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Berkholz J, Karle W. Unravelling the molecular interplay: SUMOylation, PML nuclear bodies and vascular cell activity in health and disease. Cell Signal 2024; 119:111156. [PMID: 38574938 DOI: 10.1016/j.cellsig.2024.111156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
In the seemingly well-researched field of vascular research, there are still many underestimated factors and molecular mechanisms. In recent years, SUMOylation has become increasingly important. SUMOylation is a post-translational modification in which small ubiquitin-related modifiers (SUMO) are covalently attached to target proteins. Sites where these SUMO modification processes take place in the cell nucleus are PML nuclear bodies (PML-NBs) - multiprotein complexes with their essential main component and organizer, the PML protein. PML and SUMO, either alone or as partners, influence a variety of cellular processes, including regulation of transcription, senescence, DNA damage response and defence against microorganisms, and are involved in innate immunity and inflammatory responses. They also play an important role in maintaining homeostasis in the vascular system and in pathological processes leading to the development and progression of cardiovascular diseases. This review summarizes information about the function of SUMO(ylation) and PML(-NBs) in the human vasculature from angiogenesis to disease and highlights their clinical potential as drug targets.
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Affiliation(s)
- Janine Berkholz
- Institute of Physiology, Charité - Universitätsmedizin, Berlin, Germany; DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.
| | - Weronika Karle
- Institute of Physiology, Charité - Universitätsmedizin, Berlin, Germany
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2
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Bregnard TA, Fairchild D, Erlandsen H, Semenova IV, Szczepaniak R, Ahmed A, Weller SK, Korzhnev DM, Bezsonova I. Conformational exchange at a C 2H 2 zinc-binding site facilitates redox sensing by the PML protein. Structure 2023; 31:1086-1099.e6. [PMID: 37473756 PMCID: PMC10528520 DOI: 10.1016/j.str.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The promyelocytic leukemia protein, PML, plays a vital role in the cellular response to oxidative stress; however, the molecular mechanism of its action remains poorly understood. Here, we identify redox-sensitive sites of PML. A molecule of PML is cysteine-rich and contains three zinc-binding domains including RING, B-box1, and B-box2. Using in vitro assays, we have compared the sensitivity of the isolated RING and B-box1 domains and shown that B-box1 is more sensitive to oxidation. NMR studies of PML dynamics showed that one of the Zn-coordination sites within the B-box1 undergoes significant conformational exchange, revealing a hotspot for exposure of reactive cysteines. In agreement with the in vitro data, enhancement of the B-box1 Zn-coordination dynamics led to more efficient recruitment of PML into PML nuclear bodies in cells. Overall, our results suggest that the increased sensitivity of B-box1 to oxidative stress makes this domain an important redox-sensing component of PML.
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Affiliation(s)
- Thomas A Bregnard
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Daniel Fairchild
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment, UCONN, Storrs, CT 06269, USA
| | - Irina V Semenova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Renata Szczepaniak
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Affrin Ahmed
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Sandra K Weller
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA.
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3
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Cobb AM, De Silva SA, Hayward R, Sek K, Ulferts S, Grosse R, Shanahan CM. Filamentous nuclear actin regulation of PML NBs during the DNA damage response is deregulated by prelamin A. Cell Death Dis 2022; 13:1042. [PMID: 36522328 PMCID: PMC9755150 DOI: 10.1038/s41419-022-05491-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/16/2022]
Abstract
Nuclear actin participates in a continuously expanding list of core processes within eukaryotic nuclei, including the maintenance of genomic integrity. In response to DNA damage, nuclear actin polymerises into filaments that are involved in the repair of damaged DNA through incompletely defined mechanisms. We present data to show that the formation of nuclear F-actin in response to genotoxic stress acts as a scaffold for PML NBs and that these filamentous networks are essential for PML NB fission and recruitment of microbodies to DNA lesions. Further to this, we demonstrate that the accumulation of the toxic lamin A precursor prelamin A induces mislocalisation of nuclear actin to the nuclear envelope and prevents the establishment of nucleoplasmic F-actin networks in response to stress. Consequently, PML NB dynamics and recruitment to DNA lesions is ablated, resulting in impaired DNA damage repair. Inhibition of nuclear export of formin mDia2 restores nuclear F-actin formation by augmenting polymerisation of nuclear actin in response to stress and rescues PML NB localisation to sites of DNA repair, leading to reduced levels of DNA damage.
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Affiliation(s)
- Andrew M. Cobb
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Shanelle A. De Silva
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Robert Hayward
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Karolina Sek
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
| | - Svenja Ulferts
- grid.5963.9Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Robert Grosse
- grid.5963.9Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Catherine M. Shanahan
- grid.13097.3c0000 0001 2322 6764BHF Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King’s College London, The James Black Centre, 125 Coldharbour Lane, London, SE5 9NU United Kingdom
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4
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Lussier-Price M, Wahba HM, Mascle XH, Cappadocia L, Bourdeau V, Gagnon C, Igelmann S, Sakaguchi K, Ferbeyre G, Omichinski J. Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1. Nucleic Acids Res 2022; 50:8331-8348. [PMID: 35871297 PMCID: PMC9371903 DOI: 10.1093/nar/gkac620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/22/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
SUMO proteins are important regulators of many key cellular functions in part through their ability to form interactions with other proteins containing SUMO interacting motifs (SIMs). One characteristic feature of all SUMO proteins is the presence of a highly divergent intrinsically disordered region at their N-terminus. In this study, we examine the role of this N-terminal region of SUMO proteins in SUMO–SIM interactions required for the formation of nuclear bodies by the promyelocytic leukemia (PML) protein (PML-NBs). We demonstrate that the N-terminal region of SUMO1 functions in a paralog specific manner as an auto-inhibition domain by blocking its binding to the phosphorylated SIMs of PML and Daxx. Interestingly, we find that this auto-inhibition in SUMO1 is relieved by zinc, and structurally show that zinc stabilizes the complex between SUMO1 and a phospho-mimetic form of the SIM of PML. In addition, we demonstrate that increasing cellular zinc levels enhances PML-NB formation in senescent cells. Taken together, these results provide important insights into a paralog specific function of SUMO1, and suggest that zinc levels could play a crucial role in regulating SUMO1-SIM interactions required for PML-NB formation and function.
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Affiliation(s)
- Mathieu Lussier-Price
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - Haytham M Wahba
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
- Department of Biochemistry, Beni-Suef University , Beni-Suef, Egypt
| | - Xavier H Mascle
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - Laurent Cappadocia
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - Veronique Bourdeau
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - Christina Gagnon
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - Sebastian Igelmann
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - Kazuyasu Sakaguchi
- Department of Chemistry, Faculty of Science, Hokkaido University , Sapporo, Japan
| | - Gerardo Ferbeyre
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
| | - James G Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal , Montréal, QC, Canada
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Scherer M, Read C, Neusser G, Kranz C, Kuderna AK, Müller R, Full F, Woerz S, Reichel A, Schilling EM, Walther P, Stamminger T. Dual signaling via interferon and DNA damage response elicits entrapment by giant PML nuclear bodies. eLife 2022; 11:73006. [PMID: 35319461 PMCID: PMC8975554 DOI: 10.7554/elife.73006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
PML nuclear bodies (PML-NBs) are dynamic interchromosomal macromolecular complexes implicated in epigenetic regulation as well as antiviral defense. During herpesvirus infection, PML-NBs induce epigenetic silencing of viral genomes, however, this defense is antagonized by viral regulatory proteins such as IE1 of human cytomegalovirus (HCMV). Here, we show that PML-NBs undergo a drastic rearrangement into highly enlarged PML cages upon infection with IE1-deficient HCMV. Importantly, our results demonstrate that dual signaling by interferon and DNA damage response is required to elicit giant PML-NBs. DNA labeling revealed that invading HCMV genomes are entrapped inside PML-NBs and remain stably associated with PML cages in a transcriptionally repressed state. Intriguingly, by correlative light and transmission electron microscopy (EM), we observed that PML cages also entrap newly assembled viral capsids demonstrating a second defense layer in cells with incomplete first line response. Further characterization by 3D EM showed that hundreds of viral capsids are tightly packed into several layers of fibrous PML. Overall, our data indicate that giant PML-NBs arise via combined interferon and DNA damage signaling which triggers entrapment of both nucleic acids and proteinaceous components. This represents a multilayered defense strategy to act in a cytoprotective manner and to combat viral infections.
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Affiliation(s)
- Myriam Scherer
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Clarissa Read
- Central Facility for Electron Microscopy, ULM University, Ulm, Germany
| | - Gregor Neusser
- Institute of Analytical and Bioanalytical Chemistry, ULM University, Ulm, Germany
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, ULM University, Ulm, Germany
| | - Anna K Kuderna
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Regina Müller
- Institute of Clinical and Molecular Virology, Friedrich Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Florian Full
- Institute of Clinical and Molecular Virology, Friedrich Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sonja Woerz
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Anna Reichel
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Paul Walther
- Central Facility for Electron Microscopy, ULM University, Ulm, Germany
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6
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Pack CG. Application of quantitative cell imaging using label-free optical diffraction tomography. Biophys Physicobiol 2021; 18:244-253. [PMID: 34745809 PMCID: PMC8550874 DOI: 10.2142/biophysico.bppb-v18.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/11/2021] [Indexed: 12/01/2022] Open
Abstract
The cell is three-dimensionally and dynamically organized into cellular compartments, including the endoplasmic reticulum, mitochondria, vesicles, and nucleus, which have high relative molecular density. The structure and functions of these compartments and organelles may be deduced from the diffusion and interaction of related biomolecules. Among these cellular components, various protein molecules can freely access the nucleolus or mitotic chromosome through Brownian diffusion, even though they have a densely packed structure. However, physicochemical properties of the nucleolus and chromosomes, such as molecular density and volume, are not yet fully understood under changing cellular conditions. Many studies have been conducted based on high-resolution imaging and analysis techniques using fluorescence. However, there are limitations in imaging only fluorescently labeled molecules, and cytotoxicity occurs during three-dimensional imaging. Alternatively, the recently developed label-free three-dimensional optical diffraction tomography (ODT) imaging technique can divide various organelles in cells into volumes and analyze them by refractive index, although specific molecules cannot be observed. A previous study established an analytical method that provides comprehensive insights into the physical properties of the nucleolus and mitotic chromosome by utilizing the advantages of ODT and fluorescence techniques, such as fluorescence correlation spectroscopy and confocal laser scanning microscopy. This review article summarizes a recent study and discusses the future aspects of the ODT for cellular compartments.
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Affiliation(s)
- Chan-Gi Pack
- Convergence Medicine Research Center (CREDIT), Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Republic of Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
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7
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Ismail H, Liu X, Yang F, Li J, Zahid A, Dou Z, Liu X, Yao X. Mechanisms and regulation underlying membraneless organelle plasticity control. J Mol Cell Biol 2021; 13:239-258. [PMID: 33914074 PMCID: PMC8339361 DOI: 10.1093/jmcb/mjab028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Evolution has enabled living cells to adopt their structural and functional complexity by organizing intricate cellular compartments, such as membrane-bound and membraneless organelles (MLOs), for spatiotemporal catalysis of physiochemical reactions essential for cell plasticity control. Emerging evidence and view support the notion that MLOs are built by multivalent interactions of biomolecules via phase separation and transition mechanisms. In healthy cells, dynamic chemical modifications regulate MLO plasticity, and reversible phase separation is essential for cell homeostasis. Emerging evidence revealed that aberrant phase separation results in numerous neurodegenerative disorders, cancer, and other diseases. In this review, we provide molecular underpinnings on (i) mechanistic understanding of phase separation, (ii) unifying structural and mechanistic principles that underlie this phenomenon, (iii) various mechanisms that are used by cells for the regulation of phase separation, and (iv) emerging therapeutic and other applications.
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Affiliation(s)
- Hazrat Ismail
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xu Liu
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity Control, Atlanta, GA 30310, USA
| | - Fengrui Yang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity Control, Atlanta, GA 30310, USA
| | - Junying Li
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
| | - Ayesha Zahid
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Zhen Dou
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics and CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230027, China
- Anhui Key Laboratory for Cellular Dynamics & Chemical Biology, Hefei 230027, China
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8
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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: 94] [Impact Index Per Article: 23.5] [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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9
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Hasenson SE, Shav‐Tal Y. Speculating on the Roles of Nuclear Speckles: How RNA‐Protein Nuclear Assemblies Affect Gene Expression. Bioessays 2020; 42:e2000104. [DOI: 10.1002/bies.202000104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah E. Hasenson
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
| | - Yaron Shav‐Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
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10
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Kohata K, Miyoshi D. RNA phase separation-mediated direction of molecular trafficking under conditions of molecular crowding. Biophys Rev 2020; 12:669-676. [PMID: 32415614 DOI: 10.1007/s12551-020-00696-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Living cells are highly crowded with large and small biomolecules. The total concentration of biomolecules can reach 400 mg/ml, and 40% of the cell volume is occupied by biomolecules. Droplet formation in cells via liquid-liquid phase separation may play a role in controlling biochemical reactions in this complex molecular environment. Liquid-liquid phase separation generally involves nucleic acids and proteins as anionic and cationic components, respectively. Significant characteristics of droplets, which make them different from protein aggregation or fibril formation, are reversibility of formation and responsiveness to the molecular environment. In this review, we quantitatively describe the molecular environment inside cells and droplets that participate in controlling central dogma reactions. Finally, we discuss the importance of droplets under conditions of molecular crowding within living cells.
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Affiliation(s)
- Kazuki Kohata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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11
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Critical role of CRAG, a splicing variant of centaurin-γ3/AGAP3, in ELK1-dependent SRF activation at PML bodies. Sci Rep 2019; 9:20107. [PMID: 31882856 PMCID: PMC6934726 DOI: 10.1038/s41598-019-56559-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
CRMP-5-associated GTPase (CRAG), a short splicing variant of centaurin-γ3/AGAP3, is predominantly expressed in the developing brain. We previously demonstrated that CRAG, but not centaurin-γ3, translocates to the nucleus and activates the serum response factor (SRF)-c-Fos pathway in cultured neuronal cells. However, the physiological relevance of CRAG in vivo is unknown. Here, we found that CRAG/centaurin-γ3-knockout mice showed intensively suppressed kainic acid-induced c-fos expression in the hippocampus. Analyses of molecular mechanisms underlying CRAG-mediated SRF activation revealed that CRAG has an essential role in GTPase activity, interacts with ELK1 (a co-activator of SRF), and activates SRF in an ELK1-dependent manner. Furthermore, CRAG and ELK1 interact with promyelocytic leukaemia bodies through SUMO-interacting motifs, which is required for SRF activation. These results suggest that CRAG plays a critical role in ELK1-dependent SRF-c-fos activation at promyelocytic leukaemia bodies in the developing brain.
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12
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Martin N. Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation. Chembiochem 2019; 20:2553-2568. [PMID: 31039282 DOI: 10.1002/cbic.201900183] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 12/16/2022]
Abstract
Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom-up construction of cell-like models capable of reproducing aspects of such dynamic organisation. Liquid-liquid phase-separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher-order structures and behaviour.
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Affiliation(s)
- Nicolas Martin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 Avenue du Dr. Albert Schweitzer, 33600, Pessac, France
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13
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Zhao S, Shi P, Zhong Q, Shao S, Huang Y, Sun Y, Wu C, Zhu HH. Identification of a point mutation PML S214L-RARα that alters PML body organization, dynamics and SUMOylation. Biochem Biophys Res Commun 2019; 511:518-523. [PMID: 30824184 DOI: 10.1016/j.bbrc.2019.02.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
Genetic mutations on PML-RARα in acute promyelocytic leukemia (APL) are reported to associate with arsenic trioxide (ATO) or all-trans retinoic acid (ATRA) resistance. Here we performed a retrospective analysis of APL patients and identified that the patient with S214L mutation on the PML moiety of PML-RARα showed resistance to both ATO and ATRA. Super-resolution microcopy was used to examine the structural response of PML bodies in wild-type or the S214L mutant cells upon drug treatment. Different protein density and fluidity were identified with the S214L mutant PML bodies by single particle quantification and FRAP analysis. We discovered that altered SUMOylation and ubiquitination might contribute to the drug resistance. Taken together, we have revealed that the S214L mutation on PML-RARα disrupted the organization of PML body and dynamics changes, perturbing structural responses to ATRA and subsequent oncoprotein degradation. Our findings shed new light on the structural alterations of PML bodies and mechanisms of APL drug resistance.
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Affiliation(s)
- Shanshan Zhao
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Peng Shi
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qihang Zhong
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shipeng Shao
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yuxing Huang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Congying Wu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Hong-Hu Zhu
- Department of Hematology& Institute of Hematology, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China; Institute of Hematology, China Three Gorges University, Yichang, 443002, China.
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14
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Berchtold D, Battich N, Pelkmans L. A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells. Mol Cell 2018; 72:1035-1049.e5. [DOI: 10.1016/j.molcel.2018.10.036] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/11/2018] [Accepted: 10/19/2018] [Indexed: 01/06/2023]
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15
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Sawyer IA, Sturgill D, Dundr M. Membraneless nuclear organelles and the search for phases within phases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1514. [DOI: 10.1002/wrna.1514] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/20/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago Illinois
- Laboratory of Receptor Biology and Gene Expression National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression National Cancer Institute, National Institutes of Health Bethesda Maryland
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School Rosalind Franklin University of Medicine and Science North Chicago Illinois
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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: 21] [Impact Index Per Article: 3.5] [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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Burroughs AF, Eluhu S, Whalen D, Goodwin JS, Sakwe AM, Arinze IJ. PML-Nuclear Bodies Regulate the Stability of the Fusion Protein Dendra2-Nrf2 in the Nucleus. Cell Physiol Biochem 2018; 47:800-816. [PMID: 29807365 PMCID: PMC6503657 DOI: 10.1159/000490033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/11/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND/AIMS Nuclear factor erythroid 2-related factor 2 (Nrf2) is a basic leucine-zipper transcription factor essential for cellular responses to oxidative stress. Degradation of Nrf2 in the cytoplasm, mediated by Keap1-Cullin3/RING box1 (Cul3-Rbx1) E3 ubiquitin ligase and the proteasome, is considered the primary pathway controlling the cellular abundance of Nrf2. Although the nucleus has been implicated in the degradation of Nrf2, little information is available on how this compartment participates in degrading Nrf2. METHODS Here, we fused the photoconvertible fluorescent protein Dendra2 to Nrf2 and capitalized on the irreversible change in color (green to red) that occurs when Dendra2 undergoes photoconversion to study degradation of Dendra2-Nrf2 in single live cells. RESULTS Using this approach, we show that the half-life (t1/2) of Dendra2-Nrf2 in the whole cell, under homeostatic conditions, is 35 min. Inhibition of the proteasome with MG-132 or induction of oxidative stress with tert-butylhydroquinone (tBHQ) extended the half-life of Dendra2-Nrf2 by 6- and 28-fold, respectively. By inhibiting nuclear export using Leptomycin B, we provide direct evidence that degradation of Nrf2 also occurs in the nucleus and involves PML-NBs (Promyelocytic Leukemia-nuclear bodies). We further demonstrate that co-expression of Dendra2-Nrf2 and Crimson-PML-I lacking two PML-I sumoylation sites (K65R and K490R) changed the decay rate of Dendra2-Nrf2 in the nucleus and stabilized the nuclear derived Nrf2 levels in whole cells. CONCLUSION Altogether, our findings provide direct evidence for degradation of Nrf2 in the nucleus and suggest that modification of Nrf2 in PML nuclear bodies contributes to its degradation in intact cells.
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Affiliation(s)
| | - Sylvia Eluhu
- Department of Biochemistry and Cancer Biology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, USA
| | - Diva Whalen
- Department of Biochemistry and Cancer Biology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, USA
| | - J. Shawn Goodwin
- Department of Biochemistry and Cancer Biology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, USA
| | - Amos M. Sakwe
- Department of Biochemistry and Cancer Biology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, USA
| | - Ifeanyi J. Arinze
- Department of Physiology, School of Medicine, Meharry Medical College, Nashville, TN, USA
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Abstract
As obligate intracellular parasites, viruses are dependent on their infected hosts for survival. Consequently, viruses are under enormous selective pressure to utilize available cellular components and processes to their own advantage. As most, if not all, cellular activities are regulated at some level via protein interactions, host protein interaction networks are particularly vulnerable to viral exploitation. Indeed, viral proteins frequently target highly connected “hub” proteins to “hack” the cellular network, defining the molecular basis for viral control over the host. This widespread and successful strategy of network intrusion and exploitation has evolved convergently among numerous genetically distinct viruses as a result of the endless evolutionary arms race between pathogens and hosts. Here we examine the means by which a particularly well-connected viral hub protein, human adenovirus E1A, compromises and exploits the vulnerabilities of eukaryotic protein interaction networks. Importantly, these interactions identify critical regulatory hubs in the human proteome and help define the molecular basis of their function.
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Chang HR, Munkhjargal A, Kim MJ, Park SY, Jung E, Ryu JH, Yang Y, Lim JS, Kim Y. The functional roles of PML nuclear bodies in genome maintenance. Mutat Res 2017; 809:99-107. [PMID: 28521962 DOI: 10.1016/j.mrfmmm.2017.05.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
Abstract
In the nucleus, there are several membraneless structures called nuclear bodies. Among them, promyelocytic leukemia nuclear bodies (PML-NBs) are involved in multiple genome maintenance pathways including the DNA damage response, DNA repair, telomere homeostasis, and p53-associated apoptosis. In response to DNA damage, PML-NBs are coalesced and divided by a fission mechanism, thus increasing their number. PML-NBs also play a role in repairing DNA double-strand breaks (DSBs) by homologous recombination (HR). Clinically, the dominant negative PML-RARα fusion protein expressed in acute promyelocytic leukemia (APL) inhibits the transactivation of downstream factors and disrupts PML function, revealing the tumor suppressor role of PML-NBs. All-trans retinoic acid and arsenic trioxide treatment has been implemented for promyelocytic leukemia to target the PML-RARα fusion protein. PML-NBs are associated with various factors implicated in genome maintenance, and are found at the sites of DNA damage. Their interaction with proteins such as p53 indicates that PML-NBs may play a significant role in apoptosis and cancer. Decades of research have revealed the importance of PML-NBs in diverse cellular pathways, yet the underlying molecular mechanisms and exact functions of PML-NBs remain elusive. In this review, PML protein modifications and the functional relevance of PML-NB and its associated factors in genome maintenance will be discussed.
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Affiliation(s)
- Hae Ryung Chang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Anudari Munkhjargal
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Myung-Jin Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Seon Young Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jae-Ha Ryu
- Research Center for Cell Fate Control, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jong-Seok Lim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yonghwan Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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20
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Tessier S, Martin-Martin N, de Thé H, Carracedo A, Lallemand-Breitenbach V. Promyelocytic Leukemia Protein, a Protein at the Crossroad of Oxidative Stress and Metabolism. Antioxid Redox Signal 2017; 26:432-444. [PMID: 27758112 DOI: 10.1089/ars.2016.6898] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE Cellular metabolic activity impacts the production of reactive oxygen species (ROS), both positively through mitochondrial oxidative processes and negatively by promoting the production of reducing agents (including NADPH and reduced glutathione). A defined metabolic state in cancer cells is critical for cell growth and long-term self-renewal, and such state is intrinsically associated with redox balance. Promyelocytic leukemia protein (PML) regulates several biological processes, at least in part, through its ability to control the assembly of PML nuclear bodies (PML NBs). Recent Advances: PML is oxidation-prone, and oxidative stress promotes NB biogenesis. These nuclear subdomains recruit many nuclear proteins and regulate their SUMOylation and other post-translational modifications. Some of these cargos-such as p53, SIRT1, AKT, and mammalian target of rapamycin (mTOR)-are key regulators of cell fate. PML was also recently shown to regulate oxidation. CRITICAL ISSUES While it was long considered primarily as a tumor suppressor protein, PML-regulated metabolic switch uncovered that this protein could promote survival and/or stemness of some normal or cancer cells. In this study, we review the recent findings on this multifunctional protein. FUTURE DIRECTIONS Studying PML scaffolding functions as well as its fine role in the activation of p53 or fatty acid oxidation will bring new insights in how PML could bridge oxidative stress, senescence, cell death, and metabolism. Antioxid. Redox Signal. 26, 432-444.
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Affiliation(s)
- Sarah Tessier
- 1 Collège de France , Paris, France .,2 INSERM UMR 944, Equipe labellisée par la Ligue Nationale contre le Cancer, Institut Universitaire d'Hématologie , Paris, France .,3 CNRS UMR 7212 , Paris France .,4 Université Paris Diderot-Sorbonne Paris Cité , Paris, France
| | | | - Hugues de Thé
- 1 Collège de France , Paris, France .,2 INSERM UMR 944, Equipe labellisée par la Ligue Nationale contre le Cancer, Institut Universitaire d'Hématologie , Paris, France .,3 CNRS UMR 7212 , Paris France .,4 Université Paris Diderot-Sorbonne Paris Cité , Paris, France .,6 AP-HP, Service de Biochimie, Hôpital St. Louis , Paris, France
| | - Arkaitz Carracedo
- 5 CIC bioGUNE , Bizkaia Technology Part, Derio, Spain .,7 IKERBASQUE , Basque Foundation for Science, Bilbao, Spain .,8 Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU) , Bilbao, Spain
| | - Valérie Lallemand-Breitenbach
- 1 Collège de France , Paris, France .,2 INSERM UMR 944, Equipe labellisée par la Ligue Nationale contre le Cancer, Institut Universitaire d'Hématologie , Paris, France .,3 CNRS UMR 7212 , Paris France .,4 Université Paris Diderot-Sorbonne Paris Cité , Paris, France
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21
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Fukuda T, Kigoshi-Tansho Y, Naganuma T, Kazaana A, Okajima T, Tsuruta F, Chiba T. CACUL1/CAC1 attenuates p53 activity through PML post-translational modification. Biochem Biophys Res Commun 2016; 482:863-869. [PMID: 27889610 DOI: 10.1016/j.bbrc.2016.11.125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 11/22/2016] [Indexed: 12/30/2022]
Abstract
Promyelocytic leukaemia (PML) is a tumor suppressor protein covalently conjugated with SUMO family proteins, leading to the formation of PML nuclear bodies (NBs). PML-NBs provide a platform for efficient posttranslational modification of targets and protein-protein interaction, contributing to the adjustment of gene expression and chromatin integrity. Although PML SUMOylation is thought to play important roles in diverse cellular functions, the control mechanisms of adequate modification levels have remained unsolved. Here, we report that Cullin-related protein CACUL1/CAC1 (CACUL1) inhibits PML posttranslational modification. CACUL1 interacts with PML and suppresses PML SUMOylation, leading to the regulation of PML-NB size in the nucleus. We also found that Ubc9, a SUMO-conjugating enzyme, binds to CACUL1 and antagonizes the interaction between CACUL1 and PML. Furthermore, CACUL1 attenuates p53 transcriptional activity. These data suggest that CACUL1 is a novel regulator that negatively controls p53 activity through the regulation of PML SUMOylation.
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Affiliation(s)
- Tomomi Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yu Kigoshi-Tansho
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takao Naganuma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akira Kazaana
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Tomomi Okajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Fuminori Tsuruta
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Ph.D. Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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22
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Neumann F, Czech-Sioli M, Dobner T, Grundhoff A, Schreiner S, Fischer N. Replication of Merkel cell polyomavirus induces reorganization of promyelocytic leukemia nuclear bodies. J Gen Virol 2016; 97:2926-2938. [PMID: 27580912 DOI: 10.1099/jgv.0.000593] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma (MCC), a rare but aggressive skin cancer. The virus is highly prevalent: 60-80 % of adults are seropositive; however, cells permissive for MCPyV infection are unknown. Consequently, very little information about the MCPyV life cycle is available. Until recently, MCPyV replication could only be studied using a semi-permissive in vitro replication system (Neumann et al., 2011; Feng et al., 2011, Schowalter et al., 2011). MCPyV replication most likely depends on subnuclear structures such as promyelocytic leukemia protein nuclear bodies (PML-NBs), which are known to play regulatory roles in the infection of many DNA viruses. Here, we investigated PML-NB components as candidate host factors to control MCPyV DNA replication. We showed that PML-NBs change in number and size in cells actively replicating MCPyV proviral DNA. We observed a significant increase in PML-NBs in cells positive for MCPyV viral DNA replication. Interestingly, a significant amount of cells actively replicating MCPyV did not show any Sp100 expression. While PML and Daxx had no effect on MCPyV DNA replication, MCPyV replication was increased in cells depleted for Sp100, strongly suggesting that Sp100 is a negative regulator of MCPyV DNA replication.
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MESH Headings
- Antigens, Nuclear/genetics
- Antigens, Nuclear/metabolism
- Autoantigens/genetics
- Autoantigens/metabolism
- Carcinoma, Merkel Cell/genetics
- Carcinoma, Merkel Cell/metabolism
- Carcinoma, Merkel Cell/virology
- DNA Replication
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Humans
- Inclusion Bodies, Viral/genetics
- Inclusion Bodies, Viral/metabolism
- Inclusion Bodies, Viral/virology
- Merkel cell polyomavirus/genetics
- Merkel cell polyomavirus/physiology
- Polyomavirus Infections/genetics
- Polyomavirus Infections/metabolism
- Polyomavirus Infections/virology
- Promyelocytic Leukemia Protein/genetics
- Promyelocytic Leukemia Protein/metabolism
- Tumor Virus Infections/genetics
- Tumor Virus Infections/metabolism
- Tumor Virus Infections/virology
- Virus Replication
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Affiliation(s)
- Friederike Neumann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manja Czech-Sioli
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Dobner
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabrina Schreiner
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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23
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Abstract
The human adenovirus genome is transported into the nucleus, where viral gene transcription, viral DNA replication, and virion assembly take place. Posttranslational modifications by small ubiquitin-like modifiers (SUMOs) are implicated in the regulation of diverse cellular processes, particularly nuclear events. It is not surprising, therefore, that adenovirus modulates and utilizes the host sumoylation system. Adenovirus early proteins play an important role in establishing optimal host environments for virus replication within infected cells by stimulating the cell cycle and counteracting host antiviral defenses. Here, we review findings on the mechanisms and functional consequences of the interplay between human adenovirus early proteins and the host sumoylation system.
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24
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A novel single cell method to identify the genetic composition at a single nuclear body. Sci Rep 2016; 6:29191. [PMID: 27389808 PMCID: PMC4937434 DOI: 10.1038/srep29191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/14/2016] [Indexed: 11/24/2022] Open
Abstract
Gene loci make specific associations with compartments of the nucleus (e.g. the nuclear envelope, nucleolus, and transcription factories) and this association may determine or reflect a mechanism of genetic control. With current methods, it is not possible to identify sets of genes that converge to form a “gene hub” as there is a reliance on loci-specific probes, or immunoprecipitation of a particular protein from bulk cells. We introduce a method that will allow for the identification of loci contained within the vicinity of a single nuclear body in a single cell. For the first time, we demonstrate that the DNA sequences originating from a single sub-nuclear structure in a single cell targeted by two-photon irradiation can be determined, and mapped to a particular locus. Its application to single PML nuclear bodies reveals ontologically related loci that frequently associate with each other and with PML bodies in a population of cells, and a possible nuclear body targeting role for specific transcription factor binding sites.
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25
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Mitrea DM, Kriwacki RW. Phase separation in biology; functional organization of a higher order. Cell Commun Signal 2016; 14:1. [PMID: 26727894 PMCID: PMC4700675 DOI: 10.1186/s12964-015-0125-7] [Citation(s) in RCA: 458] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/29/2015] [Indexed: 12/18/2022] Open
Abstract
Inside eukaryotic cells, macromolecules are partitioned into membrane-bounded compartments and, within these, some are further organized into non-membrane-bounded structures termed membrane-less organelles. The latter structures are comprised of heterogeneous mixtures of proteins and nucleic acids and assemble through a phase separation phenomenon similar to polymer condensation. Membrane-less organelles are dynamic structures maintained through multivalent interactions that mediate diverse biological processes, many involved in RNA metabolism. They rapidly exchange components with the cellular milieu and their properties are readily altered in response to environmental cues, often implicating membrane-less organelles in responses to stress signaling. In this review, we discuss: (1) the functional roles of membrane-less organelles, (2) unifying structural and mechanistic principles that underlie their assembly and disassembly, and (3) established and emerging methods used in structural investigations of membrane-less organelles.
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Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA.
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26
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Solarczyk KJ, Kordon M, Berniak K, Dobrucki JW. Two stages of XRCC1 recruitment and two classes of XRCC1 foci formed in response to low level DNA damage induced by visible light, or stress triggered by heat shock. DNA Repair (Amst) 2016; 37:12-21. [PMID: 26630398 DOI: 10.1016/j.dnarep.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 12/18/2022]
Abstract
Induction of local photosensitised DNA damage has been used to study recruitment of repair factors, spatial organisation and subsequent stages of the repair processes. However, the damage induced by a focused laser beam interacting with a photosensitiser may not fully reflect the types of damage and repair encountered in cells of an animal under typical conditions in vivo. We report on two characteristic stages of recruitment of XRCC1 (a protein engaged in BER and SSB repair pathways), in response to low level DNA damage induced by visible light. We demonstrate that, when just a few DNA breaks are induced in a small region of the nucleus, the recruited XRCC1 is initially distributed uniformly throughout this region, and rearranges into several small stationary foci within minutes. In contrast, when heavy damage of various types (including oxidative damage) is induced in cells pre-sensitized with a DNA-binding drug ethidium bromide, XRCC1 is also recruited but fails to rearrange from the stage of the uniform distribution to the stage of several small foci, indicating that this heavy damage interferes with the progress and completion of the repair processes. We hypothesize that that first stage may reflect recruitment of XRCC1 to poly(ADP-ribose) moieties in the region surrounding the single-strand break, while the second-binding directly to the DNA lesions. We also show that moderate damage or stress induces formation of two types of XRCC1-containing foci differing in their mobility. A large subset of DNA damage-induced XRCC1 foci is associated with a major component of PML nuclear bodies--the Sp100 protein.
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Affiliation(s)
- Kamil J Solarczyk
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Magdalena Kordon
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Krzysztof Berniak
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Jurek W Dobrucki
- Division of Cell Biophysics Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University ul. Gronostajowa 7, 30-387 Kraków, Poland.
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Quetol 651: Not just a low viscosity resin. Microsc Res Tech 2015; 79:50-7. [DOI: 10.1002/jemt.22597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/12/2015] [Indexed: 11/07/2022]
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Pinder J, Salsman J, Dellaire G. Nuclear domain 'knock-in' screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing. Nucleic Acids Res 2015; 43:9379-92. [PMID: 26429972 PMCID: PMC4627099 DOI: 10.1093/nar/gkv993] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 09/21/2015] [Indexed: 12/31/2022] Open
Abstract
CRISPR is a genome-editing platform that makes use of the bacterially-derived endonuclease Cas9 to introduce DNA double-strand breaks at precise locations in the genome using complementary guide RNAs. We developed a nuclear domain knock-in screen, whereby the insertion of a gene encoding the green fluorescent protein variant Clover is inserted by Cas9-mediated homology directed repair (HDR) within the first exon of genes that are required for the structural integrity of subnuclear domains such as the nuclear lamina and promyelocytic leukemia nuclear bodies (PML NBs). Using this approach, we compared strategies for enhancing CRISPR-mediated HDR, focusing on known genes and small molecules that impact non-homologous end joining (NHEJ) and homologous recombination (HR). Ultimately, we identified the small molecule RS-1 as a potent enhancer of CRISPR-based genome editing, enhancing HDR 3- to 6-fold depending on the locus and transfection method. We also characterized U2OS human osteosarcoma cells expressing Clover-tagged PML and demonstrate that this strategy generates cell lines with PML NBs that are structurally and functionally similar to bodies in the parental cell line. Thus, the nuclear domain knock-in screen that we describe provides a simple means of rapidly evaluating methods and small molecules that have the potential to enhance Cas9-mediated HDR.
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Affiliation(s)
- Jordan Pinder
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, B3H 4R2, Canada
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Hall MH, Magalska A, Malinowska M, Ruszczycki B, Czaban I, Patel S, Ambrożek-Latecka M, Zołocińska E, Broszkiewicz H, Parobczak K, Nair RR, Rylski M, Pawlak R, Bramham CR, Wilczyński GM. Localization and regulation of PML bodies in the adult mouse brain. Brain Struct Funct 2015; 221:2511-25. [PMID: 25956166 DOI: 10.1007/s00429-015-1053-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/28/2015] [Indexed: 01/19/2023]
Abstract
PML is a tumor suppressor protein involved in the pathogenesis of promyelocytic leukemia. In non-neuronal cells, PML is a principal component of characteristic nuclear bodies. In the brain, PML has been implicated in the control of embryonic neurogenesis, and in certain physiological and pathological phenomena in the adult brain. Yet, the cellular and subcellular localization of the PML protein in the brain, including its presence in the nuclear bodies, has not been investigated comprehensively. Because the formation of PML bodies appears to be a key aspect in the function of the PML protein, we investigated the presence of these structures and their anatomical distribution, throughout the adult mouse brain. We found that PML is broadly expressed across the gray matter, with the highest levels in the cerebral and cerebellar cortices. In the cerebral cortex PML is present exclusively in neurons, in which it forms well-defined nuclear inclusions containing SUMO-1, SUMO 2/3, but not Daxx. At the ultrastructural level, the appearance of neuronal PML bodies differs from the classic one, i.e., the solitary structure with more or less distinctive capsule. Rather, neuronal PML bodies have the form of small PML protein aggregates located in the close vicinity of chromatin threads. The number, size, and signal intensity of neuronal PML bodies are dynamically influenced by immobilization stress and seizures. Our study indicates that PML bodies are broadly involved in activity-dependent nuclear phenomena in adult neurons.
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Affiliation(s)
- Małgorzata H Hall
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Adriana Magalska
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Monika Malinowska
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Błażej Ruszczycki
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Satyam Patel
- Department of Cell Physiology and Pharmacology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Magdalena Ambrożek-Latecka
- Department of Clinical Cytology, Center of Postgraduate Medical Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Ewa Zołocińska
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Hanna Broszkiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Kamil Parobczak
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland
| | - Rajeevkumar R Nair
- Neuroscience Research Group, Department of Biomedicine and KG Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Marcin Rylski
- Department of Clinical Cytology, Center of Postgraduate Medical Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Robert Pawlak
- Department of Cell Physiology and Pharmacology, University of Leicester, University Road, Leicester, LE1 7RH, UK.,Hatherley Laboratories, University of Exeter Medical School, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Clive R Bramham
- Neuroscience Research Group, Department of Biomedicine and KG Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Grzegorz M Wilczyński
- Laboratory of Molecular and Systemic Neuromorphology, Department of Neurophysiology, Nencki Institute of Experimental Biology, Pasteura 3, 02-093, Warsaw, Poland.
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Shigella infection interferes with SUMOylation and increases PML-NB number. PLoS One 2015; 10:e0122585. [PMID: 25848798 PMCID: PMC4388590 DOI: 10.1371/journal.pone.0122585] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 02/20/2015] [Indexed: 01/08/2023] Open
Abstract
Shigellosis is a severe diarrheal disease that affects hundreds of thousands of individuals resulting in significant morbidity and mortality worldwide. Shigellosis is caused by Shigella spp., a gram-negative bacterium that uses a Type 3 Secretion System (T3SS) to deliver effector proteins into the cytosol of infected human cells. Shigella infection triggers multiple signaling programs that result in a robust host transcriptional response that includes the induction of multiple proinflammatory cytokines. PML nuclear bodies (PML-NBs) are dynamic subnuclear structures that coordinate immune signaling programs and have a demonstrated role in controlling viral infection. We show that PML-NB number increases upon Shigella infection. We examined the effects of Shigella infection on SUMOylation and found that upon Shigella infection the localization of SUMOylated proteins is altered and the level of SUMOylated proteins decreases. Although Shigella infection does not alter the abundance of SUMO activating enzymes SAE1 or SAE2, it dramatically decreases the level of the SUMO conjugating enzyme Ubc9. All Shigella-induced alterations to the SUMOylation system are dependent upon a T3SS. Thus, we demonstrate that Shigella uses one or more T3SS effectors to influence both PML-NB number and the SUMOylation machinery in human cells.
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Gallina I, Colding C, Henriksen P, Beli P, Nakamura K, Offman J, Mathiasen DP, Silva S, Hoffmann E, Groth A, Choudhary C, Lisby M. Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control. Nat Commun 2015; 6:6533. [PMID: 25817432 PMCID: PMC4389229 DOI: 10.1038/ncomms7533] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 02/05/2015] [Indexed: 11/09/2022] Open
Abstract
DNA replication stress is a source of genomic instability. Here we identify changed mutation rate 1 (Cmr1) as a factor involved in the response to DNA replication stress in Saccharomyces cerevisiae and show that Cmr1--together with Mrc1/Claspin, Pph3, the chaperonin containing TCP1 (CCT) and 25 other proteins--define a novel intranuclear quality control compartment (INQ) that sequesters misfolded, ubiquitylated and sumoylated proteins in response to genotoxic stress. The diversity of proteins that localize to INQ indicates that other biological processes such as cell cycle progression, chromatin and mitotic spindle organization may also be regulated through INQ. Similar to Cmr1, its human orthologue WDR76 responds to proteasome inhibition and DNA damage by relocalizing to nuclear foci and physically associating with CCT, suggesting an evolutionarily conserved biological function. We propose that Cmr1/WDR76 plays a role in the recovery from genotoxic stress through regulation of the turnover of sumoylated and phosphorylated proteins.
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Affiliation(s)
- Irene Gallina
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Camilla Colding
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Peter Henriksen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Petra Beli
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Kyosuke Nakamura
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Judith Offman
- MRC, Centre for Genome Damage and Stability, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - David P Mathiasen
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Sonia Silva
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
| | - Eva Hoffmann
- MRC, Centre for Genome Damage and Stability, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N DK-2200, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Room 4.1.07, Copenhagen N DK-2200, Denmark
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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The elastin peptide (VGVAPG)3 induces the 3D reorganisation of PML-NBs and SC35 speckles architecture, and accelerates proliferation of fibroblasts and melanoma cells. Histochem Cell Biol 2014; 143:245-58. [PMID: 25274422 DOI: 10.1007/s00418-014-1274-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2014] [Indexed: 01/28/2023]
Abstract
During melanoma tumour growth, cancerous cells are exposed to the immediate surrounding the micro- and macro environment, which is largely modified through the degradation of the extracellular matrix by fibroblast-derived metalloproteinases. Among the degradation products, (VGVAPG)3, an elastin peptide is known to stimulate the proliferation of both fibroblasts and cancerous cells by binding to the elastin-binding receptor and activating the MEK/ERK signal transduction pathway. As this process strongly modifies mRNA synthesis, we investigated its effect on the relative three-dimensional organisation of the major partners of the mRNA splicing machinery: promyelocytic nuclear bodies (PML-NBs ) and splicing component 35 speckles (SC35) of normal fibroblasts and melanoma SK-MEL-28 cells. SC35 and PML-NBs proteins were immunolabeled and imaged by confocal microscopy within these cells cultured with (VGVAPG)3. Three-dimensional reconstruction was performed to elucidate the organisation of PML-NBs and SC35 speckles and their spatial relationship. In G0 cells, SC35 speckles were sequestered in PML-NBs. Shortly after (VGVAPG)3 stimulation, the three-dimensional organisation of PML-NBs and SC35 speckles changed markedly. In particular, SC35 speckles gradually enlarged and adopted a heterogeneous organisation, intermingled with PML-NBs. Conversely, inhibition of the elastin-binding protein or MEK/ERK pathway induced a remarkable early sequestration of condensed SC35 speckles in PML-NBs, the hallmark of splicing inhibition. The 3D architecture of speckles/PML-NBs highlights the modulation in their spatial relationship, the multiple roles of PML-NBs in activation, inhibition and sequestration, and provides the first demonstration of the dependence of PML-NBs and SC35 speckles on the elastin peptide for these functions.
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Adenovirus E1A targets the DREF nuclear factor to regulate virus gene expression, DNA replication, and growth. J Virol 2014; 88:13469-81. [PMID: 25210186 DOI: 10.1128/jvi.02538-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The adenovirus E1A gene is the first gene expressed upon viral infection. E1A remodels the cellular environment to maximize permissivity for viral replication. E1A is also the major transactivator of viral early gene expression and a coregulator of a large number of cellular genes. E1A carries out its functions predominantly by binding to cellular regulatory proteins and altering their activities. The unstructured nature of E1A enables it to bind to a large variety of cellular proteins and form new molecular complexes with novel functions. The C terminus of E1A is the least-characterized region of the protein, with few known binding partners. Here we report the identification of cellular factor DREF (ZBED1) as a novel and direct binding partner of E1A. Our studies identify a dual role for DREF in the viral life cycle. DREF contributes to activation of gene expression from all viral promoters early in infection. Unexpectedly, it also functions as a growth restriction factor for adenovirus as knockdown of DREF enhances virus growth and increases viral genome copy number late in the infection. We also identify DREF as a component of viral replication centers. E1A affects the subcellular distribution of DREF within PML bodies and enhances DREF SUMOylation. Our findings identify DREF as a novel E1A C terminus binding partner and provide evidence supporting a role for DREF in viral replication. IMPORTANCE This work identifies the putative transcription factor DREF as a new target of the E1A oncoproteins of human adenovirus. DREF was found to primarily localize with PML nuclear bodies in uninfected cells and to relocalize into virus replication centers during infection. DREF was also found to be SUMOylated, and this was enhanced in the presence of E1A. Knockdown of DREF reduced the levels of viral transcripts detected at 20 h, but not at 40 h, postinfection, increased overall virus yield, and enhanced viral DNA replication. DREF was also found to localize to viral promoters during infection together with E1A. These results suggest that DREF contributes to activation of viral gene expression. However, like several other PML-associated proteins, DREF also appears to function as a growth restriction factor for adenovirus infection.
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Guo S, Cheng X, Lim JH, Liu Y, Kao HY. Control of antioxidative response by the tumor suppressor protein PML through regulating Nrf2 activity. Mol Biol Cell 2014; 25:2485-98. [PMID: 24943846 PMCID: PMC4142619 DOI: 10.1091/mbc.e13-11-0692] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PML plays a critical role in the maintenance of ROS homeostasis via a unique mechanism in which PML functions as an oxidative sensor to regulate the expression of antioxidant genes through Nrf2. PML is also indispensable for sulforaphane-mediated ROS generation, Nrf2 activation, antiproliferation, antimigration, and antiangiogenesis. Oxidative stress is a consequence of an imbalance between reactive oxygen species (ROS) production and the ability of the cytoprotective system to detoxify the reactive intermediates. The tumor suppressor promyelocytic leukemia protein (PML) functions as a stress sensor. Loss of PML results in impaired mitochondrial complex II activity, increased ROS, and subsequent activation of nuclear factor erythroid 2–related factor 2 (Nrf2) antioxidative pathway. We also demonstrate that sulforaphane (SFN), an antioxidant, regulates Nrf2 activity by controlling abundance and subcellular distribution of PML and that PML is essential for SFN-mediated ROS increase, Nrf2 activation, antiproliferation, antimigration, and antiangiogenesis. Taking the results together, we have uncovered a novel antioxidative mechanism by which PML regulates cellular oxidant homeostasis by controlling complex II integrity and Nrf2 activity and identified PML as an indispensable mediator of SFN activity.
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Affiliation(s)
- Shuang Guo
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Xiwen Cheng
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Jun-Hee Lim
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Yu Liu
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106
| | - Hung-Ying Kao
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106Comprehensive Cancer Center of Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH 44106
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Sahin U, Ferhi O, Jeanne M, Benhenda S, Berthier C, Jollivet F, Niwa-Kawakita M, Faklaris O, Setterblad N, de Thé H, Lallemand-Breitenbach V. Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins. ACTA ACUST UNITED AC 2014; 204:931-45. [PMID: 24637324 PMCID: PMC3998805 DOI: 10.1083/jcb.201305148] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PML multimerization into nuclear bodies following its oxidation promotes sumoylation and sequestration of partner proteins in these structures. The promyelocytic leukemia (PML) protein organizes PML nuclear bodies (NBs), which are stress-responsive domains where many partner proteins accumulate. Here, we clarify the basis for NB formation and identify stress-induced partner sumoylation as the primary NB function. NB nucleation does not rely primarily on intermolecular interactions between the PML SUMO-interacting motif (SIM) and SUMO, but instead results from oxidation-mediated PML multimerization. Oxidized PML spherical meshes recruit UBC9, which enhances PML sumoylation, allow partner recruitment through SIM interactions, and ultimately enhance partner sumoylation. Intermolecular SUMO–SIM interactions then enforce partner sequestration within the NB inner core. Accordingly, oxidative stress enhances NB formation and global sumoylation in vivo. Some NB-associated sumoylated partners also become polyubiquitinated by RNF4, precipitating their proteasomal degradation. As several partners are protein-modifying enzymes, NBs could act as sensors that facilitate and confer oxidative stress sensitivity not only to sumoylation but also to other post-translational modifications, thereby explaining alterations of stress response upon PML or NB loss.
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Affiliation(s)
- Umut Sahin
- Université Paris Diderot, Sorbonne Paris Cité, Hôpital St. Louis 1, 75475 Paris Cedex 10, France
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Cheng X, Guo S, Liu Y, Chu H, Hakimi P, Berger NA, Hanson RW, Kao HY. Ablation of promyelocytic leukemia protein (PML) re-patterns energy balance and protects mice from obesity induced by a Western diet. J Biol Chem 2013; 288:29746-59. [PMID: 23986437 DOI: 10.1074/jbc.m113.487595] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The promyelocytic leukemia protein is a well known tumor suppressor, but its role in metabolism is largely unknown. Mice with a deletion in the gene for PML (KO mice) exhibit altered gene expression in liver, adipose tissue, and skeletal muscle, an accelerated rate of fatty acid metabolism, abnormal glucose metabolism, constitutive AMP-activating kinase (AMPK) activation, and insulin resistance in skeletal muscle. Last, an increased rate of energy expenditure protects PML KO mice from the effects of obesity induced by a Western diet. Collectively, our study uncovers a previously unappreciated role of PML in the regulation of metabolism and energy balance in mice.
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Rivera-Molina YA, Martínez FP, Tang Q. Nuclear domain 10 of the viral aspect. World J Virol 2013; 2:110-122. [PMID: 24255882 PMCID: PMC3832855 DOI: 10.5501/wjv.v2.i3.110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/31/2013] [Accepted: 07/11/2013] [Indexed: 02/05/2023] Open
Abstract
Nuclear domain 10 (ND10) are spherical bodies distributed throughout the nucleoplasm and measuring around 0.2-1.0 μm. First observed under an electron microscope, they were originally described as dense bodies found in the nucleus. They are known by a number of other names, including Promyelocytic Leukemia bodies (PML bodies), Kremer bodies, and PML oncogenic domains. ND10 are frequently associated with Cajal bodies and cleavage bodies. It has been suggested that they play a role in regulating gene transcription. ND10 were originally characterized using human autoantisera, which recognizes Speckled Protein of 100 kDa, from patients with primary biliary cirrhosis. At the immunohistochemical level, ND10 appear as nuclear punctate structures, with 10 indicating the approximate number of dots per nucleus observed. ND10 do not colocalize with kinetochores, centromeres, sites of mRNA processing, or chromosomes. Resistance of ND10 antigens to nuclease digestion and salt extraction suggest that ND10 are associated with the nuclear matrix. They are often identified by immunofluorescent assay using specific antibodies against PML, Death domain-associated protein, nuclear dot protein (NDP55), and so on. The role of ND10 has long been the subject of investigation, with the specific connection of ND10 and viral infection having been a particular focus for almost 20 years. This review summarizes the relationship of ND10 and viral infection. Some future study directions are also discussed.
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Soares IN, Caetano FA, Pinder J, Rodrigues BR, Beraldo FH, Ostapchenko VG, Durette C, Pereira GS, Lopes MH, Queiroz-Hazarbassanov N, Cunha IW, Sanematsu PI, Suzuki S, Bleggi-Torres LF, Schild-Poulter C, Thibault P, Dellaire G, Martins VR, Prado VF, Prado MAM. Regulation of stress-inducible phosphoprotein 1 nuclear retention by protein inhibitor of activated STAT PIAS1. Mol Cell Proteomics 2013; 12:3253-70. [PMID: 23938469 DOI: 10.1074/mcp.m113.031005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stress-inducible phosphoprotein 1 (STI1), a cochaperone for Hsp90, has been shown to regulate multiple pathways in astrocytes, but its contributions to cellular stress responses are not fully understood. We show that in response to irradiation-mediated DNA damage stress STI1 accumulates in the nucleus of astrocytes. Also, STI1 haploinsufficiency decreases astrocyte survival after irradiation. Using yeast two-hybrid screenings we identified several nuclear proteins as STI1 interactors. Overexpression of one of these interactors, PIAS1, seems to be specifically involved in STI1 nuclear retention and in directing STI1 and Hsp90 to specific sub-nuclear regions. PIAS1 and STI1 co-immunoprecipitate and PIAS1 can function as an E3 SUMO ligase for STI. Using mass spectrometry we identified five SUMOylation sites in STI1. A STI1 mutant lacking these five sites is not SUMOylated, but still accumulates in the nucleus in response to increased expression of PIAS1, suggesting the possibility that a direct interaction with PIAS1 could be responsible for STI1 nuclear retention. To test this possibility, we mapped the interaction sites between PIAS1 and STI1 using yeast-two hybrid assays and surface plasmon resonance and found that a large domain in the N-terminal region of STI1 interacts with high affinity with amino acids 450-480 of PIAS1. Knockdown of PIAS1 in astrocytes impairs the accumulation of nuclear STI1 in response to irradiation. Moreover, a PIAS1 mutant lacking the STI1 binding site is unable to increase STI1 nuclear retention. Interestingly, in human glioblastoma multiforme PIAS1 expression is increased and we found a significant correlation between increased PIAS1 expression and STI1 nuclear localization. These experiments provide evidence that direct interaction between STI1 and PIAS1 is involved in the accumulation of nuclear STI1. This retention mechanism could facilitate nuclear chaperone activity.
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Affiliation(s)
- Iaci N Soares
- Robarts Research Institute, The University of Western Ontario, London, ON, Canada
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PML-mediated signaling and its role in cancer stem cells. Oncogene 2013; 33:1475-84. [PMID: 23563177 DOI: 10.1038/onc.2013.111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/06/2013] [Accepted: 02/09/2013] [Indexed: 02/08/2023]
Abstract
The promyelocytic leukemia (PML) protein, initially discovered as a part of the PML/retinoic acid receptor alpha fusion protein, has been found to be a critical player in oncogenesis and tumor progression. Multiple cellular activities, including DNA repair, alternative lengthening of telomeres, transcriptional control, apoptosis and senescence, are regulated by PML and its featured subcellular structure, the PML nuclear body. In correspondence with its role in many important life processes, PML mediates several complex downstream signaling pathways. The determinant function of PML in tumorigenesis and cancer progression raises the interest in its involvement in cancer stem cells (CSCs), a subpopulation of cancer cells that share properties with stem cells and are critical for tumor propagation. Recently, there are exciting discoveries concerning the requirement of PML in CSC maintenance. Growing evidences strongly suggest a positive role of PML in regulating CSCs in both hematopoietic cancers and solid tumors, whereas the underlying mechanisms may be different and remain elusive. Here we summarize and discuss the PML-mediated signaling pathways in cancers and their potential roles in regulating CSCs.
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Malloy MT, McIntosh DJ, Walters TS, Flores A, Goodwin JS, Arinze IJ. Trafficking of the transcription factor Nrf2 to promyelocytic leukemia-nuclear bodies: implications for degradation of NRF2 in the nucleus. J Biol Chem 2013; 288:14569-14583. [PMID: 23543742 DOI: 10.1074/jbc.m112.437392] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ubiquitylation of Nrf2 by the Keap1-Cullin3/RING box1 (Cul3-Rbx1) E3 ubiquitin ligase complex targets Nrf2 for proteasomal degradation in the cytoplasm and is an extensively studied mechanism for regulating the cellular level of Nrf2. Although mechanistic details are lacking, reports abound that Nrf2 can also be degraded in the nucleus. Here, we demonstrate that Nrf2 is a target for sumoylation by both SUMO-1 and SUMO-2. HepG2 cells treated with As2O3, which enhances attachment of SUMO-2/3 to target proteins, increased SUMO-2/3-modification (polysumoylation) of Nrf2. We show that Nrf2 traffics, in part, to promyelocytic leukemia-nuclear bodies (PML-NBs). Cell fractions harboring key components of PML-NBs did not contain biologically active Keap1 but contained modified Nrf2 as well as RING finger protein 4 (RNF4), a poly-SUMO-specific E3 ubiquitin ligase. Overexpression of wild-type RNF4, but not the catalytically inactive mutant, decreased the steady-state levels of Nrf2, measured in the PML-NB-enriched cell fraction. The proteasome inhibitor MG-132 interfered with this decrease, resulting in elevated levels of polysumoylated Nrf2 that was also ubiquitylated. Wild-type RNF4 accelerated the half-life (t½) of Nrf2, measured in PML-NB-enriched cell fractions. These results suggest that RNF4 mediates polyubiquitylation of polysumoylated Nrf2, leading to its subsequent degradation in PML-NBs. Overall, this work identifies Nrf2 as a target for sumoylation and provides a novel mechanism for its degradation in the nucleus, independent of Keap1.
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Affiliation(s)
- Melanie Theodore Malloy
- Department of Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208-3599
| | - Deneshia J McIntosh
- Department of Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208-3599
| | - Treniqka S Walters
- Department of Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208-3599
| | - Andrea Flores
- Department of Neuroscience and Pharmacology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208-3599
| | - J Shawn Goodwin
- Department of Biochemistry and Cancer Biology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208-3599
| | - Ifeanyi J Arinze
- Department of Physiology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208-3599.
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Cheng X, Kao HY. Post-translational modifications of PML: consequences and implications. Front Oncol 2013; 2:210. [PMID: 23316480 PMCID: PMC3539660 DOI: 10.3389/fonc.2012.00210] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/16/2012] [Indexed: 12/23/2022] Open
Abstract
The tumor suppressor promyelocytic leukemia protein (PML) predominantly resides in a structurally distinct sub-nuclear domain called PML nuclear bodies. Emerging evidences indicated that PML actively participates in many aspects of cellular processes, but the molecular mechanisms underlying PML regulation in response to stress and environmental cues are not complete. Post-translational modifications, such as SUMOylation, phosphorylation, acetylation, and ubiquitination of PML add a complex layer of regulation to the physiological function of PML. In this review, we discuss the fast-moving horizon of post-translational modifications targeting PML.
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Affiliation(s)
- Xiwen Cheng
- Department of Biochemistry, School of Medicine, Case Western Reserve UniversityCleveland, OH, USA
- Comprehensive Cancer Center, Case Western Reserve UniversityCleveland, OH, USA
- University Hospital of Cleveland, Case Western Reserve UniversityCleveland, OH, USA
| | - Hung-Ying Kao
- Department of Biochemistry, School of Medicine, Case Western Reserve UniversityCleveland, OH, USA
- Comprehensive Cancer Center, Case Western Reserve UniversityCleveland, OH, USA
- University Hospital of Cleveland, Case Western Reserve UniversityCleveland, OH, USA
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Kruhlak MJ. Correlative fluorescence and EFTEM imaging of the organized components of the mammalian nucleus. Methods Mol Biol 2013; 950:397-416. [PMID: 23086887 PMCID: PMC7581281 DOI: 10.1007/978-1-62703-137-0_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The cell nucleus contains many distinct subnuclear compartments, domains, and bodies that vary in their composition, structure, and function. While the cellular constituents that occupy the subnuclear regions may be well known, defining the structural details of the molecular assembly of the constituents has been more difficult. A correlative fluorescence and energy-filtering transmission electron microscopy (EFTEM) imaging method has the ability to provide these details. The correlative microscopy method described here allows the tracking of subnuclear structures from specific cells by fluorescence microscopy and then, using electron energy loss imaging in the transmission electron microscope, reveals the ultrastructural features of the nuclear components along with endogenous elemental information that relates directly to the biochemical composition of the structure. The ultrastructural features and composition of well-characterized PML bodies and interchromatin granule clusters are compared to those of ligand-activated glucocorticoid receptor (GR) foci, with GR foci containing fibrogranular nucleic acid-containing features and PML bodies being devoid of nucleic acid.
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Affiliation(s)
- Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Berscheminski J, Groitl P, Dobner T, Wimmer P, Schreiner S. The adenoviral oncogene E1A-13S interacts with a specific isoform of the tumor suppressor PML to enhance viral transcription. J Virol 2013; 87:965-77. [PMID: 23135708 PMCID: PMC3554061 DOI: 10.1128/jvi.02023-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/20/2012] [Indexed: 12/21/2022] Open
Abstract
PML nuclear bodies (PML NBs), also called ND10, are matrix-bound nuclear structures that have been implicated in a variety of functions, including DNA repair, transcriptional regulation, protein degradation, and tumor suppression. These domains are also known for their potential to mediate an intracellular defense mechanism against many virus types. This is likely why they are targeted and subsequently manipulated by numerous viral proteins. Paradoxically, the genomes of various DNA viruses become associated with PML NBs, and initial sites of viral transcription/replication centers are often juxtaposed to these domains. The question is why viruses start their transcription and replication next to their supposed antagonists. Here, we report that PML NBs are targeted by the adenoviral (Ad) transactivator protein E1A-13S. Alternatively spliced E1A isoforms (E1A-12S and E1A-13S) are the first proteins expressed upon Ad infection. E1A-13S is essential for activating viral transcription in the early phase of infection. Coimmunoprecipitation assays showed that E1A-13S preferentially interacts with only one (PML-II) of at least six nuclear human PML isoforms. Deletion mapping located the interaction site within E1A conserved region 3 (CR3), which was previously described as the transcription factor binding region of E1A-13S. Indeed, cooperation with PML-II enhanced E1A-mediated transcriptional activation, while deleting the SUMO-interacting motif (SIM) of PML proved even more effective. Our results suggest that in contrast to PML NB-associated antiviral defense, PML-II may help transactivate viral gene expression and therefore play a novel role in activating Ad transcription during the early viral life cycle.
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Affiliation(s)
- Julia Berscheminski
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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46
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de Thé H, Le Bras M, Lallemand-Breitenbach V. The cell biology of disease: Acute promyelocytic leukemia, arsenic, and PML bodies. J Cell Biol 2012; 198:11-21. [PMID: 22778276 PMCID: PMC3392943 DOI: 10.1083/jcb.201112044] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 06/15/2012] [Indexed: 12/12/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is driven by a chromosomal translocation whose product, the PML/retinoic acid (RA) receptor α (RARA) fusion protein, affects both nuclear receptor signaling and PML body assembly. Dissection of APL pathogenesis has led to the rediscovery of PML bodies and revealed their role in cell senescence, disease pathogenesis, and responsiveness to treatment. APL is remarkable because of the fortuitous identification of two clinically effective therapies, RA and arsenic, both of which degrade PML/RARA oncoprotein and, together, cure APL. Analysis of arsenic-induced PML or PML/RARA degradation has implicated oxidative stress in the biogenesis of nuclear bodies and SUMO in their degradation.
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Affiliation(s)
- Hugues de Thé
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 944, Equipe labellisée par la Ligue Nationale contre le Cancer, 2 University Paris-Diderot, Sorbonne Paris Cité, Paris, France.
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47
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Londoño-Vallejo JA, Wellinger RJ. Telomeres and telomerase dance to the rhythm of the cell cycle. Trends Biochem Sci 2012; 37:391-9. [PMID: 22727244 DOI: 10.1016/j.tibs.2012.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/21/2012] [Accepted: 05/25/2012] [Indexed: 11/27/2022]
Abstract
The stability of the ends of linear eukaryotic chromosomes is ensured by functional telomeres, which are composed of short, species-specific direct repeat sequences. The maintenance of telomeres depends on a specialized ribonucleoprotein (RNP) called telomerase. Both telomeres and telomerase are dynamic entities with different physical behaviors and, given their substrate-enzyme relation, they must establish a productive interaction. Regulatory mechanisms controlling this interaction are key missing elements in our understanding of telomere functions. Here, we review the dynamic properties of telomeres and the maturing telomerase RNPs, and summarize how tracking the timing of their dance during the cell cycle will yield insights into chromosome stability mechanisms. Cancer cells often display loss of genome integrity; therefore, these issues are of particular interest for our understanding of cancer initiation or progression.
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Affiliation(s)
- J Arturo Londoño-Vallejo
- Laboratoire Télomères et Cancer, UMR3244, Institut Curie, 26 rue d'Ulm, 75248 Paris, France; UPMC Université Paris 06, F-75005 Paris, France
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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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Batty EC, Jensen K, Freemont PS. PML nuclear bodies and other TRIM-defined subcellular compartments. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 770:39-58. [PMID: 23630999 DOI: 10.1007/978-1-4614-5398-7_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Tripartite motif (TRIM) proteins are defined by their possession of a RING, B-box and predicted coiled coil (RBCC) domain. The coiled-coil region facilitates the oligomerisation of TRIMs and contributes to the formation of high molecular weight complexes that show interesting subcellular compartmentalisations and structures. TRIM protein compartments include both nuclear and cytoplasmic filaments and aggregates (bodies), as well as diffuse subcellular distributions. TRIM 19, otherwise known as promyelocytic leukaemia (PML) protein forms nuclear aggregates termed PML nuclear bodies (PML NBs), at which a number of functionally diverse proteins transiently or covalently associate. PML NBs are therefore implicated in a wide variety of cellular functions such as transcriptional regulation, viral response, apoptosis and nuclear protein storage.
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Affiliation(s)
- Elizabeth C Batty
- Macromolecular Structure and Function Group, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK
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50
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Cho S, Park JS, Kang YK. Dual functions of histone-lysine N-methyltransferase Setdb1 protein at promyelocytic leukemia-nuclear body (PML-NB): maintaining PML-NB structure and regulating the expression of its associated genes. J Biol Chem 2011; 286:41115-24. [PMID: 21921037 PMCID: PMC3220519 DOI: 10.1074/jbc.m111.248534] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 09/14/2011] [Indexed: 11/06/2022] Open
Abstract
Setdb1/Eset is a histone H3 lysine 9 (H3K9)-specific methyltransferase that associates with various transcription factors to regulate gene expression via chromatin remodeling. Here, we report that Setdb1 associates with promyelocytic leukemia (Pml) protein from the early stage of mouse development and is a constitutive member of promyelocytic leukemia (PML)-nuclear bodies (PML-NBs) that have been linked to many cellular processes such as apoptosis, DNA damage responses, and transcriptional regulation. Arsenic treatment, which induces Pml degradation, caused Setdb1 signals to disappear. Setdb1 knockdown resulted in dismantlement of PML-NBs. Immunoprecipitation results demonstrated physical interactions between Setdb1 and Pml. Chromatin immunoprecipitation revealed that, within the frame of PML-NBs, Setdb1 binds the promoter of Id2 and suppresses its expression through installing H3K9 methylation. Our findings suggest that Setdb1 performs dual, but inseparable, functions at PML-NBs to maintain the structural integrity of PML-NBs and to control PML-NB-associated genes transcriptionally.
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Affiliation(s)
- Sunwha Cho
- From the Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology and
- the Department of Functional Genomics, University of Science and Technology, 113 Gwahangno, Yuseong-gu, 305-806 Daejeon, South Korea
| | - Jung Sun Park
- From the Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology and
| | - Yong-Kook Kang
- From the Development and Differentiation Research Center, Korea Research Institute of Bioscience and Biotechnology and
- the Department of Functional Genomics, University of Science and Technology, 113 Gwahangno, Yuseong-gu, 305-806 Daejeon, South Korea
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