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Furuhata T, Devadasan Racheal PA, Murayama I, Toyoda U, Okamoto A. One-Pot, Photocontrolled Enzymatic Assembly of the Structure-Defined Heterotypic Polyubiquitin Chain. J Am Chem Soc 2023; 145:11690-11700. [PMID: 37200097 DOI: 10.1021/jacs.3c01912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterotypic polyubiquitins are an emerging class of polyubiquitins that have attracted interest because of their potential diversity of structures and physiological functions. There is an increasing demand for structure-defined synthesis of heterotypic chains to investigate the topological factors underlying the intracellular signals that are characteristically mediated by the heterotypic chain. However, the applicability of chemical and enzymatic polyubiquitin synthesis developed to date has been limited by laborious rounds of ligation and purification or by a lack of modularity of the chain structure with respect to the length and the branch position. Here, we established a one-pot, photocontrolled synthesis of structurally defined heterotypic polyubiquitin chains. We designed ubiquitin derivatives with a photolabile protecting group at a lysine residue used for polymerization. Repetitive cycles of linkage-specific enzymatic elongation and photoinduced deprotection of the protected ubiquitin units enabled stepwise addition of ubiquitins with appropriate functionalities to control the length and branching positions. The positional control of branching was achieved without isolation of intermediates, allowing one-pot synthesis of K63 triubiqutin chains and a K63/K48 heterotypic tetraubiquitin chain with defined branching positions. The present study provides a chemical platform for the efficient construction of long polyubiquitin chains with defined branch structures that will facilitate the understanding of the essential relationships between functions and structures of the heterotypic chain that have hitherto been overlooked.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Phebee Angeline Devadasan Racheal
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Iori Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Usano Toyoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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2
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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3
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Paudel P, Banos CM, Liu Y, Zhuang Z. Triubiquitin Probes for Identification of Reader and Eraser Proteins of Branched Polyubiquitin Chains. ACS Chem Biol 2023; 18:837-847. [PMID: 36972492 PMCID: PMC10894068 DOI: 10.1021/acschembio.2c00898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The important roles played by branched polyubiquitin chains were recently uncovered in proteasomal protein degradation, mitotic regulation, and NF-κB signaling. With the new realization of a wide presence of branched ubiquitin chains in mammalian cells, there is an urgent need of identifying the reader and eraser proteins of the various branched ubiquitin chains. In this work, we report the generation of noncleavable branched triubiquitin probes with combinations of K11-, K48-, and K63-linkages. Through a pulldown approach using the branched triUb probes, we identified human proteins that recognize branched triubiquitin structures including ubiquitin-binding proteins and deubiquitinases (DUBs). Proteomics analysis of the identified proteins enriched by the branched triubiquitin probes points to possible roles of branched ubiquitin chains in cellular processes including DNA damage response, autophagy, and receptor endocytosis. In vitro characterization of several identified UIM-containing proteins demonstrated their binding to branch triubiquitin chains with moderate to high affinities. Availability of this new class of branched triubiquitin probes will enable future investigation into the roles of branched polyubiquitin chains through identification of specific reader and eraser proteins, and the modes of branched ubiquitin chain recognition and processing using biochemical and biophysical methods.
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Affiliation(s)
| | | | - Yujue Liu
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware, USA, 19716
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware, USA, 19716
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4
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Vogel K, Nagel MK, Isono E. Measuring the DUB Activity of Arabidopsis Deubiquitylating Enzymes. Methods Mol Biol 2023; 2581:69-79. [PMID: 36413311 DOI: 10.1007/978-1-0716-2784-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Deubiquitylating enzymes, or DUBs, are important regulators of ubiquitin homeostasis and substrate stability, though the molecular mechanisms of most of the DUBs in plants are not yet understood. As different ubiquitin chain types are implicated in different biological pathways, it is important to analyze the enzyme characteristic for studying a DUB. Quantitative analysis of DUB activity is also important to determine enzyme kinetics and the influence of DUB binding proteins on the enzyme activity. Here we show methods to analyze DUB activity using immunodetection, Coomassie brilliant blue staining, and fluorescence measurement that can be useful for understanding the basic characteristic of DUBs.
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Affiliation(s)
- Karin Vogel
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz, Germany.
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5
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Waltho A, Sommer T. Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions. Methods Mol Biol 2023; 2602:19-38. [PMID: 36446964 DOI: 10.1007/978-1-0716-2859-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nearly 20 years since the first branched ubiquitin (Ub) chains were identified by mass spectrometry, our understanding of these chains and their function is still evolving. This is due to the limitations of classical Ub research techniques in identifying these chains and the vast complexity of potential branched chains. Considering only lysine or N-terminal methionine attachment sites, there are already 28 different possible branch points. Taking into account recently discovered ester-linked ubiquitination, branch points of more than two linkage types, and the higher-order chain structures within which branch points exist, the diversity of branched chains is nearly infinite. This review breaks down the complexity of these chains into their general functions, what we know so far about the different linkage combinations, branched chain-optimized methodologies, and the future perspectives of branched chain research.
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Affiliation(s)
- Anita Waltho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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6
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Yang K, Xiao W. Functions and mechanisms of the Ubc13-UEV complex and lysine 63-linked polyubiquitination in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5372-5387. [PMID: 35640002 DOI: 10.1093/jxb/erac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitination is one of the best-known post-translational modifications in eukaryotes, in which different linkage types of polyubiquitination result in different outputs of the target proteins. Distinct from the well-characterized K48-linked polyubiquitination that usually serves as a signal for degradation of the target protein, K63-linked polyubiquitination often requires a unique E2 heterodimer Ubc13-UEV and alters the target protein activity instead of marking it for degradation. This review focuses on recent advances on the roles of Ubc13-UEV-mediated K63-linked polyubiquitination in plant growth, development, and response to environmental stresses.
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Affiliation(s)
- Kun Yang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, China
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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7
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Wegmann S, Meister C, Renz C, Yakoub G, Wollscheid HP, Takahashi DT, Mikicic I, Beli P, Ulrich HD. Linkage reprogramming by tailor-made E3s reveals polyubiquitin chain requirements in DNA-damage bypass. Mol Cell 2022; 82:1589-1602.e5. [PMID: 35263628 PMCID: PMC9098123 DOI: 10.1016/j.molcel.2022.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 01/05/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
A polyubiquitin chain can adopt a variety of shapes, depending on how the ubiquitin monomers are joined. However, the relevance of linkage for the signaling functions of polyubiquitin chains is often poorly understood because of our inability to control or manipulate this parameter in vivo. Here, we present a strategy for reprogramming polyubiquitin chain linkage by means of tailor-made, linkage- and substrate-selective ubiquitin ligases. Using the polyubiquitylation of the budding yeast replication factor PCNA in response to DNA damage as a model case, we show that altering the features of a polyubiquitin chain in vivo can change the fate of the modified substrate. We also provide evidence for redundancy between distinct but structurally similar linkages, and we demonstrate by proof-of-principle experiments that the method can be generalized to targets beyond PCNA. Our study illustrates a promising approach toward the in vivo analysis of polyubiquitin signaling.
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Affiliation(s)
- Sabrina Wegmann
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Cindy Meister
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Christian Renz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - George Yakoub
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | | | - Diane T Takahashi
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, 10413 Illkirch, Strasbourg, France
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany; Institute for Developmental Biology and Neurobiology, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, 55128 Mainz, Germany.
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8
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Pashkova N, Gakhar L, Yu L, Schnicker NJ, Minard AY, Winistorfer S, Johnson IE, Piper RC. ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals. eLife 2021; 10:72583. [PMID: 34821552 PMCID: PMC8648300 DOI: 10.7554/elife.72583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Attachment of ubiquitin (Ub) to cell surface proteins serves as a signal for internalization via clathrin-mediated endocytosis (CME). How ubiquitinated membrane proteins engage the internalization apparatus remains unclear. The internalization apparatus contains proteins such as Epsin and Eps15, which bind Ub, potentially acting as adaptors for Ub-based internalization signals. Here, we show that additional components of the endocytic machinery including CALM, HIP1R, and Sla2 bind Ub via their N-terminal ANTH domain, a domain belonging to the superfamily of ENTH and VHS domains. Structural studies revealed that Ub binds with µM affinity to a unique C-terminal region within the ANTH domain not found in ENTH domains. Functional studies showed that combined loss of Ub-binding by ANTH-domain proteins and other Ub-binding domains within the yeast internalization apparatus caused defects in the Ub-dependent internalization of the GPCR Ste2 that was engineered to rely exclusively on Ub as an internalization signal. In contrast, these mutations had no effect on the internalization of Ste2 engineered to use an alternate Ub-independent internalization signal. These studies define new components of the internalization machinery that work collectively with Epsin and Eps15 to specify recognition of Ub as an internalization signal.
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Affiliation(s)
- Natalya Pashkova
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Lokesh Gakhar
- Carver College of Medicine Protein Crystallography Core, University of Iowa, Iowa City, United States.,Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, United States
| | - Liping Yu
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, United States.,Carver College of Medicine NMR Core, University of Iowa, Iowa City, United States
| | - Nicholas J Schnicker
- Carver College of Medicine Protein Crystallography Core, University of Iowa, Iowa City, United States
| | - Annabel Y Minard
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Stanley Winistorfer
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Ivan E Johnson
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, United States
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9
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Kajikawa M, Imaizumi N, Machii S, Nakamura T, Harigane N, Kimura M, Miyano K, Ishido S, Kanamoto T. Kaposi's sarcoma-associated herpesvirus ubiquitin ligases downregulate cell surface expression of l-selectin. J Gen Virol 2021; 102. [PMID: 34726593 DOI: 10.1099/jgv.0.001678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic etiological factor for Kaposi's sarcoma and primary effusion lymphoma in immunocompromised patients. KSHV utilizes two immune evasion E3 ubiquitin ligases, namely K3 and K5, to downregulate the expression of antigen-presenting molecules and ligands of natural killer (NK) cells in the host cells through an ubiquitin-dependent endocytic mechanism. This allows the infected cells to evade surveillance and elimination by cytotoxic lymphocytes and NK cells. The number of host cell molecular substrates reported for these ubiquitin ligases is limited. The identification of novel substrates for these ligases will aid in elucidating the mechanism underlying immune evasion of KSHV. This study demonstrated that K5 downregulated the cell surface expression of l-selectin, a C-type lectin-like adhesion receptor expressed in the lymphocytes. Tryptophan residue located at the centre of the E2-binding site in the K5 RINGv domain was essential to downregulate l-selectin expression. Additionally, the lysine residues located at the cytoplasmic tail of l-selectin were required for the K5-mediated downregulation of l-selectin. K5 promoted the degradation of l-selectin through polyubiquitination. These results suggest that K5 downregulates l-selectin expression on the cell surface by promoting polyubiquitination and ubiquitin-dependent endocytosis, which indicated that l-selectin is a novel substrate for K5. Additionally, K3 downregulated l-selectin expression. The findings of this study will aid in the elucidation of a novel immune evasion mechanism in KSHV.
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Affiliation(s)
- Mizuho Kajikawa
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Nanae Imaizumi
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Shiho Machii
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Tomoka Nakamura
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Nana Harigane
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Minako Kimura
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Kei Miyano
- Department of Biochemistry, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Satoshi Ishido
- Department of Microbiology, Hyogo College of Medicine, 1-1 Mukogawa-cho, Nishinomiya, Hyogo 663-8501, Japan
| | - Taisei Kanamoto
- Laboratory of Microbiology, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
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10
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Shukla A, Cloutier M, Appiya Santharam M, Ramanathan S, Ilangumaran S. The MHC Class-I Transactivator NLRC5: Implications to Cancer Immunology and Potential Applications to Cancer Immunotherapy. Int J Mol Sci 2021; 22:ijms22041964. [PMID: 33671123 PMCID: PMC7922096 DOI: 10.3390/ijms22041964] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The immune system constantly monitors the emergence of cancerous cells and eliminates them. CD8+ cytotoxic T lymphocytes (CTLs), which kill tumor cells and provide antitumor immunity, select their targets by recognizing tumor antigenic peptides presented by MHC class-I (MHC-I) molecules. Cancer cells circumvent immune surveillance using diverse strategies. A key mechanism of cancer immune evasion is downregulation of MHC-I and key proteins of the antigen processing and presentation machinery (APM). Even though impaired MHC-I expression in cancers is well-known, reversing the MHC-I defects remains the least advanced area of tumor immunology. The discoveries that NLRC5 is the key transcriptional activator of MHC-I and APM genes, and genetic lesions and epigenetic modifications of NLRC5 are the most common cause of MHC-I defects in cancers, have raised the hopes for restoring MHC-I expression. Here, we provide an overview of cancer immunity mediated by CD8+ T cells and the functions of NLRC5 in MHC-I antigen presentation pathways. We describe the impressive advances made in understanding the regulation of NLRC5 expression, the data supporting the antitumor functions of NLRC5 and a few reports that argue for a pro-tumorigenic role. Finally, we explore the possible avenues of exploiting NLRC5 for cancer immunotherapy.
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Affiliation(s)
- Akhil Shukla
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Madanraj Appiya Santharam
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
- Correspondence: ; Tel.: +1-819-346-1110 (ext. 14834)
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11
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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12
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Abstract
Ubiquitylation is a critical post-translational modification that controls a wide variety of processes in eukaryotes. Ubiquitin chains of different topologies are specialized for different cellular functions and control the stability, activity, interaction properties, and localization of many different proteins. Recent work has highlighted a role for branched ubiquitin chains in the regulation of cell signaling and protein degradation pathways. Similar to their unbranched counterparts, branched ubiquitin chains are remarkably diverse in terms of their chemical linkages, structures, and the biological information they transmit. In this review, we discuss emerging themes related to the architecture, synthesis, and functions of branched ubiquitin chains. We also describe methodologies that have recently been developed to identify and decode the functions of these branched polymers.
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13
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Wu Y, Zhang W. The Role of E3s in Regulating Pluripotency of Embryonic Stem Cells and Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:1168. [PMID: 33503896 PMCID: PMC7865285 DOI: 10.3390/ijms22031168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are derived from early embryos and can differentiate into any type of cells in living organisms. Induced pluripotent stem cells (iPSCs) resemble ESCs, both of which serve as excellent sources to study early embryonic development and realize cell replacement therapies for age-related degenerative diseases and other cell dysfunction-related illnesses. To achieve these valuable applications, comprehensively understanding of the mechanisms underlying pluripotency maintenance and acquisition is critical. Ubiquitination modifies proteins with Ubiquitin (Ub) at the post-translational level to monitor protein stability and activity. It is extensively involved in pluripotency-specific regulatory networks in ESCs and iPSCs. Ubiquitination is achieved by sequential actions of the Ub-activating enzyme E1, Ub-conjugating enzyme E2, and Ub ligase E3. Compared with E1s and E2s, E3s are most abundant, responsible for substrate selectivity and functional diversity. In this review, we focus on E3 ligases to discuss recent progresses in understanding how they regulate pluripotency and somatic cell reprogramming through ubiquitinating core ESC regulators.
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Affiliation(s)
| | - Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China;
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14
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Vere G, Kealy R, Kessler BM, Pinto-Fernandez A. Ubiquitomics: An Overview and Future. Biomolecules 2020; 10:E1453. [PMID: 33080838 PMCID: PMC7603029 DOI: 10.3390/biom10101453] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
| | - Rachel Kealy
- St Anne’s College, University of Oxford, Oxford OX2 6HS, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute (CAMS), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
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15
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Musaus M, Navabpour S, Jarome TJ. The diversity of linkage-specific polyubiquitin chains and their role in synaptic plasticity and memory formation. Neurobiol Learn Mem 2020; 174:107286. [PMID: 32745599 DOI: 10.1016/j.nlm.2020.107286] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/15/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022]
Abstract
Over the last 20 years, a number of studies have provided strong support for protein degradation mediated by the ubiquitin-proteasome system in synaptic plasticity and memory formation. In this system, target substrates become covalently modified by the small protein ubiquitin through a series of enzymatic reactions involving hundreds of different ligases. While some substrates will acquire only a single ubiquitin, most will be marked by multiple ubiquitin modifications, which link together at specific lysine sites or the N-terminal methionine on the previous ubiquitin to form a polyubiquitin chain. There are at least eight known linkage-specific polyubiquitin chains a target protein can acquire, many of which are independent of the proteasome, and these chains can be homogenous, mixed, or branched in nature, all of which result in different functional outcomes and fates for the target substrate. However, as the focus has remained on protein degradation, much remains unknown about the role of these diverse ubiquitin chains in the brain, particularly during activity- and learning-dependent synaptic plasticity. Here, we review the different types and functions of ubiquitin chains and summarize evidence suggesting a role for these diverse ubiquitin modifications in synaptic plasticity and memory formation. We conclude by discussing how technological limitations have limited our ability to identify and elucidate the role of different ubiquitin chains in the brain and speculate on the future directions and implications of understanding linkage-specific ubiquitin modifications in activity- and learning-dependent synaptic plasticity.
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Affiliation(s)
- Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Timothy J Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA; Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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16
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Hua X, Chu GC, Li YM. The Ubiquitin Enigma: Progress in the Detection and Chemical Synthesis of Branched Ubiquitin Chains. Chembiochem 2020; 21:3313-3318. [PMID: 32621561 DOI: 10.1002/cbic.202000295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/01/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitin chains with distinct topologies play essential roles in eukaryotic cells. Recently, it was discovered that multiple ubiquitin units can be ligated to more than one lysine residue in the same ubiquitin to form diverse branched ubiquitin chains. Although there is increasing evidence implicating these branched chains in a plethora of biological functions, few mechanistic details have been elucidated. This concept article introduces the function, detection and chemical synthesis of branched ubiquitin chains; and offers some future perspective for this exciting new field.
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Affiliation(s)
- Xiao Hua
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases, Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, China.,Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Guo-Chao Chu
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases, Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui, 230009, China.,Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
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17
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Alix E, Godlee C, Cerny O, Blundell S, Tocci R, Matthews S, Liu M, Pruneda JN, Swatek KN, Komander D, Sleap T, Holden DW. The Tumour Suppressor TMEM127 Is a Nedd4-Family E3 Ligase Adaptor Required by Salmonella SteD to Ubiquitinate and Degrade MHC Class II Molecules. Cell Host Microbe 2020; 28:54-68.e7. [PMID: 32526160 PMCID: PMC7342019 DOI: 10.1016/j.chom.2020.04.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/13/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022]
Abstract
The Salmonella enterica effector SteD depletes mature MHC class II (mMHCII) molecules from the surface of infected antigen-presenting cells through ubiquitination of the cytoplasmic tail of the mMHCII β chain. Here, through a genome-wide mutant screen of human antigen-presenting cells, we show that the NEDD4 family HECT E3 ubiquitin ligase WWP2 and a tumor-suppressing transmembrane protein of unknown biochemical function, TMEM127, are required for SteD-dependent ubiquitination of mMHCII. Although evidently not involved in normal regulation of mMHCII, TMEM127 was essential for SteD to suppress both mMHCII antigen presentation in mouse dendritic cells and MHCII-dependent CD4+ T cell activation. We found that TMEM127 contains a canonical PPxY motif, which was required for binding to WWP2. SteD bound to TMEM127 and enabled TMEM127 to interact with and induce ubiquitination of mature MHCII. Furthermore, SteD also underwent TMEM127- and WWP2-dependent ubiquitination, which both contributed to its degradation and augmented its activity on mMHCII.
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Affiliation(s)
- Eric Alix
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Camilla Godlee
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Ondrej Cerny
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Samkeliso Blundell
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Romina Tocci
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Sophie Matthews
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Mei Liu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - Jonathan N Pruneda
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239, USA
| | - Kirby N Swatek
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royale Parade, 3052 Parkville, Melbourne, Australia
| | - David Komander
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Tabitha Sleap
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
| | - David W Holden
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK.
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18
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Deng L, Meng T, Chen L, Wei W, Wang P. The role of ubiquitination in tumorigenesis and targeted drug discovery. Signal Transduct Target Ther 2020; 5:11. [PMID: 32296023 PMCID: PMC7048745 DOI: 10.1038/s41392-020-0107-0] [Citation(s) in RCA: 345] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 02/08/2023] Open
Abstract
Ubiquitination, an important type of protein posttranslational modification (PTM), plays a crucial role in controlling substrate degradation and subsequently mediates the "quantity" and "quality" of various proteins, serving to ensure cell homeostasis and guarantee life activities. The regulation of ubiquitination is multifaceted and works not only at the transcriptional and posttranslational levels (phosphorylation, acetylation, methylation, etc.) but also at the protein level (activators or repressors). When regulatory mechanisms are aberrant, the altered biological processes may subsequently induce serious human diseases, especially various types of cancer. In tumorigenesis, the altered biological processes involve tumor metabolism, the immunological tumor microenvironment (TME), cancer stem cell (CSC) stemness and so on. With regard to tumor metabolism, the ubiquitination of some key proteins such as RagA, mTOR, PTEN, AKT, c-Myc and P53 significantly regulates the activity of the mTORC1, AMPK and PTEN-AKT signaling pathways. In addition, ubiquitination in the TLR, RLR and STING-dependent signaling pathways also modulates the TME. Moreover, the ubiquitination of core stem cell regulator triplets (Nanog, Oct4 and Sox2) and members of the Wnt and Hippo-YAP signaling pathways participates in the maintenance of CSC stemness. Based on the altered components, including the proteasome, E3 ligases, E1, E2 and deubiquitinases (DUBs), many molecular targeted drugs have been developed to combat cancer. Among them, small molecule inhibitors targeting the proteasome, such as bortezomib, carfilzomib, oprozomib and ixazomib, have achieved tangible success. In addition, MLN7243 and MLN4924 (targeting the E1 enzyme), Leucettamol A and CC0651 (targeting the E2 enzyme), nutlin and MI-219 (targeting the E3 enzyme), and compounds G5 and F6 (targeting DUB activity) have also shown potential in preclinical cancer treatment. In this review, we summarize the latest progress in understanding the substrates for ubiquitination and their special functions in tumor metabolism regulation, TME modulation and CSC stemness maintenance. Moreover, potential therapeutic targets for cancer are reviewed, as are the therapeutic effects of targeted drugs.
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Affiliation(s)
- Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, 712100, China.
| | - Tong Meng
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China
| | - Lei Chen
- Division of Laboratory Safety and Services, Northwest A&F University, Yangling Shaanxi, 712100, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai, 200092, China.
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19
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Boughton AJ, Krueger S, Fushman D. Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1. Structure 2020; 28:29-43.e6. [PMID: 31677892 PMCID: PMC6996796 DOI: 10.1016/j.str.2019.10.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/17/2019] [Accepted: 10/10/2019] [Indexed: 01/04/2023]
Abstract
Post-translational substrate modification with ubiquitin is essential for eukaryotic cellular signaling. Polymeric ubiquitin chains are assembled with specific architectures, which convey distinct signaling outcomes depending on the linkages involved. Recently, branched K11/K48-linked polyubiquitins were shown to enhance proteasomal degradation during mitosis. To better understand the underlying structural mechanisms, we determined the crystal and NMR structures of branched K11/K48-linked tri-ubiquitin and discovered a previously unobserved interdomain interface between the distal ubiquitins. Small-angle neutron scattering and site-directed mutagenesis corroborated the presence of this interface, which we hypothesized to be influential in the physiological role of branched K11/K48-linked chains. Yet, experiments probing polyubiquitin interactions-deubiquitination assays, binding to proteasomal shuttle hHR23A-showed negligible differences between branched K11/K48-linked tri-ubiquitin and related di-ubiquitins. However, significantly stronger binding affinity for branched K11/K48-linked tri-ubiquitin was observed with proteasomal subunit Rpn1, thereby suggesting a functional impact of this interdomain interface and pinpointing the mechanistic site of enhanced degradation.
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Affiliation(s)
- Andrew J Boughton
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
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20
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Mendes ML, Fougeras MR, Dittmar G. Analysis of ubiquitin signaling and chain topology cross-talk. J Proteomics 2020; 215:103634. [PMID: 31918034 DOI: 10.1016/j.jprot.2020.103634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/13/2019] [Accepted: 01/05/2020] [Indexed: 12/12/2022]
Abstract
Protein ubiquitination is a powerful post-translational modification implicated in many cellular processes. Although ubiquitination is associated with protein degradation, depending on the topology of polyubiquitin chains, protein ubiquitination is connected to non-degradative events in DNA damage response, cell cycle control, immune response, trafficking, intracellular localization, and vesicle fusion events. It has been shown that a ubiquitin chain can contain two or more topologies at the same time. These branched chains add another level of complexity to ubiquitin signaling, increasing its versatility and specificity. Mass spectrometry-based proteomics has been playing an important role in the identification of all types of ubiquitin chains and linkages. This review aims to provide an overview of ubiquitin chain topology and associated signaling pathways and discusses the MS-based proteomic methodologies used to determine such topologies. SIGNIFICANCE: Ubiquitination plays important roles in many cellular processes. Proteins can be monoubiquitinated or polyubiquitinated forming non-branched or branched chains in a high number of possible combinations, each associated with different cellular processes. The detection and the topology of ubiquitin chains is thus of extreme importance in order to explain such processes. Advances in mass spectrometry based proteomics allowed for the discovery and topology mapping of many ubiquitin chains. This review revisits the state of the art in ubiquitin chain identification by mass spectrometry and gives an insight on the implication of such chains in many cellular processes.
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Affiliation(s)
- Marta L Mendes
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Miriam R Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Faculty of Science, Technology and Communication, University of Luxembourg, 2 avenue de l'Université, 4365, Esch-sur-Alzette, Luxembourg.
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21
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Sharma A, Trivedi AK. Regulation of apoptosis by E3 ubiquitin ligases in ubiquitin proteasome system. Cell Biol Int 2019; 44:721-734. [PMID: 31814188 DOI: 10.1002/cbin.11277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/06/2019] [Indexed: 11/10/2022]
Abstract
Apoptosis is an organised ATP-dependent programmed cell death that organisms have evolved to maintain homoeostatic cell numbers and eliminate unnecessary or unhealthy cells from the system. Dysregulation of apoptosis can have serious manifestations culminating into various diseases, especially cancer. Accurate control of apoptosis requires regulation of a wide range of growth enhancing as well as anti-oncogenic factors. Appropriate regulation of magnitude and temporal expression of key proteins is vital to maintain functional apoptotic signalling. Controlled protein turnover is thus critical to the unhindered operation of the apoptotic machinery, disruption of which can have severe consequences, foremost being oncogenic transformation of cells. The ubiquitin proteasome system (UPS) is one such major cellular pathway that maintains homoeostatic protein levels. Recent studies have found interesting links between these two fundamental cellular processes, wherein UPS depending on the cue can either inhibit or promote apoptosis. A diverse range of E3 ligases are involved in regulating the turnover of key proteins of the apoptotic pathway. This review summarises an overview of key E3 ubiquitin ligases involved in the regulation of the fundamental proteins involved in apoptosis, linking UPS to apoptosis and attempts to emphasize the significance of this relationship in context of cancer.
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Affiliation(s)
- Akshay Sharma
- LSS008, Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, India
| | - Arun K Trivedi
- LSS008, Division of Cancer Biology, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow, 226031, India
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22
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Kon E, Calvo-Jiménez E, Cossard A, Na Y, Cooper JA, Jossin Y. N-cadherin-regulated FGFR ubiquitination and degradation control mammalian neocortical projection neuron migration. eLife 2019; 8:47673. [PMID: 31577229 PMCID: PMC6786859 DOI: 10.7554/elife.47673] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 10/01/2019] [Indexed: 12/18/2022] Open
Abstract
The functions of FGF receptors (FGFRs) in early development of the cerebral cortex are well established. Their functions in the migration of neocortical projection neurons, however, are unclear. We have found that FGFRs regulate multipolar neuron orientation and the morphological change into bipolar cells necessary to enter the cortical plate. Mechanistically, our results suggest that FGFRs are activated by N-Cadherin. N-Cadherin cell-autonomously binds FGFRs and inhibits FGFR K27- and K29-linked polyubiquitination and lysosomal degradation. Accordingly, FGFRs accumulate and stimulate prolonged Erk1/2 phosphorylation. Neurons inhibited for Erk1/2 are stalled in the multipolar zone. Moreover, Reelin, a secreted protein regulating neuronal positioning, prevents FGFR degradation through N-Cadherin, causing Erk1/2 phosphorylation. These findings reveal novel functions for FGFRs in cortical projection neuron migration, suggest a physiological role for FGFR and N-Cadherin interaction in vivo and identify Reelin as an extracellular upstream regulator and Erk1/2 as downstream effectors of FGFRs during neuron migration.
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Affiliation(s)
- Elif Kon
- Laboratory of Mammalian Development & Cell Biology, Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
| | - Elisa Calvo-Jiménez
- Laboratory of Mammalian Development & Cell Biology, Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
| | - Alexia Cossard
- Laboratory of Mammalian Development & Cell Biology, Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
| | - Youn Na
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jonathan A Cooper
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Yves Jossin
- Laboratory of Mammalian Development & Cell Biology, Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
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23
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Abstract
The small protein ubiquitin and its multiple polymers are encountered free in cells and as post-translational modifications on all proteins. Different polyubiquitin three dimensional structures are shown to correlate uniquely with different cellular functions as part of the diverse ubiquitin signaling. At the same time, this multiplicity of structures provides serious challenges to the analytical biochemist. Globally applicable strategies are presented here for the analyses of polyubiquitins and of ubiquitinated proteins, which take advantage of the speed, specificity and sensitivity of top-down tandem mass spectrometry. Particular attention is given to the supervised interpretation of fragmentation as revealed in the MS/MS spectra of these branched proteins. The strategy is compatible with any MS activation technology, is applicable to all polyubiquitin linkage and chain types, can be extended to ubiquitin-like proteins, and will be compatible with and enhanced by continuing advances in LC-MS/MS instrumentation and interpretation software.
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Affiliation(s)
- Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - Amanda E Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States.
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24
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Kudriaeva AA, Belogurov AA. Proteasome: a Nanomachinery of Creative Destruction. BIOCHEMISTRY (MOSCOW) 2019; 84:S159-S192. [PMID: 31213201 DOI: 10.1134/s0006297919140104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the middle of the 20th century, it was postulated that degradation of intracellular proteins is a stochastic process. More than fifty years of intense studies have finally proven that protein degradation is a very complex and tightly regulated in time and space process that plays an incredibly important role in the vast majority of metabolic pathways. Degradation of more than a half of intracellular proteins is controlled by a hierarchically aligned and evolutionarily perfect system consisting of many components, the main ones being ubiquitin ligases and proteasomes, together referred to as the ubiquitin-proteasome system (UPS). The UPS includes more than 1000 individual components, and most of them are critical for the cell functioning and survival. In addition to the well-known signaling functions of ubiquitination, such as modification of substrates for proteasomal degradation and DNA repair, polyubiquitin (polyUb) chains are involved in other important cellular processes, e.g., cell cycle regulation, immunity, protein degradation in mitochondria, and even mRNA stability. This incredible variety of ubiquitination functions is related to the ubiquitin ability to form branching chains through the ε-amino group of any of seven lysine residues in its sequence. Deubiquitination is accomplished by proteins of the deubiquitinating enzyme family. The second main component of the UPS is proteasome, a multisubunit proteinase complex that, in addition to the degradation of functionally exhausted and damaged proteins, regulates many important cellular processes through controlled degradation of substrates, for example, transcription factors and cyclins. In addition to the ubiquitin-dependent-mediated degradation, there is also ubiquitin-independent degradation, when the proteolytic signal is either an intrinsic protein sequence or shuttle molecule. Protein hydrolysis is a critically important cellular function; therefore, any abnormalities in this process lead to systemic impairments further transforming into serious diseases, such as diabetes, malignant transformation, and neurodegenerative disorders (multiple sclerosis, Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease and Huntington's disease). In this review, we discuss the mechanisms that orchestrate all components of the UPS, as well as the plurality of the fine-tuning pathways of proteasomal degradation.
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Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
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25
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Nguyen T, Ho M, Kim K, Yun SI, Mizar P, Easton JW, Lee SS, Kim KK. Suppression of the Ubiquitin Pathway by Small Molecule Binding to Ubiquitin Enhances Doxorubicin Sensitivity of the Cancer Cells. Molecules 2019; 24:molecules24061073. [PMID: 30893775 PMCID: PMC6471062 DOI: 10.3390/molecules24061073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Development of inhibitors for ubiquitin pathway has been suggested as a promising strategy to treat several types of cancers, which has been showcased by recent success of a series of novel anticancer drugs based on inhibition of ubiquitin pathways. Although the druggability of enzymes in ubiquitin pathways has been demonstrated, ubiquitin itself, the main agent of the pathway, has not been targeted. Whereas conventional enzyme inhibitors are used to silence the ubiquitination or reverse it, they cannot disrupt the binding activity of ubiquitin. Herein, we report that the scaffolds of sulfonated aryl diazo compounds, particularly Congo red, could disrupt the binding activity of ubiquitin, resulting in the activity equivalent to inhibition of ubiquitination. NMR mapping assay demonstrated that the chemical directly binds to the recognition site for ubiquitin processing enzymes on the surface of ubiquitin, and thereby blocks the binding of ubiquitin to its cognate receptors. As a proof of concept for the druggability of the ubiquitin molecule, we demonstrated that Congo red acted as an intracellular inhibitor of ubiquitin recognition and binding, which led to inhibition of ubiquitination, and thereby, could be used as a sensitizer for conventional anticancer drugs, doxorubicin.
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Affiliation(s)
- Thanh Nguyen
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
| | - Minh Ho
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
| | - Kyungmin Kim
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Sun-Il Yun
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
| | - Pushpak Mizar
- Chemistry, Faculty of Engineering & Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - James W Easton
- Chemistry, Faculty of Engineering & Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Seung Seo Lee
- Chemistry, Faculty of Engineering & Physical Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
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26
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Stefanovic-Barrett S, Dickson AS, Burr SP, Williamson JC, Lobb IT, van den Boomen DJ, Lehner PJ, Nathan JA. MARCH6 and TRC8 facilitate the quality control of cytosolic and tail-anchored proteins. EMBO Rep 2018; 19:e45603. [PMID: 29519897 PMCID: PMC5934766 DOI: 10.15252/embr.201745603] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/26/2022] Open
Abstract
Misfolded or damaged proteins are typically targeted for destruction by proteasome-mediated degradation, but the mammalian ubiquitin machinery involved is incompletely understood. Here, using forward genetic screens in human cells, we find that the proteasome-mediated degradation of the soluble misfolded reporter, mCherry-CL1, involves two ER-resident E3 ligases, MARCH6 and TRC8. mCherry-CL1 degradation is routed via the ER membrane and dependent on the hydrophobicity of the substrate, with complete stabilisation only observed in double knockout MARCH6/TRC8 cells. To identify a more physiological correlate, we used quantitative mass spectrometry and found that TRC8 and MARCH6 depletion altered the turnover of the tail-anchored protein heme oxygenase-1 (HO-1). These E3 ligases associate with the intramembrane cleaving signal peptide peptidase (SPP) and facilitate the degradation of HO-1 following intramembrane proteolysis. Our results highlight how ER-resident ligases may target the same substrates, but work independently of each other, to optimise the protein quality control of selected soluble and tail-anchored proteins.
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Affiliation(s)
- Sandra Stefanovic-Barrett
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Anna S Dickson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Stephen P Burr
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - James C Williamson
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Ian T Lobb
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Dick Jh van den Boomen
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - James A Nathan
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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27
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Cheng X, Zheng J, Li G, Göbel V, Zhang H. Degradation for better survival? Role of ubiquitination in epithelial morphogenesis. Biol Rev Camb Philos Soc 2018; 93:1438-1460. [PMID: 29493067 DOI: 10.1111/brv.12404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 02/06/2023]
Abstract
As a prevalent post-translational modification, ubiquitination is essential for many developmental processes. Once covalently attached to the small and conserved polypeptide ubiquitin (Ub), a substrate protein can be directed to perform specific biological functions via its Ub-modified form. Three sequential catalytic reactions contribute to this process, among which E3 ligases serve to identify target substrates and promote the activated Ub to conjugate to substrate proteins. Ubiquitination has great plasticity, with diverse numbers, topologies and modifications of Ub chains conjugated at different substrate residues adding a layer of complexity that facilitates a huge range of cellular functions. Herein, we highlight key advances in the understanding of ubiquitination in epithelial morphogenesis, with an emphasis on the latest insights into its roles in cellular events involved in polarized epithelial tissue, including cell adhesion, asymmetric localization of polarity determinants and cytoskeletal organization. In addition, the physiological roles of ubiquitination are discussed for typical examples of epithelial morphogenesis, such as lung branching, vascular development and synaptic formation and plasticity. Our increased understanding of ubiquitination in epithelial morphogenesis may provide novel insights into the molecular mechanisms underlying epithelial regeneration and maintenance.
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Affiliation(s)
- Xiaoxiang Cheng
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Jun Zheng
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Gang Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Verena Göbel
- Department of Pediatrics, Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114,, U.S.A
| | - Hongjie Zhang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
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28
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Michel MA, Swatek KN, Hospenthal MK, Komander D. Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol Cell 2017; 68:233-246.e5. [PMID: 28943312 PMCID: PMC5640506 DOI: 10.1016/j.molcel.2017.08.020] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/13/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022]
Abstract
Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific "affimer" reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
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Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kirby N Swatek
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Manuela K Hospenthal
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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29
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Rana ASJB, Ge Y, Strieter ER. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry (UbiChEM-MS) Reveals Cell-Cycle Dependent Formation of Lys11/Lys48 Branched Ubiquitin Chains. J Proteome Res 2017; 16:3363-3369. [PMID: 28737031 DOI: 10.1021/acs.jproteome.7b00381] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics of cellular signaling events are tightly regulated by a diverse set of ubiquitin chains. Recent work has suggested that branched ubiquitin chains composed of Lys11 and Lys48 isopeptide linkages play a critical role in regulating cell cycle progression. Yet, endogenous Lys11/Lys48 branched chains could not be detected. By combining a Lys11 linkage specific antibody with high-resolution middle-down mass spectrometry (an approach termed UbiChEM-MS) we sought to identify endogenous Lys11/Lys48 branched ubiquitin chains in cells. Using asynchronous cells, we find that Lys11-linked branched chains can only be detected upon cotreatment with a proteasome and nonselective deubiquitinase inhibitor. Releasing cells from mitotic arrest results in a marked accumulation of Lys11/Lys48 branched chains in which branch points represent ∼3-4% of the total ubiquitin population. This report highlights the utility of UbiChEM-MS in characterizing the architecture of Lys11 Ub chains under various cellular conditions and corroborates the formation of Lys11/Lys48 branched chains during mitosis.
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Affiliation(s)
- Ambar S J B Rana
- Department of Chemistry, University of Massachusetts - Amherst , Amherst, Massachusetts 01003, United States.,Department of Chemistry, University of Wisconsin - Madison , Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin - Madison , Madison, Wisconsin 53706, United States.,Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison , Madison, Wisconsin 53706, United States.,Human Proteomics Program, University of Wisconsin - Madison , Madison, Wisconsin 53706, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts - Amherst , Amherst, Massachusetts 01003, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts - Amherst , Amherst, Massachusetts 01003, United States
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30
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Ebner P, Versteeg GA, Ikeda F. Ubiquitin enzymes in the regulation of immune responses. Crit Rev Biochem Mol Biol 2017; 52:425-460. [PMID: 28524749 PMCID: PMC5490640 DOI: 10.1080/10409238.2017.1325829] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/06/2017] [Accepted: 04/28/2017] [Indexed: 12/25/2022]
Abstract
Ubiquitination plays a central role in the regulation of various biological functions including immune responses. Ubiquitination is induced by a cascade of enzymatic reactions by E1 ubiquitin activating enzyme, E2 ubiquitin conjugating enzyme, and E3 ubiquitin ligase, and reversed by deubiquitinases. Depending on the enzymes, specific linkage types of ubiquitin chains are generated or hydrolyzed. Because different linkage types of ubiquitin chains control the fate of the substrate, understanding the regulatory mechanisms of ubiquitin enzymes is central. In this review, we highlight the most recent knowledge of ubiquitination in the immune signaling cascades including the T cell and B cell signaling cascades as well as the TNF signaling cascade regulated by various ubiquitin enzymes. Furthermore, we highlight the TRIM ubiquitin ligase family as one of the examples of critical E3 ubiquitin ligases in the regulation of immune responses.
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31
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Molecular basis for specificity of the Met1-linked polyubiquitin signal. Biochem Soc Trans 2017; 44:1581-1602. [PMID: 27913667 PMCID: PMC5135002 DOI: 10.1042/bst20160227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/03/2016] [Accepted: 10/07/2016] [Indexed: 12/27/2022]
Abstract
The post-translational modification of proteins provides a rapid and versatile system for regulating all signalling pathways. Protein ubiquitination is one such type of post-translational modification involved in controlling numerous cellular processes. The unique ability of ubiquitin to form polyubiquitin chains creates a highly complex code responsible for different subsequent signalling outcomes. Specialised enzymes ('writers') generate the ubiquitin code, whereas other enzymes ('erasers') disassemble it. Importantly, the ubiquitin code is deciphered by different ubiquitin-binding proteins ('readers') functioning to elicit particular cellular responses. Ten years ago, the methionine1 (Met1)-linked (linear) polyubiquitin code was first identified and the intervening years have witnessed a seismic shift in our understanding of Met1-linked polyubiquitin in cellular processes, particularly inflammatory signalling. This review will discuss the molecular mechanisms of specificity determination within Met1-linked polyubiquitin signalling.
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32
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Ohtake F, Tsuchiya H. The emerging complexity of ubiquitin architecture. J Biochem 2017; 161:125-133. [PMID: 28011818 DOI: 10.1093/jb/mvw088] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022] Open
Abstract
Ubiquitylation is an essential post-translational modification (PTM) of proteins with diverse cellular functions. Polyubiquitin chains with different topologies have different cellular roles, and are referred to as a 'ubiquitin code'. Recent studies have begun to reveal that more complex ubiquitin architectures function as important signals in several biological pathways. These include PTMs of ubiquitin itself, such as acetylated ubiquitin and phospho-ubiquitin. Moreover, important roles for heterogeneous polyubiquitin chains, such as mixed or branched chains, have been reported, which significantly increase the diversity of the ubiquitin code. In this review, we describe mass spectrometry-based methods to characterize the ubiquitin signal. We also describe recent advances in our understanding of complex ubiquitin architectures, including our own findings concerning ubiquitin acetylation and branching within polyubiquitin chains.
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Affiliation(s)
- Fumiaki Ohtake
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Sciences, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Sciences, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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33
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Abstract
Ubiquitylation is essential for signal transduction as well as cell division and differentiation in all eukaryotes. Substrate modifications range from a single ubiquitin molecule to complex polymeric chains, with different types of ubiquitylation often eliciting distinct outcomes. The recent identification of novel chain topologies has improved our understanding of how ubiquitylation establishes precise communication within cells. Here, we discuss how the increasing complexity of ubiquitylation is employed to ensure robust and faithful signal transduction in eukaryotic cells.
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34
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Crowe SO, Rana ASJB, Deol KK, Ge Y, Strieter ER. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in Cellulo. Anal Chem 2017; 89:4428-4434. [PMID: 28291339 PMCID: PMC5541364 DOI: 10.1021/acs.analchem.6b03675] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ubiquitin (Ub) has a broad functional range that has been ascribed to the formation of an array of polymeric ubiquitin chains. Understanding the precise roles of ubiquitin chains, however, is difficult due to their complex chain topologies. Branched ubiquitin chains are particularly challenging, as multiple modifications on a single ubiquitin preclude the use of standard bottom-up proteomic approaches. Developing methods to overcome these challenges is crucial considering evidence suggesting branched chains regulate the stability of proteins. In this study, we employ Ubiquitin Chain Enrichment Middle-down Mass Spectrometry (UbiChEM-MS) to identify branched chains that cannot be detected using bottom-up proteomic methods. Specifically, we employ tandem ubiquitin binding entities (TUBEs) and the K29-selective Npl4 Zinc Finger 1 (NZF1) domain from the deubiquitinase TRABID to enrich for chains from human cells. Minimal trypsinolysis followed by high resolution mass spectrometric analysis reveals that Ub chain branching can indeed be detected using both Ub binding domains (UBDs) tested at endogenous levels. We find that ∼1% of chains isolated with TUBEs contain Ub branch points, with this value rising to ∼4% after proteasome inhibition. Electron-transfer dissociation (ETD) analysis indicates the presence of K48 in these branched chains. The use of the NZF1 domain reveals that ∼4% of the isolated chains contain branch points with no apparent dependence on proteasome inhibition. Our results demonstrate an effective strategy for detecting and characterizing the dynamics of branched conjugates under different cellular conditions.
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Affiliation(s)
- Sean O. Crowe
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ambar S. J. B. Rana
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirandeep K. Deol
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Eric R. Strieter
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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35
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Zinngrebe J, Walczak H. TLRs Go Linear – On the Ubiquitin Edge. Trends Mol Med 2017; 23:296-309. [DOI: 10.1016/j.molmed.2017.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 02/07/2023]
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36
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Abstract
The ubiquitin proteasome system controls the concentrations of regulatory proteins and removes damaged and misfolded proteins from cells. Proteins are targeted to the protease at the center of this system, the proteasome, by ubiquitin tags, but ubiquitin is also used as a signal in other cellular processes. Specificity is conferred by the size and structure of the ubiquitin tags, which are recognized by receptors associated with the different cellular processes. However, the ubiquitin code remains ambiguous, and the same ubiquitin tag can target different proteins to different fates. After binding substrate protein at the ubiquitin tag, the proteasome initiates degradation at a disordered region in the substrate. The proteasome has pronounced preferences for the initiation site, and its recognition represents a second component of the degradation signal.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
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37
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Zhang X, Kim KM. Multifactorial Regulation of G Protein-Coupled Receptor Endocytosis. Biomol Ther (Seoul) 2017; 25:26-43. [PMID: 28035080 PMCID: PMC5207461 DOI: 10.4062/biomolther.2016.186] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/21/2016] [Accepted: 11/30/2016] [Indexed: 12/26/2022] Open
Abstract
Endocytosis is a process by which cells absorb extracellular materials via the inward budding of vesicles formed from the plasma membrane. Receptor-mediated endocytosis is a highly selective process where receptors with specific binding sites for extracellular molecules internalize via vesicles. G protein-coupled receptors (GPCRs) are the largest single family of plasma-membrane receptors with more than 1000 family members. But the molecular mechanisms involved in the regulation of GPCRs are believed to be highly conserved. For example, receptor phosphorylation in collaboration with β-arrestins plays major roles in desensitization and endocytosis of most GPCRs. Nevertheless, a number of subsequent studies showed that GPCR regulation, such as that by endocytosis, occurs through various pathways with a multitude of cellular components and processes. This review focused on i) functional interactions between homologous and heterologous pathways, ii) methodologies applied for determining receptor endocytosis, iii) experimental tools to determine specific endocytic routes, iv) roles of small guanosine triphosphate-binding proteins in GPCR endocytosis, and v) role of post-translational modification of the receptors in endocytosis.
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Affiliation(s)
- Xiaohan Zhang
- Pharmacology Laboratory, College of Pharmacy, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyeong-Man Kim
- Pharmacology Laboratory, College of Pharmacy, Chonnam National University, Gwangju 61186, Republic of Korea
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38
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Abstract
Protein complexes form the critical foundation for a wide range of biological process, however understanding the intricate details of their activities is often challenging. In this review we describe how mass spectrometry plays a key role in the analysis of protein assemblies and the cellular pathways which they are involved in. Specifically, we discuss how the versatility of mass spectrometric approaches provides unprecedented information on multiple levels. We demonstrate this on the ubiquitin-proteasome proteolytic pathway, a process that is responsible for protein turnover. We follow the various steps of this degradation route and illustrate the different mass spectrometry workflows that were applied for elucidating molecular information. Overall, this review aims to stimulate the integrated use of multiple mass spectrometry approaches for analyzing complex biological systems.
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39
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Gao S, Pan M, Zheng Y, Huang Y, Zheng Q, Sun D, Lu L, Tan X, Tan X, Lan H, Wang J, Wang T, Wang J, Liu L. Monomer/Oligomer Quasi-Racemic Protein Crystallography. J Am Chem Soc 2016; 138:14497-14502. [PMID: 27768314 DOI: 10.1021/jacs.6b09545] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub. This monomer/oligomer cocrystallization phenomenon expands the concept of racemic crystallography. Using the monomer/oligomer cocrystallization technology we obtained, for the first time the X-ray structures of linear M1-linked tri- and tetra-Ubs and a K11/K63-branched tri-Ub.
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Affiliation(s)
- Shuai Gao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yong Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Yichao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Demeng Sun
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lining Lu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Xiaodan Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Xianglong Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Huan Lan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Jiaxing Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Tian Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Jiawei Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry and ‡State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
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40
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Lee AE, Geis-Asteggiante L, Dixon EK, Miller M, Wang Y, Fushman D, Fenselau C. Preparing to read the ubiquitin code: top-down analysis of unanchored ubiquitin tetramers. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:629-637. [PMID: 28239975 PMCID: PMC5618806 DOI: 10.1002/jms.3787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 05/13/2023]
Abstract
The characterization of polyubiquitin chains has been an analytical challenge for several decades. It has been shown that anchored and unanchored polyubiquitin chains with different isopeptide linkages and lengths exhibit a wide range of profoundly different cellular functions. However, structure function studies have been hindered by the difficulty of characterizing these complex chain structures. This report presents a broadly applicable workflow to characterize ubiquitin tetramers without the need for genetic mutations or reiterative immunoprecipitations. We use a top-down proteomic strategy that exploits ETciD activation on an orbitrap Fusion Lumos and manual interpretation aided by graphical interpretation of mass shifts to facilitate characterization of chain topography and lysine linkage sites. Our workflow differentiates all topological features of the numerous isomers of tetraubiquitin, which have molecular masses in excess of 34 000 Da and identifies linkage sites in these branched proteins. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Amanda E Lee
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive University of Maryland, College Park, MD, 20742, USA
| | - Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive University of Maryland, College Park, MD, 20742, USA
| | - Emma K Dixon
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive University of Maryland, College Park, MD, 20742, USA
| | - Meredith Miller
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive University of Maryland, College Park, MD, 20742, USA
| | - Yan Wang
- Proteomics Core Facility, University of Maryland, College Park, MD, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive University of Maryland, College Park, MD, 20742, USA
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive University of Maryland, College Park, MD, 20742, USA
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41
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Morimoto D, Shirakawa M. The evolving world of ubiquitin: transformed polyubiquitin chains. Biomol Concepts 2016; 7:157-67. [PMID: 27226101 DOI: 10.1515/bmc-2016-0009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
The regulation of diverse cellular events by proteins that have undergone post-translational modification with ubiquitin is well documented. Ubiquitin can be polymerized and eight types of polyubiquitin chain contribute to the complexity and specificity of the ubiquitin signal. Unexpectedly, recent studies have shown that ubiquitin itself undergoes post-translational modification by acetylation and phosphorylation; moreover, amyloid-like fibrils comprised of polyubiquitin chains have been discovered. Thus, ubiquitin is not only conjugated to substrate proteins, but also modified and transformed itself. Here, we review these novel forms of ubiquitin signal, with a focus on fibril formation of polyubiquitin chains and its underlying biological relevance.
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42
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Rebmann V, König L, Nardi FDS, Wagner B, Manvailer LFS, Horn PA. The Potential of HLA-G-Bearing Extracellular Vesicles as a Future Element in HLA-G Immune Biology. Front Immunol 2016; 7:173. [PMID: 27199995 PMCID: PMC4854879 DOI: 10.3389/fimmu.2016.00173] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/19/2016] [Indexed: 12/21/2022] Open
Abstract
The HLA-G molecule is a member of the non-classical HLA class I family. Its surface expression is physiologically restricted to the maternal–fetal interface and to immune privileged adult tissues. Despite the restricted tissue expression, HLA-G is detectable in body fluids as secreted soluble molecules. A unique feature of HLA-G is the structural diversity as surface expressed and as secreted molecules. Secreted HLA-G can be found in various body fluids either as free soluble HLA-G or as part of extracellular vesicles (EVs), which are composed of various antigens/ligands/receptors, bioactive lipids, cytokines, growth factors, and genetic information, such as mRNA and microRNA. Functionally, HLA-G and its secreted forms are considered to play a crucial role in the network of immune-regulatory tolerance mechanisms, preferentially interacting with the cognate inhibitory receptors LILRB1 and LILRB2. The HLA-G mediated tolerance is described in processes of pregnancy, inflammation, and cancer. However, almost all functional and clinical implications of HLA-G in vivo and in vitro have been established based on simple single ligand/receptor interactions at the cell surface, whereas HLA-G-bearing EVs were in minor research focus. Indeed, cytotrophoblast cells, mesenchymal stem cells, and cancer cells were recently described to secrete HLA-G-bearing EVs, displaying immunosuppressive effects and modulating the tumor microenvironment. However, numerous functional and clinical open questions persist. Here, we (i) introduce basic aspects of EVs biology, (ii) summarize the functional knowledge, clinical implications and open questions of HLA-G-bearing EVs, and (iii) discuss HLA-G-bearing EVs as a future element in HLA-G biology.
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Affiliation(s)
- Vera Rebmann
- Institute for Transfusion Medicine, University Hospital Essen , Essen , Germany
| | - Lisa König
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany; Department of Gynecology and Obstetrics, Essen, Germany
| | - Fabiola da Silva Nardi
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany; Laboratory of Immunogenetics and Histocompatibility (LIGH), Federal University of Paraná Genetics Department, Curitiba, Paraná, Brazil; CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District, Brazil
| | - Bettina Wagner
- Institute for Transfusion Medicine, University Hospital Essen , Essen , Germany
| | - Luis Felipe Santos Manvailer
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany; CAPES Foundation, Ministry of Education of Brazil, Brasília, Federal District, Brazil
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen , Essen , Germany
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43
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Lee AE, Geis-Asteggiante L, Dixon EK, Kim Y, Kashyap TR, Wang Y, Fushman D, Fenselau C. Preparing to read the ubiquitin code: characterization of ubiquitin trimers by top-down mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:315-21. [PMID: 27041663 PMCID: PMC4909354 DOI: 10.1002/jms.3759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 05/12/2023]
Abstract
The profound effects of ubiquitination on the movement and processing of cellular proteins depend exquisitely on the structures of monoubiquitin and polyubiquitin modifications. Unconjugated polyubiquitins also have a variety of intracellular functions. Structures and functions are not well correlated yet, because the structures of polyubiquitins and polyubiquitin modifications of proteins are difficult to decipher. We are moving towards a robust strategy to provide that structural information. In this report electron transfer dissociation mass spectra of six synthetic ubiquitin trimers (multiply branched proteins with molecular masses exceeding 25,600 Da) are examined using an Orbitrap Fusion Lumos instrument to determine how top-down mass spectrometry can characterize the chain topology and linkage sites in a single, facile workflow. The efficacy of this method relies on the formation, detection, and interpretation of extensive fragmentation.
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Affiliation(s)
- Amanda E Lee
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Emma K Dixon
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Yeji Kim
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Tanuja R Kashyap
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Yan Wang
- Proteomics Core Facility, University of Maryland, College Park, MD, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD, 20742, USA
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44
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Abstract
Protein ubiquitination is a dynamic multifaceted post-translational modification involved in nearly all aspects of eukaryotic biology. Once attached to a substrate, the 76-amino acid protein ubiquitin is subjected to further modifications, creating a multitude of distinct signals with distinct cellular outcomes, referred to as the 'ubiquitin code'. Ubiquitin can be ubiquitinated on seven lysine (Lys) residues or on the N-terminus, leading to polyubiquitin chains that can encompass complex topologies. Alternatively or in addition, ubiquitin Lys residues can be modified by ubiquitin-like molecules (such as SUMO or NEDD8). Finally, ubiquitin can also be acetylated on Lys, or phosphorylated on Ser, Thr or Tyr residues, and each modification has the potential to dramatically alter the signaling outcome. While the number of distinctly modified ubiquitin species in cells is mind-boggling, much progress has been made to characterize the roles of distinct ubiquitin modifications, and many enzymes and receptors have been identified that create, recognize or remove these ubiquitin modifications. We here provide an overview of the various ubiquitin modifications present in cells, and highlight recent progress on ubiquitin chain biology. We then discuss the recent findings in the field of ubiquitin acetylation and phosphorylation, with a focus on Ser65-phosphorylation and its role in mitophagy and Parkin activation.
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Affiliation(s)
- Kirby N Swatek
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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45
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Ronau JA, Beckmann JF, Hochstrasser M. Substrate specificity of the ubiquitin and Ubl proteases. Cell Res 2016; 26:441-56. [PMID: 27012468 PMCID: PMC4822132 DOI: 10.1038/cr.2016.38] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families.
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Affiliation(s)
- Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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46
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He F, Wollscheid HP, Nowicka U, Biancospino M, Valentini E, Ehlinger A, Acconcia F, Magistrati E, Polo S, Walters KJ. Myosin VI Contains a Compact Structural Motif that Binds to Ubiquitin Chains. Cell Rep 2016; 14:2683-94. [PMID: 26971995 DOI: 10.1016/j.celrep.2016.01.079] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 11/24/2015] [Accepted: 01/27/2016] [Indexed: 12/13/2022] Open
Abstract
Myosin VI is critical for cargo trafficking and sorting during early endocytosis and autophagosome maturation, and abnormalities in these processes are linked to cancers, neurodegeneration, deafness, and hypertropic cardiomyopathy. We identify a structured domain in myosin VI, myosin VI ubiquitin-binding domain (MyUb), that binds to ubiquitin chains, especially those linked via K63, K11, and K29. Herein, we solve the solution structure of MyUb and MyUb:K63-linked diubiquitin. MyUb folds as a compact helix-turn-helix-like motif and nestles between the ubiquitins of K63-linked diubiquitin, interacting with distinct surfaces of each. A nine-amino-acid extension at the C-terminal helix (Helix2) of MyUb is required for myosin VI interaction with endocytic and autophagic adaptors. Structure-guided mutations revealed that a functional MyUb is necessary for optineurin interaction. In addition, we found that an isoform-specific helix restricts MyUb binding to ubiquitin chains. This work provides fundamental insights into myosin VI interaction with ubiquitinated cargo and functional adaptors.
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Affiliation(s)
- Fahu He
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hans-Peter Wollscheid
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Urszula Nowicka
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Matteo Biancospino
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Eleonora Valentini
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Aaron Ehlinger
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Filippo Acconcia
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Elisa Magistrati
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy; DIPO, Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, Via di Rudinì 8, 20122 Milan, Italy.
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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47
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Nardi FDS, Slowik R, Michelon T, Manvailer LFDS, Wagner B, Neumann J, Horn P, Bicalho MDG, Rebmann V. High Amounts of Total and Extracellular Vesicle-Derived Soluble HLA-G are Associated with HLA-G 14-bp Deletion Variant in Women with Embryo Implantation Failure. Am J Reprod Immunol 2016; 75:661-71. [PMID: 26959830 DOI: 10.1111/aji.12507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/15/2016] [Indexed: 12/31/2022] Open
Abstract
PROBLEM Human leukocyte antigen-G (HLA-G) expression is related to 14-bp insertion/deletion polymorphism at the 3'UTR of the HLA-G gene. Soluble forms of HLA-G are released as free molecules or via extracellular vesicles (EVs). Due to the crucial role of HLA-G during pregnancy, we analyzed the 14-bp polymorphism and the two secreted forms in implantation failure women (IF) and in fertile women (FW). METHOD OF STUDY For the genetic analysis, 49 IF and 34 FW were genotyped. For sHLA-G quantification, serum samples from 35 IF and 23 FW were available. ExoQuick(™) kit was used for EVs precipitation. The total soluble HLA-G (sHLA-Gtot ) and vesicular sHLA-GEV were quantified by ELISA. The EVs size and concentration were determined by nanoparticle tracking analysis (NTA). RESULTS An increased proportion of IF presented high levels of sHLA-Gtot (P = 0.02) and vesicular sHLA-GEV (P = 0.0003) compared to FW. The 14-bp deletion allele is more frequent in IF (P = 0.0002) and associated with high levels of sHLA-Gtot and vesicular sHLA-GEV . CONCLUSION The high expression of sHLA-Gtot and sHLA-GEV , together with the presence of the 14-bp deletion allele, might be involved in implantation failure.
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Affiliation(s)
- Fabiola da Silva Nardi
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany.,Laboratory of Immunogenetics and Histocompatibility (LIGH), Genetics Department, Federal University of Paraná, Curitiba, Brazil.,Capes Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Renata Slowik
- Laboratory of Immunogenetics and Histocompatibility (LIGH), Genetics Department, Federal University of Paraná, Curitiba, Brazil
| | | | - Luis Felipe Dos Santos Manvailer
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany.,Capes Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Bettina Wagner
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Jorge Neumann
- Reproductive Immunology Center, Porto Alegre, Brazil
| | - Peter Horn
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Maria da Graça Bicalho
- Laboratory of Immunogenetics and Histocompatibility (LIGH), Genetics Department, Federal University of Paraná, Curitiba, Brazil
| | - Vera Rebmann
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
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48
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Kalinowska K, Nagel MK, Isono E. Measuring the Enzyme Activity of Arabidopsis Deubiquitylating Enzymes. Methods Mol Biol 2016; 1450:35-44. [PMID: 27424744 DOI: 10.1007/978-1-4939-3759-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Deubiquitylating enzymes, or DUBs, are important regulators of ubiquitin homeostasis and substrate stability, though the molecular mechanisms of most of the DUBs in plants are not yet understood. As different ubiquitin chain types are implicated in different biological pathways, it is important to analyze the enzyme characteristic for studying a DUB. Quantitative analysis of DUB activity is also important to determine enzyme kinetics and the influence of DUB binding proteins on the enzyme activity. Here, we show methods to analyze DUB activity using immunodetection, Coomassie Brilliant Blue staining, and fluorescence measurement that can be useful for understanding the basic characteristic of DUBs.
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Affiliation(s)
- Kamila Kalinowska
- Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Marie-Kristin Nagel
- Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany
| | - Erika Isono
- Department of Plant Systems Biology, Technische Universität München, Emil-Ramann-Str. 4, 85354, Freising, Germany.
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49
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Cano F, Rapiteanu R, Sebastiaan Winkler G, Lehner PJ. A non-proteolytic role for ubiquitin in deadenylation of MHC-I mRNA by the RNA-binding E3-ligase MEX-3C. Nat Commun 2015; 6:8670. [PMID: 26471122 PMCID: PMC4617606 DOI: 10.1038/ncomms9670] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 09/17/2015] [Indexed: 11/27/2022] Open
Abstract
The regulation of protein and mRNA turnover is essential for many cellular processes. We recently showed that ubiquitin—traditionally linked to protein degradation—directly regulates the degradation of mRNAs through the action of a newly identified family of RNA-binding E3 ubiquitin ligases. How ubiquitin regulates mRNA decay remains unclear. Here, we identify a new role for ubiquitin in regulating deadenylation, the initial and often rate-limiting step in mRNA degradation. MEX-3C, a canonical member of this family of RNA-binding ubiquitin ligases, associates with the cytoplasmic deadenylation complexes and ubiquitinates CNOT7(Caf1), the main catalytic subunit of the CCR4-NOT deadenylation machinery. We establish a new role for ubiquitin in regulating MHC-I mRNA deadenylation as ubiquitination of CNOT7 by MEX-3C regulates its deadenylation activity and is required for MHC-I mRNA degradation. Since neither proteasome nor lysosome inhibitors rescued MEX-3C-mediated MHC-I mRNA degradation, our findings suggest a new non-proteolytic function for ubiquitin in the regulation of mRNA decay. mRNA deadenylation, the first step in regulated degradation, is mediated by the action of the CCR4-NOT and PAN2-PAN3 complexes. Here the authors show that the RNA-binding E3 ubiquitin-ligase MEX-3C associates with the CCR4-NOT complex and ubiquitinates the catalytic subunit CNOT7 to regulate its deadenylation activity.
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Affiliation(s)
- Florencia Cano
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.,Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge CB22 3AT, UK
| | - Radu Rapiteanu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - G Sebastiaan Winkler
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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50
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Parkinson MDJ, Piper SC, Bright NA, Evans JL, Boname JM, Bowers K, Lehner PJ, Luzio JP. A non-canonical ESCRT pathway, including histidine domain phosphotyrosine phosphatase (HD-PTP), is used for down-regulation of virally ubiquitinated MHC class I. Biochem J 2015; 471:79-88. [PMID: 26221024 PMCID: PMC4613529 DOI: 10.1042/bj20150336] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/21/2015] [Accepted: 07/28/2015] [Indexed: 11/17/2022]
Abstract
The Kaposi's sarcoma-associated herpes virus (KSHV) K3 viral gene product effectively down-regulates cell surface MHC class I. K3 is an E3 ubiquitin ligase that promotes Lys(63)-linked polyubiquitination of MHC class I, providing the signal for clathrin-mediated endocytosis. Endocytosis is followed by sorting into the intralumenal vesicles (ILVs) of multivesicular bodies (MVBs) and eventual delivery to lysosomes. The sorting of MHC class I into MVBs requires many individual proteins of the four endosomal sorting complexes required for transport (ESCRTs). In HeLa cells expressing the KSHV K3 ubiquitin ligase, the effect of RNAi-mediated depletion of individual proteins of the ESCRT-0 and ESCRT-I complexes and three ESCRT-III proteins showed that these are required to down-regulate MHC class I. However, depletion of proteins of the ESCRT-II complex or of the ESCRT-III protein, VPS20 (vacuolar protein sorting 20)/CHMP6 (charged MVB protein 6), failed to prevent the loss of MHC class I from the cell surface. Depletion of histidine domain phosphotyrosine phosphatase (HD-PTP) resulted in an increase in the cell surface concentration of MHC class I in HeLa cells expressing the KSHV K3 ubiquitin ligase. Rescue experiments with wild-type (WT) and mutant HD-PTP supported the conclusion that HD-PTP acts as an alternative to ESCRT-II and VPS20/CHMP6 as a link between the ESCRT-I and those ESCRT-III protein(s) necessary for ILV formation. Thus, the down-regulation of cell surface MHC class I, polyubiquitinated by the KSHV K3 ubiquitin ligase, does not employ the canonical ESCRT pathway, but instead utilizes an alternative pathway in which HD-PTP replaces ESCRT-II and VPS20/CHMP6.
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Affiliation(s)
- Michael D J Parkinson
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - Siân C Piper
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - Nicholas A Bright
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - Jennifer L Evans
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - Jessica M Boname
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - Katherine Bowers
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K
| | - J Paul Luzio
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Wellcome Trust/MRC Building, Biomedical Campus, Hills Road, Cambridge, CB2 0XY, U.K.
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