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Hegde S, Soory A, Kaduskar B, Ratnaparkhi GS. SUMO conjugation regulates immune signalling. Fly (Austin) 2020; 14:62-79. [PMID: 32777975 PMCID: PMC7714519 DOI: 10.1080/19336934.2020.1808402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) are critical drivers and attenuators for proteins that regulate immune signalling cascades in host defence. In this review, we explore functional roles for one such PTM, the small ubiquitin-like modifier (SUMO). Very few of the SUMO conjugation targets identified by proteomic studies have been validated in terms of their roles in host defence. Here, we compare and contrast potential SUMO substrate proteins in immune signalling for flies and mammals, with an emphasis on NFκB pathways. We discuss, using the few mechanistic studies that exist for validated targets, the effect of SUMO conjugation on signalling and also explore current molecular models that explain regulation by SUMO. We also discuss in detail roles of evolutionary conservation of mechanisms, SUMO interaction motifs, crosstalk of SUMO with other PTMs, emerging concepts such as group SUMOylation and finally, the potentially transforming roles for genome-editing technologies in studying the effect of PTMs.
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Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
| | - Amarendranath Soory
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
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52
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van Kruijsbergen I, Mulder MPC, Uckelmann M, van Welsem T, de Widt J, Spanjaard A, Jacobs H, El Oualid F, Ovaa H, van Leeuwen F. Strategy for Development of Site-Specific Ubiquitin Antibodies. Front Chem 2020; 8:111. [PMID: 32154221 PMCID: PMC7047734 DOI: 10.3389/fchem.2020.00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification regulating a wide range of biological processes. Ubiquitination involves the covalent attachment of the small protein ubiquitin to a lysine of a protein substrate. In addition to its well-established role in protein degradation, protein ubiquitination plays a role in protein-protein interactions, DNA repair, transcriptional regulation, and other cellular functions. Understanding the mechanisms and functional relevance of ubiquitin as a signaling system requires the generation of antibodies or alternative reagents that specifically detect ubiquitin in a site-specific manner. However, in contrast to other post-translational modifications such as acetylation, phosphorylation, and methylation, the instability and size of ubiquitin-76 amino acids-complicate the preparation of suitable antigens and the generation antibodies detecting such site-specific modifications. As a result, the field of ubiquitin research has limited access to specific antibodies. This severely hampers progress in understanding the regulation and function of site-specific ubiquitination in many areas of biology, specifically in epigenetics and cancer. Therefore, there is a high demand for antibodies recognizing site-specific ubiquitin modifications. Here we describe a strategy for the development of site-specific ubiquitin antibodies. Based on a recently developed antibody against site-specific ubiquitination of histone H2B, we provide detailed protocols for chemical synthesis methods for antigen preparation and discuss considerations for screening and quality control experiments.
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Affiliation(s)
- Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Monique P C Mulder
- Leiden Institute for Chemical Immunology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Michael Uckelmann
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - John de Widt
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Huib Ovaa
- Leiden Institute for Chemical Immunology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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53
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van Huizen M, Kikkert M. The Role of Atypical Ubiquitin Chains in the Regulation of the Antiviral Innate Immune Response. Front Cell Dev Biol 2020; 7:392. [PMID: 32039206 PMCID: PMC6987411 DOI: 10.3389/fcell.2019.00392] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022] Open
Abstract
It is well established that polyubiquitin chains, in particular those linked through K48 and K63, play a key role in the regulation of the antiviral innate immune response. However, the role of the atypical chains linked via any of the other lysine residues (K6, K11, K27, K29, and K33) and the M1-linked linear chains have not been investigated very well yet in this context. This is partially due to a lack of tools to study these linkages in their biological context. Interestingly though, recent findings underscore the importance of the atypical chains in the regulation of the antiviral immune response. This review will highlight the most important advances in the study of the role of atypical ubiquitin chains, particularly in the regulation of intracellular antiviral innate immune signaling pathways. We will also discuss the development of new tools and how these can increase our knowledge of the role of atypical ubiquitin chains.
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Affiliation(s)
- Mariska van Huizen
- Department of Medical Microbiology, LUMC Center for Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, LUMC Center for Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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54
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Dittmar G, Winklhofer KF. Linear Ubiquitin Chains: Cellular Functions and Strategies for Detection and Quantification. Front Chem 2020; 7:915. [PMID: 31998699 PMCID: PMC6966713 DOI: 10.3389/fchem.2019.00915] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/16/2019] [Indexed: 01/06/2023] Open
Abstract
Ubiquitination of proteins is a sophisticated post-translational modification implicated in the regulation of an ever-growing abundance of cellular processes. Recent insights into different layers of complexity have shaped the concept of the ubiquitin code. Key players in determining this code are the number of ubiquitin moieties attached to a substrate, the architecture of polyubiquitin chains, and post-translational modifications of ubiquitin itself. Ubiquitination can induce conformational changes of substrates and alter their interactive profile, resulting in the formation of signaling complexes. Here we focus on a distinct type of ubiquitination that is characterized by an inter-ubiquitin linkage through the N-terminal methionine, called M1-linked or linear ubiquitination. Formation, recognition, and disassembly of linear ubiquitin chains are highly specific processes that are implicated in immune signaling, cell death regulation and protein quality control. Consistent with their role in influencing signaling events, linear ubiquitin chains are formed in a transient and spatially regulated manner, making their detection and quantification challenging.
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Affiliation(s)
- Gunnar Dittmar
- Proteomics of Cellular Signalling, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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55
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Activation and suppression of hematopoietic integrins in hemostasis and immunity. Blood 2020; 135:7-16. [DOI: 10.1182/blood.2019003336] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022] Open
Abstract
Nolte and Margadant review the current understanding of the activation and inactivation of integrin receptors expressed by hematopoietic cells and the role of these conformational changes in modulating platelet and leukocyte function.
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56
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Gâtel P, Piechaczyk M, Bossis G. Ubiquitin, SUMO, and Nedd8 as Therapeutic Targets in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:29-54. [PMID: 32274752 DOI: 10.1007/978-3-030-38266-7_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ubiquitin defines a family of approximately 20 peptidic posttranslational modifiers collectively called the Ubiquitin-like (UbLs). They are conjugated to thousands of proteins, modifying their function and fate in many ways. Dysregulation of these modifications has been implicated in a variety of pathologies, in particular cancer. Ubiquitin, SUMO (-1 to -3), and Nedd8 are the best-characterized UbLs. They have been involved in the regulation of the activity and/or the stability of diverse components of various oncogenic or tumor suppressor pathways. Moreover, the dysregulation of enzymes responsible for their conjugation/deconjugation has also been associated with tumorigenesis and cancer resistance to therapies. The UbL system therefore constitutes an attractive target for developing novel anticancer therapeutic strategies. Here, we review the roles and dysregulations of Ubiquitin, SUMO, and Nedd8 pathways in tumorigenesis, as well as recent advances in the identification of small molecules targeting their conjugating machineries for potential application in the fight against cancer.
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Affiliation(s)
- Pierre Gâtel
- Equipe Labellisée Ligue Contre le Cancer, IGMM, Univ Montpellier, CNRS, Montpellier, France
| | - Marc Piechaczyk
- Equipe Labellisée Ligue Contre le Cancer, IGMM, Univ Montpellier, CNRS, Montpellier, France
| | - Guillaume Bossis
- Equipe Labellisée Ligue Contre le Cancer, IGMM, Univ Montpellier, CNRS, Montpellier, France.
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Wiseman RL. Lining up for quality control: linear ubiquitin and proteotoxicity. EMBO J 2019; 38:embj.2019101985. [PMID: 30975687 DOI: 10.15252/embj.2019101985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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