1
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Mousa R, Shkolnik D, Alalouf Y, Brik A. Chemical approaches to explore ubiquitin-like proteins. RSC Chem Biol 2025; 6:492-509. [PMID: 39950163 PMCID: PMC11817102 DOI: 10.1039/d4cb00220b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Accepted: 01/21/2025] [Indexed: 02/16/2025] Open
Abstract
Chemical protein synthesis has emerged as a powerful approach for producing ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in both their free and conjugated forms, particularly when recombinant or enzymatic strategies are challenging. By providing precise control over the assembly of Ub and Ubls, chemical synthesis enables the generation of complex constructs with site-specific modifications that facilitate detailed functional and structural studies. Ub and Ubls are central regulators of protein homeostasis, regulating a wide range of cellular processes such as cell cycle progression, transcription, DNA repair, and apoptosis. Ubls share an evolutionary link with Ub, resembling its structure and following a parallel conjugation pathway that results in a covalent isopeptide bond with their cellular substrates. Despite their structural similarities and sequence homology, Ub and Ubls exhibit distinct functional differences. Understanding Ubl biology is essential for unraveling how cells maintain their regulatory networks and how disruptions in these pathways contribute to various diseases. In this review, we highlight the chemical methodologies and strategies available for studying Ubls and advancing our comprehensive understanding of the Ubl system in health and disease.
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Affiliation(s)
- Reem Mousa
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Dana Shkolnik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Yam Alalouf
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa 3200008 Israel
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2
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Bergoug M, Mosrin C, Serrano A, Godin F, Doudeau M, Dundović I, Goffinont S, Normand T, Suskiewicz MJ, Vallée B, Bénédetti H. An Atypical Mechanism of SUMOylation of Neurofibromin SecPH Domain Provides New Insights into SUMOylation Site Selection. J Mol Biol 2024; 436:168768. [PMID: 39216515 DOI: 10.1016/j.jmb.2024.168768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 08/08/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Neurofibromin (Nf1) is a giant multidomain protein encoded by the tumour-suppressor gene NF1. NF1 is mutated in a common genetic disease, neurofibromatosis type I (NF1), and in various cancers. The protein has a Ras-GAP (GTPase activating protein) activity but is also connected to diverse signalling pathways through its SecPH domain, which interacts with lipids and different protein partners. We previously showed that Nf1 partially colocalized with the ProMyelocytic Leukemia (PML) protein in PML nuclear bodies, hotspots of SUMOylation, thereby suggesting the potential SUMOylation of Nf1. Here, we demonstrate that the full-length isoform 2 and a SecPH fragment of Nf1 are substrates of the SUMO pathway and identify a well-defined SUMOylation profile of SecPH with two main modified lysines. One of these sites, K1731, is highly conserved and surface-exposed. Despite the presence of an inverted SUMO consensus motif surrounding K1731, and a potential SUMO-interacting motif (SIM) within SecPH, we show that neither of these elements is necessary for K1731 SUMOylation, which is also independent of Ubc9 SUMOylation on K14. A 3D model of an interaction between SecPH and Ubc9 centred on K1731, combined with site-directed mutagenesis, identifies specific structural elements of SecPH required for K1731 SUMOylation, some of which are affected in reported NF1 pathogenic variants. This work provides a new example of SUMOylation dependent on the tertiary rather than primary protein structure surrounding the modified site, expanding our knowledge of mechanisms governing SUMOylation site selection.
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Affiliation(s)
- Mohammed Bergoug
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Christine Mosrin
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Amandine Serrano
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Fabienne Godin
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Michel Doudeau
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Iva Dundović
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Stephane Goffinont
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Thierry Normand
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Béatrice Vallée
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Affiliated to University of Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France.
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3
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Bächer J, Allweiss L, Dandri M. SMC5/6-Mediated Transcriptional Regulation of Hepatitis B Virus and Its Therapeutic Potential. Viruses 2024; 16:1667. [PMID: 39599784 PMCID: PMC11598903 DOI: 10.3390/v16111667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 10/16/2024] [Accepted: 10/23/2024] [Indexed: 11/29/2024] Open
Abstract
Cells have developed various mechanisms to counteract viral infections. In an evolutionary arms race, cells mobilize cellular restriction factors to fight off viruses, targeted by viral factors to facilitate their own replication. The hepatitis B virus (HBV) is a small dsDNA virus that causes acute and chronic infections of the liver. Its genome persists in the nuclei of infected hepatocytes as a covalently closed circular DNA (cccDNA) minichromosome, thus building up an episomal persistence reservoir. The chromosomal maintenance complex SMC5/6 acts as a restriction factor hindering cccDNA transcription, whereas the viral regulatory protein HBx targets SMC5/6 for proteasomal degradation, thus relieving transcriptional suppression of the HBV minichromosome. To date, no curative therapies are available for chronic HBV carriers. Knowledge of the factors regulating the cccDNA and the development of therapies involving silencing the minichromosome or specifically interfering with the HBx-SMC5/6 axis holds promise in achieving sustained viral control. Here, we summarize the current knowledge of the mechanism of SMC5/6-mediated HBV restriction. We also give an overview of SMC5/6 cellular functions and how this compares to the restriction of other DNA viruses. We further discuss the therapeutic potential of available and investigational drugs interfering with the HBx-SMC5/6 axis.
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Affiliation(s)
- Johannes Bächer
- I. Department of Internal Medicine, Center for Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; (J.B.); (L.A.)
| | - Lena Allweiss
- I. Department of Internal Medicine, Center for Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; (J.B.); (L.A.)
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, Germany
| | - Maura Dandri
- I. Department of Internal Medicine, Center for Internal Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany; (J.B.); (L.A.)
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, Germany
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4
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Kim D, Bhargava R, Wang SC, Lee D, Patel R, Oh S, Bowman RW, Na CH, O'Sullivan RJ, Miller KM. TRIM24 directs replicative stress responses to maintain ALT telomeres via chromatin signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.18.618947. [PMID: 39463989 PMCID: PMC11507842 DOI: 10.1101/2024.10.18.618947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
An inability to replicate the genome can cause replication stress and genome instability. Here, we develop BLOCK-ID, a proteomic method to identify and visualize proteins at stressed replication forks. This approach successfully identified novel mediators of the replication stress response, including the chromatin acetylation reader protein TRIM24. In validating TRIM24 function, we uncovered its crucial role in coordinating Alternative Lengthening of Telomeres (ALT), a cancer-specific telomere extension pathway involving replication stress. Our data reveal that TRIM24 is directed to telomeres via a p300/CBP-dependent acetylation chromatin signaling cascade, where it organizes ALT-associated PML bodies (APBs) to promote telomere DNA synthesis. Strikingly, we demonstrate that when artificially tethered at telomeres, TRIM24 can stimulate new telomere DNA synthesis in a SUMO-dependent manner, independently of p300/CBP or PML-dependent APBs. Thus, this study identifies a TRIM24 chromatin signaling pathway required for ALT telomere maintenance.
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5
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Liang X, Chen J, Yan P, Chen Z, Gao C, Bai R, Tang J. The highly conserved region within exonuclease III-like in PML-I regulates the cytoplasmic localization of PML-NBs. J Biol Chem 2024; 300:107872. [PMID: 39395810 PMCID: PMC11602975 DOI: 10.1016/j.jbc.2024.107872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 09/12/2024] [Accepted: 09/25/2024] [Indexed: 10/14/2024] Open
Abstract
The sub-nuclear protein structure PML-NB regulates a wide range of important cellular functions, while its abnormal cytoplasmic localization may have pathological consequences. However, the nature of this aberrant localization remains poorly understood. In this study, we unveil that PML-I, the most conserved and abundant structural protein of PML-NB, possesses potent cytoplasmic targeting ability within the N-terminal half of the exonuclease III-like domain encoded by its unique exon 9, independent of the known nuclear localization signal. Fusion of this region to PML-VI can relocate PML-VI from the nucleus to the cytosol. Structural and deletion analysis revealed that the cytoplasmic targeting ability of this domain was restrained by the sequences encoded by exon 8a and the 3' portion of exon 9 in PML-I. Deletion of either of these regions relocates PML-I to the cytosol. Furthermore, we observed a potential interaction between the ER-localized TREX1 and the cytoplasmic-located PML-I mutants. Our results suggest that perturbation of the EXO-like domain of PML-I may represent an important mode to translocate PMLs from the nucleus to the cytosol, thereby interfering with the normal nuclear functions of PML-NBs.
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Affiliation(s)
- Xinxin Liang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinwen Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Peijie Yan
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhongzhou Chen
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chao Gao
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rulan Bai
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jun Tang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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6
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Serrero MC, Paludan SR. Restriction factors regulating human herpesvirus infections. Trends Immunol 2024; 45:662-677. [PMID: 39198098 DOI: 10.1016/j.it.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 09/01/2024]
Abstract
Herpesviruses are DNA viruses and the cause of diseases ranging from mild skin conditions to severe brain diseases. Mammalian antiviral host defense comprises an array of mechanisms, including restriction factors (RFs), which block specific steps in viral replication cycles. In recent years, knowledge of RFs that contribute to controlling herpesvirus infections has expanded significantly, along with a new understanding of viral evasion mechanisms and disease pathogenesis. By integrating findings from human genetics, murine models, and cellular studies, this review provides a current view of RF control of herpesvirus infections. We also explore the regulation of RF expression, discuss the roles of RFs in diseases, and point towards their growing potential as candidate therapeutic targets.
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Affiliation(s)
- Manutea C Serrero
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Immunology of Viral Infections, Aarhus, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Center for Immunology of Viral Infections, Aarhus, Denmark.
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7
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Pai CP, Wang H, Seachrist DD, Agarwal N, Adams JA, Liu Z, Keri RA, Cao K, Schiemann WP, Kao HY. The PML1-WDR5 axis regulates H3K4me3 marks and promotes stemness of estrogen receptor-positive breast cancer. Cell Death Differ 2024; 31:768-778. [PMID: 38627584 PMCID: PMC11164886 DOI: 10.1038/s41418-024-01294-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/30/2024] Open
Abstract
The alternative splicing of PML precursor mRNA gives rise to various PML isoforms, yet their expression profile in breast cancer cells remains uncharted. We discovered that PML1 is the most abundant isoform in all breast cancer subtypes, and its expression is associated with unfavorable prognosis in estrogen receptor-positive (ER+) breast cancers. PML depletion reduces cell proliferation, invasion, and stemness, while heterologous PML1 expression augments these processes and fuels tumor growth and resistance to fulvestrant, an FDA-approved drug for ER+ breast cancer, in a mouse model. Moreover, PML1, rather than the well-known tumor suppressor isoform PML4, rescues the proliferation of PML knockdown cells. ChIP-seq analysis reveals significant overlap between PML-, ER-, and Myc-bound promoters, suggesting their coordinated regulation of target gene expression, including genes involved in breast cancer stem cells (BCSCs), such as JAG1, KLF4, YAP1, SNAI1, and MYC. Loss of PML reduces BCSC-related gene expression, and exogenous PML1 expression elevates their expression. Consistently, PML1 restores the association of PML with these promoters in PML-depleted cells. We identified a novel association between PML1 and WDR5, a key component of H3K4 methyltransferase (HMTs) complexes that catalyze H3K4me1 and H3K4me3. ChIP-seq analyses showed that the loss of PML1 reduces H3K4me3 in numerous loci, including BCSC-associated gene promoters. Additionally, PML1, not PML4, re-establishes the H3K4me3 mark on these promoters in PML-depleted cells. Significantly, PML1 is essential for recruiting WDR5, MLL1, and MLL2 to these gene promoters. Inactivating WDR5 by knockdown or inhibitors phenocopies the effects of PML1 loss, reducing BCSC-related gene expression and tumorsphere formation and enhancing fulvestrant's anticancer activity. Our findings challenge the conventional understanding of PML as a tumor suppressor, redefine its role as a promoter of tumor growth in breast cancer, and offer new insights into the unique roles of PML isoforms in breast cancer.
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Affiliation(s)
- Chun-Peng Pai
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Han Wang
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Darcie D Seachrist
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Neel Agarwal
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Joshua A Adams
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Zhenghao Liu
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ruth A Keri
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
- Departments of Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Kaixiang Cao
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - William P Schiemann
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Hung-Ying Kao
- Departments of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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8
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Jing S, Gao J, Tiwari N, Du Y, Zhu L, Gim B, Qian Y, Yue X, Lee I. SUMOylated Golgin45 associates with PML-NB to transcriptionally regulate lipid metabolism genes during heat shock stress. Commun Biol 2024; 7:532. [PMID: 38710927 PMCID: PMC11074300 DOI: 10.1038/s42003-024-06232-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
Golgin tethers are known to mediate vesicular transport in the secretory pathway, whereas it is relatively unknown whether they may mediate cellular stress response within the cell. Here, we describe a cellular stress response during heat shock stress via SUMOylation of a Golgin tether, Golgin45. We found that Golgin45 is a SUMOylated Golgin via SUMO1 under steady state condition. Upon heat shock stress, the Golgin enters the nucleus by interacting with Importin-β2 and gets further modified by SUMO3. Importantly, SUMOylated Golgin45 appears to interact with PML and SUMO-deficient Golgin45 mutant functions as a dominant negative for PML-NB formation during heat shock stress, suppressing transcription of lipid metabolism genes. These results indicate that Golgin45 may play a role in heat stress response by transcriptional regulation of lipid metabolism genes in SUMOylation-dependent fashion.
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Affiliation(s)
- Shuaiyang Jing
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingkai Gao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Neeraj Tiwari
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yulei Du
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lianhui Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Bopil Gim
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yi Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Xihua Yue
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Intaek Lee
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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9
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Silonov SA, Smirnov EY, Kuznetsova IM, Turoverov KK, Fonin AV. PML Body Biogenesis: A Delicate Balance of Interactions. Int J Mol Sci 2023; 24:16702. [PMID: 38069029 PMCID: PMC10705990 DOI: 10.3390/ijms242316702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
PML bodies are subnuclear protein complexes that play a crucial role in various physiological and pathological cellular processes. One of the general structural proteins of PML bodies is a member of the tripartite motif (TRIM) family-promyelocytic leukemia protein (PML). It is known that PML interacts with over a hundred partners, and the protein itself is represented by several major isoforms, differing in their variable and disordered C-terminal end due to alternative splicing. Despite nearly 30 years of research, the mechanisms underlying PML body formation and the role of PML proteins in this process remain largely unclear. In this review, we examine the literature and highlight recent progress in this field, with a particular focus on understanding the role of individual domains of the PML protein, its post-translational modifications, and polyvalent nonspecific interactions in the formation of PML bodies. Additionally, based on the available literature, we propose a new hypothetical model of PML body formation.
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Affiliation(s)
- Sergey A. Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (E.Y.S.); (I.M.K.); (K.K.T.)
| | | | | | | | - Alexander V. Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; (E.Y.S.); (I.M.K.); (K.K.T.)
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10
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Kao HY, Pai CP, Wang H, Agarwal N, Adams J, Liu Z, Seachrist D, Keri R, Schiemann W. The PML1-WDR5 axis regulates H3K4me3 marks and promotes stemness of estrogen receptor-positive breast cancer. RESEARCH SQUARE 2023:rs.3.rs-3266720. [PMID: 37720048 PMCID: PMC10503857 DOI: 10.21203/rs.3.rs-3266720/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The alternative splicing of PML precursor mRNA gives rise to various PML isoforms, yet their expression profile in breast cancer cells remains uncharted. We discovered that PML1 is the most abundant isoform in all breast cancer subtypes, and its expression is associated with unfavorable prognosis in estrogen receptor-positive (ER+) breast cancers. PML depletion reduces cell proliferation, invasion, and stemness, while heterologous PML1 expression augments these processes and fuels tumor growth and resistance to fulvestrant, an FDA-approved drug for ER + breast cancer, in a mouse model. Moreover, PML1, rather than the well-known tumor suppressor isoform PML4, rescues the proliferation of PML knockdown cells. ChIP-seq analysis reveals significant overlap between PML-, ER-, and Myc-bound promoters, suggesting their coordinated regulation of target gene expression, including genes involved in breast cancer stem cells (BCSCs), such as JAG1, KLF4, YAP1, SNAI1, and MYC. Loss of PML reduces BCSC-related gene expression, and exogenous PML1 expression elevates their expression. Consistently, PML1 restores the association of PML with these promoters in PML-depleted cells. We identified a novel association between PML1 and WDR5, a key component of H3K4 methyltransferase (HMTs) complexes that catalyze H3K4me1 and H3K4me3. ChIP-seq analyses showed that the loss of PML1 reduces H3K4me3 in numerous loci, including BCSC-associated gene promoters. Additionally, PML1, not PML4, re-establishes the H3K4me3 mark on these promoters in PML-depleted cells. Significantly, PML1 is essential for recruiting WDR5, MLL1, and MLL2 to these gene promoters. Inactivating WDR5 by knockdown or inhibitors phenocopies the effects of PML1 loss, reducing BCSC-related gene expression and tumorsphere formation and enhancing fulvestrant's anticancer activity. Our findings challenge the conventional understanding of PML as a tumor suppressor, redefine its role as a promoter of tumor growth in breast cancer and offer new insights into the unique roles of PML isoforms in breast cancer.
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Affiliation(s)
| | | | | | | | - Joshua Adams
- Washington University School of Medicine in St. Louis
| | | | | | - Ruth Keri
- Cleveland Clinic Lerner Research Institute
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11
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Boccaccio GL, Thomas MG, García CC. Membraneless Organelles and Condensates Orchestrate Innate Immunity Against Viruses. J Mol Biol 2023; 435:167976. [PMID: 36702393 DOI: 10.1016/j.jmb.2023.167976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
The cellular defense against viruses involves the assembly of oligomers, granules and membraneless organelles (MLOs) that govern the activation of several arms of the innate immune response. Upon interaction with specific pathogen-derived ligands, a number of pattern recognition receptors (PRRs) undergo phase-separation thus triggering downstream signaling pathways. Among other relevant condensates, inflammasomes, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) specks, cyclic GMP-AMP synthase (cGAS) foci, protein kinase R (PKR) clusters, ribonuclease L-induced bodies (RLBs), stress granules (SGs), processing bodies (PBs) and promyelocytic leukemia protein nuclear bodies (PML NBs) play different roles in the immune response. In turn, viruses have evolved diverse strategies to evade the host defense. Viral DNA or RNA, as well as viral proteases or proteins carrying intrinsically disordered regions may interfere with condensate formation and function in multiple ways. In this review we discuss current and hypothetical mechanisms of viral escape that involve the disassembly, repurposing, or inactivation of membraneless condensates that govern innate immunity. We summarize emerging interconnections between these diverse condensates that ultimately determine the cellular outcome.
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Affiliation(s)
- Graciela Lidia Boccaccio
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - María Gabriela Thomas
- Laboratorio de Biología Celular del ARN, Instituto Leloir (FIL) and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina. https://www.twitter.com/_gabithomas
| | - Cybele Carina García
- Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEN), and IQUIBICEN, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) and Universidad de Buenos Aires, Buenos Aires, Argentina
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Rérolle D, de Thé H. The PML hub: An emerging actor of leukemia therapies. J Exp Med 2023; 220:e20221213. [PMID: 37382966 PMCID: PMC10309189 DOI: 10.1084/jem.20221213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/29/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
PML assembles into nuclear domains that have attracted considerable attention from cell and cancer biologists. Upon stress, PML nuclear bodies modulate sumoylation and other post-translational modifications, providing an integrated molecular framework for the multiple roles of PML in apoptosis, senescence, or metabolism. PML is both a sensor and an effector of oxidative stress. Emerging data has demonstrated its key role in promoting therapy response in several hematological malignancies. While these membrane-less nuclear hubs can enforce efficient cancer cell clearance, their downstream pathways deserve better characterization. PML NBs are druggable and their known modulators may have broader clinical utilities than initially thought.
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Affiliation(s)
- Domitille Rérolle
- Center for Interdisciplinary Research in Biology, Collège de France, Inserm, PSL Research University, Paris, France
- Université Paris Cité, Inserm U944, CNRS, GenCellDis, Institut de Recherche Saint-Louis, Paris, France
| | - Hugues de Thé
- Center for Interdisciplinary Research in Biology, Collège de France, Inserm, PSL Research University, Paris, France
- Université Paris Cité, Inserm U944, CNRS, GenCellDis, Institut de Recherche Saint-Louis, Paris, France
- Chaire d'Oncologie Cellulaire et Moléculaire, Collège de France, Paris, France
- Service d'Hématologie Biologique, Assistance Publique-Hôpitaux de Paris, Hôpital St. Louis, Paris, France
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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: 9] [Impact Index Per Article: 4.5] [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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Effects of arsenic on the topology and solubility of promyelocytic leukemia (PML)-nuclear bodies. PLoS One 2022; 17:e0268835. [PMID: 35594310 PMCID: PMC9122205 DOI: 10.1371/journal.pone.0268835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/09/2022] [Indexed: 11/19/2022] Open
Abstract
Promyelocytic leukemia (PML) proteins are involved in the pathogenesis of acute promyelocytic leukemia (APL). Trivalent arsenic (As3+) is known to cure APL by binding to cysteine residues of PML and enhance the degradation of PML-retinoic acid receptor α (RARα), a t(15;17) gene translocation product in APL cells, and restore PML-nuclear bodies (NBs). The size, number, and shape of PML-NBs vary among cell types and during cell division. However, topological changes of PML-NBs in As3+-exposed cells have not been well-documented. We report that As3+-induced solubility shift underlies rapid SUMOylation of PML and late agglomeration of PML-NBs. Most PML-NBs were toroidal and granular dot-like in GFPPML-transduced CHO-K1 and HEK293 cells, respectively. Exposure to As3+ and antimony (Sb3+) greatly reduced the solubility of PML and enhanced SUMOylation within 2 h in the absence of changes in the number and size of PML-NBs. However, the prolonged exposure to As3+ and Sb3+ resulted in agglomeration of PML-NBs. Exposure to bismuth (Bi3+), another Group 15 element, did not induce any of these changes. ML792, a SUMO activation inhibitor, reduced the number of PML-NBs and increased the size of the NBs, but had little effect on the As3+-induced solubility change of PML. These results warrant the importance of As3+- or Sb3+-induced solubility shift of PML for the regulation intranuclear dynamics of PML-NBs.
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Uggè M, Simoni M, Fracassi C, Bernardi R. PML isoforms: a molecular basis for PML pleiotropic functions. Trends Biochem Sci 2022; 47:609-619. [DOI: 10.1016/j.tibs.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 10/19/2022]
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