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Ferdoush J, Abdul Kadir R, Simay Kaplanoglu S, Osborn M. SARS-CoV-2 and UPS with potentials for therapeutic interventions. Gene 2024; 912:148377. [PMID: 38490508 DOI: 10.1016/j.gene.2024.148377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The Ubiquitin proteasome system (UPS), an essential eukaryotic/host/cellular post-translational modification (PTM), plays a critical role in the regulation of diverse cellular functions including regulation of protein stability, immune signaling, antiviral activity, as well as virus replication. Although UPS regulation of viral proteins may be utilized by the host as a defense mechanism to invade viruses, viruses may have adapted to take advantage of the host UPS. This system can be manipulated by viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to stimulate various steps of the viral replication cycle and facilitate pathogenesis, thereby causing the respiratory disease COVID-19. Many SARS-CoV-2 encoded proteins including open reading frame 3a (ORF3a), ORF6, ORF7a, ORF9b, and ORF10 interact with the host's UPS machinery, influencing host immune signaling and apoptosis. Moreover, SARS-CoV-2 encoded papain-like protease (PLpro) interferes with the host UPS to facilitate viral replication and to evade the host's immune system. These alterations in SARS-CoV-2 infected cells have been revealed by various proteomic studies, suggesting potential targets for clinical treatment. To provide insight into the underlying causes of COVID-19 and suggest possible directions for therapeutic interventions, this paper reviews the intricate relationship between SARS-CoV-2 and UPS. Promising treatment strategies are also investigated in this paper including targeting PLpro with zinc-ejector drugs, as well as targeting viral non-structural protein (nsp12) via heat treatment associated ubiquitin-mediated proteasomal degradation to reduce viral pathogenesis.
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Affiliation(s)
- Jannatul Ferdoush
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA.
| | - Rizwaan Abdul Kadir
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Selin Simay Kaplanoglu
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Morgan Osborn
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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2
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Takeda Y, Ueki M, Matsuhiro J, Walinda E, Tanaka T, Yamada M, Fujita H, Takezaki S, Kobayashi I, Tamaki S, Nagata S, Miyake N, Matsumoto N, Osawa M, Yasumi T, Heike T, Ohtake F, Saito MK, Toguchida J, Takita J, Ariga T, Iwai K. A de novo dominant-negative variant is associated with OTULIN-related autoinflammatory syndrome. J Exp Med 2024; 221:e20231941. [PMID: 38652464 DOI: 10.1084/jem.20231941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
OTULIN-related autoinflammatory syndrome (ORAS), a severe autoinflammatory disease, is caused by biallelic pathogenic variants of OTULIN, a linear ubiquitin-specific deubiquitinating enzyme. Loss of OTULIN attenuates linear ubiquitination by inhibiting the linear ubiquitin chain assembly complex (LUBAC). Here, we report a patient who harbors two rare heterozygous variants of OTULIN (p.P152L and p.R306Q). We demonstrated accumulation of linear ubiquitin chains upon TNF stimulation and augmented TNF-induced cell death in mesenchymal stem cells differentiated from patient-derived iPS cells, which confirms that the patient has ORAS. However, although the de novo p.R306Q variant exhibits attenuated deubiquitination activity without reducing the amount of OTULIN, the deubiquitination activity of the p.P152L variant inherited from the mother was equivalent to that of the wild-type. Patient-derived MSCs in which the p.P152L variant was replaced with wild-type also exhibited augmented TNF-induced cell death and accumulation of linear chains. The finding that ORAS can be caused by a dominant-negative p.R306Q variant of OTULIN furthers our understanding of disease pathogenesis.
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Affiliation(s)
- Yukiko Takeda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Ueki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junpei Matsuhiro
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masafumi Yamada
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- Department of Food and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
| | - Hiroaki Fujita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunichiro Takezaki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ichiro Kobayashi
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Sakura Tamaki
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sanae Nagata
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University , Tokyo, Japan
| | - Megumu K Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junya Toguchida
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Ariga
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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3
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Grossmann J, Kratz AS, Kordonsky A, Prag G, Hoffmann I. CRL4 DCAF1 ubiquitin ligase regulates PLK4 protein levels to prevent premature centriole duplication. Life Sci Alliance 2024; 7:e202402668. [PMID: 38490717 PMCID: PMC10942865 DOI: 10.26508/lsa.202402668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Centrioles play important roles in the assembly of centrosomes and cilia. Centriole duplication occurs once per cell cycle and is dependent on polo-like kinase 4 (PLK4). To prevent centriole amplification, which is a hallmark of cancer, PLK4 protein levels need to be tightly regulated. Here, we show that the Cullin4A/B-DDB1-DCAF1, CRL4DCAF1, E3 ligase targets PLK4 for degradation in human cells. DCAF1 binds and ubiquitylates PLK4 in the G2 phase to prevent premature centriole duplication in mitosis. In contrast to the regulation of PLK4 by SCFβ-TrCP, the interaction between PLK4 and DCAF1 is independent of PLK4 kinase activity and mediated by polo-boxes 1 and 2 of PLK4, suggesting that DCAF1 promotes PLK4 ubiquitylation independently of β-TrCP. Thus, the SCFSlimb/β-TrCP pathway, targeting PLK4 for ubiquitylation based on its phosphorylation state and CRL4DCAF1, which ubiquitylates PLK4 by binding to the conserved PB1-PB2 domain, appear to be complementary ways to control PLK4 abundance to prevent centriole overduplication.
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Affiliation(s)
- Josina Grossmann
- Cell Cycle Control and Carcinogenesis, German Cancer Research Center, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Anne-Sophie Kratz
- Cell Cycle Control and Carcinogenesis, German Cancer Research Center, DKFZ, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alina Kordonsky
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ingrid Hoffmann
- Cell Cycle Control and Carcinogenesis, German Cancer Research Center, DKFZ, Heidelberg, Germany
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4
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van Vliet VJE, De Silva A, Mark BL, Kikkert M. Viral deubiquitinating proteases and the promising strategies of their inhibition. Virus Res 2024; 344:199368. [PMID: 38588924 PMCID: PMC11025011 DOI: 10.1016/j.virusres.2024.199368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Several viruses are now known to code for deubiquitinating proteases in their genomes. Ubiquitination is an essential post-translational modification of cellular substrates involved in many processes in the cell, including in innate immune signalling. This post-translational modification is regulated by the ubiquitin conjugation machinery, as well as various host deubiquitinating enzymes. The conjugation of ubiquitin chains to several innate immune related factors is often needed to induce downstream signalling, shaping the antiviral response. Viral deubiquitinating proteins, besides often having a primary function in the viral replication cycle by cleaving the viral polyprotein, are also able to cleave ubiquitin chains from such host substrates, in that way exerting a function in innate immune evasion. The presence of viral deubiquitinating enzymes has been firmly established for numerous animal-infecting viruses, such as some well-researched and clinically important nidoviruses, and their presence has now been confirmed in several plant viruses as well. Viral proteases in general have long been highlighted as promising drug targets, with a current focus on small molecule inhibitors. In this review, we will discuss the range of viral deubiquitinating proteases known to date, summarise the various avenues explored to inhibit such proteases and discuss novel strategies and models intended to inhibit and study these specific viral enzymes.
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Affiliation(s)
- Vera J E van Vliet
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands; The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands.
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5
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Banik P, Ray K, Kamps J, Chen QY, Luesch H, Winklhofer KF, Tatzelt J. VCP/p97 mediates nuclear targeting of non-ER-imported prion protein to maintain proteostasis. Life Sci Alliance 2024; 7:e202302456. [PMID: 38570188 PMCID: PMC10992997 DOI: 10.26508/lsa.202302456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
Mistargeting of secretory proteins in the cytosol can trigger their aggregation and subsequent proteostasis decline. We have identified a VCP/p97-dependent pathway that directs non-ER-imported prion protein (PrP) into the nucleus to prevent the formation of toxic aggregates in the cytosol. Upon impaired translocation into the ER, PrP interacts with VCP/p97, which facilitates nuclear import mediated by importin-ß. Notably, the cytosolic interaction of PrP with VCP/p97 and its nuclear import are independent of ubiquitination. In vitro experiments revealed that VCP/p97 binds non-ubiquitinated PrP and prevents its aggregation. Inhibiting binding of PrP to VCP/p97, or transient proteotoxic stress, promotes the formation of self-perpetuating and partially proteinase resistant PrP aggregates in the cytosol, which compromised cellular proteostasis and disrupted further nuclear targeting of PrP. In the nucleus, RNAs keep PrP in a soluble and non-toxic conformation. Our study revealed a novel ubiquitin-independent role of VCP/p97 in the nuclear targeting of non-imported secretory proteins and highlights the impact of the chemical milieu in triggering protein misfolding.
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Affiliation(s)
- Papiya Banik
- https://ror.org/04tsk2644 Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Koustav Ray
- https://ror.org/04tsk2644 Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Janine Kamps
- https://ror.org/04tsk2644 Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
| | - Qi-Yin Chen
- https://ror.org/02y3ad647 Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, USA
| | - Hendrik Luesch
- https://ror.org/02y3ad647 Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL, USA
| | - Konstanze F Winklhofer
- https://ror.org/04tsk2644 Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
| | - Jörg Tatzelt
- https://ror.org/04tsk2644 Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Cluster of Excellence RESOLV, Bochum, Germany
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6
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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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7
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Krishnamurthy K, Stillman IE, Hecht JL, Vyas M. Defining the Nature and Clinicopathologic Significance of Mallory-Denk-like Inclusions in Ovarian Fibromas: A Potential Degenerative Phenomenon Associated With Torsion. Int J Gynecol Pathol 2024; 43:290-295. [PMID: 37562060 DOI: 10.1097/pgp.0000000000000974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Mallory-Denk bodies (MBD), described in alcoholic hepatitis, are composed of intermediate filaments admixed with other proteins. These cytoplasmic inclusions are irregularly shaped and eosinophilic as seen under the light microscope. MBD-like inclusions have rarely been described outside the hepatobiliary tree. Though rare, intracytoplasmic inclusions have been reported in ovarian fibromas. This study evaluates a series of torsed ovarian fibromas with intracytoplasmic inclusions resembling MDBs. Forty-three ovarian fibromas were retrieved from the pathology archives. The H&E slides were evaluated for the presence of MBD-like inclusions and histologic evidence of torsion. The cases with histologic features of torsion were included in the study group while the nontorsed fibromas formed the control group. Among the 15 cases of fibromas with torsion, MBD-like intracytoplasmic inclusions were seen in 5 cases, predominantly in the interface between necrotic areas and viable stroma. None of the cases from the control group showed any inclusions. There was no significant difference in the size of the fibroma or patient demographics between cases with and without inclusions. The inclusions were positive for cytokeratin and ubiquitin while being negative for per acidic Schiff and periodic acid-Schiff with diastase reaction, in the 3 cases selected for immunohistochemistry and special stains. Electron microscopy of the index case revealed a predominance of type 3 Mallory hyaline. This is the first report describing MDB-like inclusions in ovarian fibromas. These MDB-like inclusions appear to be limited to a fraction of ovarian fibromas that underwent torsion, suggesting that these inclusions likely result from subacute hypoxic damage to the cells.
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8
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Ślusarz MJ, Lipińska AD. An intrinsic network of polar interactions is responsible for binding of UL49.5 C-degron by the CRL2 KLHDC3 ubiquitin ligase. Proteins 2024; 92:610-622. [PMID: 38069558 DOI: 10.1002/prot.26651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 04/13/2024]
Abstract
Bovine herpesvirus type 1 (BoHV-1) is a pathogen of cattle responsible for infectious bovine rhinotracheitis. The BoHV-1 UL49.5 is a transmembrane protein that binds to the transporter associated with antigen processing (TAP) and downregulates cell surface expression of the antigenic peptide complexes with the major histocompatibility complex class I (MHC-I). KLHDC3 is a kelch domain-containing protein 3 and a substrate receptor of a cullin2-RING (CRL2) E3 ubiquitin ligase. Recently, it has been identified that CRL2KLHDC3 is responsible for UL49.5-triggered TAP degradation via a C-degron pathway and the presence of the degron sequence does not lead to the degradation of UL49.5 itself. The molecular modeling of KLHDC3 in complexes with four UL49.5 C-terminal decapeptides (one native protein and three mutants) revealed their activity to be closely correlated with the conformation which they adopt in KLHDC3 binding cleft. To analyze the interaction between UL49.5 and KLHDC3 in detail, in this work a total of 3.6 μs long molecular dynamics simulations have been performed. The complete UL49.5-KLHDC3 complexes were embedded into the fully hydrated all-atom lipid membrane model with explicit water molecules. The network of polar interactions has been proposed to be responsible for the recognition and binding of the degron in KLHDC3. The interaction network within the binding pocket appeared to be very similar between two CRL2 substrate receptors: KLHDC3 and KLHDC2.
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Affiliation(s)
| | - Andrea D Lipińska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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Amici DR, Alhayek S, Klein AT, Wang YZ, Wilen AP, Song W, Zhu P, Thakkar A, King MA, Steffeck AW, Alasady MJ, Peek C, Savas JN, Mendillo ML. Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life. Life Sci Alliance 2024; 7:e202302370. [PMID: 38453366 PMCID: PMC10921065 DOI: 10.26508/lsa.202302370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The recently discovered HAPSTR1 protein broadly oversees cellular stress responses. This function requires HUWE1, a ubiquitin ligase that paradoxically marks HAPSTR1 for degradation, but much about this pathway remains unclear. Here, leveraging multiplexed proteomics, we find that HAPSTR1 enables nuclear localization of HUWE1 with implications for nuclear protein quality control. We show that HAPSTR1 is tightly regulated and identify ubiquitin ligase TRIP12 and deubiquitinase USP7 as upstream regulators titrating HAPSTR1 stability. Finally, we generate conditional Hapstr1 knockout mice, finding that Hapstr1-null mice are perinatal lethal, adult mice depleted of Hapstr1 have reduced fitness, and primary cells explanted from Hapstr1-null animals falter in culture coincident with HUWE1 mislocalization and broadly remodeled signaling. Notably, although HAPSTR1 potently suppresses p53, we find that Hapstr1 is essential for life even in mice lacking p53. Altogether, we identify novel components and functional insights into the conserved HAPSTR1-HUWE1 pathway and demonstrate its requirement for mammalian life.
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Affiliation(s)
- David R Amici
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sammy Alhayek
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Austin T Klein
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yi-Zhi Wang
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anika P Wilen
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Weimin Song
- https://ror.org/000e0be47 Comprehensive Metabolic Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pei Zhu
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Abhishek Thakkar
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - McKenzi A King
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam Wt Steffeck
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Milad J Alasady
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Clara Peek
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffrey N Savas
- https://ror.org/000e0be47 Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- https://ror.org/000e0be47 Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- https://ror.org/000e0be47 Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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10
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Xu J, Liu H, Zhou C, Wang J, Wang J, Han Y, Zheng N, Zhang M, Li X. The ubiquitin-proteasome system in the plant response to abiotic stress: Potential role in crop resilience improvement. Plant Sci 2024; 342:112035. [PMID: 38367822 DOI: 10.1016/j.plantsci.2024.112035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
The post-translational modification (PTM) of proteins by ubiquitination modulates many physiological processes in plants. As the major protein degradation pathway in plants, the ubiquitin-proteasome system (UPS) is considered a promising target for improving crop tolerance drought, high salinity, extreme temperatures, and other abiotic stressors. The UPS also participates in abiotic stress-related abscisic acid (ABA) signaling. E3 ligases are core components of the UPS-mediated modification process due to their substrate specificity. In this review, we focus on the abiotic stress-associated regulatory mechanisms and functions of different UPS components, emphasizing the participation of E3 ubiquitin ligases. We also summarize and discuss UPS-mediated modulation of ABA signaling. In particular, we focus our review on recent research into the UPS-mediated modulation of the abiotic stress response in major crop plants. We propose that altering the ubiquitination site of the substrate or the substrate-specificity of E3 ligase using genome editing technology such as CRISPR/Cas9 may improve the resistance of crop plants to adverse environmental conditions. Such a strategy will require continued research into the role of the UPS in mediating the abiotic stress response in plants.
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Affiliation(s)
- Jian Xu
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China; Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Hongjie Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhou
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Jinxing Wang
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua, China
| | - Junqiang Wang
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yehui Han
- Qiqihar Branch of the Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Nan Zheng
- Industrial Crop Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ming Zhang
- Industrial Crop Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiaoming Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Mandal K, Tomar SK, Kumar Santra M. Decoding the ubiquitin language: Orchestrating transcription initiation and gene expression through chromatin remodelers and histones. Gene 2024; 904:148218. [PMID: 38307220 DOI: 10.1016/j.gene.2024.148218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Eukaryotic transcription is a finely orchestrated process and it is controlled by transcription factors as well as epigenetic regulators. Transcription factors and epigenetic regulators undergo different types of posttranslational modifications including ubiquitination to control transcription process. Ubiquitination, traditionally associated with protein degradation, has emerged as a crucial contributor to the regulation of chromatin structure through ubiquitination of histone and chromatin remodelers. Ubiquitination introduces new layers of intricacy to the regulation of transcription initiation through controlling the equilibrium between euchromatin and heterochromatin states. Nucleosome, the fundamental units of chromatin, spacing in euchromatin and heterochromatin states are regulated by histone modification and chromatin remodeling complexes. Chromatin remodeling complexes actively sculpt the chromatin architecture and thereby influence the transcriptional states of genes. Therefore, understanding the dynamic behavior of nucleosome spacing is critical as it impacts various cellular functions through controlling gene expression profiles. In this comprehensive review, we discussed the intricate interplay between ubiquitination and transcription initiation, and illuminated the underlying molecular mechanisms that occur in a variety of biological contexts. This exploration sheds light on the complex regulatory networks that govern eukaryotic transcription, providing important insights into the fine orchestration of gene expression and chromatin dynamics.
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Affiliation(s)
- Kartik Mandal
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Shiva Kumar Tomar
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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12
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Bhachoo JS, Garvin AJ. SUMO and the DNA damage response. Biochem Soc Trans 2024; 52:773-792. [PMID: 38629643 DOI: 10.1042/bst20230862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
The preservation of genome integrity requires specialised DNA damage repair (DDR) signalling pathways to respond to each type of DNA damage. A key feature of DDR is the integration of numerous post-translational modification signals with DNA repair factors. These modifications influence DDR factor recruitment to damaged DNA, activity, protein-protein interactions, and ultimately eviction to enable access for subsequent repair factors or termination of DDR signalling. SUMO1-3 (small ubiquitin-like modifier 1-3) conjugation has gained much recent attention. The SUMO-modified proteome is enriched with DNA repair factors. Here we provide a snapshot of our current understanding of how SUMO signalling impacts the major DNA repair pathways in mammalian cells. We highlight repeating themes of SUMO signalling used throughout DNA repair pathways including the assembly of protein complexes, competition with ubiquitin to promote DDR factor stability and ubiquitin-dependent degradation or extraction of SUMOylated DDR factors. As SUMO 'addiction' in cancer cells is protective to genomic integrity, targeting components of the SUMO machinery to potentiate DNA damaging therapy or exacerbate existing DNA repair defects is a promising area of study.
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Affiliation(s)
- Jai S Bhachoo
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
| | - Alexander J Garvin
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
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13
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P T B, Sahu I. Decoding the ubiquitin landscape by cutting-edge ubiquitinomic approaches. Biochem Soc Trans 2024; 52:627-637. [PMID: 38572966 DOI: 10.1042/bst20230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Functional consequences of protein ubiquitination have gone far beyond the degradation regulation as was initially imagined during its discovery 40 years back. The state-of-the-art has revealed the plethora of signaling pathways that are largely regulated by ubiquitination process in eukaryotes. To no surprise, ubiquitination is often dysregulated in many human diseases, including cancer, neurodegeneration and infection. Hence it has become a major focus with high-gain research value for many investigators to unravel new proteoforms, that are the targets of this ubiquitination modification. Despite many biochemical or proteomic approaches available for ubiquitination detection, mass-spectrometry stood out to be the most efficient and transformative technology to read this complex modification script. Here in this review, we have discussed how different ubiquitin codes can be decoded qualitatively and quantitatively following various sequential proteomic approaches to date reported and indicated the current limitations with scope for improvements.
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Affiliation(s)
- Brindhavanam P T
- Division of Medical Research, SRM-Medical College Hospital and Research Centre, Faculty of Medical and Health Sciences, SRMIST, Kattankulathur, Tamil Nadu, India
| | - Indrajit Sahu
- Division of Medical Research, SRM-Medical College Hospital and Research Centre, Faculty of Medical and Health Sciences, SRMIST, Kattankulathur, Tamil Nadu, India
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14
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Nguyen DM, Rath DH, Devost D, Pétrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hébert TE, Privé GG. Structure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex. Proc Natl Acad Sci U S A 2024; 121:e2315018121. [PMID: 38625940 DOI: 10.1073/pnas.2315018121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain, engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3KCTD5) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3NTD/Gβ1γ2 assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5BTB/CUL3NTD and KCTD5CTD/Gβγ moieties of the structure. CRL3KCTD5 engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 superassembly, and extension of the structure to include full-length CUL3 with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3NTD/Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex.
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Affiliation(s)
- Duc Minh Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Deanna H Rath
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Dominic Devost
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Robert Rizk
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Alan X Ji
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Naveen Narayanan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Darren Yong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Andrew Zhai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Maha U Q Mian
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Neil C Pomroy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alexander F A Keszei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mohammad T Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - John L Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
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15
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Gahlot P, Kravic B, Rota G, van den Boom J, Levantovsky S, Schulze N, Maspero E, Polo S, Behrends C, Meyer H. Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH. Mol Cell 2024; 84:1556-1569.e10. [PMID: 38503285 DOI: 10.1016/j.molcel.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Cells respond to lysosomal membrane permeabilization by membrane repair or selective macroautophagy of damaged lysosomes, termed lysophagy, but it is not fully understood how this decision is made. Here, we uncover a pathway in human cells that detects lipid bilayer perturbations in the limiting membrane of compromised lysosomes, which fail to be repaired, and then initiates ubiquitin-triggered lysophagy. We find that SPG20 binds the repair factor IST1 on damaged lysosomes and, importantly, integrates that with the detection of damage-associated lipid-packing defects of the lysosomal membrane. Detection occurs via sensory amphipathic helices in SPG20 before rupture of the membrane. If lipid-packing defects are extensive, such as during lipid peroxidation, SPG20 recruits and activates ITCH, which marks the damaged lysosome with lysine-63-linked ubiquitin chains to initiate lysophagy and thus triages the lysosome for destruction. With SPG20 being linked to neurodegeneration, these findings highlight the relevance of a coordinated lysosomal damage response for cellular homeostasis.
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Affiliation(s)
- Pinki Gahlot
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Bojana Kravic
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Giulia Rota
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Johannes van den Boom
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Sophie Levantovsky
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Nina Schulze
- Imaging Center Campus Essen, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Hemmo Meyer
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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16
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Tajdel-Zielińska M, Janicki M, Marczak M, Ludwików A. Arabidopsis HECT and RING-type E3 Ligases Promote MAPKKK18 Degradation to Regulate Abscisic Acid Signaling. Plant Cell Physiol 2024; 65:390-404. [PMID: 38153765 PMCID: PMC11020294 DOI: 10.1093/pcp/pcad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are conserved signaling pathways that transduce extracellular signals into diverse cellular responses. Arabidopsis MAPKKK18 is a component of the MAPKKK17/18-MKK3-MPK1/2/7/14 cascades, which play critical roles in abscisic acid (ABA) signaling, drought tolerance and senescence. A very important aspect of MAP kinase signaling is both its activation and its termination, which must be tightly controlled to achieve appropriate biological responses. Recently, the ubiquitin-proteasome system (UPS) has received increasing attention as a key mechanism for maintaining the homeostasis of MAPK cascade components and other ABA signaling effectors. Previous studies have shown that the stability of MAPKKK18 is regulated by the UPS via the ABA core pathway. Here, using multiple proteomic approaches, we found that MAPKKK17/18 turnover is tightly controlled by three E3 ligases, UPL1, UPL4 and KEG. We also identified lysines 154 and 237 as critical for MAPKKK18 stability. Taken together, this study sheds new light on the mechanism that controls MAPKKK17/18 activity and function.
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Affiliation(s)
- Małgorzata Tajdel-Zielińska
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| | - Maciej Janicki
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| | - Małgorzata Marczak
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
| | - Agnieszka Ludwików
- Laboratory Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
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17
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Wu L, Zhang L, Feng S, Chen L, Lin C, Wang G, Zhu Y, Wang P, Cheng G. An evolutionarily conserved ubiquitin ligase drives infection and transmission of flaviviruses. Proc Natl Acad Sci U S A 2024; 121:e2317978121. [PMID: 38593069 PMCID: PMC11032495 DOI: 10.1073/pnas.2317978121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
Mosquito-borne flaviviruses such as dengue (DENV) and Zika (ZIKV) cause hundreds of millions of infections annually. The single-stranded RNA genome of flaviviruses is translated into a polyprotein, which is cleaved equally into individual functional proteins. While structural proteins are packaged into progeny virions and released, most of the nonstructural proteins remain intracellular and could become cytotoxic if accumulated over time. However, the mechanism by which nonstructural proteins are maintained at the levels optimal for cellular fitness and viral replication remains unknown. Here, we identified that the ubiquitin E3 ligase HRD1 is essential for flaviviruses infections in both mammalian hosts and mosquitoes. HRD1 directly interacts with flavivirus NS4A and ubiquitylates a conserved lysine residue for ER-associated degradation. This mechanism avoids excessive accumulation of NS4A, which otherwise interrupts the expression of processed flavivirus proteins in the ER. Furthermore, a small-molecule inhibitor of HRD1 named LS-102 effectively interrupts DENV2 infection in both mice and Aedes aegypti mosquitoes, and significantly disturbs DENV transmission from the infected hosts to mosquitoes owing to reduced viremia. Taken together, this study demonstrates that flaviviruses have evolved a sophisticated mechanism to exploit the ubiquitination system to balance the homeostasis of viral proteins for their own advantage and provides a potential therapeutic target to interrupt flavivirus infection and transmission.
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Affiliation(s)
- Linjuan Wu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
| | - Liming Zhang
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
| | - Shengyong Feng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
| | - Lu Chen
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
| | - Cai Lin
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
| | - Gang Wang
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
| | - Yibin Zhu
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
| | - Penghua Wang
- Department of Immunology, School of Medicine, University of Connecticut Health Center, Farmington, CT06030
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing100084, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen518000, China
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen518055, China
- Southwest United Graduate School, Kunming650092, China
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18
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An J, Zhang X. Crbn-based molecular Glues: Breakthroughs and perspectives. Bioorg Med Chem 2024; 104:117683. [PMID: 38552596 DOI: 10.1016/j.bmc.2024.117683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
CRBN is a substrate receptor for the Cullin Ring E3 ubiquitin ligase 4 (CRL4) complex. It has been observed that CRBN can be exploited by small molecules to facilitate the recruitment and ubiquitination of non-natural CRL4 substrates, resulting in the degradation of neosubstrate through the ubiquitin-proteasome system. This phenomenon, known as molecular glue-induced protein degradation, has emerged as an innovative therapeutic approach in contrast to traditional small-molecule drugs. One key advantage of molecular glues, in comparison to conventional small-molecule drugs adhering to Lipinski's Rule of Five, is their ability to operate without the necessity for specific binding pockets on target proteins. This unique characteristic empowers molecular glues to interact with conventionally intractable protein targets, such as transcription factors and scaffold proteins. The ability to induce the degradation of these previously elusive targets by hijacking the ubiquitin-proteasome system presents a promising avenue for the treatment of recalcitrant diseases. Nevertheless, the rational design of molecular glues remains a formidable challenge due to the limited understanding of their mechanisms and actions. This review offers an overview of recent advances and breakthroughs in the field of CRBN-based molecular glues, while also exploring the prospects for a systematic approach to designing these compounds.
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Affiliation(s)
- Juzeng An
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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19
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Swenson SA, Dobish KK, Peters HC, Bea Winship C, Willow Hynes-Smith R, Caplan M, Wittorf KJ, Ghosal G, Buckley SM. Ubiquitin E3 Ligase FBXO9 Regulates Pluripotency by Targeting DPPA5 for Ubiquitylation and Degradation. Stem Cells 2024; 42:317-328. [PMID: 38227647 PMCID: PMC11016844 DOI: 10.1093/stmcls/sxae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have unique characteristics where they can both contribute to all three germ layers in vivo and self-renewal indefinitely in vitro. Post-translational modifications of proteins, particularly by the ubiquitin proteasome system (UPS), control cell pluripotency, self-renewal, and differentiation. A significant number of UPS members (mainly ubiquitin ligases) regulate pluripotency and influence ESC differentiation with key elements of the ESC pluripotency network (including the "master" regulators NANOG and OCT4) being controlled by ubiquitination. To further understand the role of the UPS in pluripotency, we performed an RNAi screen during induction of cellular reprogramming and have identified FBXO9 as a novel regulator of pluripotency associated protein DPPA5. Our findings indicate that FBXO9 silencing facilitates the induction of pluripotency through decreased proteasomal degradation of DPPA5. These findings identify FBXO9 as a key regulator of pluripotency.
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Affiliation(s)
- Samantha A Swenson
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kasidy K Dobish
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT,USA
| | - Hendrik C Peters
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT,USA
| | - C Bea Winship
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT,USA
| | - R Willow Hynes-Smith
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mika Caplan
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Karli J Wittorf
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gargi Ghosal
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shannon M Buckley
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT,USA
- Department of Internal Medicine, Division of Hematology and Hematopoietic Malignancies, University of Utah, Salt Lake City, UT, USA
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20
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Kong L, Jin X. Dysregulation of deubiquitination in breast cancer. Gene 2024; 902:148175. [PMID: 38242375 DOI: 10.1016/j.gene.2024.148175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
Breast cancer (BC) is a highly frequent malignant tumor that poses a serious threat to women's health and has different molecular subtypes, histological subtypes, and biological features, which act by activating oncogenic factors and suppressing cancer inhibitors. The ubiquitin-proteasome system (UPS) is the main process contributing to protein degradation, and deubiquitinases (DUBs) are reverse enzymes that counteract this process. There is growing evidence that dysregulation of DUBs is involved in the occurrence of BC. Herein, we review recent research findings in BC-associated DUBs, describe their nature, classification, and functions, and discuss the potential mechanisms of DUB-related dysregulation in BC. Furthermore, we present the successful treatment of malignant cancer with DUB inhibitors, as well as analyzing the status of targeting aberrant DUBs in BC.
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Affiliation(s)
- Lili Kong
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo 315211, Zhejiang, China.
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21
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Nayak B, Paul P, Mishra S. Neddylation is essential for malaria transmission in Plasmodium berghei. mBio 2024; 15:e0023224. [PMID: 38411954 PMCID: PMC11005431 DOI: 10.1128/mbio.00232-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
Neddylation is a type of posttranslational modification known to regulate a wide range of cellular processes by covalently conjugating the ubiquitin-like protein Nedd8 to target proteins at lysine residues. However, the role of neddylation in malaria parasites has not been determined. Here, for the first time, we showed that neddylation plays an essential role in malaria transmission in Plasmodium berghei. We found that disruption of Nedd8 did not affect blood-stage propagation, gametocyte development, gamete formation, or zygote formation while abolishing the formation of ookinetes and further transmission of the parasites in mosquitoes. These phenotypic defects in Nedd8 knockout parasites were complemented by reintroducing the gene that restored mosquito transmission to wild-type levels. Our data establish the role of P. berghei Nedd8 in malaria parasite transmission.IMPORTANCENeddylation is a process by which Nedd8 is covalently attached to target proteins through three-step enzymatic cascades. The attachment of Nedd8 residues results in a range of diverse functions, such as cell cycle regulation, metabolism, immunity, and tumorigenesis. The potential neddylation substrates are cullin (CUL) family members, which are implicated in controlling the cell cycle. Cullin neddylation leads to the activation of cullin-RING ubiquitin ligases, which regulate a myriad of biological processes through target-specific ubiquitylation. Neddylation possibly regulates meiosis in zygotes, which subsequently develop into ookinetes. Our findings point to an essential function of this neddylation pathway and highlight its possible importance in designing novel intervention strategies.
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Affiliation(s)
- Bandita Nayak
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Plabita Paul
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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22
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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23
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Zheng K, Li Q, Jiang N, Zhang Y, Zheng Y, Zhang Y, Feng Y, Chen R, Sang X, Chen Q. Plasmodium falciparum selectively degrades α-spectrin of infected erythrocytes after invasion. mBio 2024; 15:e0351023. [PMID: 38470053 PMCID: PMC11005373 DOI: 10.1128/mbio.03510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Remodeling the erythrocyte membrane and skeleton by the malarial parasite Plasmodium falciparum is closely associated with intraerythrocytic development. However, the mechanisms underlying this association remain unclear. In this study, we present evidence that erythrocytic α-spectrin, but not β-spectrin, was dynamically ubiquitinated and progressively degraded during the intraerythrocytic development of P. falciparum, from the ring to the schizont stage. We further observed an upregulated expression of P. falciparum phosphatidylinositol 3-kinase (PfPI3K) in the infected red blood cells during the intraerythrocytic development of the parasite. The data indicated that PfPI3K phosphorylated and activated erythrocytic ubiquitin-protein ligase, leading to increased α-spectrin ubiquitination and degradation during P. falciparum development. We further revealed that inhibition of the activity of PfPI3K impaired P. falciparum development in vitro and Plasmodium berghei infectivity in mice. These findings collectively unveil an important mechanism of PfPI3K-ubiquitin-mediated degradation of α-spectrin during the intraerythrocytic development of Plasmodium species. Proteins in the PfPI3K regulatory pathway are novel targets for effective treatment of severe malaria. IMPORTANCE Plasmodium falciparum is the causative agent of severe malaria that causes millions of deaths globally. The parasite invades human red blood cells and induces a cascade of alterations in erythrocytes for development and proliferation. Remodeling the host erythrocytic cytoskeleton is a necessary process during parasitization, but its regulatory mechanisms remain to be elucidated. In this study, we observed that erythrocytic α-spectrin is selectively degraded after P. falciparum invasion, while β-spectrin remained intact. We found that the α-spectrin chain was profoundly ubiquitinated by E3 ubiquitin ligase and degraded by the 26S proteasome. E3 ubiquitin ligase activity was regulated by P. falciparum phosphatidylinositol 3-kinase (PfPI3K) signaling. Additionally, blocking the PfPI3K-ubiquitin-proteasome pathway in P. falciparum-infected red blood cells reduced parasite proliferation and infectivity. This study deepens our understanding of the regulatory mechanisms of host and malarial parasite interactions and paves the way for the exploration of novel antimalarial drugs.
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Affiliation(s)
- Kexin Zheng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
- Engineering Research Center of Food Fermentation Technology, College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Qilong Li
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yanxin Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yuxin Zheng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Yiwei Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, China
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24
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Rivera O, Sharma M, Dagar S, Shahani N, Ramĺrez-Jarquĺn UN, Crynen G, Karunadharma P, McManus F, Bonneil E, Pierre T, Subramaniam S. Rhes, a striatal enriched protein, regulates post-translational small-ubiquitin-like-modifier (SUMO) modification of nuclear proteins and alters gene expression. Cell Mol Life Sci 2024; 81:169. [PMID: 38589732 PMCID: PMC11001699 DOI: 10.1007/s00018-024-05181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
Rhes (Ras homolog enriched in the striatum), a multifunctional protein that regulates striatal functions associated with motor behaviors and neurological diseases, can shuttle from cell to cell via the formation of tunneling-like nanotubes (TNTs). However, the mechanisms by which Rhes mediates diverse functions remain unclear. Rhes is a small GTPase family member which contains a unique C-terminal Small Ubiquitin-like Modifier (SUMO) E3-like domain that promotes SUMO post-translational modification of proteins (SUMOylation) by promoting "cross-SUMOylation" of the SUMO enzyme SUMO E1 (Aos1/Uba2) and SUMO E2 ligase (Ubc-9). Nevertheless, the identity of the SUMO substrates of Rhes remains largely unknown. Here, by combining high throughput interactome and SUMO proteomics, we report that Rhes regulates the SUMOylation of nuclear proteins that are involved in the regulation of gene expression. Rhes increased the SUMOylation of histone deacetylase 1 (HDAC1) and histone 2B, while decreasing SUMOylation of heterogeneous nuclear ribonucleoprotein M (HNRNPM), protein polybromo-1 (PBRM1) and E3 SUMO-protein ligase (PIASy). We also found that Rhes itself is SUMOylated at 6 different lysine residues (K32, K110, K114, K120, K124, and K245). Furthermore, Rhes regulated the expression of genes involved in cellular morphogenesis and differentiation in the striatum, in a SUMO-dependent manner. Our findings thus provide evidence for a previously undescribed role for Rhes in regulating the SUMOylation of nuclear targets and in orchestrating striatal gene expression via SUMOylation.
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Affiliation(s)
- Oscar Rivera
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Manish Sharma
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Sunayana Dagar
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Neelam Shahani
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Uri Nimrod Ramĺrez-Jarquĺn
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
- National Institute of Cardiology Ignacio Chávez, Department of Pharmacology, Mexico, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Pabalu Karunadharma
- Genomic Core, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Francis McManus
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Thibault Pierre
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
- Department of Chemistry, Université de Montréal, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Srinivasa Subramaniam
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA.
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Norman Fixel Institute for Neurological Diseases, 3009 SW Williston Rd, Gainesville, FL, 32608, USA.
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25
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Fu Y, Li L, Zhang X, Deng Z, Wu Y, Chen W, Liu Y, He S, Wang J, Xie Y, Tu Z, Lyu Y, Wei Y, Wang S, Cui CP, Liu CH, Zhang L. Systematic HOIP interactome profiling reveals critical roles of linear ubiquitination in tissue homeostasis. Nat Commun 2024; 15:2974. [PMID: 38582895 PMCID: PMC10998861 DOI: 10.1038/s41467-024-47289-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
Linear ubiquitination catalyzed by HOIL-1-interacting protein (HOIP), the key component of the linear ubiquitination assembly complex, plays fundamental roles in tissue homeostasis by executing domain-specific regulatory functions. However, a proteome-wide analysis of the domain-specific interactome of HOIP across tissues is lacking. Here, we present a comprehensive mass spectrometry-based interactome profiling of four HOIP domains in nine mouse tissues. The interaction dataset provides a high-quality HOIP interactome resource with an average of approximately 90 interactors for each bait per tissue. HOIP tissue interactome presents a systematic understanding of linear ubiquitination functions in each tissue and also shows associations of tissue functions to genetic diseases. HOIP domain interactome characterizes a set of previously undefined linear ubiquitinated substrates and elucidates the cross-talk among HOIP domains in physiological and pathological processes. Moreover, we show that linear ubiquitination of Integrin-linked protein kinase (ILK) decreases focal adhesion formation and promotes the detachment of Shigella flexneri-infected cells. Meanwhile, Hoip deficiency decreases the linear ubiquitination of Smad ubiquitination regulatory factor 1 (SMURF1) and enhances its E3 activity, finally causing a reduced bone mass phenotype in mice. Overall, our work expands the knowledge of HOIP-interacting proteins and provides a platform for further discovery of linear ubiquitination functions in tissue homeostasis.
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Affiliation(s)
- Yesheng Fu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Lei Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Xin Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Zhikang Deng
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Ying Wu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Wenzhe Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yuchen Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Shan He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Jian Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yuping Xie
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Zhiwei Tu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yadi Lyu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yange Wei
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Shujie Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Lingqiang Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.
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26
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Zhang J, Tao P, Deuitch NT, Yu X, Askentijevich I, Zhou Q. Proteasome-Associated Syndromes: Updates on Genetics, Clinical Manifestations, Pathogenesis, and Treatment. J Clin Immunol 2024; 44:88. [PMID: 38578475 DOI: 10.1007/s10875-024-01692-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
The ubiquitin-proteasome system (UPS) has a critical role in post-translational protein modification that is essential for the maintenance of all cellular functions, including immune responses. The proteasome complex is ubiquitously expressed and is responsible for degradation of short-lived structurally abnormal, misfolded and not-needed proteins that are targeted for degradation via ubiquitin conjugation. Over the last 14 years, an increasing number of human diseases have been linked to pathogenic variants in proteasome subunits and UPS regulators. Defects of the proteasome complex or its chaperons - which have a regulatory role in the assembly of the proteasome - disrupt protein clearance and cellular homeostasis, leading to immune dysregulation, severe inflammation, and neurodevelopmental disorders in humans. Proteasome-associated diseases have complex inheritance, including monogenic, digenic and oligogenic disorders and can be dominantly or recessively inherited. In this review, we summarize the current known genetic causes of proteasomal disease, and discuss the molecular pathogenesis of these conditions based on the function and cellular expression of mutated proteins in the proteasome complex.
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Affiliation(s)
- Jiahui Zhang
- Department of Rheumatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- National Clinical Research Center for Kidney Diseases, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Panfeng Tao
- Department of Rheumatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
| | - Natalie T Deuitch
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaomin Yu
- Department of Rheumatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
| | - Ivona Askentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qing Zhou
- Department of Rheumatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, and Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
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27
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Li H, Ji Z, Paulo JA, Gygi SP, Rapoport TA. Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation. Mol Cell 2024; 84:1290-1303.e7. [PMID: 38401542 DOI: 10.1016/j.molcel.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 12/12/2023] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
Most eukaryotic proteins are degraded by the 26S proteasome after modification with a polyubiquitin chain. Substrates lacking unstructured segments cannot be degraded directly and require prior unfolding by the Cdc48 ATPase (p97 or VCP in mammals) in complex with its ubiquitin-binding partner Ufd1-Npl4 (UN). Here, we use purified yeast components to reconstitute Cdc48-dependent degradation of well-folded model substrates by the proteasome. We show that a minimal system consists of the 26S proteasome, the Cdc48-UN ATPase complex, the proteasome cofactor Rad23, and the Cdc48 cofactors Ubx5 and Shp1. Rad23 and Ubx5 stimulate polyubiquitin binding to the 26S proteasome and the Cdc48-UN complex, respectively, allowing these machines to compete for substrates before and after their unfolding. Shp1 stimulates protein unfolding by the Cdc48-UN complex rather than substrate recruitment. Experiments in yeast cells confirm that many proteins undergo bidirectional substrate shuttling between the 26S proteasome and Cdc48 ATPase before being degraded.
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Affiliation(s)
- Hao Li
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Zhejian Ji
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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28
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Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G. Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Mol Cell 2024; 84:1304-1320.e16. [PMID: 38382526 PMCID: PMC10997478 DOI: 10.1016/j.molcel.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/07/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. Substrates are recognized by substrate receptors, such as Fbox or BCbox proteins. Meanwhile, CRLs employ assorted ubiquitin-carrying enzymes (UCEs, which are a collection of E2 and ARIH-family E3s) specialized for either initial substrate ubiquitylation (priming) or forging poly-ubiquitin chains. We discovered specific human CRL-UCE pairings governing substrate priming. The results reveal pairing of CUL2-based CRLs and UBE2R-family UCEs in cells, essential for efficient PROTAC-induced neo-substrate degradation. Despite UBE2R2's intrinsic programming to catalyze poly-ubiquitylation, CUL2 employs this UCE for geometrically precise PROTAC-dependent ubiquitylation of a neo-substrate and for rapid priming of substrates recruited to diverse receptors. Cryo-EM structures illuminate how CUL2-based CRLs engage UBE2R2 to activate substrate ubiquitylation. Thus, pairing with a specific UCE overcomes E2 catalytic limitations to drive substrate ubiquitylation and targeted protein degradation.
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Affiliation(s)
- Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Holly A Byers
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Spencer Hill
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Trent Hinkle
- Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | | | | | | | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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Roberts JB, Boldvig OLG, Aubourg G, Kanchenapally ST, Deehan DJ, Rice SJ, Loughlin J. Specific isoforms of the ubiquitin ligase gene WWP2 are targets of osteoarthritis genetic risk via a differentially methylated DNA sequence. Arthritis Res Ther 2024; 26:78. [PMID: 38570801 PMCID: PMC10988806 DOI: 10.1186/s13075-024-03315-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Transitioning from a genetic association signal to an effector gene and a targetable molecular mechanism requires the application of functional fine-mapping tools such as reporter assays and genome editing. In this report, we undertook such studies on the osteoarthritis (OA) risk that is marked by single nucleotide polymorphism (SNP) rs34195470 (A > G). The OA risk-conferring G allele of this SNP associates with increased DNA methylation (DNAm) at two CpG dinucleotides within WWP2. This gene encodes a ubiquitin ligase and is the host gene of microRNA-140 (miR-140). WWP2 and miR-140 are both regulators of TGFβ signaling. METHODS Nucleic acids were extracted from adult OA (arthroplasty) and foetal cartilage. Samples were genotyped and DNAm quantified by pyrosequencing at the two CpGs plus 14 flanking CpGs. CpGs were tested for transcriptional regulatory effects using a chondrocyte cell line and reporter gene assay. DNAm was altered using epigenetic editing, with the impact on gene expression determined using RT-qPCR. In silico analysis complemented laboratory experiments. RESULTS rs34195470 genotype associates with differential methylation at 14 of the 16 CpGs in OA cartilage, forming a methylation quantitative trait locus (mQTL). The mQTL is less pronounced in foetal cartilage (5/16 CpGs). The reporter assay revealed that the CpGs reside within a transcriptional regulator. Epigenetic editing to increase their DNAm resulted in altered expression of the full-length and N-terminal transcript isoforms of WWP2. No changes in expression were observed for the C-terminal isoform of WWP2 or for miR-140. CONCLUSIONS As far as we are aware, this is the first experimental demonstration of an OA association signal targeting specific transcript isoforms of a gene. The WWP2 isoforms encode proteins with varying substrate specificities for the components of the TGFβ signaling pathway. Future analysis should focus on the substrates regulated by the two WWP2 isoforms that are the targets of this genetic risk.
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Affiliation(s)
- Jack B Roberts
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Olivia L G Boldvig
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - Guillaume Aubourg
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - S Tanishq Kanchenapally
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - David J Deehan
- Freeman Hospital, Newcastle University Teaching Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne, NE1 3BZ, UK.
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30
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Ikeda T, Yamazaki K, Okumura F, Kamura T, Nakatsukasa K. Role of the San1 ubiquitin ligase in the heat stress-induced degradation of nonnative Nup1 in the nuclear pore complex. Genetics 2024; 226:iyae017. [PMID: 38302116 DOI: 10.1093/genetics/iyae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 11/21/2022] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The nuclear pore complex (NPC) mediates the selective exchange of macromolecules between the nucleus and the cytoplasm. Neurodegenerative diseases such as amyotrophic lateral sclerosis are characterized by mislocalization of nucleoporins (Nups), transport receptors, and Ras-related nuclear proteins into nucleoplasmic or cytosolic aggregates, underscoring the importance of precise assembly of the NPC. The assembly state of large protein complexes is strictly monitored by the protein quality control system. The ubiquitin-proteasome system may eliminate aberrant, misfolded, and/or orphan components; however, the involvement of the ubiquitin-proteasome system in the degradation of nonnative Nups in the NPC remains unclear. Here, we show that in Saccharomyces cerevisiae, although Nup1 (the FG-Nup component of the central core of the NPC) was stable, C-terminally green fluorescent protein-tagged Nup1, which had been incorporated into the NPC, was degraded by the proteasome especially under heat stress conditions. The degradation was dependent on the San1 ubiquitin ligase and Cdc48/p97, as well as its cofactor Doa1. We also demonstrate that San1 weakly but certainly contributes to the degradation of nontagged endogenous Nup1 in cells defective in NPC biogenesis by the deletion of NUP120. In addition, the overexpression of SAN1 exacerbated the growth defect phenotype of nup120Δ cells, which may be caused by excess degradation of defective Nups due to the deletion of NUP120. These biochemical and genetic data suggest that San1 is involved in the degradation of nonnative Nups generated by genetic mutation or when NPC biogenesis is impaired.
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Affiliation(s)
- Takanari Ikeda
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
| | - Kenji Yamazaki
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Fukuoka 813-8529, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
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Rasool S, Shomali T, Truong L, Croteau N, Veyron S, Bustillos BA, Springer W, Fiesel FC, Trempe JF. Identification and structural characterization of small molecule inhibitors of PINK1. Sci Rep 2024; 14:7739. [PMID: 38565869 PMCID: PMC10987619 DOI: 10.1038/s41598-024-58285-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Mutations in PINK1 and Parkin cause early-onset Parkinson's Disease (PD). PINK1 is a kinase which functions as a mitochondrial damage sensor and initiates mitochondrial quality control by accumulating on the damaged organelle. There, it phosphorylates ubiquitin, which in turn recruits and activates Parkin, an E3 ubiquitin ligase. Ubiquitylation of mitochondrial proteins leads to the autophagic degradation of the damaged organelle. Pharmacological modulation of PINK1 constitutes an appealing avenue to study its physiological function and develop therapeutics. In this study, we used a thermal shift assay with insect PINK1 to identify small molecules that inhibit ATP hydrolysis and ubiquitin phosphorylation. PRT062607, an SYK inhibitor, is the most potent inhibitor in our screen and inhibits both insect and human PINK1, with an IC50 in the 0.5-3 µM range in HeLa cells and dopaminergic neurons. The crystal structures of insect PINK1 bound to PRT062607 or CYC116 reveal how the compounds interact with the ATP-binding pocket. PRT062607 notably engages with the catalytic aspartate and causes a destabilization of insert-2 at the autophosphorylation dimer interface. While PRT062607 is not selective for PINK1, it provides a scaffold for the development of more selective and potent inhibitors of PINK1 that could be used as chemical probes.
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Affiliation(s)
- Shafqat Rasool
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Tara Shomali
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Luc Truong
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | - Simon Veyron
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada
| | | | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Fabienne C Fiesel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, Centre de Recherche en Biologie Structurale, and Structural Genomics Consortium, McGill University, 3655 Prom Sir William Osler, Montréal, QC, H3G 1Y6, Canada.
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Ju D, Wu S, Li L, Xie Y. Ubiquitylation-independent cotranslational degradation of dihydrofolate reductase and ubiquitin. Biochem Biophys Res Commun 2024; 702:149651. [PMID: 38350414 DOI: 10.1016/j.bbrc.2024.149651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Nascent proteins are degraded during or immediately after synthesis, a process called cotranslational protein degradation (CTPD). Although CTPD was observed decades ago, it has never been fully explored mechanistically and functionally. We show here that dihydrofolate reductase (DHFR) and ubiquitin (Ub), two stable proteins widely used in protein degradation studies, are actually subject to CTPD. Unlike canonical posttranslational protein degradation, CTPD of DHFR and Ub does not require prior ubiquitylation. Our data also suggest that protein expression level and N-terminal folding pattern may be two critical determinants for CTPD. Thus, this study reveals that CTPD plays a role in regulating the homeostasis of long-lived proteins and provides insights into the mechanism of CTPD.
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Affiliation(s)
- Donghong Ju
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shichao Wu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Li Li
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Youming Xie
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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Zhang S, Hu N, Yu F. Insights into a functional model of key deubiquitinases UBP12/13 in plants. New Phytol 2024; 242:424-430. [PMID: 38406992 DOI: 10.1111/nph.19639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Understanding the complexities of protein ubiquitination is crucial, as it plays a multifaceted role in controlling protein stability, activity, subcellular localization, and interaction, which are central to diverse biological processes. Deubiquitinases (DUBs) serve to reverse ubiquitination, but research progress in plant DUBs is noticeably limited. Among existing studies, UBIQUITIN-SPECIFIC PROTEASE 12 (UBP12) and UBP13 have garnered attention for their extensive role in diverse biological processes in plants. This review systematically summarizes the recent advancements in UBP12/13 studies, emphasizing their function, and their substrate specificity, their relationship with E3 ubiquitin ligases, and the similarities and differences with their mammalian orthologue, USP7. By unraveling the molecular mechanisms of UBP12/13, this review offers in-depth insights into the ubiquitin-proteasome system (UPS) in plants and aims to catalyze further explorations and comprehensive understanding in this field.
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Affiliation(s)
- Shiqi Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100083, China
| | - Ningning Hu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100083, China
| | - Feifei Yu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100083, China
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34
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Liang CT, Roscow O, Zhang W. Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc 2024; 2024:pdb.over107784. [PMID: 36997275 DOI: 10.1101/pdb.over107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Ontario M5G1M1, Canada
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35
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Sergeeva KV, Tyganov SA, Zaripova KA, Bokov RO, Nikitina LV, Konstantinova TS, Kalamkarov GR, Shenkman BS. Mechanical and signaling responses of unloaded rat soleus muscle to chronically elevated β-myosin activity. Arch Biochem Biophys 2024; 754:109961. [PMID: 38492659 DOI: 10.1016/j.abb.2024.109961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
It has been reported that muscle functional unloading is accompanied by an increase in motoneuronal excitability despite the elimination of afferent input. Thus, we hypothesized that pharmacological potentiation of spontaneous contractile soleus muscle activity during hindlimb unloading could activate anabolic signaling pathways and prevent the loss of muscle mass and strength. To investigate these aspects and underlying molecular mechanisms, we used β-myosin allosteric effector Omecamtiv Mekarbil (OM). We found that OM partially prevented the loss of isometric strength and intrinsic stiffness of the soleus muscle after two weeks of disuse. Notably, OM was able to attenuate the unloading-induced decrease in the rate of muscle protein synthesis (MPS). At the same time, the use of drug neither prevented the reduction in the markers of translational capacity (18S and 28S rRNA) nor activation of the ubiquitin-proteosomal system, which is evidenced by a decrease in the cross-sectional area of fast and slow muscle fibers. These results suggest that chemically-induced increase in low-intensity spontaneous contractions of the soleus muscle during functional unloading creates prerequisites for protein synthesis. At the same time, it should be assumed that the use of OM is advisable with pharmacological drugs that inhibit the expression of ubiquitin ligases.
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Affiliation(s)
- K V Sergeeva
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia.
| | - S A Tyganov
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - K A Zaripova
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - R O Bokov
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - L V Nikitina
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - T S Konstantinova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - G R Kalamkarov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - B S Shenkman
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
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Costas-Insua C, Hermoso-López A, Moreno E, Montero-Fernández C, Álvaro-Blázquez A, Maroto IB, Sánchez-Ruiz A, Diez-Alarcia R, Blázquez C, Morales P, Canela EI, Casadó V, Urigüen L, Perea G, Bellocchio L, Rodríguez-Crespo I, Guzmán M. The CB 1 receptor interacts with cereblon and drives cereblon deficiency-associated memory shortfalls. EMBO Mol Med 2024; 16:755-783. [PMID: 38514794 PMCID: PMC11018632 DOI: 10.1038/s44321-024-00054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Cereblon/CRBN is a substrate-recognition component of the Cullin4A-DDB1-Roc1 E3 ubiquitin ligase complex. Destabilizing mutations in the human CRBN gene cause a form of autosomal recessive non-syndromic intellectual disability (ARNSID) that is modelled by knocking-out the mouse Crbn gene. A reduction in excitatory neurotransmission has been proposed as an underlying mechanism of the disease. However, the precise factors eliciting this impairment remain mostly unknown. Here we report that CRBN molecules selectively located on glutamatergic neurons are necessary for proper memory function. Combining various in vivo approaches, we show that the cannabinoid CB1 receptor (CB1R), a key suppressor of synaptic transmission, is overactivated in CRBN deficiency-linked ARNSID mouse models, and that the memory deficits observed in these animals can be rescued by acute CB1R-selective pharmacological antagonism. Molecular studies demonstrated that CRBN interacts physically with CB1R and impairs the CB1R-Gi/o-cAMP-PKA pathway in a ubiquitin ligase-independent manner. Taken together, these findings unveil that CB1R overactivation is a driving mechanism of CRBN deficiency-linked ARNSID and anticipate that the antagonism of CB1R could constitute a new therapy for this orphan disease.
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Affiliation(s)
- Carlos Costas-Insua
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Alba Hermoso-López
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Carlos Montero-Fernández
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Alicia Álvaro-Blázquez
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Irene B Maroto
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | | | - Rebeca Diez-Alarcia
- Department of Pharmacology, University of the Basque Country/Euskal Herriko Unibertsitatea, 48940, Leioa, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029, Madrid, Spain
- BioBizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Cristina Blázquez
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Paula Morales
- Instituto de Química Médica, CSIC, 28006, Madrid, Spain
| | - Enric I Canela
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Leyre Urigüen
- Department of Pharmacology, University of the Basque Country/Euskal Herriko Unibertsitatea, 48940, Leioa, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029, Madrid, Spain
- BioBizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | | | - Luigi Bellocchio
- Institut National de la Santé et de la Recherche Médicale (INSERM) and University of Bordeaux, NeuroCentre Magendie, Physiopathologie de la Plasticité Neuronale, U1215, 33077, Bordeaux, France
| | - Ignacio Rodríguez-Crespo
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Manuel Guzmán
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain.
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Hu J, Luo M, Zhou X, Wang Z, Yan L, Hong D, Yang G, Zhang X. RING-type E3 ligase BnaJUL1 ubiquitinates and degrades BnaTBCC1 to regulate drought tolerance in Brassica napus L. Plant Cell Environ 2024; 47:1023-1040. [PMID: 37984059 DOI: 10.1111/pce.14770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/26/2023] [Accepted: 09/27/2023] [Indexed: 11/22/2023]
Abstract
Drought stress poses a persistent threat to field crops and significantly limits global agricultural productivity. Plants employ ubiquitin-dependent degradation as a crucial post-translational regulatory mechanism to swiftly adapt to changing environmental conditions. JUL1 is a RING-type E3 ligase related to drought stress in Arabidopsis. In this study, we explored the function of BnaJUL1 (a homologous gene of JUL1 in Brassica napus) and discovered a novel gene BnaTBCC1 participating in drought tolerance. First, we utilised BnaJUL1-cri materials through the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 system. Second, we confirmed that BnaJUL1 regulated drought tolerance through the drought tolerance assay and transcriptome analysis. Then, we identified a series of proteins interacting with BnaJUL1 through yeast library screening, including BnaTBCC1 (a tubulin binding cofactor C domain-containing protein); whose homologous gene TBCC1 knockdown mutants (tbcc1-1) exhibited ABA-sensitive germination in Arabidopsis, we then confirmed the involvement of BnaTBCC1 in drought tolerance in both Arabidopsis and Brassica. Finally, we established that BnaJUL1 could ubiquitinate and degrade BnaTBCC1 to regulate drought tolerance. Consequently, our study unveils BnaJUL1 as a novel regulator that ubiquitinates and degrades BnaTBCC1 to modulate drought tolerance and provided desirable germplasm for further breeding of drought tolerance in rapeseed.
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Affiliation(s)
- Jin Hu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Mudan Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xianming Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhaoyang Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Li Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guangsheng Yang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohui Zhang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
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Ye F, Xia T, Zhao M, Zhao W, Min P, Wang Y, Wang Q, Zhang Y, Du J. PlexinA1 promotes gastric cancer migration through preventing MICAL1 protein ubiquitin/proteasome-mediated degradation in a Rac1-dependent manner. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167124. [PMID: 38508474 DOI: 10.1016/j.bbadis.2024.167124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
Metastasis promotes the development of tumors and is a significant cause of gastric cancer death. For metastasis to proceed, tumor cells must become mobile by modulating their cytoskeleton. MICAL1 (Molecule Interacting with CasL1) is known as an actin cytoskeleton regulator, but the mechanisms by which it drives gastric cancer cell migration are still unclear. Analysis of gastric cancer tissues revealed that MICAL1 expression is dramatically upregulated in stomach adenocarcinoma (STAD) samples as compared to noncancerous stomach tissues. Patients with high MICAL1 expression had shorter overall survival (OS), post-progression survival (PPS) and first-progression survival (FPS) compared with patients with low MICAL1 expression. RNAi-mediated silencing of MICAL1 inhibited the expression of Vimentin, a protein involved in epithelial-mesenchymal transition. This effect correlates with a significant reduction in gastric cancer cell migration. MICAL1 overexpression reversed these preventive effects. Immunoprecipitation experiments and immunofluorescence assays revealed that PlexinA1 forms a complex with MICAL1. Importantly, specific inhibition of PlexinA1 blocked the Rac1 activation and ROS production, which, in turn, impaired MICAL1 protein stability by accelerating MICAL1 ubiquitin/proteasome-dependent degradation. Overexpression of PlexinA1 enhanced Rac1 activation, ROS production, MICAL1 and Vimentin expressions, and favored cell migration. In conclusion, this study identified MICAL1 as an important facilitator of gastric cancer cell migration, at least in part, by affecting Vimentin expression and PlexinA1 promotes gastric cancer cell migration by binding to and suppressing MICAL1 degradation in a Rac1/ROS-dependent manner.
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Affiliation(s)
- Fengwen Ye
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Tianxiang Xia
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - MingYu Zhao
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Weizhen Zhao
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Pengxiang Min
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yueyuan Wang
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qianwen Wang
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yujie Zhang
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jun Du
- Department of Physiology, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
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Mughal S, Sabater-Arcis M, Artero R, Ramón-Azcón J, Fernández-Costa JM. Taurine activates the AKT-mTOR axis to restore muscle mass and contractile strength in human 3D in vitro models of steroid myopathy. Dis Model Mech 2024; 17:dmm050540. [PMID: 38655653 DOI: 10.1242/dmm.050540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/06/2024] [Indexed: 04/26/2024] Open
Abstract
Steroid myopathy is a clinically challenging condition exacerbated by prolonged corticosteroid use or adrenal tumors. In this study, we engineered a functional three-dimensional (3D) in vitro skeletal muscle model to investigate steroid myopathy. By subjecting our bioengineered muscle tissues to dexamethasone treatment, we reproduced the molecular and functional aspects of this disease. Dexamethasone caused a substantial reduction in muscle force, myotube diameter and induced fatigue. We observed nuclear translocation of the glucocorticoid receptor (GCR) and activation of the ubiquitin-proteasome system within our model, suggesting their coordinated role in muscle atrophy. We then examined the therapeutic potential of taurine in our 3D model for steroid myopathy. Our findings revealed an upregulation of phosphorylated AKT by taurine, effectively countering the hyperactivation of the ubiquitin-proteasomal pathway. Importantly, we demonstrate that discontinuing corticosteroid treatment was insufficient to restore muscle mass and function. Taurine treatment, when administered concurrently with corticosteroids, notably enhanced contractile strength and protein turnover by upregulating the AKT-mTOR axis. Our model not only identifies a promising therapeutic target, but also suggests combinatorial treatment that may benefit individuals undergoing corticosteroid treatment or those diagnosed with adrenal tumors.
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Affiliation(s)
- Sheeza Mughal
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, E08028 Barcelona, Spain
| | - Maria Sabater-Arcis
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
- Translational Genomics Group, Incliva Health Research Institute, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
- Joint Unit Incliva- CIPF, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
| | - Ruben Artero
- University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
- Translational Genomics Group, Incliva Health Research Institute, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
- Joint Unit Incliva- CIPF, Dr Moliner 50, E46100 Burjassot, Valencia, Spain
| | - Javier Ramón-Azcón
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, E08028 Barcelona, Spain
- Institució Catalana de Reserca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, E08010 Barcelona, Spain
| | - Juan M Fernández-Costa
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), C/Baldiri Reixac 10-12, E08028 Barcelona, Spain
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40
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Mariner BL, Rodriguez AS, Heath OC, McCormick MA. Induction of proteasomal activity in mammalian cells by lifespan-extending tRNA synthetase inhibitors. GeroScience 2024; 46:1755-1773. [PMID: 37749371 PMCID: PMC10828360 DOI: 10.1007/s11357-023-00938-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
We have recently shown that multiple tRNA synthetase inhibitors can greatly increase lifespan in multiple models by acting through the conserved transcription factor ATF4. Here, we show that these compounds, and several others of the same class, can greatly upregulate mammalian ATF4 in cells in vitro, in a dose dependent manner. Further, RNASeq analysis of these cells pointed toward changes in protein turnover. In subsequent experiments here we show that multiple tRNA synthetase inhibitors can greatly upregulate activity of the ubiquitin proteasome system (UPS) in cells in an ATF4-dependent manner. The UPS plays an important role in the turnover of many damaged or dysfunctional proteins in an organism. Increasing UPS activity has been shown to enhance the survival of Huntington's disease cell models, but there are few known pharmacological enhancers of the UPS. Additionally, we see separate ATF4 dependent upregulation of macroautophagy upon treatment with tRNA synthetase inhibitors. Protein degradation is an essential cellular process linked to many important human diseases of aging such as Alzheimer's disease and Huntington's disease. These drugs' ability to enhance proteostasis more broadly could have wide-ranging implications in the treatment of important age-related neurodegenerative diseases.
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Affiliation(s)
- Blaise L Mariner
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA
| | - Antonio S Rodriguez
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Olivia C Heath
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA.
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Feng Z, Yin J, Zhang Z, Chen Z, Huang L, Tang N, Wang K. O-GlcNAcylation of E3 ubiquitin ligase SKP2 promotes hepatocellular carcinoma proliferation. Oncogene 2024; 43:1149-1159. [PMID: 38396292 DOI: 10.1038/s41388-024-02977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
O-linked-β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) and ubiquitination are critical posttranslational modifications that regulate tumor development and progression. The continuous progression of the cell cycle is the fundamental cause of tumor proliferation. S-phase kinase-associated protein 2 (SKP2), an important E3 ubiquitin ligase, assumes a pivotal function in the regulation of the cell cycle. However, it is still unclear whether SKP2 is an effector of O-GlcNAcylation that affects tumor progression. In this study, we found that SKP2 interacted with O-GlcNAc transferase (OGT) and was highly O-GlcNAcylated in hepatocellular carcinoma (HCC). Mechanistically, the O-GlcNAcylation at Ser34 stabilized SKP2 by reducing its ubiquitination and degradation mediated by APC-CDH1. Moreover, the O-GlcNAcylation of SKP2 enhanced its binding ability with SKP1, thereby enhancing its ubiquitin ligase function. Consequently, SKP2 facilitated the transition from the G1-S phase of the cell cycle by promoting the ubiquitin degradation of cell cycle-dependent kinase inhibitors p27 and p21. Additionally, targeting the O-GlcNAcylation of SKP2 significantly suppressed the proliferation of HCC. Altogether, our findings reveal that O-GlcNAcylation, a novel posttranslational modification of SKP2, plays a crucial role in promoting HCC proliferation, and targeting the O-GlcNAcylation of SKP2 may become a new therapeutic strategy to impede the progression of HCC.
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Affiliation(s)
- Zhongqi Feng
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Jiaxin Yin
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Zhirong Zhang
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Zhen Chen
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Luyi Huang
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China.
| | - Ni Tang
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China.
| | - Kai Wang
- Key Laboratory of Molecular Biology for Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China.
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42
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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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Griffith-Jones S, Álvarez L, Mukhopadhyay U, Gharbi S, Rettel M, Adams M, Hennig J, Bhogaraju S. Structural basis for RAD18 regulation by MAGEA4 and its implications for RING ubiquitin ligase binding by MAGE family proteins. EMBO J 2024; 43:1273-1300. [PMID: 38448672 PMCID: PMC10987633 DOI: 10.1038/s44318-024-00058-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024] Open
Abstract
MAGEA4 is a cancer-testis antigen primarily expressed in the testes but aberrantly overexpressed in several cancers. MAGEA4 interacts with the RING ubiquitin ligase RAD18 and activates trans-lesion DNA synthesis (TLS), potentially favouring tumour evolution. Here, we employed NMR and AlphaFold2 (AF) to elucidate the interaction mode between RAD18 and MAGEA4, and reveal that the RAD6-binding domain (R6BD) of RAD18 occupies a groove in the C-terminal winged-helix subdomain of MAGEA4. We found that MAGEA4 partially displaces RAD6 from the RAD18 R6BD and inhibits degradative RAD18 autoubiquitination, which could be countered by a competing peptide of the RAD18 R6BD. AlphaFold2 and cross-linking mass spectrometry (XL-MS) also revealed an evolutionary invariant intramolecular interaction between the catalytic RING and the DNA-binding SAP domains of RAD18, which is essential for PCNA mono-ubiquitination. Using interaction proteomics, we found that another Type-I MAGE, MAGE-C2, interacts with the RING ubiquitin ligase TRIM28 in a manner similar to the MAGEA4/RAD18 complex, suggesting that the MAGEA4 peptide-binding groove also serves as a ligase-binding cleft in other type-I MAGEs. Our data provide new insights into the mechanism and regulation of RAD18-mediated PCNA mono-ubiquitination.
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Affiliation(s)
| | - Lucía Álvarez
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Urbi Mukhopadhyay
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Sarah Gharbi
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Mandy Rettel
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Michael Adams
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Janosch Hennig
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
- Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Sagar Bhogaraju
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, France.
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Cai H, Wu X, Mao J, Tong Z, Yan D, Weng Y, Zheng Q. Sequential release of interacting proteins and Ub-modifying enzymes by disulfide heterotypic ubiquitin reagents. Bioorg Chem 2024; 145:107186. [PMID: 38387394 DOI: 10.1016/j.bioorg.2024.107186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Heterotypic ubiquitin (Ub) chains have emerged as fundamental components in a wide range of cellular processes. The integrative identification of Ub-interacting proteins (readers) and Ub-modifying enzymes (writers and erasers) that selectively recognize and regulate heterotypic ubiquitination may provide crucial insights into these processes. In this study, we employed the bifunctional molecule-assisted (CAET) strategy to develop a type of disulfide bond-activated heterotypic Ub reagents, which allowed to enrich heterotypic Ub-interacting proteins and modifying enzymes simultaneously. The sequential release of readers which are non-covalently bound and writers or erasers which are covalently conjugated by using urea and reductant, respectively, combined with label-free quantitative (LFQ) MS indicated that these heterotypic Ub reagents would facilitate future investigations into functional roles played by heterotypic Ub chains.
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Affiliation(s)
- Hongyi Cai
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China; Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiangwei Wu
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Junxiong Mao
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China; Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zebin Tong
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dingfei Yan
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Yicheng Weng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qingyun Zheng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China.
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Hsieh Y, Augur ZM, Arbery M, Ashour N, Barrett K, Pearse RV, Tio ES, Duong DM, Felsky D, De Jager PL, Bennett DA, Seyfried NT, Young‐Pearse TL. Person-specific differences in ubiquitin-proteasome mediated proteostasis in human neurons. Alzheimers Dement 2024; 20:2952-2967. [PMID: 38470006 PMCID: PMC11032531 DOI: 10.1002/alz.13680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 03/13/2024]
Abstract
BACKGROUND Impairment of the ubiquitin-proteasome system (UPS) has been implicated in abnormal protein accumulation in Alzheimer's disease. It remains unclear if genetic variation affects the intrinsic properties of neurons that render some individuals more vulnerable to UPS impairment. METHODS Induced pluripotent stem cell (iPSC)-derived neurons were generated from over 50 genetically variant and highly characterized participants of cohorts of aging. Proteomic profiling, proteasome activity assays, and Western blotting were employed to examine neurons at baseline and in response to UPS perturbation. RESULTS Neurons with lower basal UPS activity were more vulnerable to tau accumulation following mild UPS inhibition. Chronic reduction in proteasome activity in human neurons induced compensatory elevation of regulatory proteins involved in proteostasis and several proteasome subunits. DISCUSSION These findings reveal that genetic variation influences basal UPS activity in human neurons and differentially sensitizes them to external factors perturbing the UPS, leading to the accumulation of aggregation-prone proteins such as tau. HIGHLIGHTS Polygenic risk score for AD is associated with the ubiquitin-proteasome system (UPS) in neurons. Basal proteasome activity correlates with aggregation-prone protein levels in neurons. Genetic variation affects the response to proteasome inhibition in neurons. Neuronal proteasome perturbation induces an elevation in specific proteins involved in proteostasis. Low basal proteasome activity leads to enhanced tau accumulation with UPS challenge.
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Affiliation(s)
- Yi‐Chen Hsieh
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Zachary M. Augur
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Mason Arbery
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Nancy Ashour
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Katharine Barrett
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Richard V. Pearse
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Earvin S. Tio
- Department of Psychiatry and Institute of Medical ScienceUniversity of TorontoTorontoOntarioCanada
| | - Duc M. Duong
- Department of BiochemistryEmory University School of MedicineAtlantaGeorgiaUSA
| | - Daniel Felsky
- Department of Psychiatry and Institute of Medical ScienceUniversity of TorontoTorontoOntarioCanada
- Krembil Centre for NeuroinformaticsCentre for Addiction and Mental HealthTorontoOntarioCanada
| | - Philip L. De Jager
- Center for Translational and Computational NeuroimmunologyDepartment of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging BrainColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Nicholas T. Seyfried
- Department of BiochemistryEmory University School of MedicineAtlantaGeorgiaUSA
- Department of NeurologyEmory University School of MedicineAtlantaGeorgiaUSA
| | - Tracy L. Young‐Pearse
- Ann Romney Centerfor Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
- Harvard Stem Cell InstituteHarvard UniversityCambridgeMassachusettsUSA
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Li Q, Kang J, Liu N, Huang J, Zhang X, Pang K, Zhang S, Wang M, Zhao Y, Dong S, Li H, Zhao D, Lu F, Zhang W. Hydrogen sulfide improves endothelial barrier function by modulating the ubiquitination degradation of KLF4 through TRAF7 S-sulfhydration in diabetic aorta. Free Radic Biol Med 2024; 216:118-138. [PMID: 38479633 DOI: 10.1016/j.freeradbiomed.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Anomalous vascular endothelium significantly contributes to various cardiovascular diseases. VE-cadherin plays a vital role in governing the endothelial barrier. Krüppel-like factor 4(KLF4), as a transcription factor, which binds the VE-cadherin promoter and enhances its transcription. Tumor necrosis factor receptor-associated factor 7 (TRAF7) is an E3 ubiquitin ligase that has been shown to modulate the degradation of KLF4. H2S can covalently modify cysteine residues on proteins through S-sulfhydration, thereby influencing the structure and functionality of the target protein. However, the role of S-sulfhydration on endothelial barrier integrity remains to be comprehensively elucidated. This study aims to investigate whether protein S-sulfhydration in the endothelium regulates endothelial integrity and its underlying mechanism. In this study, we observed that protein S-sulfhydration was reduced in the endothelium during diabetes and TRAF7 was the main target. Overexpression of TRAF7-Cys327 mutant could mitigate the endothelial barrier damage by weakening TRAF7 interaction with KLF4 and reducing ubiquitination degradation of KLF4. In conclusion, our research demonstrates that H2S plays a pivotal role in regulating S-sulfhydration of TRAF7 at Cys327. This regulation effectively inhibits the ubiquitin-mediated degradation of KLF4, resulting in an upregulation of VE-cadherin levels. This molecular mechanism contributes to the prevention of endothelial barrier damage.
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Affiliation(s)
- Qianzhu Li
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Jiaxin Kang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Ning Liu
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Jiayi Huang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Xueya Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Kemiao Pang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Shiwu Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Mengyi Wang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Yajun Zhao
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Shiyun Dong
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Hongxia Li
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China
| | - Dechao Zhao
- Department of Cardiology, First Affiliated Hospital of Harbin Medical University, Harbin 150001, China.
| | - Fanghao Lu
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China.
| | - Weihua Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin 150086, China.
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47
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Li K, Zhang J, Lyu H, Yang J, Wei W, Wang Y, Luo H, Zhang Y, Jiang X, Yi H, Wang M, Zhang C, Wu K, Xiao L, Wen W, Xu H, Li G, Wan Y, Yang F, Yang R, Fu X, Qin B, Zhou Z, Zhang H, Lee M. CSN6-SPOP-HMGCS1 Axis Promotes Hepatocellular Carcinoma Progression via YAP1 Activation. Adv Sci (Weinh) 2024; 11:e2306827. [PMID: 38308184 PMCID: PMC11005689 DOI: 10.1002/advs.202306827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/15/2024] [Indexed: 02/04/2024]
Abstract
Cholesterol metabolism has important roles in maintaining membrane integrity and countering the development of diseases such as obesity and cancers. Cancer cells sustain cholesterol biogenesis for their proliferation and microenvironment reprograming even when sterols are abundant. However, efficacy of targeting cholesterol metabolism for cancer treatment is always compromised. Here it is shown that CSN6 is elevated in HCC and is a positive regulator of hydroxymethylglutaryl-CoA synthase 1 (HMGCS1) of mevalonate (MVA) pathway to promote tumorigenesis. Mechanistically, CSN6 antagonizes speckle-type POZ protein (SPOP) ubiquitin ligase to stabilize HMGCS1, which in turn activates YAP1 to promote tumor growth. In orthotopic liver cancer models, targeting CSN6 and HMGCS1 hinders tumor growth in both normal and high fat diet. Significantly, HMGCS1 depletion improves YAP inhibitor efficacy in patient derived xenograft models. The results identify a CSN6-HMGCS1-YAP1 axis mediating tumor outgrowth in HCC and propose a therapeutic strategy of targeting non-alcoholic fatty liver diseases- associated HCC.
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48
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Son Y, Su Yang J, Chul Shin S, Kyoung Park S, Kim Y, Park J, Yu J. Structural optimization and biological evaluation of ML364 based derivatives as USP2a inhibitors. Bioorg Chem 2024; 145:107222. [PMID: 38401359 DOI: 10.1016/j.bioorg.2024.107222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/29/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Ubiquitination is a representative post-translational modification that tags target proteins with ubiquitin to induce protein degradation or modify their functions. Deubiquitinating enzymes (DUBs) play a crucial role in reversing this process by removing ubiquitin from target proteins. Among them, USP2a has emerged as a promising target for cancer therapy due to its oncogenic properties in various cancer types, but its inhibitors have been limited. In this study, our aim was to optimize the structure of ML364, a USP2a inhibitor, and synthesize a series of its derivatives to develop potent USP2a inhibitors. Compound 8v emerged as a potential USP2a inhibitor with lower cytotoxicity compared to ML364. Cellular assays demonstrated that compound 8v effectively reduced the levels of USP2a substrates and attenuated cancer cell growth. We confirmed its direct interaction with the catalytic domain of USP2a and its selective inhibitory activity against USP2a over other USP subfamily proteins (USP7, 8, or 15). In conclusion, compound 8v has been identified as a potent USP2a inhibitor with substantial potential for cancer therapy.
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Affiliation(s)
- Youngchai Son
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Su Yang
- Biomedical Research Division, Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sang Chul Shin
- Research Resources Division, Technological Convergence Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seo Kyoung Park
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeojin Kim
- Biomedical Research Division, Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jinyoung Park
- Biomedical Research Division, Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio‑Medical Science and Technology, KIST‑School, University of Science and Technology (UST), Seoul 02792, Republic of Korea.
| | - Jinha Yu
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea.
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49
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Radko-Juettner S, Yue H, Myers JA, Carter RD, Robertson AN, Mittal P, Zhu Z, Hansen BS, Donovan KA, Hunkeler M, Rosikiewicz W, Wu Z, McReynolds MG, Roy Burman SS, Schmoker AM, Mageed N, Brown SA, Mobley RJ, Partridge JF, Stewart EA, Pruett-Miller SM, Nabet B, Peng J, Gray NS, Fischer ES, Roberts CWM. Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF. Nature 2024; 628:442-449. [PMID: 38538798 DOI: 10.1038/s41586-024-07250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
Whereas oncogenes can potentially be inhibited with small molecules, the loss of tumour suppressors is more common and is problematic because the tumour-suppressor proteins are no longer present to be targeted. Notable examples include SMARCB1-mutant cancers, which are highly lethal malignancies driven by the inactivation of a subunit of SWI/SNF (also known as BAF) chromatin-remodelling complexes. Here, to generate mechanistic insights into the consequences of SMARCB1 mutation and to identify vulnerabilities, we contributed 14 SMARCB1-mutant cell lines to a near genome-wide CRISPR screen as part of the Cancer Dependency Map Project1-3. We report that the little-studied gene DDB1-CUL4-associated factor 5 (DCAF5) is required for the survival of SMARCB1-mutant cancers. We show that DCAF5 has a quality-control function for SWI/SNF complexes and promotes the degradation of incompletely assembled SWI/SNF complexes in the absence of SMARCB1. After depletion of DCAF5, SMARCB1-deficient SWI/SNF complexes reaccumulate, bind to target loci and restore SWI/SNF-mediated gene expression to levels that are sufficient to reverse the cancer state, including in vivo. Consequently, cancer results not from the loss of SMARCB1 function per se, but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of ubiquitin-mediated quality-control factors may effectively reverse the malignant state of some cancers driven by disruption of tumour suppressor complexes.
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Affiliation(s)
- Sandi Radko-Juettner
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jacquelyn A Myers
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Raymond D Carter
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Alexis N Robertson
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Priya Mittal
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhexin Zhu
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Baranda S Hansen
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- The Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhiping Wu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Meghan G McReynolds
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shourya S Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott A Brown
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert J Mobley
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Janet F Partridge
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth A Stewart
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- The Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Junmin Peng
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford Medicine, Stanford, CA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
- Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA.
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50
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Abdul Rehman SA, Cazzaniga C, Di Nisio E, Antico O, Knebel A, Johnson C, Şahin AT, Ibrahim PEGF, Lamoliatte F, Negri R, Muqit MMK, De Cesare V. Discovery and characterization of noncanonical E2-conjugating enzymes. Sci Adv 2024; 10:eadh0123. [PMID: 38536929 PMCID: PMC10971424 DOI: 10.1126/sciadv.adh0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
E2-conjugating enzymes (E2s) play a central role in the enzymatic cascade that leads to the attachment of ubiquitin to a substrate. This process, termed ubiquitylation, is required to maintain cellular homeostasis and affects almost all cellular process. By interacting with multiple E3 ligases, E2s dictate the ubiquitylation landscape within the cell. Since its discovery, ubiquitylation has been regarded as a posttranslational modification that specifically targets lysine side chains (canonical ubiquitylation). We used Matrix-Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry to identify and characterize a family of E2s that are instead able to conjugate ubiquitin to serine and/or threonine. We used structural modeling and prediction tools to identify the key activity determinants that these E2s use to interact with ubiquitin as well as their substrates. Our results unveil the missing E2s necessary for noncanonical ubiquitylation, underscoring the adaptability and versatility of ubiquitin modifications.
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Chiara Cazzaniga
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Elena Di Nisio
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Clare Johnson
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Alp T Şahin
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow St, Dundee DD1 5EH, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Rodolfo Negri
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli 4, 00185 Rome, Italy
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
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