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Ryabchenko B, Šroller V, Horníková L, Lovtsov A, Forstová J, Huérfano S. The interactions between PML nuclear bodies and small and medium size DNA viruses. Virol J 2023; 20:82. [PMID: 37127643 PMCID: PMC10152602 DOI: 10.1186/s12985-023-02049-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PM NBs), often referred to as membraneless organelles, are dynamic macromolecular protein complexes composed of a PML protein core and other transient or permanent components. PML NBs have been shown to play a role in a wide variety of cellular processes. This review describes in detail the diverse and complex interactions between small and medium size DNA viruses and PML NBs that have been described to date. The PML NB components that interact with small and medium size DNA viruses include PML protein isoforms, ATRX/Daxx, Sp100, Sp110, HP1, and p53, among others. Interaction between viruses and components of these NBs can result in different outcomes, such as influencing viral genome expression and/or replication or impacting IFN-mediated or apoptotic cell responses to viral infection. We discuss how PML NB components abrogate the ability of adenoviruses or Hepatitis B virus to transcribe and/or replicate their genomes and how papillomaviruses use PML NBs and their components to promote their propagation. Interactions between polyomaviruses and PML NBs that are poorly understood but nevertheless suggest that the NBs can serve as scaffolds for viral replication or assembly are also presented. Furthermore, complex interactions between the HBx protein of hepadnaviruses and several PML NBs-associated proteins are also described. Finally, current but scarce information regarding the interactions of VP3/apoptin of the avian anellovirus with PML NBs is provided. Despite the considerable number of studies that have investigated the functions of the PML NBs in the context of viral infection, gaps in our understanding of the fine interactions between viruses and the very dynamic PML NBs remain. The complexity of the bodies is undoubtedly a great challenge that needs to be further addressed.
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Affiliation(s)
- Boris Ryabchenko
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Vojtěch Šroller
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Lenka Horníková
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Alexey Lovtsov
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Jitka Forstová
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Sandra Huérfano
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic.
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2
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Lacroix E, Audas TE. Keeping up with the condensates: The retention, gain, and loss of nuclear membrane-less organelles. Front Mol Biosci 2022; 9:998363. [PMID: 36203874 PMCID: PMC9530788 DOI: 10.3389/fmolb.2022.998363] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/19/2022] [Indexed: 12/04/2022] Open
Abstract
In recent decades, a growing number of biomolecular condensates have been identified in eukaryotic cells. These structures form through phase separation and have been linked to a diverse array of cellular processes. While a checklist of established membrane-bound organelles is present across the eukaryotic domain, less is known about the conservation of membrane-less subcellular structures. Many of these structures can be seen throughout eukaryotes, while others are only thought to be present in metazoans or a limited subset of species. In particular, the nucleus is a hub of biomolecular condensates. Some of these subnuclear domains have been found in a broad range of organisms, which is a characteristic often attributed to essential functionality. However, this does not always appear to be the case. For example, the nucleolus is critical for ribosomal biogenesis and is present throughout the eukaryotic domain, while the Cajal bodies are believed to be similarly conserved, yet these structures are dispensable for organismal survival. Likewise, depletion of the Drosophila melanogaster omega speckles reduces viability, despite the apparent absence of this domain in higher eukaryotes. By reviewing primary research that has analyzed the presence of specific condensates (nucleoli, Cajal bodies, amyloid bodies, nucleolar aggresomes, nuclear speckles, nuclear paraspeckles, nuclear stress bodies, PML bodies, omega speckles, NUN bodies, mei2 dots) in a cross-section of organisms (e.g., human, mouse, D. melanogaster, Caenorhabditis elegans, yeast), we adopt a human-centric view to explore the emergence, retention, and absence of a subset of nuclear biomolecular condensates. This overview is particularly important as numerous biomolecular condensates have been linked to human disease, and their presence in additional species could unlock new and well characterized model systems for health research.
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Affiliation(s)
- Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Timothy E. Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
- *Correspondence: Timothy E. Audas,
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3
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Ly CY, Yu C, McDonald PR, Roy A, Johnson DK, Davido DJ. Simple and rapid high-throughput assay to identify HSV-1 ICP0 transactivation inhibitors. Antiviral Res 2021; 194:105160. [PMID: 34384824 DOI: 10.1016/j.antiviral.2021.105160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/30/2021] [Accepted: 08/07/2021] [Indexed: 10/20/2022]
Abstract
Herpes simplex virus 1 (HSV-1) is a ubiquitous virus that results in lifelong infections due to its ability to cycle between lytic replication and latency. As an obligate intracellular pathogen, HSV-1 exploits host cellular factors to replicate and aid in its life cycle. HSV-1 expresses infected cell protein 0 (ICP0), an immediate-early regulator, to stimulate the transcription of all classes of viral genes via its E3 ubiquitin ligase activity. Here we report an automated, inexpensive, and rapid high-throughput approach to examine the effects of small molecule compounds on ICP0 transactivator function in cells. Two HSV-1 reporter viruses, KOS6β (wt) and dlx3.1-6β (ICP0-null mutant), were used to monitor ICP0 transactivation activity through the HSV-1 ICP6 promoter:lacz expression cassette. A ≥10-fold difference in β-galactosidase activity was observed in cells infected with KOS6β compared to dlx3.1-6β, demonstrating that ICP0 potently transactivates the ICP6 promoter. We established the robustness and reproducibility with a Z'-factor score of ≥0.69, an important criterium for high-throughput analyses. Approximately 19,000 structurally diverse compounds were screened and 76 potential inhibitors of the HSV-1 transactivator ICP0 were identified. We expect this assay will aid in the discovery of novel inhibitors and tools against HSV-1 ICP0. Using well-annotated compounds could identify potential novel factors and pathways that interact with ICP0 to promote HSV-1 gene expression.
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Affiliation(s)
- Cindy Y Ly
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA
| | - Chunmiao Yu
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA
| | - Peter R McDonald
- High Throughput Screening Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, The University of Kansas, Lawrence, KS, 66047, USA
| | - David K Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, KS, 66047, USA
| | - David J Davido
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA.
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4
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PML Regulates the Epidermal Differentiation Complex and Skin Morphogenesis during Mouse Embryogenesis. Genes (Basel) 2020; 11:genes11101130. [PMID: 32992884 PMCID: PMC7600374 DOI: 10.3390/genes11101130] [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: 08/10/2020] [Revised: 09/13/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022] Open
Abstract
The promyelocytic leukemia (PML) protein is an essential component of nuclear compartments called PML bodies. This protein participates in several cellular processes, including growth control, senescence, apoptosis, and differentiation. Previous studies have suggested that PML regulates gene expression at a subset of loci through a function in chromatin remodeling. Here we have studied global gene expression patterns in mouse embryonic skin derived from Pml depleted and wild type mouse embryos. Differential gene expression analysis at different developmental stages revealed a key role of PML in regulating genes involved in epidermal stratification. In particular, we observed dysregulation of the late cornified envelope gene cluster, which is a sub-region of the epidermal differentiation complex. In agreement with these data, PML body numbers are elevated in basal keratinocytes during embryogenesis, and we observed reduced epidermal thickness and defective hair follicle development in PML depleted mouse embryos.
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5
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Zheng B, Mora RA, Fritzler MJ, Satoh M, Bloch DB, Garcia-De La Torre I, Boylan K, Kohl K, Wener MH, Andrade LEC, Chan EKL. Establishment of international autoantibody reference standards for the detection of autoantibodies directed against PML bodies, GW bodies, and NuMA protein. Clin Chem Lab Med 2020; 59:197-207. [PMID: 32776893 PMCID: PMC7855248 DOI: 10.1515/cclm-2020-0981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/21/2020] [Indexed: 12/16/2022]
Abstract
Objectives: Reference materials are important in the standardization of autoantibody testing and only a few are freely available for many known autoantibodies. Our goal was to develop three reference materials for antibodies to PML bodies/multiple nuclear dots (MND), antibodies to GW bodies (GWB), and antibodies to the nuclear mitotic apparatus (NuMA). Methods: Reference materials for identifying autoantibodies to MND (MND-REF), GWB (GWB-REF), and NuMA (NuMA-REF) were obtained from three donors and validated independently by seven laboratories. The sera were characterized using indirect immunofluorescence assay (IFA) on HEp-2 cell substrates including two-color immunofluorescence using antigen-specific markers, western blot (WB), immunoprecipitation (IP), line immunoassay (LIA), addressable laser bead immunoassay (ALBIA), enzyme-linked immunosorbent assay (ELISA), and immunoprecipitation–mass spectrometry (IP-MS). Results: MND-REF stained 6–20 discrete nuclear dots that colocalized with PML bodies. Antibodies to Sp100 and PML were detected by LIA and antibodies to Sp100 were also detected by ELISA. GWB-REF stained discrete cytoplasmic dots in interphase cells, which were confirmed to be GWB using two-color immunofluorescence. Anti-Ge-1 antibodies were identified in GWB-REF by ALBIA, IP, and IP-MS. All reference materials produced patterns at dilutions of 1:160 or greater. NuMA-REF produced fine speckled nuclear staining in interphase cells and staining of spindle fibers and spindle poles. The presence of antibodies to NuMA was verified by IP, WB, ALBIA, and IP-MS. Conclusions: MND-REF, GWB-REF, and NuMA-REF are suitable reference materials for the corresponding antinuclear antibodies staining patterns and will be accessible to qualified laboratories.
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Affiliation(s)
- Bing Zheng
- Department of Oral Biology,University of Florida, Gainesville, FL, USA.,Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Rodrigo A Mora
- Department of Oral Biology,University of Florida, Gainesville, FL, USA
| | - Marvin J Fritzler
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Minoru Satoh
- Department of Clinical Nursing, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Donald B Bloch
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ignacio Garcia-De La Torre
- Department of Immunology and Rheumatology, Hospital General de Occidente and University of Guadalajara, Guadalajara, Mexico
| | - Katherine Boylan
- Scientific & Clinical Affairs, Plasma Services Group Inc., Huntingdon Valley, PA, USA
| | - Kathryn Kohl
- Scientific & Clinical Affairs, Plasma Services Group Inc., Huntingdon Valley, PA, USA
| | - Mark H Wener
- Division of Rheumatology and Department of Laboratory Medicine,University of Washington, Seattle, WA, USA
| | - Luis E C Andrade
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Immunology Division, Fleury Laboratories, São Paulo, Brazil
| | - Edward K L Chan
- Department of Oral Biology,University of Florida, Gainesville, FL, USA
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6
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Zhang H, Zhao R, Tones J, Liu M, Dilley RL, Chenoweth DM, Greenberg RA, Lampson MA. Nuclear body phase separation drives telomere clustering in ALT cancer cells. Mol Biol Cell 2020; 31:2048-2056. [PMID: 32579423 PMCID: PMC7543070 DOI: 10.1091/mbc.e19-10-0589] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Telomerase-free cancer cells employ a recombination-based alternative lengthening of telomeres (ALT) pathway that depends on ALT-associated promyelocytic leukemia nuclear bodies (APBs), whose function is unclear. We find that APBs behave as liquid condensates in response to telomere DNA damage, suggesting two potential functions: condensation to enrich DNA repair factors and coalescence to cluster telomeres. To test these models, we developed a chemically induced dimerization approach to induce de novo APB condensation in live cells without DNA damage. We show that telomere-binding protein sumoylation nucleates APB condensation via interactions between small ubiquitin-like modifier (SUMO) and SUMO interaction motif (SIM), and that APB coalescence drives telomere clustering. The induced APBs lack DNA repair factors, indicating that APB functions in promoting telomere clustering can be uncoupled from enriching DNA repair factors. Indeed, telomere clustering relies only on liquid properties of the condensate, as an alternative condensation chemistry also induces clustering independent of sumoylation. Our findings introduce a chemical dimerization approach to manipulate phase separation and demonstrate how the material properties and chemical composition of APBs independently contribute to ALT, suggesting a general framework for how chromatin condensates promote cellular functions.
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Affiliation(s)
- Huaiying Zhang
- Departments of Biology, University of Pennsylvania, Philadelphia, PA 19104.,Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Rongwei Zhao
- Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Jason Tones
- Departments of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Michel Liu
- Departments of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert L Dilley
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
| | - David M Chenoweth
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine
| | - Roger A Greenberg
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael A Lampson
- Penn Center for Genome Integrity, University of Pennsylvania, Philadelphia, PA 19104
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7
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Li Y, Ma X, Wu W, Chen Z, Meng G. PML Nuclear Body Biogenesis, Carcinogenesis, and Targeted Therapy. Trends Cancer 2020; 6:889-906. [PMID: 32527650 DOI: 10.1016/j.trecan.2020.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 01/16/2023]
Abstract
Targeted therapy has become increasingly important in cancer therapy. For example, targeting the promyelocytic leukemia PML protein in leukemia has proved to be an effective treatment. PML is the core component of super-assembled structures called PML nuclear bodies (NBs). Although this nuclear megaDalton complex was first observed in the 1960s, the mechanism of its assembly remains poorly understood. We review recent breakthroughs in the PML field ranging from a revised assembly mechanism to PML-driven genome organization and carcinogenesis. In addition, we highlight that oncogenic oligomerization might also represent a promising target in the treatment of leukemias and solid tumors.
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Affiliation(s)
- Yuwen Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaodan Ma
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenyu Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guoyu Meng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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8
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Wang M, Wang L, Qian M, Tang X, Liu Z, Lai Y, Ao Y, Huang Y, Meng Y, Shi L, Peng L, Cao X, Wang Z, Qin B, Liu B. PML2-mediated thread-like nuclear bodies mark late senescence in Hutchinson-Gilford progeria syndrome. Aging Cell 2020; 19:e13147. [PMID: 32351002 PMCID: PMC7294779 DOI: 10.1111/acel.13147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/20/2020] [Accepted: 02/23/2020] [Indexed: 01/10/2023] Open
Abstract
Progerin accumulation disrupts nuclear lamina integrity and causes nuclear structure abnormalities, leading to premature aging, that is, Hutchinson–Gilford progeria syndrome (HGPS). The roles of nuclear subcompartments, such as PML nuclear bodies (PML NBs), in HGPS pathogenesis, are unclear. Here, we show that classical dot‐like PML NBs are reorganized into thread‐like structures in HGPS patient fibroblasts and their presence is associated with late stage of senescence. By co‐immunoprecipitation analysis, we show that farnesylated Progerin interacts with human PML2, which accounts for the formation of thread‐like PML NBs. Specifically, human PML2 but not PML1 overexpression in HGPS cells promotes PML thread development and accelerates senescence. Further immunofluorescence microscopy, immuno‐TRAP, and deep sequencing data suggest that these irregular PML NBs might promote senescence by perturbing NB‐associated DNA repair and gene expression in HGPS cells. These data identify irregular structures of PML NBs in senescent HGPS cells and support that the thread‐like PML NBs might be a novel, morphological, and functional biomarker of late senescence.
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Affiliation(s)
- Ming Wang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou China
| | - Lulu Wang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou China
| | - Minxian Qian
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Xiaolong Tang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Zuojun Liu
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Yiwei Lai
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou China
| | - Ying Ao
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Yinghua Huang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou China
| | - Yuan Meng
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Lei Shi
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Linyuan Peng
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Xinyue Cao
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
| | - Zimei Wang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
- Carson International Cancer Center Shenzhen University Health Science Center Shenzhen China
| | - Baoming Qin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences Guangzhou China
| | - Baohua Liu
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SAI) National Engineering Research Center for Biotechnology (Shenzhen) Medical Research Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention Department of Biochemistry & Molecular Biology School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
- Carson International Cancer Center Shenzhen University Health Science Center Shenzhen China
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases School of Basic Medical Sciences Shenzhen University Health Science Center Shenzhen China
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9
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Lee J, Salsman J, Foster J, Dellaire G, Ridgway ND. Lipid-associated PML structures assemble nuclear lipid droplets containing CCTα and Lipin1. Life Sci Alliance 2020; 3:3/8/e202000751. [PMID: 32461215 PMCID: PMC7266991 DOI: 10.26508/lsa.202000751] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/24/2022] Open
Abstract
PML proteins assemble into noncanonical lipid-associated PML structures (LAPS) on nuclear lipid droplets, which recruit CCTα and Lipin1 for the synthesis of phosphatidylcholine and triacylglycerol. Nuclear lipid droplets (nLDs) form on the inner nuclear membrane by a mechanism involving promyelocytic leukemia (PML), the protein scaffold of PML nuclear bodies. We report that PML structures on nLDs in oleate-treated U2OS cells, referred to as lipid-associated PML structures (LAPS), differ from canonical PML nuclear bodies by the relative absence of SUMO1, SP100, and DAXX. These nLDs were also enriched in CTP:phosphocholine cytidylyltransferase α (CCTα), the phosphatidic acid phosphatase Lipin1, and DAG. Translocation of CCTα onto nLDs was mediated by its α-helical M-domain but was not correlated with its activator DAG. High-resolution imaging revealed that CCTα and LAPS occupied distinct polarized regions on nLDs. PML knockout U2OS (PML KO) cells lacking LAPS had a 40–50% reduction in nLDs with associated CCTα, and residual nLDs were almost devoid of Lipin1 and DAG. As a result, phosphatidylcholine and triacylglycerol synthesis was inhibited in PML KO cells. We conclude that in response to excess exogenous fatty acids, LAPS are required to assemble nLDs that are competent to recruit CCTα and Lipin1.
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Affiliation(s)
- Jonghwa Lee
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, Canada
| | - Jason Foster
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Graham Dellaire
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada .,Department of Pathology, Dalhousie University, Halifax, Canada
| | - Neale D Ridgway
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada .,Department of Pediatrics, Dalhousie University, Halifax, Canada
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10
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Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y. Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion. Mol Cell 2020; 78:493-505.e8. [PMID: 32353257 DOI: 10.1016/j.molcel.2020.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/06/2019] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Abstract
The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.
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Affiliation(s)
- Misuzu Kurihara
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan
| | - Kagayaki Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Center for Novel Science Initiatives (CNSI), National Institutes of Natural Sciences (NINS), Okazaki, 444-8787, Japan
| | - Chiaki Sanbo
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan
| | - Yasuyuki Ohkawa
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Takeshi Fuchigami
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Yusuke Miyanari
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan.
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11
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Attwood KM, Salsman J, Chung D, Mathavarajah S, Van Iderstine C, Dellaire G. PML isoform expression and DNA break location relative to PML nuclear bodies impacts the efficiency of homologous recombination. Biochem Cell Biol 2019; 98:314-326. [PMID: 31671275 DOI: 10.1139/bcb-2019-0115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PML NBs) are nuclear subdomains that respond to genotoxic stress by increasing in number via changes in chromatin structure. However, the role of the PML protein and PML NBs in specific mechanisms of DNA repair has not been fully characterized. Here, we have directly examined the role of PML in homologous recombination (HR) using I-SceI extrachromosomal and chromosome-based homology-directed repair (HDR) assays, and in HDR by CRISPR/Cas9-mediated gene editing. We determined that PML loss can inhibit HR in an extrachromosomal HDR assay but had less of an effect on CRISPR/Cas9-mediated chromosomal HDR. Overexpression of PML also inhibited both CRISPR HDR and I-SceI-induced HDR using a chromosomal reporter, and in an isoform-specific manner. However, the impact of PML overexpression on the chromosomal HDR reporter was dependent on the intranuclear chromosomal positioning of the reporter. Specifically, HDR at the TAP1 gene locus, which is associated with PML NBs, was reduced compared with a locus not associated with a PML NB; yet, HDR could be reduced at the non-PML NB-associated locus by PML overexpression. Thus, both loss and overexpression of PML isoforms can inhibit HDR, and proximity of a chromosomal break to a PML NB can impact HDR efficiency.
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Affiliation(s)
- Kathleen M Attwood
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | | | - Graham Dellaire
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
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12
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Lång A, Lång E, Bøe SO. PML Bodies in Mitosis. Cells 2019; 8:cells8080893. [PMID: 31416160 PMCID: PMC6721746 DOI: 10.3390/cells8080893] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies are dynamic intracellular structures that recruit and release a variety of different proteins in response to stress, virus infection, DNA damage and cell cycle progression. While PML bodies primarily are regarded as nuclear compartments, they are forced to travel to the cytoplasm each time a cell divides, due to breakdown of the nuclear membrane at entry into mitosis and subsequent nuclear exclusion of nuclear material at exit from mitosis. Here we review the biochemical and biophysical transitions that occur in PML bodies during mitosis and discuss this in light of post-mitotic nuclear import, cell fate decision and acute promyelocytic leukemia therapy.
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Affiliation(s)
- Anna Lång
- Oslo University Hospital, Department of Molecular Microbiology, Forskningsveien 1, 0373 Oslo, Norway
| | - Emma Lång
- Oslo University Hospital, Department of Molecular Microbiology, Forskningsveien 1, 0373 Oslo, Norway
| | - Stig Ove Bøe
- Oslo University Hospital, Department of Molecular Microbiology, Forskningsveien 1, 0373 Oslo, Norway.
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13
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Gao M, Lin Y, Liu X, Li Y, Zhang C, Wang Z, Wang Z, Wang Y, Guo Z. ISG20 promotes local tumor immunity and contributes to poor survival in human glioma. Oncoimmunology 2018; 8:e1534038. [PMID: 30713788 PMCID: PMC6343791 DOI: 10.1080/2162402x.2018.1534038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022] Open
Abstract
Recent evidence has confirmed that a mutation of the isocitrate dehydrogenase (IDH) gene occurs early in gliomagenesis and contributes to suppressed immunity. The present study aimed to determine the candidate genes associated with IDH mutation status that could serve as biomarkers of immune suppression for improved prognosis prediction. Clinical information and RNA-seq gene expression data were collected for 932 glioma samples from the CGGA and TCGA databases, and differentially expressed genes in both lower-grade glioma (LGG) and glioblastoma (GBM) samples were identified according to IDH mutation status. Only one gene, interferon-stimulated exonuclease gene 20 (ISG20), with reduced expression in IDH mutant tumors, demonstrated significant prognostic value. ISG20 expression level significantly increased with increasing tumor grade, and its high expression was associated with a poor clinical outcome. Moreover, increased ISG20 expression was associated with increased infiltration of monocyte-derived macrophages and neutrophils, and suppressed adaptive immune response. ISG20 expression was also positively correlated with PD-1, PD-L1, and CTLA4 expression, along with the levels of several chemokines. We conclude that ISG20 is a useful biomarker to identify IDH-mediated immune processes in glioma and may serve as a potential therapeutic target.
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Affiliation(s)
- Mengqi Gao
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Yi Lin
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Xing Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zhiliang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yulin Wang
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Zongze Guo
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
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14
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Coordinated collective migration and asymmetric cell division in confluent human keratinocytes without wounding. Nat Commun 2018; 9:3665. [PMID: 30202009 PMCID: PMC6131553 DOI: 10.1038/s41467-018-05578-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 07/16/2018] [Indexed: 12/19/2022] Open
Abstract
Epithelial sheet spreading is a fundamental cellular process that must be coordinated with cell division and differentiation to restore tissue integrity. Here we use consecutive serum deprivation and re-stimulation to reconstruct biphasic collective migration and proliferation in cultured sheets of human keratinocytes. In this system, a burst of long-range coordinated locomotion is rapidly generated throughout the cell sheet in the absence of wound edges. Migrating cohorts reach correlation lengths of several millimeters and display dependencies on epidermal growth factor receptor-mediated signaling, self-propelled polarized migration, and a G1/G0 cell cycle environment. The migration phase is temporally and spatially aligned with polarized cell divisions characterized by pre-mitotic nuclear migration to the cell front and asymmetric partitioning of nuclear promyelocytic leukemia bodies and lysosomes to opposite daughter cells. This study investigates underlying mechanisms contributing to the stark contrast between cells in a static quiescent state compared to the long-range coordinated collective migration seen in contact with blood serum. Epithelial sheet migration requires polarized and coordinated cell movement. Here, the authors demonstrate serum-activated collective migration followed by polarized asymmetric cell divisions in otherwise quiescent human keratinocyte monolayers in the absence of wound edges.
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15
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Shah FR, Bhat YA, Wani AH. Subnuclear distribution of proteins: Links with genome architecture. Nucleus 2018; 9:42-55. [PMID: 28910577 PMCID: PMC5973252 DOI: 10.1080/19491034.2017.1361578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 02/08/2023] Open
Abstract
Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both. Several evidences suggest that the distribution of proteins within the nuclear space is linked to the organization and function of genome. Here, we describe advances made in understanding the relationship between subnuclear distribution of proteins and genome architecture.
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Affiliation(s)
- Fouziya R. Shah
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Younus A. Bhat
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Ajazul H. Wani
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
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16
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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17
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Salsman J, Rapkin LM, Margam NN, Duncan R, Bazett-Jones DP, Dellaire G. Myogenic differentiation triggers PML nuclear body loss and DAXX relocalization to chromocentres. Cell Death Dis 2017; 8:e2724. [PMID: 28358373 PMCID: PMC5386546 DOI: 10.1038/cddis.2017.151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/05/2017] [Accepted: 03/07/2017] [Indexed: 12/12/2022]
Abstract
The promyelocytic leukemia protein (PML) is expressed in most normal human tissues and forms nuclear bodies (NBs) that have roles in gene regulation and cellular processes such as DNA repair, cell cycle control, and cell fate decisions. Using murine C2C12 myoblasts, we demonstrate that activation of skeletal muscle differentiation results in loss of PML and PML NBs prior to myotube fusion. Myotube formation was associated with marked chromatin reorganization and the relocalization of DAXX from PML NBs to chromocentres. MyoD expression was sufficient to cause PML NB loss, and silencing of PML induced DAXX relocalization. Fusion of C2C12 cells using the reptilian reovirus p14 fusogenic protein failed to disrupt PML NBs yet still promoted DAXX redistribution and loss; whereas ectopic expression of PML in differentiated cells only partially restored PML NB formation and DAXX localization at NBs. Finally, we determined that the C-terminal SUMO-interacting motif of DAXX is required for its colocalization with ATRX in heterochromatin domains during myotube formation. These data support a model in which activation of myogenic differentiation results in PML NB loss, chromatin reorganization and DAXX relocalization, and provides a paradigm for understanding the consequence of PML loss in other cellular contexts, such as during cancer development and progression.
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Affiliation(s)
- Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
| | - Lindsy M Rapkin
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada, M5G 1X8
| | - Nandini N Margam
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
| | - Roy Duncan
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
| | - David P Bazett-Jones
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada, M5G 1X8
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS, Canada, B3H 4R2.,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
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18
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PML nuclear bodies contribute to the basal expression of the mTOR inhibitor DDIT4. Sci Rep 2017; 7:45038. [PMID: 28332630 PMCID: PMC5362932 DOI: 10.1038/srep45038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/20/2017] [Indexed: 11/16/2022] Open
Abstract
The promyelocytic leukemia (PML) protein is an essential component of PML nuclear bodies (PML NBs) frequently lost in cancer. PML NBs coordinate chromosomal regions via modification of nuclear proteins that in turn may regulate genes in the vicinity of these bodies. However, few PML NB-associated genes have been identified. PML and PML NBs can also regulate mTOR and cell fate decisions in response to cellular stresses. We now demonstrate that PML depletion in U2OS cells or TERT-immortalized normal human diploid fibroblasts results in decreased expression of the mTOR inhibitor DDIT4 (REDD1). DNA and RNA immuno-FISH reveal that PML NBs are closely associated with actively transcribed DDIT4 loci, implicating these bodies in regulation of basal DDIT4 expression. Although PML silencing did reduce the sensitivity of U2OS cells to metabolic stress induced by metformin, PML loss did not inhibit the upregulation of DDIT4 in response to metformin, hypoxia-like (CoCl2) or genotoxic stress. Analysis of publicly available cancer data also revealed a significant correlation between PML and DDIT4 expression in several cancer types (e.g. lung, breast, prostate). Thus, these findings uncover a novel mechanism by which PML loss may contribute to mTOR activation and cancer progression via dysregulation of basal DDIT4 gene expression.
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19
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Abstract
Promyelocytic Leukemia (PML) is a nuclear protein that forms sub-nuclear structures termed nuclear bodies associated with transcriptionally active genomic regions. PML is a tumour suppressor and regulator of cell differentiation. We demonstrate that PML promotes TNFα-induced transcriptional responses by promoting NF-κB activity. TNFα-treated PML-/- cells show normal IκBα degradation and NF-κB nuclear translocation but significantly reduced NF-κB DNA binding and phosphorylation of NF-κB p65. We also demonstrate that the PML retinoic acid receptor-α (PML-RARα) oncofusion protein, which causes acute promyelocytic leukemia, inhibits TNFα induced gene expression and phosphorylation of NF-κB. This study establishes PML as an important regulator of NF-κB and demonstrates that PML-RARα dysregulates NF-κB.
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20
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Lomonte P. Herpesvirus Latency: On the Importance of Positioning Oneself. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 223:95-117. [PMID: 28528441 DOI: 10.1007/978-3-319-53168-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nucleus is composed of multiple compartments and domains, which directly or indirectly influence many cellular processes including gene expression, RNA splicing and maturation, protein post-translational modifications, and chromosome segregation. Nuclear-replicating viruses, especially herpesviruses, have co-evolved with the cell, adopting strategies to counteract and eventually hijack this hostile environment for their own benefit. This allows them to persist in the host for the entire life of an individual and to ensure their maintenance in the target species. Herpesviruses establish latency in dividing or postmitotic cells from which they can efficiently reactivate after sometimes years of a seemingly dormant state. Therefore, herpesviruses circumvent the threat of permanent silencing by reactivating their dormant genomes just enough to escape extinction, but not too much to avoid life-threatening damage to the host. In addition, herpesviruses that establish latency in dividing cells must adopt strategies to maintain their genomes in the daughter cells to avoid extinction by dilution of their genomes following multiple cell divisions. From a biochemical point of view, reactivation and maintenance of viral genomes in dividing cells occur successfully because the viral genomes interact with the nuclear architecture in a way that allows the genomes to be transmitted faithfully and to benefit from the nuclear micro-environments that allow reactivation following specific stimuli. Therefore, spatial positioning of the viral genomes within the nucleus is likely to be essential for the success of the latent infection and, beyond that, for the maintenance of herpesviruses in their respective hosts.
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Affiliation(s)
- Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Assembly, Nuclear Domains, Virus, 69008, Lyon, France.
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21
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The Role of Nuclear Antiviral Factors against Invading DNA Viruses: The Immediate Fate of Incoming Viral Genomes. Viruses 2016; 8:v8100290. [PMID: 27782081 PMCID: PMC5086622 DOI: 10.3390/v8100290] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has been suggested that host cells exert intrinsic mechanisms to control nuclear replicating DNA viruses. This cellular response involves nuclear antiviral factors targeting incoming viral genomes. Herpes simplex virus-1 (HSV-1) is the best-studied model in this context, and it was shown that upon nuclear entry HSV-1 genomes are immediately targeted by components of promyelocytic leukemia nuclear bodies (PML-NBs) and the nuclear DNA sensor IFI16 (interferon gamma inducible protein 16). Based on HSV-1 studies, together with limited examples in other viral systems, these phenomena are widely believed to be a common cellular response to incoming viral genomes, although formal evidence for each virus is lacking. Indeed, recent studies suggest that the case may be different for adenovirus infection. Here we summarize the existing experimental evidence for the roles of nuclear antiviral factors against incoming viral genomes to better understand cellular responses on a virus-by-virus basis. We emphasize that cells seem to respond differently to different incoming viral genomes and discuss possible arguments for and against a unifying cellular mechanism targeting the incoming genomes of different virus families.
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22
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Root H, Larsen A, Komosa M, Al-Azri F, Li R, Bazett-Jones DP, Stephen Meyn M. FANCD2 limits BLM-dependent telomere instability in the alternative lengthening of telomeres pathway. Hum Mol Genet 2016; 25:3255-3268. [DOI: 10.1093/hmg/ddw175] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/02/2016] [Accepted: 06/06/2016] [Indexed: 11/12/2022] Open
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23
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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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24
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Komatsu T, Nagata K, Wodrich H. An Adenovirus DNA Replication Factor, but Not Incoming Genome Complexes, Targets PML Nuclear Bodies. J Virol 2016; 90:1657-67. [PMID: 26608315 PMCID: PMC4719639 DOI: 10.1128/jvi.02545-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/19/2015] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Promyelocytic leukemia protein nuclear bodies (PML-NBs) are subnuclear domains implicated in cellular antiviral responses. Despite the antiviral activity, several nuclear replicating DNA viruses use the domains as deposition sites for the incoming viral genomes and/or as sites for viral DNA replication, suggesting that PML-NBs are functionally relevant during early viral infection to establish productive replication. Although PML-NBs and their components have also been implicated in the adenoviral life cycle, it remains unclear whether incoming adenoviral genome complexes target PML-NBs. Here we show using immunofluorescence and live-cell imaging analyses that incoming adenovirus genome complexes neither localize at nor recruit components of PML-NBs during early phases of infection. We further show that the viral DNA binding protein (DBP), an early expressed viral gene and essential DNA replication factor, independently targets PML-NBs. We show that DBP oligomerization is required to selectively recruit the PML-NB components Sp100 and USP7. Depletion experiments suggest that the absence of one PML-NB component might not affect the recruitment of other components toward DBP oligomers. Thus, our findings suggest a model in which an adenoviral DNA replication factor, but not incoming viral genome complexes, targets and modulates PML-NBs to support a conducive state for viral DNA replication and argue against a generalized concept that PML-NBs target incoming viral genomes. IMPORTANCE The immediate fate upon nuclear delivery of genomes of incoming DNA viruses is largely unclear. Early reports suggested that incoming genomes of herpesviruses are targeted and repressed by PML-NBs immediately upon nuclear import. Genome localization and/or viral DNA replication has also been observed at PML-NBs for other DNA viruses. Thus, it was suggested that PML-NBs may immediately sense and target nuclear viral genomes and hence serve as sites for deposition of incoming viral genomes and/or subsequent viral DNA replication. Here we performed a detailed analyses of the spatiotemporal distribution of incoming adenoviral genome complexes and found, in contrast to the expectation, that an adenoviral DNA replication factor, but not incoming genomes, targets PML-NBs. Thus, our findings may explain why adenoviral genomes could be observed at PML-NBs in earlier reports but argue against a generalized role for PML-NBs in targeting invading viral genomes.
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Affiliation(s)
- Tetsuro Komatsu
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
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25
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SP140L, an Evolutionarily Recent Member of the SP100 Family, Is an Autoantigen in Primary Biliary Cirrhosis. J Immunol Res 2015; 2015:526518. [PMID: 26347895 PMCID: PMC4548144 DOI: 10.1155/2015/526518] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/07/2015] [Indexed: 12/21/2022] Open
Abstract
The SP100 family members comprise a set of closely related genes on chromosome 2q37.1. The widely expressed SP100 and the leukocyte-specific proteins SP110 and SP140 have been associated with transcriptional regulation and various human diseases. Here, we have characterized the SP100 family member SP140L. The genome sequence analysis showed the formation of SP140L gene through rearrangements of the two neighboring genes, SP100 and SP140, during the evolution of higher primates. The SP140L expression is interferon-inducible with high transcript levels in B cells and other peripheral blood mononuclear cells. Subcellularly, SP140L colocalizes with SP100 and SP140 in nuclear structures that are devoid of SP110, PML, or p300 proteins. Similarly to SP100 and SP140 protein, we detected serum autoantibodies to SP140L in patients with primary biliary cirrhosis using luciferase immunoprecipitation system and immunoblotting assays. In conclusion, our results show that SP140L is phylogenetically recent member of SP100 proteins and acts as an autoantigen in primary biliary cirrhosis patients.
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26
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Chen BK, Anchel D, Gong Z, Cotton R, Li R, Sun Y, Bazett-Jones DP. Nano-dissection and sequencing of DNA at single sub-nuclear structures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:3267-74. [PMID: 24799430 DOI: 10.1002/smll.201400075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/05/2014] [Indexed: 05/03/2023]
Abstract
The relative positioning of gene loci within a mammalian nucleus is non-random and plays a role in gene regulation. Some sub-nuclear structures may represent "hubs" that bring specific genetic loci into close proximity where co-regulatory mechanisms can operate. The identification of loci in proximity to a shared sub-nuclear structure can provide insights into the function of the associated structure, and reveal relationships between the loci sharing a common association. A technique is introduced based on the nano-dissection of DNA from thin sections of cells by high-precision nano-tools operated inside a scanning electron microscope. The ability to dissect and identify gene loci occupying a shared site at a single sub-nuclear structure is demonstrated here for the first time. The technique is applied to the nano-dissection of DNA in vicinity of a single promyelocytic leukemia nuclear body (PML NB), and reveals novel loci from several chromosomes that are confirmed to associate at PML NBs with statistical significance in a cell population. Furthermore, it is demonstrated that pairs of loci from different chromosomes congregate at the same nuclear body. It is proposed that this technique is the first that allows the de novo determination of gene loci associations with single nuclear sub-structures.
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Affiliation(s)
- Brandon K Chen
- Department of Mechanical Engineering, University of Toronto, M5S 3G8
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Günther T, Schreiner S, Dobner T, Tessmer U, Grundhoff A. Influence of ND10 components on epigenetic determinants of early KSHV latency establishment. PLoS Pathog 2014; 10:e1004274. [PMID: 25033267 PMCID: PMC4102598 DOI: 10.1371/journal.ppat.1004274] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/05/2014] [Indexed: 12/15/2022] Open
Abstract
We have previously demonstrated that acquisition of intricate patterns of activating (H3K4me3, H3K9/K14ac) and repressive (H3K27me3) histone modifications is a hallmark of KSHV latency establishment. The precise molecular mechanisms that shape the latent histone modification landscape, however, remain unknown. Promyelocytic leukemia nuclear bodies (PML-NB), also called nuclear domain 10 (ND10), have emerged as mediators of innate immune responses that can limit viral gene expression via chromatin based mechanisms. Consequently, although ND10 functions thus far have been almost exclusively investigated in models of productive herpesvirus infection, it has been proposed that they also may contribute to the establishment of viral latency. Here, we report the first systematic study of the role of ND10 during KSHV latency establishment, and link alterations in the subcellular distribution of ND10 components to a temporal analysis of histone modification acquisition and host cell gene expression during the early infection phase. Our study demonstrates that KSHV infection results in a transient interferon response that leads to induction of the ND10 components PML and Sp100, but that repression by ND10 bodies is unlikely to contribute to KSHV latency establishment. Instead, we uncover an unexpected role for soluble Sp100 protein, which is efficiently and permanently relocalized from nucleoplasmic and chromatin-associated fractions into the insoluble matrix. We show that LANA expression is sufficient to induce Sp100 relocalization, likely via mediating SUMOylation of Sp100. Furthermore, we demonstrate that depletion of soluble Sp100 occurs precisely when repressive H3K27me3 marks first accumulate on viral genomes, and that knock-down of Sp100 (but not PML or Daxx) facilitates H3K27me3 acquisition. Collectively, our data support a model in which non-ND10 resident Sp100 acts as a negative regulator of polycomb repressive complex-2 (PRC2) recruitment, and suggest that KSHV may actively escape ND10 silencing mechanisms to promote establishment of latent chromatin.
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Affiliation(s)
- Thomas Günther
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabrina Schreiner
- Research Unit Viral Transformation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Thomas Dobner
- Research Unit Viral Transformation, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Uwe Tessmer
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Research Group Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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Rieder D, Ploner C, Krogsdam AM, Stocker G, Fischer M, Scheideler M, Dani C, Amri EZ, Müller WG, McNally JG, Trajanoski Z. Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories. Cell Mol Life Sci 2013; 71:1741-59. [PMID: 24026398 DOI: 10.1007/s00018-013-1465-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/02/2013] [Accepted: 08/28/2013] [Indexed: 11/26/2022]
Abstract
Chromosomally separated, co-expressed genes can be in spatial proximity, but there is still debate about how this nuclear organization is achieved. Proposed mechanisms include global genome organization, preferential positioning of chromosome territories, or gene-gene sharing of various nuclear bodies. To investigate this question, we selected a set of genes that were co-expressed upon differentiation of human multipotent stem cells. We applied a novel multi-dimensional analysis procedure which revealed that prior to gene expression, the relative position of these genes was conserved in nuclei. Upon stem cell differentiation and concomitant gene expression, we found that co-expressed genes were closer together. In addition, we found that genes in the same 1-μm-diameter neighborhood associated with either the same splicing speckle or to a lesser extent with the same transcription factory. Dispersal of speckles by overexpression of the serine-arginine (SR) protein kinase cdc2-like kinase Clk2 led to a significant drop in the number of genes in shared neighborhoods. We demonstrate quantitatively that the frequencies of speckle and factory sharing can be explained by assuming stochastic selection of a nuclear body within a restricted sub-volume defined by the original global gene positioning present prior to gene expression. We conclude that the spatial organization of these genes is a two-step process in which transcription-induced association with nuclear bodies enhances and refines a pre-existing global organization.
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Affiliation(s)
- Dietmar Rieder
- Division of Bioinformatics, Biocenter, Innsbruck Medical University, Innrain 80, 6020, Innsbruck, Austria
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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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Razin SV, Gavrilov AA, Ioudinkova ES, Iarovaia OV. Communication of genome regulatory elements in a folded chromosome. FEBS Lett 2013; 587:1840-7. [PMID: 23651551 DOI: 10.1016/j.febslet.2013.04.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
The most popular model of gene activation by remote enhancers postulates that the enhancers interact directly with target promoters via the looping of intervening DNA fragments. This interaction is thought to be necessary for the stabilization of the Pol II pre-initiation complex and/or for the transfer of transcription factors and Pol II, which are initially accumulated at the enhancer, to the promoter. The direct interaction of enhancer(s) and promoter(s) is only possible when these elements are located in close proximity within the nuclear space. Here, we discuss the molecular mechanisms for maintaining the close proximity of the remote regulatory elements of the eukaryotic genome. The models of an active chromatin hub (ACH) and an active nuclear compartment are considered, focusing on the role of chromatin folding in juxtaposing remote DNA sequences. The interconnection between the functionally dependent architecture of the interphase chromosome and nuclear compartmentalization is also discussed.
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Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia.
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Foltánková V, Matula P, Sorokin D, Kozubek S, Bártová E. Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body colocalization in DNA lesions. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:360-369. [PMID: 23410959 DOI: 10.1017/s1431927612014353] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We used hybrid detectors (HyDs) to monitor the trajectories and interactions of promyelocytic leukemia (GFP-PML) nuclear bodies (NBs) and mCherry-53BP1-positive DNA lesions. 53BP1 protein accumulates in NBs that occur spontaneously in the genome or in γ-irradiation-induced foci. When we induced local DNA damage by ultraviolet irradiation, we also observed accumulation of 53BP1 proteins into discrete bodies, instead of the expected dispersed pattern. In comparison with photomultiplier tubes, which are used for standard analysis by confocal laser scanning microscopy, HyDs significantly eliminated photobleaching of GFP and mCherry fluorochromes during image acquisition. The low laser intensities used for HyD-based confocal analysis enabled us to observe NBs for the longer time periods, necessary for studies of the trajectories and interactions of PML and 53BP1 NBs. To further characterize protein interactions, we used resonance scanning and a novel bioinformatics approach to register and analyze the movements of individual PML and 53BP1 NBs. The combination of improved HyD-based confocal microscopy with a tailored bioinformatics approach enabled us to reveal damage-specific properties of PML and 53BP1 NBs.
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Affiliation(s)
- Veronika Foltánková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65, Brno, Czech Republic
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Chang FTM, McGhie JD, Chan FL, Tang MC, Anderson MA, Mann JR, Andy Choo KH, Wong LH. PML bodies provide an important platform for the maintenance of telomeric chromatin integrity in embryonic stem cells. Nucleic Acids Res 2013; 41:4447-58. [PMID: 23444137 PMCID: PMC3632112 DOI: 10.1093/nar/gkt114] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have previously shown that α-thalassemia mental retardation X-linked (ATRX) and histone H3.3 are key regulators of telomeric chromatin in mouse embryonic stem cells. The function of ATRX and H3.3 in the maintenance of telomere chromatin integrity is further demonstrated by recent studies that show the strong association of ATRX/H3.3 mutations with alternative lengthening of telomeres in telomerase-negative human cancer cells. Here, we demonstrate that ATRX and H3.3 co-localize with the telomeric DNA and associated proteins within the promyelocytic leukemia (PML) bodies in mouse ES cells. The assembly of these telomere-associated PML bodies is most prominent at S phase. RNA interference (RNAi)-mediated knockdown of PML expression induces the disassembly of these nuclear bodies and a telomere dysfunction phenotype in mouse ES cells. Loss of function of PML bodies in mouse ES cells also disrupts binding of ATRX/H3.3 and proper establishment of histone methylation pattern at the telomere. Our study demonstrates that PML bodies act as epigenetic regulators by serving as platforms for the assembly of the telomeric chromatin to ensure a faithful inheritance of epigenetic information at the telomere.
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Affiliation(s)
- Fiona T M Chang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Mostafa HH, Thompson TW, Davido DJ. N-terminal phosphorylation sites of herpes simplex virus 1 ICP0 differentially regulate its activities and enhance viral replication. J Virol 2013; 87:2109-19. [PMID: 23221554 PMCID: PMC3571471 DOI: 10.1128/jvi.02588-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 11/27/2012] [Indexed: 02/06/2023] Open
Abstract
The herpes simplex virus 1 (HSV-1) infected cell protein 0 (ICP0) is an immediate-early phosphoprotein that transactivates viral gene expression. Evidence suggests that phosphorylation regulates the functions of ICP0, and three regions (termed regions I, II, and III) in the protein are known to be phosphorylated. Mutation of the putative phosphorylation sites within region I, termed Phos 1, which lies in the N-terminal portion of ICP0, impairs the E3 ubiquitin (Ub) ligase and ND10-disrupting activities of ICP0 in cell culture and diminishes viral replication. To identify the specific phosphorylation site(s) or residues responsible for the phenotypes observed with Phos 1, individual residues within region I were mutated to alanine (S224A, T226A, T231A, and T232A) and one double mutant S224A/T226A was constructed. Tissue culture studies demonstrated that the S224A, S224A/T226A, T231A, and T232A mutants were unable to dissociate the cellular protein PML from ND10 and that the S224/T226A mutant was defective in its ability to dissociate the cellular protein Sp100 from ND10. Additionally, the transactivation activity of ICP0 was impaired in the S224A and S224A/T226A mutants. The S224A and S224A/T226A mutant forms were more stable than wild-type ICP0, suggesting that their ability to autoubiquitinate was limited. Moreover, one ICP0 ubiquitination target, USP-7, was also more stable after infection with these two mutants. Lastly, the replication of the S224A and S224A/T226A mutant viruses was reduced in cell culture and in vivo. Overall, our data suggest that specific phosphorylation sites within region I differentially regulate the activities of ICP0, which are required for efficient viral replication.
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Affiliation(s)
- Heba H Mostafa
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
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Ulbricht T, Alzrigat M, Horch A, Reuter N, von Mikecz A, Steimle V, Schmitt E, Krämer OH, Stamminger T, Hemmerich P. PML promotes MHC class II gene expression by stabilizing the class II transactivator. ACTA ACUST UNITED AC 2012; 199:49-63. [PMID: 23007646 PMCID: PMC3461510 DOI: 10.1083/jcb.201112015] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Promyelocytic leukemia (PML) nuclear bodies selectively associate with transcriptionally active genomic regions, including the gene-rich major histocompatibility (MHC) locus. In this paper, we have explored potential links between PML and interferon (IFN)-γ-induced MHC class II expression. IFN-γ induced a substantial increase in the spatial proximity between PML bodies and the MHC class II gene cluster in different human cell types. Knockdown experiments show that PML is required for efficient IFN-γ-induced MHC II gene transcription through regulation of the class II transactivator (CIITA). PML mediates this function through protection of CIITA from proteasomal degradation. We also show that PML isoform II specifically forms a stable complex with CIITA at PML bodies. These observations establish PML as a coregulator of IFN-γ-induced MHC class II expression.
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Affiliation(s)
- Tobias Ulbricht
- Leibniz Institute for Age Research, Fritz-Lipmann Institute, 07745 Jena, Germany
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HSV-1 genome subnuclear positioning and associations with host-cell PML-NBs and centromeres regulate LAT locus transcription during latency in neurons. PLoS Pathog 2012; 8:e1002852. [PMID: 22912575 PMCID: PMC3415458 DOI: 10.1371/journal.ppat.1002852] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/26/2012] [Indexed: 02/04/2023] Open
Abstract
Major human pathologies are caused by nuclear replicative viruses establishing life-long latent infection in their host. During latency the genomes of these viruses are intimately interacting with the cell nucleus environment. A hallmark of herpes simplex virus type 1 (HSV-1) latency establishment is the shutdown of lytic genes expression and the concomitant induction of the latency associated (LAT) transcripts. Although the setting up and the maintenance of the latent genetic program is most likely dependent on a subtle interplay between viral and nuclear factors, this remains uninvestigated. Combining the use of in situ fluorescent-based approaches and high-resolution microscopic analysis, we show that HSV-1 genomes adopt specific nuclear patterns in sensory neurons of latently infected mice (28 days post-inoculation, d.p.i.). Latent HSV-1 genomes display two major patterns, called “Single” and “Multiple”, which associate with centromeres, and with promyelocytic leukemia nuclear bodies (PML-NBs) as viral DNA-containing PML-NBs (DCP-NBs). 3D-image reconstruction of DCP-NBs shows that PML forms a shell around viral genomes and associated Daxx and ATRX, two PML partners within PML-NBs. During latency establishment (6 d.p.i.), infected mouse TGs display, at the level of the whole TG and in individual cells, a substantial increase of PML amount consistent with the interferon-mediated antiviral role of PML. “Single” and “Multiple” patterns are reminiscent of low and high-viral genome copy-containing neurons. We show that LAT expression is significantly favored within the “Multiple” pattern, which underlines a heterogeneity of LAT expression dependent on the viral genome copy number, pattern acquisition, and association with nuclear domains. Infection of PML-knockout mice demonstrates that PML/PML-NBs are involved in virus nuclear pattern acquisition, and negatively regulate the expression of the LAT. This study demonstrates that nuclear domains including PML-NBs and centromeres are functionally involved in the control of HSV-1 latency, and represent a key level of host/virus interaction. After an initial lytic infection, many viruses establish a lifelong latent infection that hides them from the host immune system activity until reactivation. To understand the resurgence of the associated diseases, it is indispensable to acquire a better knowledge of the different mechanisms involved in the antiviral defense. During latency, viral genomes of nuclear-replicative viruses, such as herpes simplex virus type 1 (HSV-1), are stored in the nucleus of host cells in a non-integrated form. Latency establishment is associated with a drastic change in HSV-1 gene expression program that is maintained until reactivation occurs. The last two decades of research has revealed that the functional organization of the cell nucleus, so-called nuclear architecture, is a major factor of regulation of cellular genes expression. Nonetheless, the role of nuclear architecture on HSV-1 gene expression has been widely overlooked. Here we describe that the genome of HSV-1 selectively interacts with two major nuclear structures, the promyelocytic nuclear bodies (PMLNBs or ND10) and the centromeres. We provide evidence supporting that these nuclear domains directly influence the behavior of latent viral genomes and their transcriptional activity. Overall, this study demonstrates that nuclear architecture is a major parameter driving the highly complex HSV-1 latency process.
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YB-1 functions as a porter to lead influenza virus ribonucleoprotein complexes to microtubules. J Virol 2012; 86:11086-95. [PMID: 22855482 DOI: 10.1128/jvi.00453-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
De novo-synthesized RNAs are under the regulation of multiple posttranscriptional processes by a variety of RNA-binding proteins. The influenza virus genome consists of single-stranded RNAs and exists as viral ribonucleoprotein (vRNP) complexes. After the replication of vRNP in the nucleus, it is exported to the cytoplasm and then reaches the budding site beneath the cell surface in a process mediated by Rab11a-positive recycling endosomes along microtubules. However, the regulatory mechanisms of the postreplicational processes of vRNP are largely unknown. Here we identified, as a novel vRNP-interacting protein, Y-box-binding protein 1 (YB-1), a cellular protein that is involved in regulation of cellular transcription and translation. YB-1 translocated to the nucleus from the cytoplasm and accumulated in PML nuclear bodies in response to influenza virus infection. vRNP assembled into the exporting complexes with YB-1 at PML nuclear bodies. After nuclear export, using YB-1 knockdown cells and in vitro reconstituted systems, YB-1 was shown to be required for the interaction of vRNP exported from the nucleus with microtubules around the microtubule-organizing center (MTOC), where Rab11a-positive recycling endosomes were located. Further, we also found that YB-1 overexpression stimulates the production of progeny virions in an Rab11a-dependent manner. Taking these findings together, we propose that YB-1 is a porter that leads vRNP to microtubules from the nucleus and puts it into the vesicular trafficking system.
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Stixová L, Matula P, Kozubek S, Gombitová A, Cmarko D, Raška I, Bártová E. Trajectories and nuclear arrangement of PML bodies are influenced by A-type lamin deficiency. Biol Cell 2012; 104:418-32. [PMID: 22443097 DOI: 10.1111/boc.201100053] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 03/16/2012] [Indexed: 01/08/2023]
Abstract
BACKGROUND INFORMATION Promyelocytic leukaemia (PML) bodies are specific nuclear structures with functional significance for acute promyelocytic leukaemia. In this study, we analysed the trajectories of PML bodies using single-particle tracking. RESULTS We observed that the recovery of PML protein after photobleaching was ATP dependent in both wild-type (wt) and A-type lamin-deficient cells. The movement of PML bodies was faster and the nuclear area occupied by particular PML bodies was larger in A-type lamin-deficient fibroblasts compared with their wt counterparts. Moreover, dysfunction of the LMNA gene increased the frequency of mutual interactions between individual PML bodies and influenced the morphology of these domains at the ultrastructural level. As a consequence of A-type lamin deficiency, PML protein accumulated in nuclear blebs and frequently appeared at the nuclear periphery. CONCLUSIONS We suggest that the physiological function of lamin A proteins is important for events that occur in the compartment of PML bodies. This observation was confirmed in other experimental models characterised by lamin changes, including apoptosis or the differentiation of mouse embryonic stem cells.
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Affiliation(s)
- Lenka Stixová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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TRIM involvement in transcriptional regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 770:59-76. [PMID: 23631000 DOI: 10.1007/978-1-4614-5398-7_5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Members of the tripartite motif (TRIM) protein family are found in all multicellular eukaryotes and function in a wide range of cellular processes such as cell cycle regulation, differentiation, development, oncogenesis and viral response. Over the past few years, several TRIM proteins have been reported to control gene expression through regulation of the transcriptional activity of numerous sequence-specific transcription factors. These proteins include the transcriptional intermediary factor 1 (TIF1) regulators, the promyelocytic leukemia tumor suppressor PML and the RET finger protein (RFP). In this chapter, we will consider the molecular interactions made by these TRIM proteins and will attempt to clarify some of the molecular mechanisms underlying their regulatory effect on transcription.
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Georges A, Benayoun BA, Marongiu M, Dipietromaria A, L'Hôte D, Todeschini AL, Auer J, Crisponi L, Veitia RA. SUMOylation of the Forkhead transcription factor FOXL2 promotes its stabilization/activation through transient recruitment to PML bodies. PLoS One 2011; 6:e25463. [PMID: 22022399 PMCID: PMC3192040 DOI: 10.1371/journal.pone.0025463] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 09/05/2011] [Indexed: 01/28/2023] Open
Abstract
Background FOXL2 is a transcription factor essential for ovarian development and maintenance. It is mutated in the genetic condition called Blepharophimosis Ptosis Epicantus inversus Syndrome (BPES) and in cases of isolated premature ovarian failure. We and others have previously shown that FOXL2 undergoes several post-translational modifications. Methods and Principal Findings Here, using cells in culture, we show that interference with FOXL2 SUMOylation leads to a robust inhibition of its transactivation ability, which correlates with a decreased stability. Interestingly, FOXL2 SUMOylation promotes its transient recruitment to subnuclear structures that we demonstrate to be PML (Promyelocytic Leukemia) Nuclear Bodies. Since PML bodies are known to be sites where post-translational modifications of nuclear factors take place, we used tandem mass spectrometry to identify new post-translational modifications of FOXL2. Specifically, we detected four phosphorylated, one sulfated and three acetylated sites. Conclusions By analogy with other transcription factors, we propose that PML Nuclear Bodies might transiently recruit FOXL2 to the vicinity of locally concentrated enzymes that could be involved in the post-translational maturation of FOXL2. FOXL2 acetylation, sulfation, phosphorylation as well as other modifications yet to be discovered might alter the transactivation capacity of FOXL2 and/or its stability, thus modulating its global intracellular activity.
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Affiliation(s)
- Adrien Georges
- Programme de Pathologie Moléculaire et Cellulaire, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
- Université Paris-Diderot/Paris VII, Paris, France
- Ecole Normale Supérieure de Paris, Paris, France
| | - Bérénice A. Benayoun
- Programme de Pathologie Moléculaire et Cellulaire, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
- Université Paris-Diderot/Paris VII, Paris, France
| | - Mara Marongiu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Aurélie Dipietromaria
- Programme de Pathologie Moléculaire et Cellulaire, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
- Université Paris-Diderot/Paris VII, Paris, France
- Université Paris-Sud/Paris XI, Orsay, France
| | - David L'Hôte
- Programme de Pathologie Moléculaire et Cellulaire, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
- Université Paris-Diderot/Paris VII, Paris, France
| | - Anne-Laure Todeschini
- Programme de Pathologie Moléculaire et Cellulaire, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
- Université Paris-Diderot/Paris VII, Paris, France
| | - Jana Auer
- Faculté de Médecine Cochin-Port-Royal, Université Paris Descartes/Paris V, Paris, France
| | - Laura Crisponi
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Reiner A. Veitia
- Programme de Pathologie Moléculaire et Cellulaire, Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
- Université Paris-Diderot/Paris VII, Paris, France
- * E-mail:
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41
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PML contributes to p53-independent p21 up-regulation in gamma-irradiation induced DNA damage responses. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4566-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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42
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Martínez-Guinó L, Ballester M, Segalés J, Kekarainen T. Expression profile and subcellular localization of Torque teno sus virus proteins. J Gen Virol 2011; 92:2446-2457. [PMID: 21715596 DOI: 10.1099/vir.0.033134-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In the present study, the expression, generation and subcellular localization of Torque teno sus virus (TTSuV) proteins were characterized into two genetically distinct TTSuV species (TTSuV1 and TTSuV2). Following transfection of three TTSuV1 and TTSuV2 full-length ORF (ORF1, ORF2 and ORF3) expression constructs into porcine kidney cells, alternative splice variants encoding new TTSuV protein isoforms were identified for the first time. Proteins encoded from ORF1 and ORF3 were localized in the nucleoli of porcine kidney cells and that of ORF2 in the cytoplasm and nucleus excluding the nucleoli. The subcellular localization of the different protein isoforms was not only similar between distinct TTSuV species but also to the ones described in human Torque teno virus (TTV). Results of the present in vitro study were not based on full-length viral clones but suggested that alternative splicing strategy to generate TTSuV protein isoforms probably occurs in vivo. Obtained data provide new information on molecular biology of TTSuV and anelloviruses, which until now has been solely based on results obtained from human TTV.
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Affiliation(s)
- Laura Martínez-Guinó
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria Ballester
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.,Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Tuija Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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43
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Herpes simplex virus immediate-early protein ICP0 is targeted by SIAH-1 for proteasomal degradation. J Virol 2011; 85:7644-57. [PMID: 21632771 DOI: 10.1128/jvi.02207-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Herpes simplex virus (HSV) immediate-early protein ICP0 is a transcriptional activator with E3 ubiquitin ligase activity that induces the degradation of ND10 proteins, including the promyelocytic leukemia protein (PML) and Sp100. Moreover, ICP0 has a role in the derepression of viral genomes and in the modulation of the host interferon response to virus infection. Here, we report that ICP0 interacts with SIAH-1, a cellular E3 ubiquitin ligase that is involved in multiple cellular pathways and is itself capable of mediating PML degradation. This novel virus-host interaction profoundly stabilized SIAH-1 and recruited this cellular E3 ligase into ICP0-containing nuclear bodies. Moreover, SIAH-1 mediated the polyubiquitination of HSV ICP0 in vitro and in vivo. After infection of SIAH-1 knockdown cells with HSV, higher levels of ICP0 were produced, ICP0 was less ubiquitinated, and the half-life of this multifunctional viral regulatory protein was increased. These results indicate an inhibitory role of SIAH-1 during lytic infection by targeting ICP0 for proteasomal degradation.
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44
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Sides MD, Block GJ, Shan B, Esteves KC, Lin Z, Flemington EK, Lasky JA. Arsenic mediated disruption of promyelocytic leukemia protein nuclear bodies induces ganciclovir susceptibility in Epstein-Barr positive epithelial cells. Virology 2011; 416:86-97. [PMID: 21605886 DOI: 10.1016/j.virol.2011.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 02/04/2011] [Accepted: 04/18/2011] [Indexed: 02/04/2023]
Abstract
Promyelocytic leukemia protein nuclear bodies (PML NBs) have been implicated in host immune response to viral infection. PML NBs are targeted for degradation during reactivation of herpes viruses, suggesting that disruption of PML NB function supports this aspect of the viral life cycle. The Epstein-Barr virus (EBV) Latent Membrane Protein 1 (LMP1) has been shown to suppress EBV reactivation. Our finding that LMP1 induces PML NB immunofluorescence intensity led to the hypothesis that LMP1 may modulate PML NBs as a means of maintaining EBV latency. Increased PML protein and morphometric changes in PML NBs were observed in EBV infected alveolar epithelial cells and nasopharyngeal carcinoma cells. Treatment with low dose arsenic trioxide disrupted PML NBs, induced expression of EBV lytic proteins, and conferred ganciclovir susceptibility. This study introduces an effective modality to induce susceptibility to ganciclovir in epithelial cells with implications for the treatment of EBV associated pathologies.
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Affiliation(s)
- Mark D Sides
- Department of Medicine, Section of Pulmonary Disease and Critical Care, Tulane University School of Medicine, New Orleans, LA, USA
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45
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Knoblach T, Grandel B, Seiler J, Nevels M, Paulus C. Human cytomegalovirus IE1 protein elicits a type II interferon-like host cell response that depends on activated STAT1 but not interferon-γ. PLoS Pathog 2011; 7:e1002016. [PMID: 21533215 PMCID: PMC3077363 DOI: 10.1371/journal.ppat.1002016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 02/02/2011] [Indexed: 12/12/2022] Open
Abstract
Human cytomegalovirus (hCMV) is a highly prevalent pathogen that, upon primary infection, establishes life-long persistence in all infected individuals. Acute hCMV infections cause a variety of diseases in humans with developmental or acquired immune deficits. In addition, persistent hCMV infection may contribute to various chronic disease conditions even in immunologically normal people. The pathogenesis of hCMV disease has been frequently linked to inflammatory host immune responses triggered by virus-infected cells. Moreover, hCMV infection activates numerous host genes many of which encode pro-inflammatory proteins. However, little is known about the relative contributions of individual viral gene products to these changes in cellular transcription. We systematically analyzed the effects of the hCMV 72-kDa immediate-early 1 (IE1) protein, a major transcriptional activator and antagonist of type I interferon (IFN) signaling, on the human transcriptome. Following expression under conditions closely mimicking the situation during productive infection, IE1 elicits a global type II IFN-like host cell response. This response is dominated by the selective up-regulation of immune stimulatory genes normally controlled by IFN-γ and includes the synthesis and secretion of pro-inflammatory chemokines. IE1-mediated induction of IFN-stimulated genes strictly depends on tyrosine-phosphorylated signal transducer and activator of transcription 1 (STAT1) and correlates with the nuclear accumulation and sequence-specific binding of STAT1 to IFN-γ-responsive promoters. However, neither synthesis nor secretion of IFN-γ or other IFNs seems to be required for the IE1-dependent effects on cellular gene expression. Our results demonstrate that a single hCMV protein can trigger a pro-inflammatory host transcriptional response via an unexpected STAT1-dependent but IFN-independent mechanism and identify IE1 as a candidate determinant of hCMV pathogenicity.
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Affiliation(s)
- Theresa Knoblach
- Institute for Medical Microbiology and Hygiene, University of Regensburg,
Regensburg, Germany
| | - Benedikt Grandel
- Institute for Medical Microbiology and Hygiene, University of Regensburg,
Regensburg, Germany
| | - Jana Seiler
- Institute for Medical Microbiology and Hygiene, University of Regensburg,
Regensburg, Germany
| | - Michael Nevels
- Institute for Medical Microbiology and Hygiene, University of Regensburg,
Regensburg, Germany
| | - Christina Paulus
- Institute for Medical Microbiology and Hygiene, University of Regensburg,
Regensburg, Germany
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46
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Khalfin-Rabinovich Y, Weinstein A, Levi BZ. PML is a key component for the differentiation of myeloid progenitor cells to macrophages. Int Immunol 2011; 23:287-96. [PMID: 21427174 DOI: 10.1093/intimm/dxr004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
IFN regulatory factor-8 (IRF-8, previously known as ICSBP) is a key transcription factor driving the differentiation of granulocyte\monocyte progenitor (GMP) cells toward monocyte\macrophage lineage. The promyelocytic leukemia (PML) gene is an immediate target gene regulated by IRF-8 in response to IFN-γ activation. PML is a multifunctional protein that has many isoforms serving as the scaffold components for nuclear bodies (NBs) engaged in numerous proteins interactions. The role of PML in the retinoic acid pathway that drives GMPs to granulopoiesis is documented in the literature. Here, we show that PML is also involved in monopoiesis by mediating some of the IRF-8 activities during the differentiation of murine-derived bone marrow macrophages (BMMs). PML silencing resulted in altered expression level of key transcription factors essential for monopoiesis that was accompanied by silencing of typical myeloid-specific genes. Interestingly, this altered expression resembled that of the GMPs and that of BMMs derived from IRF-8(-/-) mice altogether supporting the role of PML in monopoiesis. Further, PML silencing led to reduced colony-forming capacity of bone marrow cells highlighting the dual function of PML in myelopoiesis. Last, PML overexpression only partially rescued the phenotype of IRF-8(-/-) BMMs. Together, our data show that PML is an important factor for monopoiesis and not solely for granulopoiesis. This suggests that PML-NBs respond to an incoming signal that affects the fate of GMP driving cell differentiation to granulocytes or monocytes.
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Affiliation(s)
- Yana Khalfin-Rabinovich
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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47
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Shishido-Hara Y. Progressive multifocal leukoencephalopathy and promyelocytic leukemia nuclear bodies: a review of clinical, neuropathological, and virological aspects of JC virus-induced demyelinating disease. Acta Neuropathol 2010; 120:403-17. [PMID: 20464404 PMCID: PMC2910879 DOI: 10.1007/s00401-010-0694-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/11/2010] [Accepted: 05/02/2010] [Indexed: 12/01/2022]
Abstract
Progressive multifocal leukoencephalopathy is a fatal viral-induced demyelinating disease that was once rare but has become more prevalent today. Over the past decades, much has been learned about the disease from molecular study of the etiological agent of the disease, JC virus. Recently, promyelocytic leukemia nuclear bodies (PML-NBs), punctuate structures for important nuclear functions in eukaryotic cells, were identified as an intranuclear target of JC virus infection. Neuropathologically, JC virus-infected glial cells display diffuse amphophilic viral inclusions by hematoxylin–eosin staining (full inclusions), a diagnostic hallmark of this disease. Recent results using immunohistochemistry, however, revealed the presence of punctate viral inclusions preferentially located along the inner nuclear periphery (dot-shaped inclusions). Dot-shaped inclusions reflect the accumulation of viral progeny at PML-NBs, which may be disrupted after viral replication. Structural changes to PML-NBs have been reported for a variety of human diseases, including cancers and neurodegenerative disorders. Thus, PML-NBs may provide clues to the further pathogenesis of JC virus-induced demyelinating disease. Here, we review what we have learned since the disease entity establishment, including a look at recent progress in understanding the relationship between JC virus, etiology and PML-NBs.
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Affiliation(s)
- Yukiko Shishido-Hara
- Department of Pathology, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611, Japan.
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48
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Adenoviral oncoprotein E1B55K mediates colocalization of SSBP2 and PML in response to stress. J Mol Signal 2010; 5:6. [PMID: 20540776 PMCID: PMC2896343 DOI: 10.1186/1750-2187-5-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 06/11/2010] [Indexed: 12/19/2022] Open
Abstract
Transient expression of adenoviral oncoprotein E1B55K in normal cells induces aggresome formation and sequestration of critical host proteins in aggresomes. Our previous studies reported that Sequence Specific Binding Protein 2 (SSBP2), a candidate tumor suppressor is recruited to aggresomes in adenovirally transformed human embryonal kidney 293 (HEK293) cells. To understand the extent and significance of the E1B55K-SSBP2 interactions in these cells, we have examined SSBP2 localization under conditions of stress in HEK293 cells. SSBP2 localizes to PML- Nuclear Bodies (PML-NBs) in response to inhibition of nuclear export, treatment with etoposide, hydroxyurea or gamma irradiation only in HEK293 cells. Furthermore, the PML-NBs grow in size and number in response to radiation over a 24 hour period in HEK293 cells analogous to previous findings for other cell types. Nonetheless, we conclude that E1B55K subverts SSBP2 function in HEK293 cells. These findings demonstrate the limitations in using HEK293 cells to study DNA damage response and other cellular processes since SSBP2 and similar regulatory proteins are aberrantly localized due to constitutive E1B55K expression.
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49
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Abstract
PML nuclear bodies are matrix-associated domains that recruit an astonishing variety of seemingly unrelated proteins. Since their discovery in the early 1960s, PML bodies have fascinated cell biologists because of their beauty and their tight association with cellular disorders. The identification of PML, a gene involved in an oncogenic chromosomal translocation, as the key organizer of these domains drew instant interest onto them. The multiple levels of PML body regulation by a specific posttranslational modification, sumoylation, have raised several unsolved issues. Functionally, PML bodies may sequester, modify or degrade partner proteins, but in many ways, PML bodies still constitute an enigma.
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Affiliation(s)
- Valérie Lallemand-Breitenbach
- INSERM/CNRS/Université Paris Diderot/Institut Universitaire Hématologie U944/ UMR7212, Laboratoire associé de la Ligue Nationale contre le Cancer, Hôpital St. Louis, 1, Av. C. Vellefaux 75475 Paris Cedex 10, France
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50
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Mohamad N, Bodén M. The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. BMC SYSTEMS BIOLOGY 2010; 4:44. [PMID: 20388198 PMCID: PMC2859750 DOI: 10.1186/1752-0509-4-44] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 04/13/2010] [Indexed: 12/21/2022]
Abstract
Background Cajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement. Results By collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases. Conclusions The large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to be identified.
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Affiliation(s)
- Nurul Mohamad
- Institute for Molecular Bioscience, The University of Queensland QLD 4072, Australia
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