51
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Kim ET, Dybas JM, Kulej K, Reyes ED, Price AM, Akhtar LN, Orr A, Garcia BA, Boutell C, Weitzman MD. Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription. Nat Microbiol 2021; 6:234-245. [PMID: 33432153 PMCID: PMC7856100 DOI: 10.1038/s41564-020-00826-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
Intrinsic antiviral host factors confer cellular defence by limiting virus replication and are often counteracted by viral countermeasures. We reasoned that host factors that inhibit viral gene expression could be identified by determining proteins bound to viral DNA (vDNA) in the absence of key viral antagonists. Herpes simplex virus 1 (HSV-1) expresses E3 ubiquitin-protein ligase ICP0 (ICP0), which functions as an E3 ubiquitin ligase required to promote infection. Cellular substrates of ICP0 have been discovered as host barriers to infection but the mechanisms for inhibition of viral gene expression are not fully understood. To identify restriction factors antagonized by ICP0, we compared proteomes associated with vDNA during HSV-1 infection with wild-type virus and a mutant lacking functional ICP0 (ΔICP0). We identified the cellular protein Schlafen family member 5 (SLFN5) as an ICP0 target that binds vDNA during HSV-1 ΔICP0 infection. We demonstrated that ICP0 mediates ubiquitination of SLFN5, which leads to its proteasomal degradation. In the absence of ICP0, SLFN5 binds vDNA to repress HSV-1 transcription by limiting accessibility of RNA polymerase II to viral promoters. These results highlight how comparative proteomics of proteins associated with viral genomes can identify host restriction factors and reveal that viral countermeasures can overcome SLFN antiviral activity.
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Affiliation(s)
- Eui Tae Kim
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Department of Microbiology and Immunology, Jeju National University School of Medicine, Jeju, Republic of Korea
| | - Joseph M. Dybas
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Katarzyna Kulej
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Emigdio D. Reyes
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alexander M. Price
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lisa N. Akhtar
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Division of Infectious Diseases, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Pennsylvania, USA
| | - Ann Orr
- MRC-University of Glasgow Center for Virus Research, Glasgow, Scotland, United Kingdom
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Chris Boutell
- MRC-University of Glasgow Center for Virus Research, Glasgow, Scotland, United Kingdom
| | - Matthew D. Weitzman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Epigenetics Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA,Correspondence: All correspondence and request for materials should be addressed to Matthew D. Weitzman (, )
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Morozko EL, Smith-Geater C, Monteys AM, Pradhan S, Lim RG, Langfelder P, Kachemov M, Kulkarni JA, Zaifman J, Hill A, Stocksdale JT, Cullis PR, Wu J, Ochaba J, Miramontes R, Chakraborty A, Hazra TK, Lau A, St-Cyr S, Orellana I, Kopan L, Wang KQ, Yeung S, Leavitt BR, Reidling JC, Yang XW, Steffan JS, Davidson BL, Sarkar PS, Thompson LM. PIAS1 modulates striatal transcription, DNA damage repair, and SUMOylation with relevance to Huntington's disease. Proc Natl Acad Sci U S A 2021; 118:e2021836118. [PMID: 33468657 PMCID: PMC7848703 DOI: 10.1073/pnas.2021836118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA damage repair genes are modifiers of disease onset in Huntington's disease (HD), but how this process intersects with associated disease pathways remains unclear. Here we evaluated the mechanistic contributions of protein inhibitor of activated STAT-1 (PIAS1) in HD mice and HD patient-derived induced pluripotent stem cells (iPSCs) and find a link between PIAS1 and DNA damage repair pathways. We show that PIAS1 is a component of the transcription-coupled repair complex, that includes the DNA damage end processing enzyme polynucleotide kinase-phosphatase (PNKP), and that PIAS1 is a SUMO E3 ligase for PNKP. Pias1 knockdown (KD) in HD mice had a normalizing effect on HD transcriptional dysregulation associated with synaptic function and disease-associated transcriptional coexpression modules enriched for DNA damage repair mechanisms as did reduction of PIAS1 in HD iPSC-derived neurons. KD also restored mutant HTT-perturbed enzymatic activity of PNKP and modulated genomic integrity of several transcriptionally normalized genes. The findings here now link SUMO modifying machinery to DNA damage repair responses and transcriptional modulation in neurodegenerative disease.
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Affiliation(s)
- Eva L Morozko
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Charlene Smith-Geater
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Alejandro Mas Monteys
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Subrata Pradhan
- Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555
| | - Ryan G Lim
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Peter Langfelder
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, CA 90095
| | - Marketta Kachemov
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Josh Zaifman
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
| | - Austin Hill
- Incisive Genetics Inc., Vancouver, BC, Canada V6A 0H9
| | | | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
- NanoMedicines Innovation Network, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA 92697
| | - Joseph Ochaba
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697
| | - Ricardo Miramontes
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Tapas K Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555
| | - Alice Lau
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Sophie St-Cyr
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Iliana Orellana
- Sue and Bill Gross Stem Cell Institute, University of California, Irvine, CA 92697
| | - Lexi Kopan
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Keona Q Wang
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
| | - Sylvia Yeung
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Jack C Reidling
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095
| | - Joan S Steffan
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cell and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Partha S Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, TX 77555
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697;
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697
- Institute of Memory Impairments and Neurological Disorders, University of California, Irvine, CA 92697
- Department of Biological Chemistry, University of California, Irvine, CA 92697
- Sue and Bill Gross Stem Cell Institute, University of California, Irvine, CA 92697
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53
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González-Prieto R, Eifler-Olivi K, Claessens LA, Willemstein E, Xiao Z, Talavera Ormeno CMP, Ovaa H, Ulrich HD, Vertegaal ACO. Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex. Cell Rep 2021; 34:108691. [PMID: 33503430 DOI: 10.1016/j.celrep.2021.108691] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/11/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
In contrast to our extensive knowledge on covalent small ubiquitin-like modifier (SUMO) target proteins, we are limited in our understanding of non-covalent SUMO-binding proteins. We identify interactors of different SUMO isoforms-monomeric SUMO1, monomeric SUMO2, or linear trimeric SUMO2 chains-using a mass spectrometry-based proteomics approach. We identify 379 proteins that bind to different SUMO isoforms, mainly in a preferential manner. Interestingly, XRCC4 is the only DNA repair protein in our screen with a preference for SUMO2 trimers over mono-SUMO2, as well as the only protein in our screen that belongs to the non-homologous end joining (NHEJ) DNA double-strand break repair pathway. A SUMO interaction motif (SIM) in XRCC4 regulates its recruitment to sites of DNA damage and phosphorylation of S320 by DNA-PKcs. Our data highlight the importance of non-covalent and covalent sumoylation for DNA double-strand break repair via the NHEJ pathway and provide a resource of SUMO isoform interactors.
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Affiliation(s)
- Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Karolin Eifler-Olivi
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Laura A Claessens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Edwin Willemstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Zhenyu Xiao
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Cami M P Talavera Ormeno
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Oncode Institute, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Oncode Institute, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
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54
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F-box only and CUE proteins are crucial ubiquitination-associated components for conidiation and pathogenicity in the rice blast fungus, Magnaporthe oryzae. Fungal Genet Biol 2020; 144:103473. [DOI: 10.1016/j.fgb.2020.103473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 08/11/2020] [Accepted: 09/19/2020] [Indexed: 11/21/2022]
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55
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Jansen NS, Vertegaal ACO. A Chain of Events: Regulating Target Proteins by SUMO Polymers. Trends Biochem Sci 2020; 46:113-123. [PMID: 33008689 DOI: 10.1016/j.tibs.2020.09.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/21/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
Small ubiquitin-like modifiers (SUMOs) regulate virtually all nuclear processes. The fate of the target protein is determined by the architecture of the attached SUMO protein, which can be of polymeric nature. Here, we highlight the multifunctional aspects of dynamic signal transduction by SUMO polymers. The SUMO-targeted ubiquitin ligases (STUbLs) RING-finger protein 4 (RNF4) and RNF111 recognize SUMO polymers in a chain-architecture-dependent manner, leading to the formation of hybrid chains, which could enable proteasomal destruction of proteins. Recent publications have highlighted essential roles for SUMO chain disassembly by the mammalian SUMO proteases SENP6 and SENP7 and the yeast SUMO protease Ulp2. SENP6 is particularly important for centromere assembly. These recent findings demonstrate the diversity of SUMO polymer signal transduction for proteolytic and nonproteolytic purposes.
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Affiliation(s)
- Nicolette S Jansen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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56
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Zhang Y, Zeng L. Crosstalk between Ubiquitination and Other Post-translational Protein Modifications in Plant Immunity. PLANT COMMUNICATIONS 2020; 1:100041. [PMID: 33367245 PMCID: PMC7748009 DOI: 10.1016/j.xplc.2020.100041] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/07/2020] [Accepted: 03/19/2020] [Indexed: 05/05/2023]
Abstract
Post-translational modifications (PTMs) are central to the modulation of protein activity, stability, subcellular localization, and interaction with partners. They greatly expand the diversity and functionality of the proteome and have taken the center stage as key players in regulating numerous cellular and physiological processes. Increasing evidence indicates that in addition to a single regulatory PTM, many proteins are modified by multiple different types of PTMs in an orchestrated manner to collectively modulate the biological outcome. Such PTM crosstalk creates a combinatorial explosion in the number of proteoforms in a cell and greatly improves the ability of plants to rapidly mount and fine-tune responses to different external and internal cues. While PTM crosstalk has been investigated in depth in humans, animals, and yeast, the study of interplay between different PTMs in plants is still at its infant stage. In the past decade, investigations showed that PTMs are widely involved and play critical roles in the regulation of interactions between plants and pathogens. In particular, ubiquitination has emerged as a key regulator of plant immunity. This review discusses recent studies of the crosstalk between ubiquitination and six other PTMs, i.e., phosphorylation, SUMOylation, poly(ADP-ribosyl)ation, acetylation, redox modification, and glycosylation, in the regulation of plant immunity. The two basic ways by which PTMs communicate as well as the underlying mechanisms and diverse outcomes of the PTM crosstalk in plant immunity are highlighted.
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57
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Keiten-Schmitz J, Wagner K, Piller T, Kaulich M, Alberti S, Müller S. The Nuclear SUMO-Targeted Ubiquitin Quality Control Network Regulates the Dynamics of Cytoplasmic Stress Granules. Mol Cell 2020; 79:54-67.e7. [PMID: 32521226 DOI: 10.1016/j.molcel.2020.05.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 01/01/2023]
Abstract
Exposure of cells to heat or oxidative stress causes misfolding of proteins. To avoid toxic protein aggregation, cells have evolved nuclear and cytosolic protein quality control (PQC) systems. In response to proteotoxic stress, cells also limit protein synthesis by triggering transient storage of mRNAs and RNA-binding proteins (RBPs) in cytosolic stress granules (SGs). We demonstrate that the SUMO-targeted ubiquitin ligase (StUbL) pathway, which is part of the nuclear proteostasis network, regulates SG dynamics. We provide evidence that inactivation of SUMO deconjugases under proteotoxic stress initiates SUMO-primed, RNF4-dependent ubiquitylation of RBPs that typically condense into SGs. Impairment of SUMO-primed ubiquitylation drastically delays SG resolution upon stress release. Importantly, the StUbL system regulates compartmentalization of an amyotrophic lateral sclerosis (ALS)-associated FUS mutant in SGs. We propose that the StUbL system functions as surveillance pathway for aggregation-prone RBPs in the nucleus, thereby linking the nuclear and cytosolic axis of proteotoxic stress response.
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Affiliation(s)
- Jan Keiten-Schmitz
- Institute of Biochemistry II, Goethe University, Faculty of Medicine, Frankfurt, Germany
| | - Kristina Wagner
- Institute of Biochemistry II, Goethe University, Faculty of Medicine, Frankfurt, Germany
| | - Tanja Piller
- Institute of Biochemistry II, Goethe University, Faculty of Medicine, Frankfurt, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University, Faculty of Medicine, Frankfurt, Germany
| | - Simon Alberti
- CMCB/BIOTEC, Technical University Dresden, Dresden, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University, Faculty of Medicine, Frankfurt, Germany.
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58
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Nakka VP, Mohammed AQ. A Critical Role for ISGylation, Ubiquitination and, SUMOylation in Brain Damage: Implications for Neuroprotection. Neurochem Res 2020; 45:1975-1985. [DOI: 10.1007/s11064-020-03066-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/12/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
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59
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Excoffon KJDA. The coxsackievirus and adenovirus receptor: virological and biological beauty. FEBS Lett 2020; 594:1828-1837. [PMID: 32298477 DOI: 10.1002/1873-3468.13794] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 12/17/2022]
Abstract
The coxsackievirus and adenovirus receptor (CAR) is an essential multifunctional cellular protein that is only beginning to be understood. CAR serves as a receptor for many adenoviruses, human group B coxsackieviruses, swine vesicular disease virus, and possibly other viruses. While named for its function as a viral receptor, CAR is also involved in cell adhesion, immune cell activation, synaptic transmission, and signaling. Knockout mouse models were first to identify some of these biological functions; however, tissue-specific model systems have shed light on the complexity of different CAR isoforms and their specific activities. Many of these functions are mediated by the large number of interacting proteins described so far, and several new putative interactions have recently been discovered. As antiviral and gene therapy strategies that target CAR continue to emerge, future work poised to understand the biological implications of manipulating CAR in vivo is critical.
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Affiliation(s)
- Katherine J D A Excoffon
- Biological Sciences, Wright State University, Dayton, OH, USA.,Spirovant Sciences, Inc, Philadelphia, PA, USA
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60
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Guérillon C, Smedegaard S, Hendriks IA, Nielsen ML, Mailand N. Multisite SUMOylation restrains DNA polymerase η interactions with DNA damage sites. J Biol Chem 2020; 295:8350-8362. [PMID: 32350109 PMCID: PMC7307195 DOI: 10.1074/jbc.ra120.013780] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/25/2020] [Indexed: 12/26/2022] Open
Abstract
Translesion DNA synthesis (TLS) mediated by low-fidelity DNA polymerases is an essential cellular mechanism for bypassing DNA lesions that obstruct DNA replication progression. However, the access of TLS polymerases to the replication machinery must be kept tightly in check to avoid excessive mutagenesis. Recruitment of DNA polymerase η (Pol η) and other Y-family TLS polymerases to damaged DNA relies on proliferating cell nuclear antigen (PCNA) monoubiquitylation and is regulated at several levels. Using a microscopy-based RNAi screen, here we identified an important role of the SUMO modification pathway in limiting Pol η interactions with DNA damage sites in human cells. We found that Pol η undergoes DNA damage- and protein inhibitor of activated STAT 1 (PIAS1)-dependent polySUMOylation upon its association with monoubiquitylated PCNA, rendering it susceptible to extraction from DNA damage sites by SUMO-targeted ubiquitin ligase (STUbL) activity. Using proteomic profiling, we demonstrate that Pol η is targeted for multisite SUMOylation, and that collectively these SUMO modifications are essential for PIAS1- and STUbL-mediated displacement of Pol η from DNA damage sites. These findings suggest that a SUMO-driven feedback inhibition mechanism is an intrinsic feature of TLS-mediated lesion bypass functioning to curtail the interaction of Pol η with PCNA at damaged DNA to prevent harmful mutagenesis.
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Affiliation(s)
- Claire Guérillon
- Ubiquitin Signaling Group, Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Stine Smedegaard
- Ubiquitin Signaling Group, Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
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61
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Avitan-Hersh E, Feng Y, Oknin Vaisman A, Abu Ahmad Y, Zohar Y, Zhang T, Lee JS, Lazar I, Sheikh Khalil S, Feiler Y, Kluger H, Kahana C, Brown K, Ruppin E, Ronai ZA, Orian A. Regulation of eIF2α by RNF4 Promotes Melanoma Tumorigenesis and Therapy Resistance. J Invest Dermatol 2020; 140:2466-2477. [PMID: 32360601 DOI: 10.1016/j.jid.2020.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 01/07/2023]
Abstract
Among the hallmarks of melanoma are impaired proteostasis and rapid development of resistance to targeted therapy that represent a major clinical challenge. However, the molecular machinery that links these processes is unknown. Here we describe that by stabilizing key melanoma oncoproteins, the ubiquitin ligase RNF4 promotes tumorigenesis and confers resistance to targeted therapy in melanoma cells, xenograft mouse models, and patient samples. In patients, RNF4 protein and mRNA levels correlate with poor prognosis and with resistance to MAPK inhibitors. Remarkably, RNF4 tumorigenic properties, including therapy resistance, require the translation initiation factor initiation elongation factor alpha (eIF2α). RNF4 binds, ubiquitinates, and stabilizes the phosphorylated eIF2α (p-eIF2α) but not activating transcription factor 4 or C/EBP homologous protein that mediates the eIF2α-dependent integrated stress response. In accordance, p-eIF2α levels were significantly elevated in high-RNF4 patient-derived melanomas. Thus, RNF4 and p-eIF2α establish a positive feed-forward loop connecting oncogenic translation and ubiquitin-dependent protein stabilization in melanoma.
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Affiliation(s)
- Emily Avitan-Hersh
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel; Rambam Health Care Campus, Haifa, Israel
| | - Yongmei Feng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Avital Oknin Vaisman
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yamen Abu Ahmad
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yaniv Zohar
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel; Rambam Health Care Campus, Haifa, Israel
| | - Tongwu Zhang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joo Sang Lee
- Cancer Data Science Lab, National Cancer Institute, NIH, Maryland, USA; Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Ikrame Lazar
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Saeed Sheikh Khalil
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yulia Feiler
- Deprtament of Molecular Genetics Weizmann Institute of Science, Rehovot, Israel
| | - Harriet Kluger
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chaim Kahana
- Deprtament of Molecular Genetics Weizmann Institute of Science, Rehovot, Israel
| | - Kevin Brown
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, NIH, Maryland, USA
| | - Ze'ev A Ronai
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion Integrative Cancer Center, Technion-Israel Institute of Technology, Haifa, Israel.
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62
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Rinfret Robert C, McManus FP, Lamoliatte F, Thibault P. Interplay of Ubiquitin-Like Modifiers Following Arsenic Trioxide Treatment. J Proteome Res 2020; 19:1999-2010. [PMID: 32223133 DOI: 10.1021/acs.jproteome.9b00807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Arsenic trioxide (ATO) is a therapeutic agent used to treat acute promyelocytic leukemia (APL), a disease caused by a chromosomal translocation of the retinoic acid receptor α (RARα) gene that can occur reciprocally with the promyelocytic leukemia (PML) gene. The mechanisms through which ATO exerts its effects on cells are not fully characterized though they involve the SUMOylation, the ubiquitylation, and the degradation of the PML/RARα oncoprotein through the PML moiety. To better understand the mechanisms that underlie the cytotoxicity induced with increasing ATO levels, we profiled the changes in protein SUMOylation, phosphorylation, and ubiquitylation on HEK293 cells following exposure to low (1 μM) or elevated (10 μM) ATO for 4 h. Our analyses revealed that a low dose of ATO resulted in the differential modification of selected substrates including the SUMOylation (K380, K394, K490, and K497) and ubiquitylation (K337, K401) of PML. These experiments also highlighted a number of unexpected SUMOylated substrates involved in DNA damage response (e.g., PCNA, YY1, and poly[ADP-ribose] polymerase 1 (PARP1)) and messenger RNA (mRNA) splicing (e.g., ACIN1, USP39, and SART1) that were regulated at higher ATO concentrations. Interestingly, additional enzymatic assays revealed that SUMOylation of PARP1 impeded its proteolytic cleavage by caspase-3, suggesting that SUMOylation could have a protective role in delaying cell apoptosis.
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Affiliation(s)
- Clémence Rinfret Robert
- Institute for Research in Immunology and Cancer, Montreal, Québec H3T 1J4, Canada.,Department of Biochemistry, University of Montréal, Montreal, Québec H3T 1J4, Canada
| | - Francis P McManus
- Institute for Research in Immunology and Cancer, Montreal, Québec H3T 1J4, Canada
| | - Frédéric Lamoliatte
- Institute for Research in Immunology and Cancer, Montreal, Québec H3T 1J4, Canada.,Department of Chemistry, University of Montréal, P.O. Box 6128, Station Centre-Ville, Montreal, Québec H3T 1J4, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Montreal, Québec H3T 1J4, Canada.,Department of Biochemistry, University of Montréal, Montreal, Québec H3T 1J4, Canada.,Department of Chemistry, University of Montréal, P.O. Box 6128, Station Centre-Ville, Montreal, Québec H3T 1J4, Canada
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63
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Keiten-Schmitz J, Schunck K, Müller S. SUMO Chains Rule on Chromatin Occupancy. Front Cell Dev Biol 2020; 7:343. [PMID: 31998715 PMCID: PMC6965010 DOI: 10.3389/fcell.2019.00343] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
The dynamic and reversible post-translational modification of proteins and protein complexes with the ubiquitin-related SUMO modifier regulates a wide variety of nuclear functions, such as transcription, replication and DNA repair. SUMO can be attached as a monomer to its targets, but can also form polymeric SUMO chains. While monoSUMOylation is generally involved in the assembly of protein complexes, multi- or polySUMOylation may have very different consequences. The evolutionary conserved paradigmatic signaling process initiated by multi- or polySUMOylation is the SUMO-targeted Ubiquitin ligase (StUbL) pathway, where the presence of multiple SUMO moieties primes ubiquitylation by the mammalian E3 ubiquitin ligases RNF4 or RNF111, or the yeast Slx5/8 heterodimer. The mammalian SUMO chain-specific isopeptidases SENP6 or SENP7, or yeast Ulp2, counterbalance chain formation thereby limiting StUbL activity. Many facets of SUMO chain signaling are still incompletely understood, mainly because only a limited number of polySUMOylated substrates have been identified. Here we summarize recent work that revealed a highly interconnected network of candidate polySUMO modified proteins functioning in DNA damage response and chromatin organization. Based on these datasets and published work on distinct polySUMO-regulated processes we discuss overarching concepts in SUMO chain function. We propose an evolutionary conserved role of polySUMOylation in orchestrating chromatin dynamics and genome stability networks by balancing chromatin-residency of protein complexes. This concept will be exemplified in processes, such as centromere/kinetochore organization, sister chromatid cohesion, DNA repair and replication.
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Affiliation(s)
- Jan Keiten-Schmitz
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Kathrin Schunck
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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Salas-Lloret D, Agabitini G, González-Prieto R. TULIP2: An Improved Method for the Identification of Ubiquitin E3-Specific Targets. Front Chem 2019; 7:802. [PMID: 31850303 PMCID: PMC6901917 DOI: 10.3389/fchem.2019.00802] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/07/2019] [Indexed: 01/27/2023] Open
Abstract
Protein modification by Ubiquitin or Ubiquitin-like modifiers is mediated by an enzyme cascade composed of E1, E2, and E3 enzymes. E1s, or ubiquitin-activating enzymes, perform ubiquitin activation. Next, ubiquitin is transferred to ubiquitin-conjugating enzymes or E2s. Finally, ubiquitin ligases or E3s catalyze the transfer of ubiquitin to the acceptor proteins. E3 enzymes are responsible for determining the substrate specificity. Determining which E3 enzyme maps to which substrate is a major challenge that is greatly facilitated by the TULIP2 methodology. TULIP2 methodology is fast, precise, and cost-effective. Compared to the previous TULIP methodology protocol, TULIP2 methodology achieves a more than 50-fold improvement in the purification yield and two orders of magnitude improvement in the signal-to-background ratio after label free quantification by mass spectrometry analysis. The method includes the generation of TULIP2 cell lines, subsequent purification of TULIP2 conjugates, preparation, and analysis of samples by mass spectrometry.
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Affiliation(s)
- Daniel Salas-Lloret
- González-Prieto Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Giulia Agabitini
- González-Prieto Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Román González-Prieto
- González-Prieto Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, Netherlands
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65
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Kumar R, Sabapathy K. RNF4—A Paradigm for SUMOylation‐Mediated Ubiquitination. Proteomics 2019; 19:e1900185. [DOI: 10.1002/pmic.201900185] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/13/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Ramesh Kumar
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
| | - Kanaga Sabapathy
- Cancer & Stem Cell Biology Program Duke–NUS Medical School 8 College Road Singapore 169857 Singapore
- Laboratory of Molecular Carcinogenesis Division of Cellular & Molecular Research Humphrey Oei Institute of Cancer Research National Cancer Centre Singapore 11 Hospital Drive Singapore 169610 Singapore
- Department of Biochemistry National University of Singapore 8 Medical Drive Singapore 117597 Singapore
- Institute of Molecular and Cellular Biology 61 Biopolis Drive Singapore 138673 Singapore
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66
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Wu Z, Huang R, Yuan L. Crosstalk of intracellular post-translational modifications in cancer. Arch Biochem Biophys 2019; 676:108138. [PMID: 31606391 DOI: 10.1016/j.abb.2019.108138] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/29/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022]
Abstract
Post-translational modifications (PTMs) have been reported to play pivotal roles in numerous cellular biochemical and physiological processes. Multiple PTMs can influence the actions of each other positively or negatively, termed as PTM crosstalk or PTM code. During recent years, development of identification strategies for PTMs co-occurrence has revealed abundant information of interplay between PTMs. Increasing evidence demonstrates that deregulation of PTMs crosstalk is involved in the genesis and development of various diseases. Insight into the complexity of PTMs crosstalk will help us better understand etiology and provide novel targets for drug therapy. In the present review, we will discuss the important functional roles of PTMs crosstalk in proteins associated with cancer diseases.
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Affiliation(s)
- Zheng Wu
- School of Kinesiology and Health, Capital University of Physical Education and Sports, Beijing, 100191, China.
| | - Rongting Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Liang Yuan
- Peking University International Hospital, Beijing, 102200, China
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67
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Wagner K, Kunz K, Piller T, Tascher G, Hölper S, Stehmeier P, Keiten-Schmitz J, Schick M, Keller U, Müller S. The SUMO Isopeptidase SENP6 Functions as a Rheostat of Chromatin Residency in Genome Maintenance and Chromosome Dynamics. Cell Rep 2019; 29:480-494.e5. [PMID: 31597105 DOI: 10.1016/j.celrep.2019.08.106] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/21/2019] [Accepted: 08/29/2019] [Indexed: 11/20/2022] Open
Abstract
Signaling by the ubiquitin-related SUMO pathway relies on coordinated conjugation and deconjugation events. SUMO-specific deconjugating enzymes counterbalance SUMOylation, but comprehensive insight into their substrate specificity and regulation is missing. By characterizing SENP6, we define an N-terminal multi-SIM domain as a critical determinant in targeting SENP6 to SUMO chains. Proteomic profiling reveals a network of SENP6 functions at the crossroads of chromatin organization and DNA damage response (DDR). SENP6 acts as a SUMO eraser at telomeric and centromeric chromatin domains and determines the SUMOylation status and chromatin association of the cohesin complex. Importantly, SENP6 is part of the hPSO4/PRP19 complex that drives ATR-Chk1 activation. SENP6 deficiency impairs chromatin association of the ATR cofactor ATRIP, thereby compromising the activation of Chk1 signaling in response to aphidicolin-induced replicative stress and sensitizing cells to DNA damage. We propose a general role of SENP6 in orchestrating chromatin dynamics and genome stability networks by balancing chromatin residency of protein complexes.
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Affiliation(s)
- Kristina Wagner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Kathrin Kunz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Tanja Piller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Soraya Hölper
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Per Stehmeier
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jan Keiten-Schmitz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Markus Schick
- Internal Medicine III, School of Medicine, Technische Universität München, Ismaninger Strasse 22, 81675 Munich, Germany; Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Ulrich Keller
- Internal Medicine III, School of Medicine, Technische Universität München, Ismaninger Strasse 22, 81675 Munich, Germany; Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
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68
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The poly-SUMO2/3 protease SENP6 enables assembly of the constitutive centromere-associated network by group deSUMOylation. Nat Commun 2019; 10:3987. [PMID: 31485003 PMCID: PMC6726658 DOI: 10.1038/s41467-019-11773-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/26/2019] [Indexed: 12/20/2022] Open
Abstract
In contrast to our extensive knowledge on ubiquitin polymer signaling, we are severely limited in our understanding of poly-SUMO signaling. We set out to identify substrates conjugated to SUMO polymers, using knockdown of the poly-SUMO2/3 protease SENP6. We identify over 180 SENP6 regulated proteins that represent highly interconnected functional groups of proteins including the constitutive centromere-associated network (CCAN), the CENP-A loading factors Mis18BP1 and Mis18A and DNA damage response factors. Our results indicate a striking protein group de-modification by SENP6. SENP6 deficient cells are severely compromised for proliferation, accumulate in G2/M and frequently form micronuclei. Accumulation of CENP-T, CENP-W and CENP-A to centromeres is impaired in the absence of SENP6. Surprisingly, the increase of SUMO chains does not lead to ubiquitin-dependent proteasomal degradation of the CCAN subunits. Our results indicate that SUMO polymers can act in a proteolysis-independent manner and consequently, have a more diverse signaling function than previously expected. While the biological roles of ubiquitin chains are well studied, little is known about the functions of SUMO polymers. Here, the authors identify poly-SUMOylation substrates and provide evidence that SUMO polymers regulate the accumulation of CCAN subunits at chromatin and centromeres.
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69
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Abrieu A, Liakopoulos D. How Does SUMO Participate in Spindle Organization? Cells 2019; 8:E801. [PMID: 31370271 PMCID: PMC6721559 DOI: 10.3390/cells8080801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-like protein SUMO is a regulator involved in most cellular mechanisms. Recent studies have discovered new modes of function for this protein. Of particular interest is the ability of SUMO to organize proteins in larger assemblies, as well as the role of SUMO-dependent ubiquitylation in their disassembly. These mechanisms have been largely described in the context of DNA repair, transcriptional regulation, or signaling, while much less is known on how SUMO facilitates organization of microtubule-dependent processes during mitosis. Remarkably however, SUMO has been known for a long time to modify kinetochore proteins, while more recently, extensive proteomic screens have identified a large number of microtubule- and spindle-associated proteins that are SUMOylated. The aim of this review is to focus on the possible role of SUMOylation in organization of the spindle and kinetochore complexes. We summarize mitotic and microtubule/spindle-associated proteins that have been identified as SUMO conjugates and present examples regarding their regulation by SUMO. Moreover, we discuss the possible contribution of SUMOylation in organization of larger protein assemblies on the spindle, as well as the role of SUMO-targeted ubiquitylation in control of kinetochore assembly and function. Finally, we propose future directions regarding the study of SUMOylation in regulation of spindle organization and examine the potential of SUMO and SUMO-mediated degradation as target for antimitotic-based therapies.
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Affiliation(s)
- Ariane Abrieu
- CRBM, CNRS UMR5237, Université de Montpellier, 1919 route de Mende, 34090 Montpellier, France.
| | - Dimitris Liakopoulos
- CRBM, CNRS UMR5237, Université de Montpellier, 1919 route de Mende, 34090 Montpellier, France.
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70
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Sha Z, Blyszcz T, González-Prieto R, Vertegaal ACO, Goldberg AL. Inhibiting ubiquitination causes an accumulation of SUMOylated newly synthesized nuclear proteins at PML bodies. J Biol Chem 2019; 294:15218-15234. [PMID: 31285264 PMCID: PMC6802522 DOI: 10.1074/jbc.ra119.009147] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/21/2019] [Indexed: 12/31/2022] Open
Abstract
Protein ubiquitination and SUMOylation are required for the maintenance of cellular protein homeostasis, and both increase in proteotoxic conditions (e.g. heat shock or proteasome inhibition). However, we found that when ubiquitination was blocked in several human cell lines by inhibiting the ubiquitin-activating enzyme with TAK243, there was an unexpected, large accumulation of proteins modified by SUMO2/3 chains or SUMO1, but not by several other ubiquitin-like proteins. This buildup of SUMOylated proteins was evident within 3–4 h. It required the small ubiquitin-like modifier (SUMO)-conjugating enzyme, UBC9, and the promyelocytic leukemia protein (PML) and thus was not due to nonspecific SUMO conjugation by ubiquitination enzymes. The SUMOylated proteins accumulated predominantly bound to chromatin and were localized to PML nuclear bodies. Because blocking protein synthesis with cycloheximide prevented the buildup of SUMOylated proteins, they appeared to be newly-synthesized proteins. The proteins SUMOylated after inhibition of ubiquitination were purified and analyzed by MS. In HeLa and U2OS cells, there was a cycloheximide-sensitive increase in a similar set of SUMOylated proteins (including transcription factors and proteins involved in DNA damage repair). Surprisingly, the inhibition of ubiquitination also caused a cycloheximide-sensitive decrease in a distinct set of SUMOylated proteins (including proteins for chromosome modification and mRNA splicing). More than 80% of the SUMOylated proteins whose levels rose or fell upon inhibiting ubiquitination inhibition underwent similar cycloheximide-sensitive increases or decreases upon proteasome inhibition. Thus, when nuclear substrates of the ubiquitin–proteasome pathway are not efficiently degraded, many become SUMO-modified and accumulate in PML bodies.
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Affiliation(s)
- Zhe Sha
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Tamara Blyszcz
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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71
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Zhao X. SUMO-Mediated Regulation of Nuclear Functions and Signaling Processes. Mol Cell 2019; 71:409-418. [PMID: 30075142 DOI: 10.1016/j.molcel.2018.07.027] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022]
Abstract
Since the discovery of SUMO twenty years ago, SUMO conjugation has become a widely recognized post-translational modification that targets a myriad of proteins in many processes. Great progress has been made in understanding the SUMO pathway enzymes, substrate sumoylation, and the interplay between sumoylation and other regulatory mechanisms in a variety of contexts. As these research directions continue to generate insights into SUMO-based regulation, several mechanisms by which sumoylation and desumoylation can orchestrate large biological effects are emerging. These include the ability to target multiple proteins within the same cellular structure or process, respond dynamically to external and internal stimuli, and modulate signaling pathways involving other post-translational modifications. Focusing on nuclear function and intracellular signaling, this review highlights a broad spectrum of historical data and recent advances with the aim of providing an overview of mechanisms underlying SUMO-mediated global effects to stimulate further inquiry into intriguing roles of SUMO.
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Affiliation(s)
- Xiaolan Zhao
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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72
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Garvin AJ, Walker AK, Densham RM, Chauhan AS, Stone HR, Mackay HL, Jamshad M, Starowicz K, Daza-Martin M, Ronson GE, Lanz AJ, Beesley JF, Morris JR. The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms. Genes Dev 2019; 33:333-347. [PMID: 30796017 PMCID: PMC6411010 DOI: 10.1101/gad.321125.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 12/18/2022]
Abstract
SUMOylation (small ubiquitin-like modifier) in the DNA double-strand break (DSB) response regulates recruitment, activity, and clearance of repair factors. However, our understanding of a role for deSUMOylation in this process is limited. Here we identify different mechanistic roles for deSUMOylation in homologous recombination (HR) and nonhomologous end joining (NHEJ) through the investigation of the deSUMOylase SENP2. We found that regulated deSUMOylation of MDC1 prevents excessive SUMOylation and its RNF4-VCP mediated clearance from DSBs, thereby promoting NHEJ. In contrast, we show that HR is differentially sensitive to SUMO availability and SENP2 activity is needed to provide SUMO. SENP2 is amplified as part of the chromosome 3q amplification in many cancers. Increased SENP2 expression prolongs MDC1 focus retention and increases NHEJ and radioresistance. Collectively, our data reveal that deSUMOylation differentially primes cells for responding to DSBs and demonstrates the ability of SENP2 to tune DSB repair responses.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexandra K Walker
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ruth M Densham
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Anoop Singh Chauhan
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Helen R Stone
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Hannah L Mackay
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Mohammed Jamshad
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Daza-Martin
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - George E Ronson
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alexander J Lanz
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James F Beesley
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Joanna R Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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De La Cruz-Herrera CF, Shire K, Siddiqi UZ, Frappier L. A genome-wide screen of Epstein-Barr virus proteins that modulate host SUMOylation identifies a SUMO E3 ligase conserved in herpesviruses. PLoS Pathog 2018; 14:e1007176. [PMID: 29979787 PMCID: PMC6051671 DOI: 10.1371/journal.ppat.1007176] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/18/2018] [Accepted: 06/22/2018] [Indexed: 12/30/2022] Open
Abstract
Many cellular processes pertinent for viral infection are regulated by the addition of small ubiquitin-like modifiers (SUMO) to key regulatory proteins, making SUMOylation an important mechanism by which viruses can commandeer cellular pathways. Epstein-Barr virus (EBV) is a master at manipulating of cellular processes, which enables life-long infection but can also lead to the induction of a variety of EBV-associated cancers. To identify new mechanisms by which EBV proteins alter cells, we screened a library of 51 EBV proteins for global effects on cellular SUMO1 and SUMO2 modifications (SUMOylation), identifying several proteins not previously known to manipulate this pathway. One EBV protein (BRLF1) globally induced the loss of SUMOylated proteins, in a proteasome-dependent manner, as well as the loss of promeylocytic leukemia nuclear bodies. However, unlike its homologue (Rta) in Kaposi's sarcoma associated herpesvirus, it did not appear to have ubiquitin ligase activity. In addition we identified the EBV SM protein as globally upregulating SUMOylation and showed that this activity was conserved in its homologues in herpes simplex virus 1 (HSV1 UL54/ICP27) and cytomegalovirus (CMV UL69). All three viral homologues were shown to bind SUMO and Ubc9 and to have E3 SUMO ligase activity in a purified system. These are the first SUMO E3 ligases discovered for EBV, HSV1 and CMV. Interestingly the homologues had different specificities for SUMO1 and SUMO2, with SM and UL69 preferentially binding SUMO1 and inducing SUMO1 modifications, and UL54 preferentially binding SUMO2 and inducing SUMO2 modifications. The results provide new insights into the function of this family of conserved herpesvirus proteins, and the conservation of this SUMO E3 ligase activity across diverse herpesviruses suggests the importance of this activity for herpesvirus infections.
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Affiliation(s)
| | - Kathy Shire
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Umama Z. Siddiqi
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Alagu J, Itahana Y, Sim F, Chao SH, Bi X, Itahana K. Tumor Suppressor p14ARF Enhances IFN-γ–Activated Immune Response by Inhibiting PIAS1 via SUMOylation. THE JOURNAL OF IMMUNOLOGY 2018; 201:451-464. [DOI: 10.4049/jimmunol.1800327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022]
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75
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Probing ubiquitin and SUMO conjugation and deconjugation. Biochem Soc Trans 2018; 46:423-436. [PMID: 29588386 DOI: 10.1042/bst20170086] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 12/24/2022]
Abstract
Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins including small Ubl modifier (SUMO) are small proteins which are covalently linked to target proteins to regulate their functions. In this review, we discuss the current state of the art and point out what we feel this field urgently needs in order to delineate the wiring of the system. We discuss what is needed to unravel the connections between different components of the conjugation machineries for ubiquitylation and SUMOylation, and to unravel the connections between the conjugation machineries and their substrates. Chemical probes are key tools to probe signal transduction by these small proteins that may help understand their action. This rapidly moving field has resulted in various small molecules that will help us to further understand Ub and SUMO function and that may lead to the development of new drugs.
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The Biology of SUMO-Targeted Ubiquitin Ligases in Drosophila Development, Immunity, and Cancer. J Dev Biol 2018; 6:jdb6010002. [PMID: 29615551 PMCID: PMC5875560 DOI: 10.3390/jdb6010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin and SUMO (small ubiquitin-like modifier) pathways modify proteins that in turn regulate diverse cellular processes, embryonic development, and adult tissue physiology. These pathways were originally discovered biochemically in vitro, leading to a long-standing challenge of elucidating both the molecular cross-talk between these pathways and their biological importance. Recent discoveries in Drosophila established that ubiquitin and SUMO pathways are interconnected via evolutionally conserved SUMO-targeted ubiquitin ligase (STUbL) proteins. STUbL are RING ubiquitin ligases that recognize SUMOylated substrates and catalyze their ubiquitination, and include Degringolade (Dgrn) in Drosophila and RNF4 and RNF111 in humans. STUbL are essential for early development of both the fly and mouse embryos. In the fly embryo, Dgrn regulates early cell cycle progression, sex determination, zygotic gene transcription, segmentation, and neurogenesis, among other processes. In the fly adult, Dgrn is required for systemic immune response to pathogens and intestinal stem cell regeneration upon infection. These functions of Dgrn are highly conserved in humans, where RNF4-dependent ubiquitination potentiates key oncoproteins, thereby accelerating tumorigenesis. Here, we review the lessons learned to date in Drosophila and highlight their relevance to cancer biology.
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