conformation at sites of cytoskeleton contacts seem to be key for withstanding nuclear mechanical stress. Mechanical perturbations of the nucleus normally occur during nuclear positioning and migration. In addition, cell contraction or expansion occurring for instance during cell migration or upon changes in osmotic conditions also result innuclear mechanical stress. Recent studies in Schizosaccharomyces pombe (fission yeast) have revealed unexpected functions of cytoplasmic microtubules in nuclear architecture and chromosome behavior, and have pointed to NE-chromatin tethers as protective elements during nuclear mechanics. Here, we review and discuss how fission yeast cells can be used to understand principles underlying the dynamic interplay between genome organization and function and the effect of forces applied to the nucleus by the microtubule cytoskeleton.
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Affiliation(s)
- Paola Gallardo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
| | - Silvia Salas-Pino
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas, Junta de Andalucia, 41010 Seville, Spain.
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31
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Zhurinsky J, Salas-Pino S, Iglesias-Romero AB, Torres-Mendez A, Knapp B, Flor-Parra I, Wang J, Bao K, Jia S, Chang F, Daga RR. Effects of the microtubule nucleator Mto1 on chromosomal movement, DNA repair, and sister chromatid cohesion in fission yeast. Mol Biol Cell 2019; 30:2695-2708. [PMID: 31483748 PMCID: PMC6761766 DOI: 10.1091/mbc.e19-05-0301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 11/11/2022] Open
Abstract
Although the function of microtubules (MTs) in chromosomal segregation during mitosis is well characterized, much less is known about the role of MTs in chromosomal functions during interphase. In the fission yeast Schizosaccharomyces pombe, dynamic cytoplasmic MT bundles move chromosomes in an oscillatory manner during interphase via linkages through the nuclear envelope (NE) at the spindle pole body (SPB) and other sites. Mto1 is a cytoplasmic factor that mediates the nucleation and attachment of cytoplasmic MTs to the nucleus. Here, we test the function of these cytoplasmic MTs and Mto1 on DNA repair and recombination during interphase. We find that mto1Δ cells exhibit defects in DNA repair and homologous recombination (HR) and abnormal DNA repair factory dynamics. In these cells, sister chromatids are not properly paired, and binding of Rad21 cohesin subunit along chromosomal arms is reduced. Our findings suggest a model in which cytoplasmic MTs and Mto1 facilitate efficient DNA repair and HR by promoting dynamic chromosomal organization and cohesion in the nucleus.
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Affiliation(s)
- Jacob Zhurinsky
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Silvia Salas-Pino
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Ana B. Iglesias-Romero
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Antonio Torres-Mendez
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Benjamin Knapp
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Ignacio Flor-Parra
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
| | - Jiyong Wang
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Kehan Bao
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Songtao Jia
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143
| | - Fred Chang
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032
| | - Rafael R. Daga
- Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Seville 41013, Spain
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32
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Irie H, Yamamoto I, Tarumoto Y, Tashiro S, Runge KW, Ishikawa F. Telomere-binding proteins Taz1 and Rap1 regulate DSB repair and suppress gross chromosomal rearrangements in fission yeast. PLoS Genet 2019; 15:e1008335. [PMID: 31454352 PMCID: PMC6733473 DOI: 10.1371/journal.pgen.1008335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 09/09/2019] [Accepted: 07/28/2019] [Indexed: 11/19/2022] Open
Abstract
Genomic rearrangements (gross chromosomal rearrangements, GCRs) threatens genome integrity and cause cell death or tumor formation. At the terminus of linear chromosomes, a telomere-binding protein complex, called shelterin, ensures chromosome stability by preventing chromosome end-to-end fusions and regulating telomere length homeostasis. As such, shelterin-mediated telomere functions play a pivotal role in suppressing GCR formation. However, it remains unclear whether the shelterin proteins play any direct role in inhibiting GCR at non-telomeric regions. Here, we have established a GCR assay for the first time in fission yeast and measured GCR rates in various mutants. We found that fission yeast cells lacking shelterin components Taz1 or Rap1 (mammalian TRF1/2 or RAP1 homologues, respectively) showed higher GCR rates compared to wild-type, accumulating large chromosome deletions. Genetic dissection of Rap1 revealed that Rap1 contributes to inhibiting GCRs via two independent pathways. The N-terminal BRCT-domain promotes faithful DSB repair, as determined by I-SceI-mediated DSB-induction experiments; moreover, association with Poz1 mediated by the central Poz1-binding domain regulates telomerase accessibility to DSBs, leading to suppression of de novo telomere additions. Our data highlight unappreciated functions of the shelterin components Taz1 and Rap1 in maintaining genome stability, specifically by preventing non-telomeric GCRs.
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Affiliation(s)
- Hiroyuki Irie
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Io Yamamoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yusuke Tarumoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sanki Tashiro
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kurt W. Runge
- Department of Molecular Genetics, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, United States of America
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail:
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33
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Kinugasa Y, Hirano Y, Sawai M, Ohno Y, Shindo T, Asakawa H, Chikashige Y, Shibata S, Kihara A, Haraguchi T, Hiraoka Y. The very-long-chain fatty acid elongase Elo2 rescues lethal defects associated with loss of the nuclear barrier function in fission yeast cells. J Cell Sci 2019; 132:jcs.229021. [PMID: 30975915 DOI: 10.1242/jcs.229021] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/03/2019] [Indexed: 12/21/2022] Open
Abstract
In eukaryotic cells, chromosomes are confined to the nucleus, which is compartmentalized by the nuclear membranes; these are continuous with the endoplasmic reticulum membranes. Maintaining the homeostasis of these membranes is an important cellular activity performed by lipid metabolic enzymes. However, how lipid metabolic enzymes affect nuclear membrane functions remains to be elucidated. We found that the very-long-chain fatty acid elongase Elo2 is located in the nuclear membrane and prevents lethal defects associated with nuclear membrane ruptures in mutants of the nuclear membrane proteins Lem2 and Bqt4 in the fission yeast Schizosaccharomyces pombe. Lipid composition analysis shows that t20:0/24:0 phytoceramide (a conjugate of C20:0 phytosphingosine and C24:0 fatty acid) is a major ceramide species in S. pombe The quantity of this ceramide is reduced in the absence of Lem2, and restored by increased expression of Elo2. Furthermore, loss of S. pombe Elo2 can be rescued by its human orthologs. These results suggest that the conserved very-long-chain fatty acid elongase producing the ceramide component is essential for nuclear membrane integrity and cell viability in eukaryotes.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yasuha Kinugasa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Megumi Sawai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Yusuke Ohno
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan .,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
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34
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Abdelfatah N, Chen R, Duff HJ, Seifer CM, Buffo I, Huculak C, Clarke S, Clegg R, Jassal DS, Gordon PMK, Ober C, Frosk P, Gerull B. Characterization of a Unique Form of Arrhythmic Cardiomyopathy Caused by Recessive Mutation in LEMD2. JACC Basic Transl Sci 2019; 4:204-221. [PMID: 31061923 PMCID: PMC6488817 DOI: 10.1016/j.jacbts.2018.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/02/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023]
Abstract
Nuclear envelope proteins have been shown to play an important role in the pathogenesis of inherited dilated cardiomyopathy. Here, we present a remarkable cardiac phenotype caused by a homozygous LEMD2 mutation in patients of the Hutterite population with juvenile cataract. Mutation carriers develop arrhythmic cardiomyopathy with mild impairment of left ventricular systolic function but severe ventricular arrhythmias leading to sudden cardiac death. Affected cardiac tissue from a deceased patient and fibroblasts exhibit elongated nuclei with abnormal condensed heterochromatin at the periphery. The patient fibroblasts demonstrate cellular senescence and reduced proliferation capacity, which may suggest an involvement of LEM domain containing protein 2 in chromatin remodeling processes and premature aging.
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Key Words
- ACM, arrhythmogenic cardiomyopathy
- BANF, barrier to autointegration factor
- CMR, cardiac magnetic resonance
- DAPI, 4′,6′-diamidino-2-phenylindole
- DCM, dilated cardiomyopathy
- DNA, deoxyribonucleic acid
- EMD, emerin
- ICD, implantable cardioverter-defibrillator
- LEMD2
- LEMD2, LEM domain containing protein 2
- LGE, late gadolinium enhancement
- LMNA, lamin A/C
- LV, left ventricular
- NE, nuclear envelope
- P, passage
- PBS, phosphate-buffered saline
- SAHF, senescence-associated heterochromatin foci
- SNV, single nucleotide variant
- chromatin remodeling
- dilated cardiomyopathy
- eGFP, enhanced green fluorescent protein
- inner nuclear membrane
- sudden death
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Affiliation(s)
- Nelly Abdelfatah
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ruping Chen
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Henry J Duff
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Colette M Seifer
- Section of Cardiology, Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ilan Buffo
- Variety Children's Heart Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Cathleen Huculak
- Department of Medical Genetics, Alberta Health Services, Calgary, Alberta, Canada
| | - Stephanie Clarke
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Robin Clegg
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Davinder S Jassal
- Section of Cardiology, Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary, Calgary, Alberta, Canada
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois
| | | | - Patrick Frosk
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brenda Gerull
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany.,Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
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35
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Nuclear membrane protein Lem2 regulates nuclear size through membrane flow. Nat Commun 2019; 10:1871. [PMID: 31015410 PMCID: PMC6478680 DOI: 10.1038/s41467-019-09623-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 03/18/2019] [Indexed: 11/08/2022] Open
Abstract
The size of the membrane-bound nucleus scales with cell size in a wide range of cell types but the mechanisms determining overall nuclear size remain largely unknown. Here we investigate the role of fission yeast inner nuclear membrane proteins in determining nuclear size, and propose that the Lap2-Emerin-Man1 domain protein Lem2 acts as a barrier to membrane flow between the nucleus and other parts of the cellular membrane system. Lem2 deletion increases membrane flow into and out of the nuclear envelope in response to changes in membrane synthesis and nucleocytoplasmic transport, altering nuclear size. The endoplasmic reticulum protein Lnp1 acts as a secondary barrier to membrane flow, functionally compensating for lack of Lem2. We propose that this is part of the mechanism that maintains nuclear size proportional to cellular membrane content and thus to cell size. Similar regulatory principles may apply to other organelles in the eukaryotic subcellular membrane network.
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36
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Thaller DJ, Allegretti M, Borah S, Ronchi P, Beck M, Lusk CP. An ESCRT-LEM protein surveillance system is poised to directly monitor the nuclear envelope and nuclear transport system. eLife 2019; 8:e45284. [PMID: 30942170 PMCID: PMC6461442 DOI: 10.7554/elife.45284] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022] Open
Abstract
The integrity of the nuclear membranes coupled to the selective barrier of nuclear pore complexes (NPCs) are essential for the segregation of nucleoplasm and cytoplasm. Mechanical membrane disruption or perturbation to NPC assembly triggers an ESCRT-dependent surveillance system that seals nuclear pores: how these pores are sensed and sealed is ill defined. Using a budding yeast model, we show that the ESCRT Chm7 and the integral inner nuclear membrane (INM) protein Heh1 are spatially segregated by nuclear transport, with Chm7 being actively exported by Xpo1/Crm1. Thus, the exposure of the INM triggers surveillance with Heh1 locally activating Chm7. Sites of Chm7 hyperactivation show fenestrated sheets at the INM and potential membrane delivery at sites of nuclear envelope herniation. Our data suggest that perturbation to the nuclear envelope barrier would lead to local nuclear membrane remodeling to promote membrane sealing. Our findings have implications for disease mechanisms linked to NPC assembly and nuclear envelope integrity.
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Affiliation(s)
- David J Thaller
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
| | - Matteo Allegretti
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - Sapan Borah
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
| | - Paolo Ronchi
- Electron Microscopy Core FacilityEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - Martin Beck
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - C Patrick Lusk
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
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37
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Iwamoto M, Fukuda Y, Osakada H, Mori C, Hiraoka Y, Haraguchi T. Identification of the evolutionarily conserved nuclear envelope proteins Lem2 and MicLem2 in Tetrahymena thermophila. Gene 2019; 721S:100006. [PMID: 32550543 PMCID: PMC7285967 DOI: 10.1016/j.gene.2019.100006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/18/2018] [Accepted: 01/11/2019] [Indexed: 11/26/2022]
Abstract
Lem2 family proteins, i.e. the LAP2-Emerin-MAN1 (LEM) domain-containing nuclear envelope proteins, are well-conserved from yeasts to humans, both of which belong to the Opisthokonta supergroup. However, whether their homologs are present in other eukaryotic phylogenies remains unclear. In this study, we identified two Lem2 homolog proteins, which we named as Lem2 and MicLem2, in a ciliate Tetrahymena thermophila belonging to the SAR supergroup. Lem2 was localized to the nuclear envelope of the macronucleus (MAC) and micronucleus (MIC), while MicLem2 was exclusively localized to the nuclear envelope of the MIC. Immunoelectron microscopy revealed that Lem2 in T. thermophila was localized to both the inner and outer nuclear envelopes of the MAC and MIC, while MicLem2 was mostly localized to the nuclear pores of the MIC. Molecular domain analysis using GFP-fused protein showed that the N-terminal and luminal domains, including the transmembrane segments, are responsible for nuclear envelope localization. During sexual reproduction, enrichment of Lem2 occurred in the nuclear envelopes of the MAC and MIC to be degraded, while MicLem2 was enriched in the nuclear envelope of the MIC that escaped degradation. These findings suggest the unique characteristics of Tetrahymena Lem2 proteins. Our findings provide insight into the evolutionary divergence of nuclear envelope proteins. Conserved nuclear envelope proteins Lem2 and MicLem2 are identified in Tetrahymena. Lem2 is localized to the nuclear envelope of the macronucleus and the micronucleus. MicLem2 is localized to the nuclear pore complex of the micronucleus. In sexual reproduction, Lem2 is enriched to the nuclei assigned to degradation. MicLem2 is enriched to the micronuclei that are escaped from degradation.
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Key Words
- BAF, barrier-to-autointegration factor
- DAPI, 4′,6‑diamidino‑2‑phenylindole
- DDW, double distilled water
- EDTA, ethylenediaminetetraacetic acid
- ER, endoplasmic reticulum
- GA, glutaraldehyde
- HeH domain
- HeH, helix-extension-helix
- LAP2, lamina associated polypeptide 2
- LEM domain
- LEM, LAP2-Emerin-MAN1
- MAC, macronucleus
- MIC, micronucleus
- MSC domain
- MSC, Man1-Src1p-C-terminal
- Man1
- Man1-Src1p-C-terminal domain
- NE, nuclear envelope
- NLS, nuclear localization signal
- NPC, nuclear pore complex
- Nuclear dimorphism
- Nuclear envelope
- ONM and INM, outer and inner nuclear membranes
- PB, phosphate buffer
- PBS, phosphate buffered saline
- Protist
- RRM, RNA recognition motif
- TM, transmembrane
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki, 989-6711, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
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38
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Hu C, Inoue H, Sun W, Takeshita Y, Huang Y, Xu Y, Kanoh J, Chen Y. The Inner Nuclear Membrane Protein Bqt4 in Fission Yeast Contains a DNA-Binding Domain Essential for Telomere Association with the Nuclear Envelope. Structure 2018; 27:335-343.e3. [PMID: 30503780 DOI: 10.1016/j.str.2018.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/30/2018] [Accepted: 10/15/2018] [Indexed: 01/07/2023]
Abstract
Telomeres, the protective caps at the end of the chromosomes, are often associated with the nuclear envelope (NE). Telomere positioning to the NE is dynamically regulated during mitosis and meiosis. One inner nuclear membrane protein, Bqt4, in Schizosaccharomyces pombe plays essential roles in connecting telomeres to the NE. However, the structural basis of Bqt4 in mediating telomere-NE association is not clear. Here, we report the crystal structure of the N-terminal domain of Bqt4. The N-terminal domain of Bqt4 structurally resembles the APSES-family DNA-binding domain and has a moderate double-stranded DNA-binding activity. Disruption of Bqt4-DNA interaction results in telomere detachment from the NE. These data suggest that the DNA-binding activity of Bqt4 may function to prime the chromosome onto the NE and promote telomere-NE association.
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Affiliation(s)
- Chunyi Hu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Haruna Inoue
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wenqi Sun
- School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China
| | - Yumiko Takeshita
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yaoguang Huang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Ying Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Junko Kanoh
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China.
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39
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Suresh S, Markossian S, Osmani AH, Osmani SA. Nup2 performs diverse interphase functions in Aspergillus nidulans. Mol Biol Cell 2018; 29:3144-3154. [PMID: 30355026 PMCID: PMC6340215 DOI: 10.1091/mbc.e18-04-0223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The nuclear pore complex (NPC) protein Nup2 plays interphase nuclear transport roles and in Aspergillus nidulans also functions to bridge NPCs at mitotic chromatin for their faithful coinheritance to daughter G1 nuclei. In this study, we further investigate the interphase functions of Nup2 in A. nidulans. Although Nup2 is not required for nuclear import of all nuclear proteins after mitosis, it is required for normal G1 nuclear accumulation of the NPC nuclear basket–associated components Mad2 and Mlp1 as well as the THO complex protein Tho2. Targeting of Mlp1 to nuclei partially rescues the interphase delay seen in nup2 mutants indicating that some of the interphase defects in Nup2-deleted cells are due to Mlp1 mislocalization. Among the inner nuclear membrane proteins, Nup2 affects the localization of Ima1, orthologues of which are involved in nuclear movement. Interestingly, nup2 mutant G1 nuclei also exhibit an abnormally long period of extensive to-and-fro movement immediately after mitosis in a manner dependent on the microtubule cytoskeleton. This indicates that Nup2 is required to limit the transient postmitotic nuclear migration typical of many filamentous fungi. The findings reveal that Nup2 is a multifunctional protein that performs diverse functions during both interphase and mitosis in A. nidulans.
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Affiliation(s)
- Subbulakshmi Suresh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210.,Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Sarine Markossian
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143
| | - Aysha H Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
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40
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Ebrahimi H, Masuda H, Jain D, Cooper JP. Distinct 'safe zones' at the nuclear envelope ensure robust replication of heterochromatic chromosome regions. eLife 2018; 7:32911. [PMID: 29722648 PMCID: PMC5933923 DOI: 10.7554/elife.32911] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/30/2018] [Indexed: 12/24/2022] Open
Abstract
Chromosome replication and transcription occur within a complex nuclear milieu whose functional subdomains are beginning to be mapped out. Here we delineate distinct domains of the fission yeast nuclear envelope (NE), focusing on regions enriched for the inner NE protein, Bqt4, or the lamin interacting domain protein, Lem2. Bqt4 is relatively mobile around the NE and acts in two capacities. First, Bqt4 tethers chromosome termini and the mat locus to the NE specifically while these regions are replicating. This positioning is required for accurate heterochromatin replication. Second, Bqt4 mobilizes a subset of Lem2 molecules around the NE to promote pericentric heterochromatin maintenance. Opposing Bqt4-dependent Lem2 mobility are factors that stabilize Lem2 beneath the centrosome, where Lem2 plays a crucial role in kinetochore maintenance. Our data prompt a model in which Bqt4-rich nuclear subdomains are 'safe zones' in which collisions between transcription and replication are averted and heterochromatin is reassembled faithfully.
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Affiliation(s)
- Hani Ebrahimi
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Hirohisa Masuda
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Devanshi Jain
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Julia Promisel Cooper
- Telomere Biology Section, Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
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41
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Zhang L, Kong H, Ma H, Yang J. Phylogenomic detection and functional prediction of genes potentially important for plant meiosis. Gene 2018; 643:83-97. [PMID: 29223357 DOI: 10.1016/j.gene.2017.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/18/2017] [Accepted: 12/04/2017] [Indexed: 11/17/2022]
Abstract
Meiosis is a specialized type of cell division necessary for sexual reproduction in eukaryotes. A better understanding of the cytological procedures of meiosis has been achieved by comprehensive cytogenetic studies in plants, while the genetic mechanisms regulating meiotic progression remain incompletely understood. The increasing accumulation of complete genome sequences and large-scale gene expression datasets has provided a powerful resource for phylogenomic inference and unsupervised identification of genes involved in plant meiosis. By integrating sequence homology and expression data, 164, 131, 124 and 162 genes potentially important for meiosis were identified in the genomes of Arabidopsis thaliana, Oryza sativa, Selaginella moellendorffii and Pogonatum aloides, respectively. The predicted genes were assigned to 45 meiotic GO terms, and their functions were related to different processes occurring during meiosis in various organisms. Most of the predicted meiotic genes underwent lineage-specific duplication events during plant evolution, with about 30% of the predicted genes retaining only a single copy in higher plant genomes. The results of this study provided clues to design experiments for better functional characterization of meiotic genes in plants, promoting the phylogenomic approach to the evolutionary dynamics of the plant meiotic machineries.
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Affiliation(s)
- Luoyan Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, Shandong, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Ma
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
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42
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Hirano Y, Kinugasa Y, Asakawa H, Chikashige Y, Obuse C, Haraguchi T, Hiraoka Y. Lem2 is retained at the nuclear envelope through its interaction with Bqt4 in fission yeast. Genes Cells 2018; 23:122-135. [PMID: 29292846 DOI: 10.1111/gtc.12557] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/04/2017] [Indexed: 12/31/2022]
Abstract
Inner nuclear membrane (INM) proteins are thought to play important roles in modulating nuclear organization and function through their interactions with chromatin. However, these INM proteins share redundant functions in metazoans that pose difficulties for functional studies. The fission yeast Schizosaccharomyces pombe exhibits a relatively small number of INM proteins, and molecular genetic tools are available to separate their redundant functions. In S. pombe, it has been reported that among potentially redundant INM proteins, Lem2 displays a unique genetic interaction with another INM protein, Bqt4, which is involved in anchoring telomeres to the nuclear envelope. Double mutations in the lem2 and bqt4 genes confer synthetic lethality during vegetative growth. Here, we show that Lem2 is retained at the nuclear envelope through its interaction with Bqt4, as the loss of Bqt4 results in the exclusive accumulation of Lem2 to the spindle pole body (SPB). An N-terminal nucleoplasmic region of Lem2 bears affinity to both Bqt4 and the SPB in a competitive manner. In contrast, the synthetic lethality of the lem2 bqt4 double mutant is suppressed by the C-terminal region of Lem2. These results indicate that the N-terminal and C-terminal domains of Lem2 show independent functions with respect to Bqt4.
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Affiliation(s)
- Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yasuha Kinugasa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Chikashi Obuse
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
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43
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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44
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Zhu Q, Zheng F, Liu AP, Qian J, Fu C, Lin Y. Shape Transformation of the Nuclear Envelope during Closed Mitosis. Biophys J 2017; 111:2309-2316. [PMID: 27851952 DOI: 10.1016/j.bpj.2016.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 09/28/2016] [Accepted: 10/07/2016] [Indexed: 11/18/2022] Open
Abstract
The nuclear envelope (NE) in lower eukaryotes such as Schizosaccharomyces pombe undergoes large morphology changes during closed mitosis. However, which physical parameters are important in governing the shape evolution of the NE, and how defects in the dividing chromosomes/microtubules are reflected in those parameters, are fundamental questions that remain unresolved. In this study, we show that improper separation of chromosomes in genetically deficient cells leads to membrane tethering or asymmetric division in contrast to the formation of two equal-sized daughter nuclei in wild-type cells. We hypothesize that the poleward force is transmitted to the nuclear membrane through its physical contact with the separated sister chromatids at the two spindle poles. A theoretical model is developed to predict the morphology evolution of the NE where key factors such as the work done by the poleward force and bending and surface energies stored in the membrane have been taken into account. Interestingly, the predicted phase diagram, summarizing the dependence of nuclear shape on the size of the load transmission regions, and the pole-to-pole distance versus surface area relationship all quantitatively agree well with our experimental observations, suggesting that this model captures the essential physics involved in closed mitosis.
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Affiliation(s)
- Qian Zhu
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Fan Zheng
- Chinese Academy of Sciences Center for Excellence in Molecular Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Jin Qian
- Department of Engineering Mechanics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chuanhai Fu
- Chinese Academy of Sciences Center for Excellence in Molecular Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
| | - Yuan Lin
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong SAR, China.
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45
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LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells. Proc Natl Acad Sci U S A 2017; 114:E2166-E2175. [PMID: 28242692 PMCID: PMC5358359 DOI: 10.1073/pnas.1613916114] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The molecular mechanism for sealing newly formed nuclear envelopes was unclear until the recent discovery that endosomal sorting complexes required for transport III (ESCRT-III) proteins mediate this process. Cmp7p (CHMP7), in particular, was identified as an early acting factor that recruits other ESCRT-III proteins to the nuclear envelope. A fundamental aspect of the varied roles of ESCRT factors is their recruitment by site-specific adaptors, yet the central question of how the ESCRT machinery is targeted to nuclear membranes has remained outstanding. Our study identifies the inner nuclear membrane protein LEM2 as a key, conserved factor that recruits CHMP7 and downstream ESCRT-III proteins to breaches in the nuclear envelope. Endosomal sorting complexes required for transport III (ESCRT-III) proteins have been implicated in sealing the nuclear envelope in mammals, spindle pole body dynamics in fission yeast, and surveillance of defective nuclear pore complexes in budding yeast. Here, we report that Lem2p (LEM2), a member of the LEM (Lap2-Emerin-Man1) family of inner nuclear membrane proteins, and the ESCRT-II/ESCRT-III hybrid protein Cmp7p (CHMP7), work together to recruit additional ESCRT-III proteins to holes in the nuclear membrane. In Schizosaccharomyces pombe, deletion of the ATPase vps4 leads to severe defects in nuclear morphology and integrity. These phenotypes are suppressed by loss-of-function mutations that arise spontaneously in lem2 or cmp7, implying that these proteins may function upstream in the same pathway. Building on these genetic interactions, we explored the role of LEM2 during nuclear envelope reformation in human cells. We found that CHMP7 and LEM2 enrich at the same region of the chromatin disk periphery during this window of cell division and that CHMP7 can bind directly to the C-terminal domain of LEM2 in vitro. We further found that, during nuclear envelope formation, recruitment of the ESCRT factors CHMP7, CHMP2A, and IST1/CHMP8 all depend on LEM2 in human cells. We conclude that Lem2p/LEM2 is a conserved nuclear site-specific adaptor that recruits Cmp7p/CHMP7 and downstream ESCRT factors to the nuclear envelope.
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46
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Collins CM, Ellis JA, Holaska JM. MAPK signaling pathways and HDAC3 activity are disrupted during differentiation of emerin-null myogenic progenitor cells. Dis Model Mech 2017; 10:385-397. [PMID: 28188262 PMCID: PMC5399572 DOI: 10.1242/dmm.028787] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/01/2017] [Indexed: 01/28/2023] Open
Abstract
Mutations in the gene encoding emerin cause Emery–Dreifuss muscular dystrophy (EDMD). Emerin is an integral inner nuclear membrane protein and a component of the nuclear lamina. EDMD is characterized by skeletal muscle wasting, cardiac conduction defects and tendon contractures. The failure to regenerate skeletal muscle is predicted to contribute to the skeletal muscle pathology of EDMD. We hypothesize that muscle regeneration defects are caused by impaired muscle stem cell differentiation. Myogenic progenitors derived from emerin-null mice were used to confirm their impaired differentiation and analyze selected myogenic molecular pathways. Emerin-null progenitors were delayed in their cell cycle exit, had decreased myosin heavy chain (MyHC) expression and formed fewer myotubes. Emerin binds to and activates histone deacetylase 3 (HDAC3). Here, we show that theophylline, an HDAC3-specific activator, improved myotube formation in emerin-null cells. Addition of the HDAC3-specific inhibitor RGFP966 blocked myotube formation and MyHC expression in wild-type and emerin-null myogenic progenitors, but did not affect cell cycle exit. Downregulation of emerin was previously shown to affect the p38 MAPK and ERK/MAPK pathways in C2C12 myoblast differentiation. Using a pure population of myogenic progenitors completely lacking emerin expression, we show that these pathways are also disrupted. ERK inhibition improved MyHC expression in emerin-null cells, but failed to rescue myotube formation or cell cycle exit. Inhibition of p38 MAPK prevented differentiation in both wild-type and emerin-null progenitors. These results show that each of these molecular pathways specifically regulates a particular stage of myogenic differentiation in an emerin-dependent manner. Thus, pharmacological targeting of multiple pathways acting at specific differentiation stages may be a better therapeutic approach in the future to rescue muscle regeneration in vivo. Editors' choice: HDAC3, p38 MAPK and ERK signaling are altered during differentiation of myogenic progenitors lacking emerin; pharmacological activation or inhibition of these signaling proteins rescues specific stages of myogenic differentiation.
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Affiliation(s)
- Carol M Collins
- University of the Sciences, Department of Pharmaceutical Sciences, 600 S. 43rd St, Philadelphia, PA 19104, USA
| | - Joseph A Ellis
- University of the Sciences, Department of Pharmaceutical Sciences, 600 S. 43rd St, Philadelphia, PA 19104, USA
| | - James M Holaska
- University of the Sciences, Department of Pharmaceutical Sciences, 600 S. 43rd St, Philadelphia, PA 19104, USA
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47
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Matsuda A, Asakawa H, Haraguchi T, Hiraoka Y. Spatial organization of the Schizosaccharomyces pombe genome within the nucleus. Yeast 2016; 34:55-66. [PMID: 27766670 DOI: 10.1002/yea.3217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/06/2016] [Accepted: 10/13/2016] [Indexed: 12/14/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a useful experimental system for studying the organization of chromosomes within the cell nucleus. S. pombe has a small genome that is organized into three chromosomes. The small size of the genome and the small number of chromosomes are advantageous for cytological and genome-wide studies of chromosomes; however, the small size of the nucleus impedes microscopic observations owing to limits in spatial resolution during imaging. Recent advances in microscopy, such as super-resolution microscopy, have greatly expanded the use of S. pombe as a model organism in a wide range of studies. In addition, biochemical studies, such as chromatin immunoprecipitation and chromosome conformation capture, have provided complementary approaches. Here, we review the spatial organization of the S. pombe genome as determined by a combination of cytological and biochemical studies. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Atsushi Matsuda
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe, 651-2492, Japan
| | - Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe, 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe, 651-2492, Japan
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48
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Braun S, Barrales RR. Beyond Tethering and the LEM domain: MSCellaneous functions of the inner nuclear membrane Lem2. Nucleus 2016; 7:523-531. [PMID: 27797637 DOI: 10.1080/19491034.2016.1252892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nuclear envelope plays a pivotal role in the functional organization of chromatin. Various inner nuclear membrane (INM) proteins associate with transcriptionally repressed chromatin, which is often found at the nuclear periphery. A prominent example is the conserved family of LEM (LAP2-Emerin-MAN1) domain proteins that interact with DNA-binding proteins and have been proposed to mediate tethering of chromatin to the nuclear membrane. We recently reported that the fission yeast protein Lem2, a homolog of metazoan LEM proteins, contributes to perinuclear localization and silencing of heterochromatin. 1 We demonstrate that binding and tethering of centromeric chromatin depends on the LEM domain of Lem2. Unexpectedly, this domain is dispensable for heterochromatin silencing, which is instead mediated by a different structural domain of Lem2, the MSC (MAN1-Src1 C-terminal) domain. Hence, silencing and tethering by Lem2 can be mechanistically separated. Notably, the MSC domain has multiple functions beyond heterochromatic silencing. Here we discuss the implications of these novel findings for the understanding of this conserved INM protein.
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Affiliation(s)
- Sigurd Braun
- a Department of Physiological Chemistry , Biomedical Center (BMC), Ludwig-Maximilians-University of Munich , Martinsried , Germany
| | - Ramón Ramos Barrales
- a Department of Physiological Chemistry , Biomedical Center (BMC), Ludwig-Maximilians-University of Munich , Martinsried , Germany.,b Present address: Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide, Sevilla-CSIC-Junta de Andalucía , Sevilla , Spain
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49
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Webster BM, Thaller DJ, Jäger J, Ochmann SE, Borah S, Lusk CP. Chm7 and Heh1 collaborate to link nuclear pore complex quality control with nuclear envelope sealing. EMBO J 2016; 35:2447-2467. [PMID: 27733427 DOI: 10.15252/embj.201694574] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022] Open
Abstract
The integrity of the nuclear envelope barrier relies on membrane remodeling by the ESCRTs, which seal nuclear envelope holes and contribute to the quality control of nuclear pore complexes (NPCs); whether these processes are mechanistically related remains poorly defined. Here, we show that the ESCRT-II/III chimera, Chm7, is recruited to a nuclear envelope subdomain that expands upon inhibition of NPC assembly and is required for the formation of the storage of improperly assembled NPCs (SINC) compartment. Recruitment to sites of NPC assembly is mediated by its ESCRT-II domain and the LAP2-emerin-MAN1 (LEM) family of integral inner nuclear membrane proteins, Heh1 and Heh2. We establish direct binding between Heh2 and the "open" forms of both Chm7 and the ESCRT-III, Snf7, and between Chm7 and Snf7. Interestingly, Chm7 is required for the viability of yeast strains where double membrane seals have been observed over defective NPCs; deletion of CHM7 in these strains leads to a loss of nuclear compartmentalization suggesting that the sealing of defective NPCs and nuclear envelope ruptures could proceed through similar mechanisms.
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Affiliation(s)
- Brant M Webster
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - David J Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Jens Jäger
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Sarah E Ochmann
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Sapan Borah
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
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Abstract
The emergence of the nucleus was a major event of eukaryogenesis. How the nuclear envelope (NE) arose and acquired functions governing chromatin organization and epigenetic control has direct bearing on origins of developmental/stage-specific expression programs. The configuration of the NE and the associated lamina in the last eukaryotic common ancestor (LECA) is of major significance and can provide insight into activities within the LECA nucleus. Subsequent lamina evolution, alterations, and adaptations inform on the variation and selection of distinct mechanisms that subtend gene expression in distinct taxa. Understanding lamina evolution has been difficult due to the diversity and limited taxonomic distributions of the three currently known highly distinct nuclear lamina. We rigorously searched available sequence data for an expanded view of the distribution of known lamina and lamina-associated proteins. While the lamina proteins of plants and trypanosomes are indeed taxonomically restricted, homologs of metazoan lamins and key lamin-binding proteins have significantly broader distributions, and a lamin gene tree supports vertical evolution from the LECA. Two protist lamins from highly divergent taxa target the nucleus in mammalian cells and polymerize into filamentous structures, suggesting functional conservation of distant lamin homologs. Significantly, a high level of divergence of lamin homologs within certain eukaryotic groups and the apparent absence of lamins and/or the presence of seemingly different lamina proteins in many eukaryotes suggests great evolutionary plasticity in structures at the NE, and hence mechanisms of chromatin tethering and epigenetic gene control.
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Affiliation(s)
- Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK
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