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Alfano C, Fichou Y, Huber K, Weiss M, Spruijt E, Ebbinghaus S, De Luca G, Morando MA, Vetri V, Temussi PA, Pastore A. Molecular Crowding: The History and Development of a Scientific Paradigm. Chem Rev 2024; 124:3186-3219. [PMID: 38466779 PMCID: PMC10979406 DOI: 10.1021/acs.chemrev.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.
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Affiliation(s)
- Caterina Alfano
- Structural
Biology and Biophysics Unit, Fondazione
Ri.MED, 90100 Palermo, Italy
| | - Yann Fichou
- CNRS,
Bordeaux INP, CBMN UMR 5248, IECB, University
of Bordeaux, F-33600 Pessac, France
| | - Klaus Huber
- Department
of Chemistry, University of Paderborn, 33098 Paderborn, Germany
| | - Matthias Weiss
- Experimental
Physics I, Physics of Living Matter, University
of Bayreuth, 95440 Bayreuth, Germany
| | - Evan Spruijt
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Simon Ebbinghaus
- Lehrstuhl
für Biophysikalische Chemie and Research Center Chemical Sciences
and Sustainability, Research Alliance Ruhr, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Giuseppe De Luca
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Valeria Vetri
- Dipartimento
di Fisica e Chimica − Emilio Segrè, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | | | - Annalisa Pastore
- King’s
College London, Denmark
Hill Campus, SE5 9RT London, United Kingdom
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Molenberghs F, Verschuuren M, Vandeweyer L, Peeters S, Bogers JJ, Novo CP, Vanden Berghe W, De Reu H, Cools N, Schelhaas M, De Vos WH. Lamin B1 curtails early human papillomavirus infection by safeguarding nuclear compartmentalization and autophagic capacity. Cell Mol Life Sci 2024; 81:141. [PMID: 38485766 PMCID: PMC10940392 DOI: 10.1007/s00018-024-05194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Human papillomavirus (HPV) infection is a primary cause of cervical and head-and-neck cancers. The HPV genome enters the nucleus during mitosis when the nuclear envelope disassembles. Given that lamins maintain nuclear integrity during interphase, we asked to what extent their loss would affect early HPV infection. To address this question, we infected human cervical cancer cells and keratinocytes lacking the major lamins with a HPV16 pseudovirus (HP-PsV) encoding an EGFP reporter. We found that a sustained reduction or complete loss of lamin B1 significantly increased HP-PsV infection rate. A corresponding greater nuclear HP-PsV load in LMNB1 knockout cells was directly related to their prolonged mitotic window and extensive nuclear rupture propensity. Despite the increased HP-PsV presence, EGFP transcript levels remained virtually unchanged, indicating an additional defect in protein turnover. Further investigation revealed that LMNB1 knockout led to a substantial decrease in autophagic capacity, possibly linked to the persistent activation of cGAS by cytoplasmic chromatin exposure. Thus, the attrition of lamin B1 increases nuclear perviousness and attenuates autophagic capacity, creating an environment conducive to unrestrained accumulation of HPV capsids. Our identification of lower lamin B1 levels and nuclear BAF foci in the basal epithelial layer of several human cervix samples suggests that this pathway may contribute to an increased individual susceptibility to HPV infection.
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Affiliation(s)
- Freya Molenberghs
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Marlies Verschuuren
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Lauran Vandeweyer
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Sarah Peeters
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Johannes J Bogers
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Claudina Perez Novo
- Cell Death Signaling Lab, Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Cell Death Signaling Lab, Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Hans De Reu
- Laboratory of Experimental Hematology, Faculty Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathalie Cools
- Laboratory of Experimental Hematology, Faculty Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Mario Schelhaas
- Institute of Cellular Virology, University of Münster, Münster, Germany
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences and Health Sciences, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
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Ainani H, Bouchmaa N, Ben Mrid R, El Fatimy R. Liquid-liquid phase separation of protein tau: An emerging process in Alzheimer's disease pathogenesis. Neurobiol Dis 2023; 178:106011. [PMID: 36702317 DOI: 10.1016/j.nbd.2023.106011] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/04/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023] Open
Abstract
Metabolic reactions within cells occur in various isolated compartments with or without borders, the latter being known as membrane-less organelles (MLOs). The MLOs show liquid-like properties and are formed by a process known as liquid-liquid phase separation (LLPS). MLOs contribute to different molecules interactions such as protein-protein, protein-RNA, and RNA-RNA driven by various factors, such as multivalency of intrinsic disorders. MLOs are involved in several cell signaling pathways such as transcription, immune response, and cellular organization. However, disruption of these processes has been found in different pathologies. Recently, it has been demonstrated that protein aggregates, a characteristic of some neurodegenerative diseases, undergo similar phase separation. Tau protein is known as a major neurofibrillary tangles component in Alzheimer's disease (AD). This protein can undergo phase separation to form a MLO known as tau droplet in vitro and in vivo, and this process can be facilitated by several factors, including crowding agents, RNA, and phosphorylation. Tau droplet has been shown to mature into insoluble aggregates suggesting that this process may precede and induce neurodegeneration in AD. Here we review major factors involved in liquid droplet formation within a cell. Additionally, we highlight recent findings concerning tau aggregation following phase separation in AD, along with the potential therapeutic strategies that could be explored in this process against the progression of this pathology.
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Affiliation(s)
- Hassan Ainani
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Najat Bouchmaa
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Reda Ben Mrid
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco
| | - Rachid El Fatimy
- Institute of Biological Sciences (ISSB), UM6P-Faculty of Medical Sciences (UM6P-FMS), Mohammed VI Polytechnic University, Ben-Guerir, Morocco.
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McPhee MJ, Salsman J, Foster J, Thompson J, Mathavarajah S, Dellaire G, Ridgway ND. Running 'LAPS' Around nLD: Nuclear Lipid Droplet Form and Function. Front Cell Dev Biol 2022; 10:837406. [PMID: 35178392 PMCID: PMC8846306 DOI: 10.3389/fcell.2022.837406] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
The nucleus harbours numerous protein subdomains and condensates that regulate chromatin organization, gene expression and genomic stress. A novel nuclear subdomain that is formed following exposure of cells to excess fatty acids is the nuclear lipid droplet (nLD), which is composed of a neutral lipid core surrounded by a phospholipid monolayer and associated regulatory and lipid biosynthetic enzymes. While structurally resembling cytoplasmic LDs, nLDs are formed by distinct but poorly understood mechanisms that involve the emergence of lipid droplets from the lumen of the nucleoplasmic reticulum and de novo lipid synthesis. Luminal lipid droplets that emerge into the nucleoplasm do so at regions of the inner nuclear membrane that become enriched in promyelocytic leukemia (PML) protein. The resulting nLDs that retain PML on their surface are termed lipid-associated PML structures (LAPS), and are distinct from canonical PML nuclear bodies (NB) as they lack key proteins and modifications associated with these NBs. PML is a key regulator of nuclear signaling events and PML NBs are sites of gene regulation and post-translational modification of transcription factors. Therefore, the subfraction of nLDs that form LAPS could regulate lipid stress responses through their recruitment and retention of the PML protein. Both nLDs and LAPS have lipid biosynthetic enzymes on their surface suggesting they are active sites for nuclear phospholipid and triacylglycerol synthesis as well as global lipid regulation. In this review we have summarized the current understanding of nLD and LAPS biogenesis in different cell types, their structure and composition relative to other PML-associated cellular structures, and their role in coordinating a nuclear response to cellular overload of fatty acids.
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Affiliation(s)
- Michael J McPhee
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Jason Foster
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jordan Thompson
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Graham Dellaire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Neale D Ridgway
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
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Warburton A, Della Fera AN, McBride AA. Dangerous Liaisons: Long-Term Replication with an Extrachromosomal HPV Genome. Viruses 2021; 13:1846. [PMID: 34578427 PMCID: PMC8472234 DOI: 10.3390/v13091846] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 01/17/2023] Open
Abstract
Papillomaviruses cause persistent, and usually self-limiting, infections in the mucosal and cutaneous surfaces of the host epithelium. However, in some cases, infection with an oncogenic HPV can lead to cancer. The viral genome is a small, double-stranded circular DNA molecule that is assembled into nucleosomes at all stages of infection. The viral minichromosome replicates at a low copy number in the nucleus of persistently infected cells using the cellular replication machinery. When the infected cells differentiate, the virus hijacks the host DNA damage and repair pathways to replicate viral DNA to a high copy number to generate progeny virions. This strategy is highly effective and requires a close association between viral and host chromatin, as well as cellular processes associated with DNA replication, repair, and transcription. However, this association can lead to accidental integration of the viral genome into host DNA, and under certain circumstances integration can promote oncogenesis. Here we describe the fate of viral DNA at each stage of the viral life cycle and how this might facilitate accidental integration and subsequent carcinogenesis.
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Affiliation(s)
| | | | - Alison A. McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (A.W.); (A.N.D.F.)
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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Farahi N, Lazar T, Wodak SJ, Tompa P, Pancsa R. Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers. Int J Mol Sci 2021; 22:ijms22063017. [PMID: 33809541 PMCID: PMC8002189 DOI: 10.3390/ijms22063017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/13/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles, representing functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integrating the data on LLPS-associated proteins from dedicated databases revealed only modest agreement between them and yielded a high-confidence dataset of 89 human LLPS drivers. Analysis of the supporting evidence for our dataset uncovered a systematic and potentially concerning difference between protein concentrations used in a good fraction of the in vitro LLPS experiments, a key parameter that governs the phase behavior, and the proteomics-derived cellular abundance levels of the corresponding proteins. Closer scrutiny of the underlying experimental data enabled us to offer a sound rationale for this systematic difference, which draws on our current understanding of the cellular organization of the proteome and the LLPS process. In support of this rationale, we find that genes coding for our human LLPS drivers tend to be dosage-sensitive, suggesting that their cellular availability is tightly regulated to preserve their functional role in direct or indirect relation to condensate formation. Our analysis offers guideposts for increasing agreement between in vitro and in vivo studies, probing the roles of proteins in LLPS.
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Affiliation(s)
- Nazanin Farahi
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Department of Biology, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Shoshana J. Wodak
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Flemish Institute for Biotechnology, 1050 Brussels, Belgium; (N.F.); (T.L.); (S.J.W.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence: (P.T.); (R.P.)
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence: (P.T.); (R.P.)
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Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res 2020; 48:11890-11912. [PMID: 33068409 PMCID: PMC7708061 DOI: 10.1093/nar/gkaa828] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
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Affiliation(s)
- Armelle Corpet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Constance Kleijwegt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Simon Roubille
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Franceline Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Karine Jacquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Pascale Texier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
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Wotherspoon D, Rogerson C, O’Shaughnessy RF. Perspective: Controlling Epidermal Terminal Differentiation with Transcriptional Bursting and RNA Bodies. J Dev Biol 2020; 8:E29. [PMID: 33291764 PMCID: PMC7768391 DOI: 10.3390/jdb8040029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/20/2020] [Accepted: 12/02/2020] [Indexed: 12/21/2022] Open
Abstract
The outer layer of the skin, the epidermis, is the principal barrier to the external environment: post-mitotic cells terminally differentiate to form a tough outer cornified layer of enucleate and flattened cells that confer the majority of skin barrier function. Nuclear degradation is required for correct cornified envelope formation. This process requires mRNA translation during the process of nuclear destruction. In this review and perspective, we address the biology of transcriptional bursting and the formation of ribonuclear particles in model organisms including mammals, and then examine the evidence that these phenomena occur as part of epidermal terminal differentiation.
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Affiliation(s)
- Duncan Wotherspoon
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London E1 2AT, UK;
| | | | - Ryan F.L. O’Shaughnessy
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London E1 2AT, UK;
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Nevers Q, Albertini AA, Lagaudrière-Gesbert C, Gaudin Y. Negri bodies and other virus membrane-less replication compartments. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118831. [PMID: 32835749 PMCID: PMC7442162 DOI: 10.1016/j.bbamcr.2020.118831] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/25/2022]
Abstract
Viruses reshape the organization of the cell interior to achieve different steps of their cellular cycle. Particularly, viral replication and assembly often take place in viral factories where specific viral and cellular proteins as well as nucleic acids concentrate. Viral factories can be either membrane-delimited or devoid of any cellular membranes. In the latter case, they are referred as membrane-less replication compartments. The most emblematic ones are the Negri bodies, which are inclusion bodies that constitute the hallmark of rabies virus infection. Interestingly, Negri bodies and several other viral replication compartments have been shown to arise from a liquid-liquid phase separation process and, thus, constitute a new class of liquid organelles. This is a paradigm shift in the field of virus replication. Here, we review the different aspects of membrane-less virus replication compartments with a focus on the Mononegavirales order and discuss their interactions with the host cell machineries and the cytoskeleton. We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells.
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Affiliation(s)
- Quentin Nevers
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie A Albertini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France.
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11
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Paulus C, Harwardt T, Walter B, Marxreiter A, Zenger M, Reuschel E, Nevels MM. Revisiting promyelocytic leukemia protein targeting by human cytomegalovirus immediate-early protein 1. PLoS Pathog 2020; 16:e1008537. [PMID: 32365141 PMCID: PMC7224577 DOI: 10.1371/journal.ppat.1008537] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/14/2020] [Accepted: 04/13/2020] [Indexed: 12/18/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies are nuclear organelles implicated in intrinsic and innate antiviral defense. The eponymous PML proteins, central to the self-organization of PML bodies, and other restriction factors found in these organelles are common targets of viral antagonism. The 72-kDa immediate-early protein 1 (IE1) is the principal antagonist of PML bodies encoded by the human cytomegalovirus (hCMV). IE1 is believed to disrupt PML bodies by inhibiting PML SUMOylation, while PML was proposed to act as an E3 ligase for IE1 SUMOylation. PML targeting by IE1 is considered to be crucial for hCMV replication at low multiplicities of infection, in part via counteracting antiviral gene induction linked to the cellular interferon (IFN) response. However, current concepts of IE1-PML interaction are largely derived from mutant IE1 proteins known or predicted to be metabolically unstable and globally misfolded. We performed systematic clustered charge-to-alanine scanning mutagenesis and identified a stable IE1 mutant protein (IE1cc172-176) with wild-type characteristics except for neither interacting with PML proteins nor inhibiting PML SUMOylation. Consequently, IE1cc172-176 does not associate with PML bodies and is selectively impaired for disrupting these organelles. Surprisingly, functional analysis of IE1cc172-176 revealed that the protein is hypermodified by mixed SUMO chains and that IE1 SUMOylation depends on nucleosome rather than PML binding. Furthermore, a mutant hCMV expressing IE1cc172-176 was only slightly attenuated compared to an IE1-null virus even at low multiplicities of infection. Finally, hCMV-induced expression of cytokine and IFN-stimulated genes turned out to be reduced rather than increased in the presence of IE1cc172-176 relative to wild-type IE1. Our findings challenge present views on the relationship of IE1 with PML and the role of PML in hCMV replication. This study also provides initial evidence for the idea that disruption of PML bodies upon viral infection is linked to activation rather than inhibition of innate immunity.
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Affiliation(s)
- Christina Paulus
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Thomas Harwardt
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Bernadette Walter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Andrea Marxreiter
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Marion Zenger
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Edith Reuschel
- Department of Obstetrics and Gynecology, Clinic St. Hedwig at Hospital Barmherzige Brüder Regensburg, Regensburg, Germany
| | - Michael M. Nevels
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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12
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Lång A, Lång E, Bøe SO. PML Bodies in Mitosis. Cells 2019; 8:cells8080893. [PMID: 31416160 PMCID: PMC6721746 DOI: 10.3390/cells8080893] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies are dynamic intracellular structures that recruit and release a variety of different proteins in response to stress, virus infection, DNA damage and cell cycle progression. While PML bodies primarily are regarded as nuclear compartments, they are forced to travel to the cytoplasm each time a cell divides, due to breakdown of the nuclear membrane at entry into mitosis and subsequent nuclear exclusion of nuclear material at exit from mitosis. Here we review the biochemical and biophysical transitions that occur in PML bodies during mitosis and discuss this in light of post-mitotic nuclear import, cell fate decision and acute promyelocytic leukemia therapy.
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Affiliation(s)
- Anna Lång
- Oslo University Hospital, Department of Molecular Microbiology, Forskningsveien 1, 0373 Oslo, Norway
| | - Emma Lång
- Oslo University Hospital, Department of Molecular Microbiology, Forskningsveien 1, 0373 Oslo, Norway
| | - Stig Ove Bøe
- Oslo University Hospital, Department of Molecular Microbiology, Forskningsveien 1, 0373 Oslo, Norway.
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13
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Ditlev JA, Vega AR, Köster DV, Su X, Tani T, Lakoduk AM, Vale RD, Mayor S, Jaqaman K, Rosen MK. A composition-dependent molecular clutch between T cell signaling condensates and actin. eLife 2019; 8:e42695. [PMID: 31268421 PMCID: PMC6624021 DOI: 10.7554/elife.42695] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/14/2019] [Indexed: 01/04/2023] Open
Abstract
During T cell activation, biomolecular condensates form at the immunological synapse (IS) through multivalency-driven phase separation of LAT, Grb2, Sos1, SLP-76, Nck, and WASP. These condensates move radially at the IS, traversing successive radially-oriented and concentric actin networks. To understand this movement, we biochemically reconstituted LAT condensates with actomyosin filaments. We found that basic regions of Nck and N-WASP/WASP promote association and co-movement of LAT condensates with actin, indicating conversion of weak individual affinities to high collective affinity upon phase separation. Condensates lacking these components were propelled differently, without strong actin adhesion. In cells, LAT condensates lost Nck as radial actin transitioned to the concentric network, and engineered condensates constitutively binding actin moved aberrantly. Our data show that Nck and WASP form a clutch between LAT condensates and actin in vitro and suggest that compositional changes may enable condensate movement by distinct actin networks in different regions of the IS.
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Affiliation(s)
- Jonathon A Ditlev
- Howard Hughes Medical Institute, Summer Institute, Marine Biological LaboratoryWoods HoleUnited States
- Department of BiophysicsHoward Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Anthony R Vega
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Darius Vasco Köster
- Howard Hughes Medical Institute, Summer Institute, Marine Biological LaboratoryWoods HoleUnited States
- National Centre for Biological Sciences, Tata Institute for Fundamental ResearchBangaloreIndia
| | - Xiaolei Su
- Howard Hughes Medical Institute, Summer Institute, Marine Biological LaboratoryWoods HoleUnited States
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Tomomi Tani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleUnited States
| | - Ashley M Lakoduk
- Department of Cell BiologyUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Ronald D Vale
- Howard Hughes Medical Institute, Summer Institute, Marine Biological LaboratoryWoods HoleUnited States
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical Institute, University of California, San FranciscoSan FranciscoUnited States
| | - Satyajit Mayor
- Howard Hughes Medical Institute, Summer Institute, Marine Biological LaboratoryWoods HoleUnited States
- National Centre for Biological Sciences, Tata Institute for Fundamental ResearchBangaloreIndia
| | - Khuloud Jaqaman
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of BioinformaticsUniversity of Texas Southwestern Medical CenterDallasUnited States
| | - Michael K Rosen
- Howard Hughes Medical Institute, Summer Institute, Marine Biological LaboratoryWoods HoleUnited States
- Department of BiophysicsHoward Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasUnited States
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14
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Guion L, Bienkowska-Haba M, DiGiuseppe S, Florin L, Sapp M. PML nuclear body-residing proteins sequentially associate with HPV genome after infectious nuclear delivery. PLoS Pathog 2019; 15:e1007590. [PMID: 30802273 PMCID: PMC6405170 DOI: 10.1371/journal.ppat.1007590] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 03/07/2019] [Accepted: 01/18/2019] [Indexed: 12/20/2022] Open
Abstract
Subnuclear promyelocytic leukemia (PML) nuclear bodies (NBs) are targeted by many DNA viruses after nuclear delivery. PML protein is essential for formation of PML NBs. Sp100 and Small Ubiquitin-Like Modifier (SUMO) are also permanently residing within PML NBs. Often, large DNA viruses disassemble and reorganize PML NBs to counteract their intrinsic antiviral activity and support establishment of infection. However, human papillomavirus (HPV) requires PML protein to retain incoming viral DNA in the nucleus for subsequent efficient transcription. In contrast, Sp100 was identified as a restriction factor for HPV. These findings suggested that PML NBs are important regulators of early stages of the HPV life cycle. Nuclear delivery of incoming HPV DNA requires mitosis. Viral particles are retained within membrane-bound transport vesicles throughout mitosis. The viral genome is released from transport vesicles by an unknown mechanism several hours after nuclear envelope reformation. The minor capsid protein L2 mediates intracellular transport by becoming transmembranous in the endocytic compartment. Herein, we tested our hypothesis that PML protein is recruited to incoming viral genome prior to egress from transport vesicles. High-resolution microscopy revealed that PML protein, SUMO-1, and Sp100 are recruited to incoming viral genomes, rather than viral genomes being targeted to preformed PML NBs. Differential immunofluorescent staining suggested that PML protein and SUMO-1 associated with transport vesicles containing viral particles prior to egress, implying that recruitment is likely mediated by L2 protein. In contrast, Sp100 recruitment to HPV-harboring PML NBs occurred after release of viral genomes from transport vesicles. The delayed recruitment of Sp100 is specific for HPV-associated PML NBs. These data suggest that the virus continuously resides within a protective environment until the transport vesicle breaks down in late G1 phase and imply that HPV might modulate PML NB assembly to achieve establishment of infection and the shift to viral maintenance.
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Affiliation(s)
- Lucile Guion
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Malgorzata Bienkowska-Haba
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Stephen DiGiuseppe
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Luise Florin
- Department of Virology and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Sapp
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
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15
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Ditlev JA, Case LB, Rosen MK. Who's In and Who's Out-Compositional Control of Biomolecular Condensates. J Mol Biol 2018; 430:4666-4684. [PMID: 30099028 PMCID: PMC6204295 DOI: 10.1016/j.jmb.2018.08.003] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.
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Affiliation(s)
- Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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16
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Hoischen C, Monajembashi S, Weisshart K, Hemmerich P. Multimodal Light Microscopy Approaches to Reveal Structural and Functional Properties of Promyelocytic Leukemia Nuclear Bodies. Front Oncol 2018; 8:125. [PMID: 29888200 PMCID: PMC5980967 DOI: 10.3389/fonc.2018.00125] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
The promyelocytic leukemia (pml) gene product PML is a tumor suppressor localized mainly in the nucleus of mammalian cells. In the cell nucleus, PML seeds the formation of macromolecular multiprotein complexes, known as PML nuclear bodies (PML NBs). While PML NBs have been implicated in many cellular functions including cell cycle regulation, survival and apoptosis their role as signaling hubs along major genome maintenance pathways emerged more clearly. However, despite extensive research over the past decades, the precise biochemical function of PML in these pathways is still elusive. It remains a big challenge to unify all the different previously suggested cellular functions of PML NBs into one mechanistic model. With the advent of genetically encoded fluorescent proteins it became possible to trace protein function in living specimens. In parallel, a variety of fluorescence fluctuation microscopy (FFM) approaches have been developed which allow precise determination of the biophysical and interaction properties of cellular factors at the single molecule level in living cells. In this report, we summarize the current knowledge on PML nuclear bodies and describe several fluorescence imaging, manipulation, FFM, and super-resolution techniques suitable to analyze PML body assembly and function. These include fluorescence redistribution after photobleaching, fluorescence resonance energy transfer, fluorescence correlation spectroscopy, raster image correlation spectroscopy, ultraviolet laser microbeam-induced DNA damage, erythrocyte-mediated force application, and super-resolution microscopy approaches. Since most if not all of the microscopic equipment to perform these techniques may be available in an institutional or nearby facility, we hope to encourage more researches to exploit sophisticated imaging tools for their research in cancer biology.
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17
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Campos SK. Subcellular Trafficking of the Papillomavirus Genome during Initial Infection: The Remarkable Abilities of Minor Capsid Protein L2. Viruses 2017; 9:v9120370. [PMID: 29207511 PMCID: PMC5744145 DOI: 10.3390/v9120370] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/24/2022] Open
Abstract
Since 2012, our understanding of human papillomavirus (HPV) subcellular trafficking has undergone a drastic paradigm shift. Work from multiple laboratories has revealed that HPV has evolved a unique means to deliver its viral genome (vDNA) to the cell nucleus, relying on myriad host cell proteins and processes. The major breakthrough finding from these recent endeavors has been the realization of L2-dependent utilization of cellular sorting factors for the retrograde transport of vDNA away from degradative endo/lysosomal compartments to the Golgi, prior to mitosis-dependent nuclear accumulation of L2/vDNA. An overview of current models of HPV entry, subcellular trafficking, and the role of L2 during initial infection is provided below, highlighting unresolved questions and gaps in knowledge.
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Affiliation(s)
- Samuel K Campos
- The Department of Immunobiology, The University of Arizona, Tucson, AZ 85721-0240, USA.
- The Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ 85721-0240, USA.
- The Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85721-0240, USA.
- The BIO5 Institute, Tucson, AZ 85721-0240, USA.
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18
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Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 2017; 18:285-298. [PMID: 28225081 PMCID: PMC7434221 DOI: 10.1038/nrm.2017.7] [Citation(s) in RCA: 3730] [Impact Index Per Article: 466.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.
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Affiliation(s)
- Salman F. Banani
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyun O. Lee
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Anthony A. Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Michael K. Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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19
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Lång A, Eriksson J, Schink KO, Lång E, Blicher P, Połeć A, Brech A, Dalhus B, Bøe SO. Visualization of PML nuclear import complexes reveals FG-repeat nucleoporins at cargo retrieval sites. Nucleus 2017; 8:404-420. [PMID: 28402725 DOI: 10.1080/19491034.2017.1306161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Selective nuclear import in eukaryotic cells involves sequential interactions between nuclear import receptors and phenylalanine-glycine (FG)-repeat nucleoporins. Traditionally, binding of cargoes to import receptors is perceived as a nuclear pore complex independent event, while interactions between import complexes and nucleoporins are thought to take place at the nuclear pores. However, studies have shown that nucleoporins are mobile and not static within the nuclear pores, suggesting that they may become engaged in nuclear import before nuclear pore entry. Here we have studied post-mitotic nuclear import of the tumor suppressor protein PML. Since this protein forms nuclear compartments called PML bodies that persist during mitosis, the assembly of putative PML import complexes can be visualized on the surface of these protein aggregates as the cell progress from an import inactive state in mitosis to an import active state in G1. We show that these post-mitotic cytoplasmic PML bodies incorporate a multitude of peripheral nucleoporins, but not scaffold or nuclear basket nucleoporins, in a manner that depends on FG-repeats, the KPNB1 import receptor, and the PML nuclear localization signal. The study suggests that nucleoporins have the ability to target certain nuclear cargo proteins in a nuclear pore-uncoupled state, before nuclear pore entry.
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Affiliation(s)
- Anna Lång
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway.,b Institute of Clinical Medicine , University of Oslo , Oslo , Norway
| | - Jens Eriksson
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
| | - Kay Oliver Schink
- c Department of Molecular Cell Biology, Institute for Cancer Research and Centre for Cancer Biomedicine , Oslo University Hospital , Oslo , Norway
| | - Emma Lång
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
| | - Pernille Blicher
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
| | - Anna Połeć
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
| | - Andreas Brech
- c Department of Molecular Cell Biology, Institute for Cancer Research and Centre for Cancer Biomedicine , Oslo University Hospital , Oslo , Norway
| | - Bjørn Dalhus
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
| | - Stig Ove Bøe
- a Department of Medical Biochemistry , Oslo University Hospital , Oslo , Norway
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20
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Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R, Rosen MK. Compositional Control of Phase-Separated Cellular Bodies. Cell 2016; 166:651-663. [PMID: 27374333 DOI: 10.1016/j.cell.2016.06.010] [Citation(s) in RCA: 874] [Impact Index Per Article: 97.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 03/13/2016] [Accepted: 06/01/2016] [Indexed: 12/12/2022]
Abstract
Cellular bodies such as P bodies and PML nuclear bodies (PML NBs) appear to be phase-separated liquids organized by multivalent interactions among proteins and RNA molecules. Although many components of various cellular bodies are known, general principles that define body composition are lacking. We modeled cellular bodies using several engineered multivalent proteins and RNA. In vitro and in cells, these scaffold molecules form phase-separated liquids that concentrate low valency client proteins. Clients partition differently depending on the ratio of scaffolds, with a sharp switch across the phase diagram diagonal. Composition can switch rapidly through changes in scaffold concentration or valency. Natural PML NBs and P bodies show analogous partitioning behavior, suggesting how their compositions could be controlled by levels of PML SUMOylation or cellular mRNA concentration, respectively. The data suggest a conceptual framework for considering the composition and control thereof of cellular bodies assembled through heterotypic multivalent interactions.
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Affiliation(s)
- Salman F Banani
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Allyson M Rice
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - William B Peeples
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuan Lin
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Saumya Jain
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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21
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SUMO5, a Novel Poly-SUMO Isoform, Regulates PML Nuclear Bodies. Sci Rep 2016; 6:26509. [PMID: 27211601 PMCID: PMC4876461 DOI: 10.1038/srep26509] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/04/2016] [Indexed: 12/23/2022] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML-NBs) are PML-based nuclear structures that regulate various cellular processes. SUMOylation, the process of covalently conjugating small ubiquitin-like modifiers (SUMOs), is required for both the formation and the disruption of PML-NBs. However, detailed mechanisms of how SUMOylation regulates these processes remain unknown. Here we report that SUMO5, a novel SUMO variant, mediates the growth and disruption of PML-NBs. PolySUMO5 conjugation of PML at lysine 160 facilitates recruitment of PML-NB components, which enlarges PML-NBs. SUMO5 also increases polySUMO2/3 conjugation of PML, resulting in RNF4-mediated disruption of PML-NBs. The acute promyelocytic leukemia oncoprotein PML-RARα blocks SUMO5 conjugation of PML, causing cytoplasmic displacement of PML and disruption of PML-NBs. Our work not only identifies a new member of the SUMO family but also reveals the mechanistic basis of the PML-NB life cycle in human cells.
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22
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Ohsaki Y, Kawai T, Yoshikawa Y, Cheng J, Jokitalo E, Fujimoto T. PML isoform II plays a critical role in nuclear lipid droplet formation. J Cell Biol 2016; 212:29-38. [PMID: 26728854 PMCID: PMC4700481 DOI: 10.1083/jcb.201507122] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PML-II plays a critical role in generating nuclear lipid droplets, which are associated with promyelocytic leukemia nuclear bodies as well as with the extension of the inner nuclear membrane. Lipid droplets (LDs) in the nucleus of hepatocyte-derived cell lines were found to be associated with premyelocytic leukemia (PML) nuclear bodies (NBs) and type I nucleoplasmic reticulum (NR) or the extension of the inner nuclear membrane. Knockdown of PML isoform II (PML-II) caused a significant decrease in both nuclear LDs and type I NR, whereas overexpression of PML-II increased both. Notably, these effects were evident only in limited types of cells, in which a moderate number of nuclear LDs exist intrinsically, and PML-II was targeted not only at PML NBs, but also at the nuclear envelope, excluding lamins and SUN proteins. Knockdown of SUN proteins induced a significant increase in the type I NR and nuclear LDs, but these effects were cancelled by simultaneous knockdown of PML-II. Nuclear LDs harbored diacylglycerol O-acyltransferase 2 and CTP:phosphocholine cytidylyltransferase α and incorporated newly synthesized lipid esters. These results corroborated that PML-II plays a critical role in generating nuclear LDs in specific cell types.
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Affiliation(s)
- Yuki Ohsaki
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Takeshi Kawai
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yukichika Yoshikawa
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Jinglei Cheng
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Toyoshi Fujimoto
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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23
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Cappadocia L, Mascle XH, Bourdeau V, Tremblay-Belzile S, Chaker-Margot M, Lussier-Price M, Wada J, Sakaguchi K, Aubry M, Ferbeyre G, Omichinski JG. Structural and functional characterization of the phosphorylation-dependent interaction between PML and SUMO1. Structure 2014; 23:126-138. [PMID: 25497731 DOI: 10.1016/j.str.2014.10.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 12/21/2022]
Abstract
PML and several other proteins localizing in PML-nuclear bodies (PML-NB) contain phosphoSIMs (SUMO-interacting motifs), and phosphorylation of this motif plays a key role in their interaction with SUMO family proteins. We examined the role that phosphorylation plays in the binding of the phosphoSIMs of PML and Daxx to SUMO1 at the atomic level. The crystal structures of SUMO1 bound to unphosphorylated and tetraphosphorylated PML-SIM peptides indicate that three phosphoserines directly contact specific positively charged residues of SUMO1. Surprisingly, the crystal structure of SUMO1 bound to a diphosphorylated Daxx-SIM peptide indicate that the hydrophobic residues of the phosphoSIM bind in a manner similar to that seen with PML, but important differences are observed when comparing the phosphorylated residues. Together, the results provide an atomic level description of how specific acetylation patterns within different SUMO family proteins can work together with phosphorylation of phosphoSIM's regions of target proteins to regulate binding specificity.
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Affiliation(s)
- Laurent Cappadocia
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Xavier H Mascle
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Véronique Bourdeau
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Samuel Tremblay-Belzile
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Malik Chaker-Margot
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Mathieu Lussier-Price
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Junya Wada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Muriel Aubry
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - James G Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, C.P. 6128 Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada.
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24
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JC virus inclusions in progressive multifocal leukoencephalopathy: scaffolding promyelocytic leukemia nuclear bodies grow with cell cycle transition through an S-to-G2-like state in enlarging oligodendrocyte nuclei. J Neuropathol Exp Neurol 2014; 73:442-53. [PMID: 24709678 PMCID: PMC3995394 DOI: 10.1097/nen.0000000000000066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In progressive multifocal leukoencephalopathy, JC virus–infected oligodendroglia display 2 distinct patterns of intranuclear viral inclusions: full inclusions in which progeny virions are present throughout enlarged nuclei and dot-shaped inclusions in which virions are clustered in subnuclear domains termed “promyelocytic leukemia nuclear bodies” (PML-NBs). Promyelocytic leukemia nuclear bodies may serve a scaffolding role in viral progeny production. We analyzed the formation process of intranuclear viral inclusions by morphometry and assessed PML-NB alterations in the brains of 2 patients with progressive multifocal leukoencephalopathy. By immunohistochemistry, proliferating cell nuclear antigen was most frequently detected in smaller nuclei; cyclin A was detected in larger nuclei. This suggests an S-to-G2 cell cycle transition in infected cells associated with nuclear enlargement. Sizes of PML-NBs were variable, but they were usually either small speckles 200 to 400 nm in diameter or distinct spherical shells with a diameter of 1 μm or more. By confocal microscopy, JC virus capsid proteins were associated with both small and large PML-NBs, but disruption of large PML-NBs was observed by ground-state depletion fluorescence nanoscopy. Clusters of progeny virions were also detected by electron microscopy. Our data suggest that, in progressive multifocal leukoencephalopathy, JC virus produces progeny virions in enlarging oligodendrocyte nuclei in association with growing PML-NBs and with cell cycle transition through an S-to-G2-like state.
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Palibrk V, Lång E, Lång A, Schink KO, Rowe AD, Bøe SO. Promyelocytic leukemia bodies tether to early endosomes during mitosis. Cell Cycle 2014; 13:1749-55. [PMID: 24675887 DOI: 10.4161/cc.28653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During mitosis the nuclear envelope breaks down, leading to potential interactions between cytoplasmic and nuclear components. PML bodies are nuclear structures with tumor suppressor and antiviral functions. Early endosomes, on the other hand, are cytoplasmic vesicles involved in transport and growth factor signaling. Here we demonstrate that PML bodies form stable interactions with early endosomes immediately following entry into mitosis. The 2 compartments remain stably associated throughout mitosis and dissociate in the cytoplasm of newly divided daughter cells. We also show that a minor subset of PML bodies becomes anchored to the mitotic spindle poles during cell division. The study demonstrates a stable mitosis-specific interaction between a cytoplasmic and a nuclear compartment.
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Affiliation(s)
- Vuk Palibrk
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Emma Lång
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Anna Lång
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Kay Oliver Schink
- Department of Biochemistry; Institute for Cancer Research; The Norwegian Radium Hospital; Oslo University Hospital; Oslo, Norway
| | - Alexander D Rowe
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
| | - Stig Ove Bøe
- Department of Microbiology and Department of Medical Biochemistry; Oslo University Hospital and University of Oslo; Oslo, Norway
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Šmigová J, Juda P, Bártová E, Raška I. Dynamics of Polycomb chromatin domains under conditions of increased molecular crowding. Biol Cell 2013; 105:519-34. [DOI: 10.1111/boc.201300022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 08/07/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Jana Šmigová
- Charles University in Prague; First Faculty of Medicine; Institute of Cellular Biology and Pathology; Czech Republic
| | - Pavel Juda
- Charles University in Prague; First Faculty of Medicine; Institute of Cellular Biology and Pathology; Czech Republic
| | - Eva Bártová
- Institute of Biophysics; Academy of Sciences of the Czech Republic, v.v.i; Brno Czech Republic
| | - Ivan Raška
- Charles University in Prague; First Faculty of Medicine; Institute of Cellular Biology and Pathology; Czech Republic
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27
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Rehman S, Day PJR, Bayat A, Westerhoff HV. Understanding Dupuytren's Disease Using Systems Biology: A Move Away from Reductionism. Front Physiol 2012; 3:316. [PMID: 22934066 PMCID: PMC3429086 DOI: 10.3389/fphys.2012.00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/18/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Samrina Rehman
- Manchester Centre for Integrative Systems Biology, University of Manchester Manchester, UK
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28
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The arsenic-based cure of acute promyelocytic leukemia promotes cytoplasmic sequestration of PML and PML/RARA through inhibition of PML body recycling. Blood 2012; 120:847-57. [DOI: 10.1182/blood-2011-10-388496] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Arsenic in the form of arsenic trioxide (ATO) is used as a therapeutic drug for treatment of acute promyelocytic leukemia (APL). The mechanism by which this agent cures this disease was previously shown to involve direct interactions between ATO and the promyelocytic leukemia protein (PML), as well as accelerated degradation of the APL-associated fusion oncoprotein PML/retinoic acid receptor α (RARA). Here we investigated the fate of PML-generated nuclear structures called PML bodies in ATO-treated cells. We found that ATO inhibits formation of progeny PML bodies while it stabilizes cytoplasmic precursor compartments, referred to as cytoplasmic assemblies of PML and nucleoporins (CyPNs), after cell division. This block in PML body recycling is readily detected at pharmacologic relevant ATO concentrations (0.02-0.5μM) that do not cause detectable cell-cycle defects, and it does not require modification of PML by SUMOylation. In addition, PML and PML/RARA carrying mutations previously identified in ATO-resistant APL patients are impeded in their ability to become sequestered within CyPNs. Thus, ATO may inhibit nuclear activities of PML and PML/RARA in postmitotic cells through CyPN-dependent cytoplasmic sequestration.
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29
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Nuclear ribonucleoprotein-containing foci increase in size in non-dividing cells from patients with myotonic dystrophy type 2. Histochem Cell Biol 2012; 138:699-707. [PMID: 22706481 DOI: 10.1007/s00418-012-0984-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
Myotonic dystrophies (DM) are genetically based neuromuscular disorders characterized by the accumulation of mutant transcripts into peculiar intranuclear foci, where different splicing factors (among which the alternative splicing regulator muscleblind-like 1 protein, MBNL1) are ectopically sequestered. The aim of the present investigation was to describe the dynamics of the DM-specific intranuclear foci in interphase nuclei and during mitosis, as well as after the exit from the cell cycle. Primary cultures of skin fibroblasts from DM2 patients were used, as a model system to reproduce in vitro, as accurately as possible, the in vivo conditions. Cycling and resting fibroblasts were investigated by immunocytochemical and morphometric techniques, and the relative amounts of MBNL1 were also estimated by western blotting. MBNL1-containing foci were exclusively found in the nucleus during most of the interphase, while being observed in the cytoplasm during mitosis when they never associate with the chromosomes; the foci remained in the cytoplasm at cytodieresis, and underwent disassembly in early G1 to be reformed in the nucleus at each cell cycle. After fibroblasts had stopped dividing in late-passage cultures, the nuclear foci were observed to progressively increase in size. Interestingly, measurements on muscle biopsies taken from the same DM2 patients at different ages demonstrated that, in the nuclei of myofibers, the MBNL1-containing foci become larger with increasing patient's age. As a whole, these results suggest that in non-dividing cells of DM2 patients the sequestration in the nuclear foci of factors needed for RNA processing would be continuous and progressive, eventually leading to the onset (and the worsening with time) of the pathological traits. This is consistent with the evidence that in DM patients the most affected organs or tissues are those where non-renewing cells are mainly present, i.e., the central nervous system, heart and skeletal muscle.
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Chung I, Osterwald S, Deeg KI, Rippe K. PML body meets telomere: the beginning of an ALTernate ending? Nucleus 2012; 3:263-75. [PMID: 22572954 PMCID: PMC3414403 DOI: 10.4161/nucl.20326] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The unlimited proliferation potential of cancer cells requires the maintenance of their telomeres. This is frequently accomplished by reactivation of telomerase. However, in a significant fraction of tumors an alternative lengthening of telomeres (ALT) mechanism is active. The molecular mechanism of the ALT pathway remains elusive. In particular, the role of characteristic complexes of promyelocytic leukemia nuclear bodies (PML-NBs) with telomeres, the ALT-associated PML-NBs (APBs), is currently under investigation. Here, we review recent findings on the assembly, structure and functions of APBs. It is discussed how genomic aberrations in ALT-positive cancer cells could result in the formation of APBs and in ALT activity. We conclude that they are important functional intermediates in what is considered the canonical ALT pathway and discuss deregulations of cellular pathways that contribute to the emergence of the ALT phenotype.
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Affiliation(s)
- Inn Chung
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Heidelberg, Germany
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31
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Abstract
The tripartite motif (TRIM)-containing proteins are involved in many cellular functions such as cell signaling, apoptosis, cell differentiation, and immune modulation. TRIM5 proteins, including TRIM5α and TRIM-Cyp, are known to possess antiretroviral activity against many different retroviruses. Besides being retroviral restriction factors, TRIM5 proteins participate in other cellular functions that have recently emerged in the study of TRIM5α. In this review, we discuss properties of TRIM5α such as cytoplasmic body formation, protein turnover, and trafficking. Also, we discuss recent insights into innate immune modulation mediated by TRIM5α, highlighting the various functions TRIM5α has in cellular processes.
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Affiliation(s)
- Zana Lukic
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, 2160 South First Avenue, Maywood, IL 60153, USA
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, 2160 South First Avenue, Maywood, IL 60153, USA
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Shishido-Hara Y, Ichinose S, Uchihara T. JC virus intranuclear inclusions associated with PML-NBs: analysis by electron microscopy and structured illumination microscopy. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 180:1095-1106. [PMID: 22266251 DOI: 10.1016/j.ajpath.2011.11.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 11/03/2011] [Accepted: 11/29/2011] [Indexed: 01/08/2023]
Abstract
Progressive multifocal leukoencephalopathy is a fatal demyelinating disorder caused by JC virus infection. JC virus was recently found to target promyelocytic leukemia nuclear bodies (PML-NBs), punctuate domains in the nuclei. Thus, the virus progenies cluster in dots as intranuclear inclusions (ie, as dot-shaped inclusions). In the present study, both the viral major and minor capsid proteins were expressed from polycistronic expression vectors with a powerful promoter, and formation into virus-like particles (VLPs) was examined by electron microscopy. When the upstream regulatory sequence including the agnogene (nt 275 to 490) was present, capsid protein expression was suppressed, but numerous VLPs were efficiently formed with restricted accumulation to PML-NBs. VLPs were uniform, and the cells were severely degraded. In contrast, when the 5' terminus of the agnogene (nt 275 to 409; 135 bp) was deleted, capsid protein expression was markedly enhanced, but VLPs were more randomly produced in the nucleus outside of PML-NBs. VLPs were pleomorphic, and cell degradation was minimal. JC virus association with PML-NBs was confirmed in human brain tissues by structured illumination microscopy. PML-NBs were shaped in spherical shells, with viral capsid proteins circumscribing the surface. These findings indicate that PML-NBs are intranuclear locations for pathogenic JC virus proliferation. Either the agnogene or its product likely supports efficient progeny production at PML-NBs, leading to subsequent degeneration of host glial cells.
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Affiliation(s)
| | - Shizuko Ichinose
- Research Center for Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshiki Uchihara
- Laboratory of Structural Neuropathology, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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Chung I, Leonhardt H, Rippe K. De novo assembly of a PML nuclear subcompartment occurs through multiple pathways and induces telomere elongation. J Cell Sci 2011; 124:3603-18. [PMID: 22045732 DOI: 10.1242/jcs.084681] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Telomerase-negative tumor cells use an alternative lengthening of telomeres (ALT) pathway that involves DNA recombination and repair to maintain their proliferative potential. The cytological hallmark of this process is the accumulation of promyelocytic leukemia (PML) nuclear protein at telomeric DNA to form ALT-associated PML bodies (APBs). Here, the de novo formation of a telomeric PML nuclear subcompartment was investigated by recruiting APB protein components. We show that functionally distinct proteins were able to initiate the formation of bona fide APBs with high efficiency in a self-organizing and self-propagating manner. These included: (1) PML and Sp100 as the constituting components of PML nuclear bodies, (2) telomere repeat binding factors 1 and 2 (TRF1 and TRF2, respectively), (3) the DNA repair protein NBS1 and (4) the SUMO E3 ligase MMS21, as well as the isolated SUMO1 domain, through an interacting domain of another protein factor. By contrast, the repair factors Rad9, Rad17 and Rad51 were less efficient in APB nucleation but were recruited to preassembled APBs. The artificially created APBs induced telomeric extension through a DNA repair mechanism, as inferred from their colocalization with sites of non-replicative DNA synthesis and histone H2A.X phosphorylation, and an increase of the telomere repeat length. These activities were absent after recruitment of the APB factors to a pericentric locus and establish APBs as functional intermediates of the ALT pathway.
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Affiliation(s)
- Inn Chung
- German Cancer Research Center & BioQuant, Research Group Genome Organization & Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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34
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Zhao R, Nakamura T, Fu Y, Lazar Z, Spector DL. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat Cell Biol 2011; 13:1295-304. [PMID: 21983563 PMCID: PMC3210065 DOI: 10.1038/ncb2341] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/10/2011] [Indexed: 12/12/2022]
Abstract
Although transmission of the gene expression program from mother to daughter cells has been suggested to be mediated by gene bookmarking, the precise mechanism by which bookmarking mediates post-mitotic transcriptional re-activation has been unclear. Here, we used a real-time gene expression system to quantitatively demonstrate that transcriptional activation of the same genetic locus occurs with a significantly more rapid kinetics in post-mitotic cells versus interphase cells. RNA polymerase II large subunit (Pol II) and bromodomain protein 4 (BRD4) were recruited to the locus in a different sequential order on interphase initiation versus post-mitotic re-activation resulting from the recognition by BRD4 of increased levels of histone H4 Lys 5 acetylation (H4K5ac) on the previously activated locus. BRD4 accelerated the dynamics of messenger RNA synthesis by de-compacting chromatin and hence facilitating transcriptional re-activation. Using a real-time quantitative approach, we identified differences in the kinetics of transcriptional activation between interphase and post-mitotic cells that are mediated by a chromatin-based epigenetic mechanism.
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Affiliation(s)
- Rui Zhao
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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35
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Abstract
The nucleus is unique amongst cellular organelles in that it contains a myriad of discrete suborganelles. These nuclear bodies are morphologically and molecularly distinct entities, and they host specific nuclear processes. Although the mode of biogenesis appears to differ widely between individual nuclear bodies, several common design principles are emerging, particularly, the ability of nuclear bodies to form de novo, a role of RNA as a structural element and self-organization as a mode of formation. The controlled biogenesis of nuclear bodies is essential for faithful maintenance of nuclear architecture during the cell cycle and is an important part of cellular responses to intra- and extracellular events.
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Affiliation(s)
- Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Ilinois 60064, USA.
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36
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Zheng R, Shen Z, Tripathi V, Xuan Z, Freier SM, Bennett CF, Prasanth SG, Prasanth KV. Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells. J Cell Sci 2010; 123:3734-44. [PMID: 20940252 DOI: 10.1242/jcs.070466] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In higher eukaryotic cells, long non-protein-coding RNAs (lncRNAs) have been implicated in a wide array of cellular functions. Cell- or tissue-specific expression of lncRNA genes encoded in the mammalian genome is thought to contribute to the complex gene networks needed to regulate cellular function. Here, we have identified a novel species of polypurine triplet repeat-rich lncRNAs, designated as GAA repeat-containing RNAs (GRC-RNAs), that localize to numerous punctate foci in the mammalian interphase nuclei. GRC-RNAs consist of a heterogeneous population of RNAs, ranging in size from ~1.5 kb to ~4 kb and localize to subnuclear domains, several of which associate with GAA.TTC-repeat-containing genomic regions. GRC-RNAs are components of the nuclear matrix and interact with various nuclear matrix-associated proteins. In mitotic cells, GRC-RNAs form distinct cytoplasmic foci and, in telophase and G1 cells, localize to the midbody, a structure involved in accurate cell division. Differentiation of tissue culture cells leads to a decrease in the number of GRC-RNA nuclear foci, albeit with an increase in size as compared with proliferating cells. Conversely, the number of GRC-RNA foci increases during cellular transformation. We propose that nuclear GRC-RNAs represent a novel family of mammalian lncRNAs that might play crucial roles in the cell nucleus.
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Affiliation(s)
- Ruiping Zheng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Chemical and Life Sciences Laboratory, 601 South Goodwin Avenue, Urbana, IL 61801, USA
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Abstract
PML nuclear bodies are matrix-associated domains that recruit an astonishing variety of seemingly unrelated proteins. Since their discovery in the early 1960s, PML bodies have fascinated cell biologists because of their beauty and their tight association with cellular disorders. The identification of PML, a gene involved in an oncogenic chromosomal translocation, as the key organizer of these domains drew instant interest onto them. The multiple levels of PML body regulation by a specific posttranslational modification, sumoylation, have raised several unsolved issues. Functionally, PML bodies may sequester, modify or degrade partner proteins, but in many ways, PML bodies still constitute an enigma.
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Affiliation(s)
- Valérie Lallemand-Breitenbach
- INSERM/CNRS/Université Paris Diderot/Institut Universitaire Hématologie U944/ UMR7212, Laboratoire associé de la Ligue Nationale contre le Cancer, Hôpital St. Louis, 1, Av. C. Vellefaux 75475 Paris Cedex 10, France
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38
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Brouwer AK, Schimmel J, Wiegant JC, Vertegaal AC, Tanke HJ, Dirks RW. Telomeric DNA mediates de novo PML body formation. Mol Biol Cell 2009; 20:4804-15. [PMID: 19793919 PMCID: PMC2777109 DOI: 10.1091/mbc.e09-04-0309] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 08/12/2009] [Accepted: 09/21/2009] [Indexed: 11/11/2022] Open
Abstract
The cell nucleus harbors a variety of different bodies that vary in number, composition, and size. Although these bodies coordinate important nuclear processes, little is known about how they are formed. Among the most intensively studied bodies in recent years is the PML body. These bodies have been implicated in gene regulation and other cellular processes and are disrupted in cells from patients suffering from acute promyelocytic leukemia. Using live cell imaging microscopy and immunofluorescence, we show in several cell types that PML bodies are formed at telomeric DNA during interphase. Recent studies revealed that both SUMO modification sites and SUMO interaction motifs in the promyelocytic leukemia (PML) protein are required for PML body formation. We show that SMC5, a component of the SUMO ligase MMS21-containing SMC5/6 complex, localizes temporarily at telomeric DNA during PML body formation, suggesting a possible role for SUMO in the formation of PML bodies at telomeric DNA. Our data identify a novel role of telomeric DNA during PML body formation.
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Affiliation(s)
- Anneke K. Brouwer
- *Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Joost Schimmel
- *Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Joop C.A.G. Wiegant
- *Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Alfred C.O. Vertegaal
- *Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Hans J. Tanke
- *Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Roeland W. Dirks
- *Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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39
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Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination. Proc Natl Acad Sci U S A 2009; 106:15726-31. [PMID: 19717459 DOI: 10.1073/pnas.0907689106] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies (also called ND10) are dynamic nuclear structures implicated in a wide variety of cellular processes. ALT-associated PML bodies (APBs) are specialized PML bodies found exclusively in telomerase-negative tumors in which telomeres are maintained by recombination-based alternative (ALT) mechanisms. Although it has been suggested that APBs are directly implicated in telomere metabolism of ALT cells, their precise role and structure have remained elusive. Here we show that PML bodies in ALT cells associate with chromosome ends forming small, spatially well-defined clusters, containing on average 2-5 telomeres. Using an innovative approach that gently enlarges PML bodies in living cells while retaining their overall organization, we show that this physical enlargement of APBs spatially resolves the single telomeres in the cluster, but does not perturb the potential of the APB to recruit chromosome extremities. We show that telomere clustering in PML bodies is cell-cycle regulated and that unique telomeres within a cluster associate with recombination proteins. Enlargement of APBs induced the accumulation of telomere-telomere recombination intermediates visible on metaphase spreads and connecting heterologous chromosomes. The strand composition of these recombination intermediates indicated that this recombination is constrained to a narrow time window in the cell cycle following replication. These data provide strong evidence that PML bodies are not only a marker for ALT cells but play a direct role in telomere recombination, both by bringing together chromosome ends and by promoting telomere-telomere interactions between heterologous chromosomes.
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40
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41
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Jul-Larsen A, Grudic A, Bjerkvig R, Bøe SO. Cell-cycle regulation and dynamics of cytoplasmic compartments containing the promyelocytic leukemia protein and nucleoporins. J Cell Sci 2009; 122:1201-10. [PMID: 19339552 DOI: 10.1242/jcs.040840] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nucleoporins and the promyelocytic leukemia protein (PML) represent structural entities of nuclear pore complexes and PML nuclear bodies, respectively. In addition, these proteins might function in a common biological mechanism, because at least two different nucleoporins, Nup98 and Nup214, as well as PML, can become aberrantly expressed as oncogenic fusion proteins in acute myeloid leukemia (AML) cells. Here we show that PML and nucleoporins become directed to common cytoplasmic compartments during the mitosis-to-G1 transition of the cell cycle. These protein assemblies, which we have termed CyPNs (cytoplasmic assemblies of PML and nucleoporins), move on the microtubular network and become stably connected to the nuclear membrane once contact with the nucleus has been made. The ability of PML to target CyPNs depends on its nuclear localization signal, and loss of PML causes an increase in cytoplasmic-bound versus nuclear-membrane-bound nucleoporins. CyPNs are also targeted by the acute promyelocytic leukemia (APL) fusion protein PML-RARalpha and can be readily detected within the APL cell line NB4. These results provide insight into a dynamic pool of cytoplasmic nucleoporins that form a complex with the tumor suppressor protein PML during the G1 phase of the cell cycle.
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Affiliation(s)
- Asne Jul-Larsen
- Department of Biomedicine, University of Bergen, Bergen, Norway
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42
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Stein GS, Davie JR, Knowlton JR, Zaidi SK. Nuclear microenvironments and cancer. J Cell Biochem 2008; 104:1949-52. [PMID: 18649350 DOI: 10.1002/jcb.21846] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Nucleic acids and regulatory proteins are architecturally organized in nuclear microenvironments. The compartmentalization of regulatory machinery for gene expression, replication and repair, is obligatory for fidelity of biological control. Perturbations in the organization, assembly and integration of regulatory machinery have been functionally linked to the onset and progression of tumorigenesis. The combined application of cellular, molecular, biochemical and in vivo genetic approaches, together with structural biology, genomics, proteomics and bioinformatics, will likely lead to new approaches in cancer diagnostics and therapy.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, S3-310, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, Massachusetts 01655, USA.
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43
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Cascianelli G, Villani M, Tosti M, Marini F, Bartoccini E, Magni MV, Albi E. Lipid microdomains in cell nucleus. Mol Biol Cell 2008; 19:5289-95. [PMID: 18923143 DOI: 10.1091/mbc.e08-05-0517] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
It is known that nuclear lipids play a role in proliferation, differentiation, and apoptotic process. Cellular nuclei contain high levels of phosphatidylcholine and sphingomyelin, which are partially linked with cholesterol and proteins to form lipid-protein complexes. These lipids are also associated with transcription factors and newly synthesized RNA but, up to date, their organization is still unknown. The aim of the present work was to study if these specific lipid-protein interactions could be nuclear membrane microdomains and to evaluate their possible role. The results obtained demonstrate for the first time the existence of nuclear microdomains characterized by a specific lipid composition similar to that of intranuclear lipid-protein complexes previously described. Nuclear microdomain lipid composition changes during cell proliferation when the content of newly synthesized RNA increases. Because previous data show a correlation between nuclear lipids and transcription process, the role of nuclear microdomains in cellular functions is discussed.
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Affiliation(s)
- Giacomo Cascianelli
- Department of Clinical and Experimental Medicine, Physiopathology Section, University School of Medicine, University of Perugia, Policlinico Monteluce, 06100 Perugia, Italy
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