1
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Wang C, Gu C, Lv Y, Liu H, Wang Y, Zuo Y, Jiang G, Liu L, Liu J. AlphaFold2 assists in providing novel mechanistic insights into the interactions among the LUBAC subunits. Acta Biochim Biophys Sin (Shanghai) 2024; 56:1034-1043. [PMID: 38655618 PMCID: PMC11322871 DOI: 10.3724/abbs.2024047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 04/26/2024] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is the only known E3 ligase complex in which the ubiquitin-like (UBL) domains of SHARPIN and HOIL-1L interact with HOIP to determine the structural stability of LUBAC. The interactions between subunits within LUBAC have been a topic of extensive research. However, the impact of the LTM motif on the interaction between the UBL domains of SHARPIN and HOIL-1L with HOIP remains unclear. Here, we discover that the absence of the LTM motif in the AlphaFold2-predicted LUBAC structure alters the HOIP-UBA structure. We employ GeoPPI to calculate the changes in binding free energy (ΔG) caused by single-point mutations between subunits, simulating their protein-protein interactions. The results reveal that the presence of the LTM motif decreases the interaction between the UBL domains of SHARPIN and HOIL-1L with HOIP, leading to a decrease in the structural stability of LUBAC. Furthermore, using the AlphaFold2-predicted results, we find that HOIP (629‒695) and HOIP-UBA bind to both sides of HOIL-1L-UBL, respectively. The experiments of Gromacs molecular dynamics simulations, SPR and ITC demonstrate that the elongated domain formed by HOIP (629‒695) and HOIP-UBA, hereafter referred to as the HOIP (466‒695) structure, interacts with HOIL-1L-UBL to form a structurally stable complex. These findings illustrate the collaborative interaction between HOIP-UBA and HOIP (629‒695) with HOIL-1L-UBL, which influences the structural stability of LUBAC.
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Affiliation(s)
- Chenchen Wang
- College of Veterinary MedicineNortheast Agricultural UniversityHarbin150030China
| | - Chunying Gu
- Department of Medical Laboratory Science and TechnologyHarbin Medical University-DaqingDaqing163319China
| | - Ying Lv
- College of Life SciencesNortheast Agricultural UniversityHarbin150030China
| | - Hongyu Liu
- Preventive and Control Center for Animal Disease of Heilongjiang ProvinceHarbin150069China
| | - Yanan Wang
- College of Basic Medical SciencesHarbin Medical University-DaqingDaqing163319China
| | - Yongmei Zuo
- Heilongjiang Institute of Animal Health InspectionHarbin150006China
| | - Guangyu Jiang
- College of Basic Medical SciencesHarbin Medical University-DaqingDaqing163319China
| | - Lili Liu
- College of Basic Medical SciencesHarbin Medical University-DaqingDaqing163319China
| | - Jiafu Liu
- College of Basic Medical SciencesHarbin Medical University-DaqingDaqing163319China
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2
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Zhang Y, Xu X, Wang Y, Wang Y, Zhou X, Pan L. Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN. Biochem Biophys Res Commun 2023; 689:149239. [PMID: 37976837 DOI: 10.1016/j.bbrc.2023.149239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/28/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
HOIL-1L and SHARPIN are two essential regulatory subunits of the linear ubiquitin chain assembly complex (LUBAC), which is the only known E3 ligase complex generating linear ubiquitin chains. In addition to their LUBAC-dependent functions, HOIL-1L and SHARPIN alone play crucial roles in many LUBAC-independent cellular processes. Importantly, deficiency of HOIL-1L or SHARPIN leads to severe disorders in humans or mice. However, the mechanistic bases underlying the multi-functions of HOIL-1L and SHARPIN are still largely unknown. Here, we uncover that HOIL-1L and SHARPIN alone can form homo-dimers through their LTM motifs. We solve two crystal structures of the dimeric LTM motifs of HOIL-1L and SHARPIN, which not only elucidate the detailed molecular mechanism underpinning the dimer formations of HOIL-1L and SHARPIN, but also reveal a general mode shared by the LTM motifs of HOIL-1L and SHARPIN for forming homo-dimer or hetero-dimer. Furthermore, we elucidate that the polyglucosan body myopathy-associated HOIL-1L A18P mutation disturbs the structural folding of HOIL-1L LTM, and disrupts the dimer formation of HOIL-1L. In summary, our study provides mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN mediated by their LTM motifs, and expands our understandings of the multi-functions of HOIL-1L and SHARPIN as well as the etiology of relevant human disease caused by defective HOIL-1L.
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Affiliation(s)
- Yan Zhang
- Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaolong Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yaru Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
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3
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SPATA2 restricts OTULIN-dependent LUBAC activity independently of CYLD. Cell Rep 2023; 42:111961. [PMID: 36640323 DOI: 10.1016/j.celrep.2022.111961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/10/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
SPATA2 mediates the recruitment of CYLD to immune receptor complexes by bridging the interaction of CYLD with the linear ubiquitylation assembly complex (LUBAC) component HOIP. Whether SPATA2 exhibits functions independently of CYLD is unclear. Here, we show that, while Cyld-/- and Spata2-/- mice are viable, double mutants exhibit highly penetrant perinatal lethality, indicating independent functions of SPATA2 and CYLD. Cyld-/-Spata2-/- fibroblasts show increased M1-linked TNFR1-SC ubiquitylation and, similar to Cyld-/-Spata2-/- macrophages and intestinal epithelial cells, elevated pro-inflammatory gene expression compared with Cyld-/- or Spata2-/- cells. We show that SPATA2 competes with OTULIN for binding to HOIP via its PUB-interacting motif (PIM) and its zinc finger domain, thereby promoting autoubiquitylation of LUBAC. Consistently, increased pro-inflammatory signaling in Cyld-/-Spata2-/- cells depends on the presence of OTULIN. Our data therefore indicate that SPATA2 counteracts, independently of CYLD, the deubiquitylation of LUBAC by OTULIN and thereby attenuates LUBAC activity and pro-inflammatory signaling.
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4
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Sato Y, Terawaki S, Oikawa D, Shimizu K, Okina Y, Ito H, Tokunaga F. Involvement of heterologous ubiquitination including linear ubiquitination in Alzheimer's disease and amyotrophic lateral sclerosis. Front Mol Biosci 2023; 10:1089213. [PMID: 36726375 PMCID: PMC9884707 DOI: 10.3389/fmolb.2023.1089213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
In neurodegenerative diseases such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS), the progressive accumulation of ubiquitin-positive cytoplasmic inclusions leads to proteinopathy and neurodegeneration. Along with the seven types of Lys-linked ubiquitin chains, the linear ubiquitin chain assembly complex (LUBAC)-mediated Met1-linked linear ubiquitin chain, which activates the canonical NF-κB pathway, is also involved in cytoplasmic inclusions of tau in AD and TAR DNA-binding protein 43 in ALS. Post-translational modifications, including heterologous ubiquitination, affect proteasomal and autophagic degradation, inflammatory responses, and neurodegeneration. Single nucleotide polymorphisms (SNPs) in SHARPIN and RBCK1 (which encodes HOIL-1L), components of LUBAC, were recently identified as genetic risk factors of AD. A structural biological simulation suggested that most of the SHARPIN SNPs that cause an amino acid replacement affect the structure and function of SHARPIN. Thus, the aberrant LUBAC activity is related to AD. Protein ubiquitination and ubiquitin-binding proteins, such as ubiquilin 2 and NEMO, facilitate liquid-liquid phase separation (LLPS), and linear ubiquitination seems to promote efficient LLPS. Therefore, the development of therapeutic approaches that target ubiquitination, such as proteolysis-targeting chimeras (PROTACs) and inhibitors of ubiquitin ligases, including LUBAC, is expected to be an additional effective strategy to treat neurodegenerative diseases.
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Affiliation(s)
- Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Graduate School of Engineering, Tottori University, Tottori, Japan,Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Seigo Terawaki
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan,Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Daisuke Oikawa
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kouhei Shimizu
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yoshinori Okina
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Hidefumi Ito
- Department of Neurology, Wakayama Medical University, Wakayama, Japan
| | - Fuminori Tokunaga
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan,*Correspondence: Fuminori Tokunaga,
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5
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Ciuffa R, Uliana F, Mannion J, Mehnert M, Tenev T, Marulli C, Satanowski A, Keller LML, Rodilla Ramírez PN, Ori A, Gstaiger M, Meier P, Aebersold R. Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics. Proc Natl Acad Sci U S A 2022; 119:e2117175119. [PMID: 36179048 PMCID: PMC9546619 DOI: 10.1073/pnas.2117175119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 07/28/2022] [Indexed: 12/03/2022] Open
Abstract
Protein-protein interactions (PPIs) represent the main mode of the proteome organization in the cell. In the last decade, several large-scale representations of PPI networks have captured generic aspects of the functional organization of network components but mostly lack the context of cellular states. However, the generation of context-dependent PPI networks is essential for structural and systems-level modeling of biological processes-a goal that remains an unsolved challenge. Here we describe an experimental/computational strategy to achieve a modeling of PPIs that considers contextual information. This strategy defines the composition, stoichiometry, temporal organization, and cellular requirements for the formation of target assemblies. We used this approach to generate an integrated model of the formation principles and architecture of a large signalosome, the TNF-receptor signaling complex (TNF-RSC). Overall, we show that the integration of systems- and structure-level information provides a generic, largely unexplored link between the modular proteome and cellular function.
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Affiliation(s)
- Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Federico Uliana
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonathan Mannion
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Cathy Marulli
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | | | | | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, SW3 6JB London, United Kingdom
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, 8093 Zurich, Switzerland
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6
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Yu B, Wang F, Wang Y. Advances in the Structural and Physiological Functions of SHARPIN. Front Immunol 2022; 13:858505. [PMID: 35547743 PMCID: PMC9084887 DOI: 10.3389/fimmu.2022.858505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
SHARPIN was initially found as a SHANK-associated protein. SHARPIN can be used as an important component to form the linear ubiquitin chain assembly complex (LUBAC) with HOIL-1L, HOIP to produce a linear ubiquitin chain connected N-terminal Met1, playing a critical role in various cellular processes including NF-κB signaling, inflammation, embryogenesis and apoptosis. SHARPIN alone can also participate in many critical physiological activities and cause various disorders such as chronic dermatitis, tumor, and Alzheimer’s disease. Mice with spontaneous autosomal recessive mutations in the SHARPIN protein mainly exhibit chronic dermatitis and immunodeficiency with elevated IgM. Additionally, SHARPIN alone also plays a key role in various cellular events, such as B cells activation and platelet aggregation. Structural studies of the SHARPIN or LUBAC have been reported continuously, advancing our understanding of it at the molecular level. However, the full-length structure of the SHARPIN or LUBAC was lagging, and the molecular mechanism underlying these physiological processes is also unclear. Herein, we summarized the currently resolved structure of SHARPIN as well as the emerging physiological role of SHARPIN alone or in LUBAC. Further structural and functional study of SHARPIN will provide insight into the role and underlying mechanism of SHARPIN in disease, as well as its potential application in therapeutic.
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Affiliation(s)
- Beiming Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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7
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Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri. Proc Natl Acad Sci U S A 2022; 119:e2116776119. [PMID: 35294289 PMCID: PMC8944867 DOI: 10.1073/pnas.2116776119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
SignificanceShigella flexneri, a deleterious bacterium, causes massive human infection cases and deaths worldwide. To facilitate survival and replication in infected host cells, S. flexneri can secrete two highly similar E3 ligase effectors, IpaH1.4 and IpaH2.5, to subvert the linear ubiquitin chain assembly complex (LUBAC), a key player involved in numerous antibacterial signaling pathways of host cells but with poorly understood mechanisms. In this study, through systematic biochemical and structural characterization, we elucidate the multiple tactics adopted by IpaH1.4/2.5 to disarm the human LUBAC and provide mechanistic insights into the subversion of host LUBAC by IpaH1.4/2.5 of S. flexneri.
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8
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Biochemical and functional characterization of the N-terminal ubiquitin-like domain of human SHARPIN. Protein Expr Purif 2021; 192:106042. [PMID: 34965468 DOI: 10.1016/j.pep.2021.106042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022]
Abstract
SHARPIN, an accessory subunit of the E3 ligase complex LUBAC, participates in the formation of LUBAC through the ubiquitin-like (UBL) domain located in the central region of SHARPIN and interacts with the ubiquitin-associated domain (UBA) of the catalytic subunit HOIP. However, the role of the N-terminal UBL domain of SHARPIN in stable LUBAC formation has not been clarified. In this study, the 1-127 domain, 128-309 domain, and UBL domain of SHARPIN expression vectors were constructed using the molecular biology method. Then the co-expression of SUMO fusion protein combined with SUMO protease (ULP enzyme) in Escherichia coli was successfully applied to improve the soluble expression of target protein. The results of circular dichroism proved that they all belong to the α+β class of proteins. The results of size exclusion chromatography showed that 128-309 domain could combine with HOIP and HOIL-1L to participate in the stability of LUBAC. Both thermal-induced and urea-induced unfolding experiment results demonstrated that the existence of the N-terminal UBL domain could make the overall structure more stable than the alone UBL domain. Biosensor experiments indicated that the existence of the N-terminal UBL domain strengthened the binding ability of the UBL domain and the UBA domain. These results were conducive to further study the structure and function of SHARPIN.
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9
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Krishnan D, Menon RN, Gopala S. SHARPIN: Role in Finding NEMO and in Amyloid-Beta Clearance and Degradation (ABCD) Pathway in Alzheimer's Disease? Cell Mol Neurobiol 2021; 42:1267-1281. [PMID: 33400084 DOI: 10.1007/s10571-020-01023-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/28/2020] [Indexed: 12/11/2022]
Abstract
SHANK- associated RH domain-interacting protein (SHARPIN) is a multifunctional protein associated with numerous physiological functions and many diseases. The primary role of the protein as a LUBAC-dependent component in regulating the activation of the transcription factor NF-κB accounts to its role in inflammation and antiapoptosis. Hence, an alteration of SHARPIN expression or genetic mutations or polymorphisms leads to the alteration of the above-mentioned primary physiological functions contributing to inflammation-associated diseases and cancer, respectively. However, there are complications of targeting SHARPIN as a therapeutic approach, which arises from the wide-range of LUBAC-independent functions and yet unknown roles of SHARPIN including neuronal functions. The identification of SHARPIN as a postsynaptic protein and the emerging studies indicating its role in several neurodegenerative diseases including Alzheimer's disease suggests a strong role of SHARPIN in neuronal functioning. This review summarizes the functional roles of SHARPIN in normal physiology and disease pathogenesis and strongly suggests a need for concentrating more studies on identifying the unknown neuronal functions of SHARPIN and hence its role in neurodegenerative diseases.
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Affiliation(s)
- Dhanya Krishnan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India
| | - Ramsekhar N Menon
- Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India
| | - Srinivas Gopala
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, 695011, Kerala, India.
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10
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Cho EA, Zhang P, Kumar V, Kavalchuk M, Zhang H, Huang Q, Duncan JS, Wu J. Phosphorylation of RIAM by src promotes integrin activation by unmasking the PH domain of RIAM. Structure 2020; 29:320-329.e4. [PMID: 33275877 DOI: 10.1016/j.str.2020.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
Integrin activation controls cell adhesion, migration, invasion, and extracellular matrix remodeling. RIAM (RAP1-GTP-interacting adaptor molecule) is recruited by activated RAP1 to the plasma membrane (PM) to mediate integrin activation via an inside-out signaling pathway. This process requires the association of the pleckstrin homology (PH) domain of RIAM with the membrane PIP2. We identify a conserved intermolecular interface that masks the PIP2-binding site in the PH domains of RIAM. Our data indicate that phosphorylation of RIAM by Src family kinases disrupts this PH-mediated interface, unmasks the membrane PIP2-binding site, and promotes integrin activation. We further demonstrate that this process requires phosphorylation of Tyr267 and Tyr427 in the RIAM PH domain by Src. Our data reveal an unorthodox regulatory mechanism of small GTPase effector proteins by phosphorylation-dependent PM association of the PH domain and provide new insights into the link between Src kinases and integrin signaling.
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Affiliation(s)
- Eun-Ah Cho
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Pingfeng Zhang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Vikas Kumar
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Mikhail Kavalchuk
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Hao Zhang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | - James S Duncan
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jinhua Wu
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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11
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Soheili-Nezhad S, Jahanshad N, Guelfi S, Khosrowabadi R, Saykin AJ, Thompson PM, Beckmann CF, Sprooten E, Zarei M. Imaging genomics discovery of a new risk variant for Alzheimer's disease in the postsynaptic SHARPIN gene. Hum Brain Mapp 2020; 41:3737-3748. [PMID: 32558014 PMCID: PMC7416020 DOI: 10.1002/hbm.25083] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
Molecular mechanisms underlying Alzheimer's disease (AD) are difficult to investigate, partly because diagnosis lags behind the insidious pathological processes. Therefore, identifying AD neuroimaging markers and their genetic modifiers may help study early mechanisms of neurodegeneration. We aimed to identify brain regions of the highest vulnerability to AD using a data-driven search in the AD Neuroimaging Initiative (ADNI, n = 1,100 subjects), and further explored genetic variants affecting this critical brain trait using both ADNI and the younger UK Biobank cohort (n = 8,428 subjects). Tensor-Based Morphometry (TBM) and Independent Component Analysis (ICA) identified the limbic system and its interconnecting white-matter as the most AD-vulnerable brain feature. Whole-genome analysis revealed a common variant in SHARPIN that was associated with this imaging feature (rs34173062, p = 2.1 × 10-10 ). This genetic association was validated in the UK Biobank, where it was correlated with entorhinal cortical thickness bilaterally (p = .002 left and p = 8.6 × 10-4 right), and with parental history of AD (p = 2.3 × 10-6 ). Our findings suggest that neuroanatomical variation in the limbic system and AD risk are associated with a novel variant in SHARPIN. The role of this postsynaptic density gene product in β1-integrin adhesion is in line with the amyloid precursor protein (APP) intracellular signaling pathway and the recent genome-wide evidence.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Institute of Medical Science and Technology, Shahid Beheshti University, Tehran, Iran.,Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands
| | - Neda Jahanshad
- Imaging Genetics Center, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey, California, USA
| | - Sebastian Guelfi
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Reza Khosrowabadi
- Institute for Cognitive and Brain Science, Shahid Beheshti University, Tehran, Iran
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Paul M Thompson
- Imaging Genetics Center, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey, California, USA
| | - Christian F Beckmann
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, The Netherlands.,Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Emma Sprooten
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Mojtaba Zarei
- Institute of Medical Science and Technology, Shahid Beheshti University, Tehran, Iran
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12
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Yang Y, Liang YH, Zheng Y, Tang LJ, Zhou ST, Zhu JN. SHARPIN regulates cell proliferation of cutaneous basal cell carcinoma via inactivation of the transcriptional factors GLI2 and c‑JUN. Mol Med Rep 2020; 21:1799-1808. [PMID: 32319607 PMCID: PMC7057814 DOI: 10.3892/mmr.2020.10981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/07/2020] [Indexed: 12/23/2022] Open
Abstract
SHANK‑associated RH domain‑interacting protein (SHARPIN) is a component of the linear ubiquitin chain assembly complex that can enhance the NF‑κB and JNK signaling pathways, acting as a tumor‑associated protein in a variety of cancer types. The present study investigated the role of SHARPIN in cutaneous basal cell carcinoma (BCC). Human BCC (n=26) and normal skin (n=5) tissues, and BCC (TE354.T) and normal skin (HaCaT) cell lines were used to evaluate SHARPIN expression level using immunohistochemistry and western blotting, respectively. A lentivirus carrying SHARPIN‑targeting or negative control short hairpin RNA was infected into TE354.T cells, and the infected stable cells were assayed to analyze tumor cell proliferation, cell cycle, apoptosis, migration and invasion by Cell Counting Kit‑8 and 5‑ethynyl‑2'‑deoxyuridine incorporation assays, flow cytometry and Transwell assays. Western blotting was performed to assess the protein expression levels of gene signaling in SHARPIN‑silenced BCC cells. SHARPIN protein expression levels were downregulated or absent in BCC cancer nests and precancerous lesions compared with normal skin samples. In addition, SHARPIN expression levels were lower in TE354.T cells compared with HaCaT cells. SHARPIN shRNA enhanced tumor cell proliferation and the S phase of the cell cycle, whereas BCC cell apoptotic rates, and migratory and invasive abilities were not significantly altered. The expression levels of cyclin D1, cyclin‑dependent kinase 4, phosphorylated‑c‑JUN and GLI family zinc finger 2 proteins were increased, whereas Patched 1 (PTCH1) and PTCH2 were decreased in the SHARPIN‑shRNA‑infected BCC cells. Therefore, the present results suggested that SHARPIN may act as a tumor suppressor during BCC development.
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Affiliation(s)
- Yao Yang
- Department of Dermatology, Cosmetology and Venereology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Yan-Hua Liang
- Department of Dermatology, Cosmetology and Venereology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Yan Zheng
- Department of Dermatology, Cosmetology and Venereology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Ling-Jie Tang
- Department of Dermatology, Cosmetology and Venereology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Si-Tong Zhou
- Department of Dermatology, Cosmetology and Venereology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Jing-Na Zhu
- Department of Dermatology, Cosmetology and Venereology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
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13
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Zheng Y, Yang Y, Wang J, Liang Y. Aberrant expression and high-frequency mutations of SHARPIN in nonmelanoma skin cancer. Exp Ther Med 2019; 17:2746-2756. [PMID: 30936956 PMCID: PMC6434243 DOI: 10.3892/etm.2019.7261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 02/05/2019] [Indexed: 12/18/2022] Open
Abstract
Squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) have exhibited a marked increase in incidence in previous decades and are the most common malignancies in Caucasian populations. Src homology 3 and multiple ankyrin repeat domains protein-associated RH domain-interacting protein (SHARPIN) has been identified as a commonly overexpressed proto-oncogene in several types of visceral cancer. However, to the best of our knowledge, the functions of SHARPIN in nonmelanoma skin cancer (NMSC) have not been described. The present study aimed to investigate the expression of SHARPIN protein and SHARPIN mutations in NMSC. A total of 85 BCC, 77 SCC and 21 keratoacanthoma (KA) formalin-fixed paraffin-embedded (FFPE) samples were collected. SHARPIN expression was detected using immunohistochemistry. DNA was extracted from the FFPE samples, and the sequences of SHARPIN were analyzed using polymerase chain reaction. In addition, high and moderate expression levels of SHARPIN were observed in normal skin tissues and KA samples. However, the expression of SHARPIN was absent in cancer nests and was significantly low in precancerous NMSC lesions. The total mutation frequency of SHARPIN was 21.8% in BCC and 17.0% in SCC. These data indicate that SHARPIN may serve a tumor-suppressing role and be a promising diagnostic, prognostic and therapeutic biomarker in NMSC.
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Affiliation(s)
- Yan Zheng
- Department of Dermatology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Yao Yang
- Department of Dermatology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Jiaman Wang
- Department of Dermatology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
| | - Yanhua Liang
- Department of Dermatology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518100, P.R. China
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14
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Liu J, Wang Y, Gong Y, Fu T, Hu S, Zhou Z, Pan L. Structural Insights into SHARPIN-Mediated Activation of HOIP for the Linear Ubiquitin Chain Assembly. Cell Rep 2018; 21:27-36. [PMID: 28978479 DOI: 10.1016/j.celrep.2017.09.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 09/07/2017] [Indexed: 11/25/2022] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is the sole identified E3 ligase complex that catalyzes the formation of linear ubiquitin chain, and it is composed of HOIP, HOIL-1L, and SHARPIN. The E3 activity of HOIP can be effectively activated by HOIL-1L or SHARPIN, deficiency of which leads to severe immune system disorders. However, the underlying mechanism governing the HOIP-SHARPIN interaction and the SHARPIN-mediated activation of HOIP remains elusive. Here, we biochemically and structurally demonstrate that the UBL domain of SHARPIN specifically binds to the UBA domain of HOIP and thereby associates with and activates HOIP. We further uncover that SHARPIN and HOIL-1L can separately or synergistically bind to distinct sites of HOIP UBA with induced allosteric effects and thereby facilitate the E2 loading of HOIP for its activation. Thus, our findings provide mechanistic insights into the assembly and activation of LUBAC.
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Affiliation(s)
- Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Yingli Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Yukang Gong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Tao Fu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Shichen Hu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Zixuan Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China.
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15
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Khan MH, Salomaa SI, Jacquemet G, Butt U, Miihkinen M, Deguchi T, Kremneva E, Lappalainen P, Humphries MJ, Pouwels J. The Sharpin interactome reveals a role for Sharpin in lamellipodium formation via the Arp2/3 complex. J Cell Sci 2017; 130:3094-3107. [PMID: 28775156 PMCID: PMC5612173 DOI: 10.1242/jcs.200329] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/25/2017] [Indexed: 12/15/2022] Open
Abstract
Sharpin, a multifunctional adaptor protein, regulates several signalling pathways. For example, Sharpin enhances signal-induced NF-κB signalling as part of the linear ubiquitin assembly complex (LUBAC) and inhibits integrins, the T cell receptor, caspase 1 and PTEN. However, despite recent insights into Sharpin and LUBAC function, a systematic approach to identify the signalling pathways regulated by Sharpin has not been reported. Here, we present the first 'Sharpin interactome', which identifies a large number of novel potential Sharpin interactors in addition to several known ones. These data suggest that Sharpin and LUBAC might regulate a larger number of biological processes than previously identified, such as endosomal trafficking, RNA processing, metabolism and cytoskeleton regulation. Importantly, using the Sharpin interactome, we have identified a novel role for Sharpin in lamellipodium formation. We demonstrate that Sharpin interacts with Arp2/3, a protein complex that catalyses actin filament branching. We have identified the Arp2/3-binding site in Sharpin and demonstrate using a specific Arp2/3-binding deficient mutant that the Sharpin-Arp2/3 interaction promotes lamellipodium formation in a LUBAC-independent fashion.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Meraj H Khan
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku 20520, Finland
| | - Siiri I Salomaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Drug Research Doctoral Programme, University of Turku, Turku 20520, Finland
| | - Guillaume Jacquemet
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Umar Butt
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku 20520, Finland
| | - Mitro Miihkinen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Drug Research Doctoral Programme, University of Turku, Turku 20520, Finland
| | - Takahiro Deguchi
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku 20520, Finland
- Laboratory of Biophysics, University of Turku, Turku 20520, Finland
| | - Elena Kremneva
- Institute of Biotechnology, University of Helsinki, Helsinki 00790, Finland
| | - Pekka Lappalainen
- Institute of Biotechnology, University of Helsinki, Helsinki 00790, Finland
| | - Martin J Humphries
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jeroen Pouwels
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
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16
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Petrie M, Esquibel J, Kabachinski G, Maciuba S, Takahashi H, Edwardson JM, Martin TFJ. The Vesicle Priming Factor CAPS Functions as a Homodimer via C2 Domain Interactions to Promote Regulated Vesicle Exocytosis. J Biol Chem 2016; 291:21257-21270. [PMID: 27528604 PMCID: PMC5076532 DOI: 10.1074/jbc.m116.728097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/29/2016] [Indexed: 11/06/2022] Open
Abstract
Neurotransmitters and peptide hormones are secreted by regulated vesicle exocytosis. CAPS (also known as CADPS) is a 145-kDa cytosolic and peripheral membrane protein required for vesicle docking and priming steps that precede Ca2+-triggered vesicle exocytosis. CAPS binds phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and SNARE proteins and is proposed to promote SNARE protein complex assembly for vesicle docking and priming. We characterized purified soluble CAPS as mainly monomer in equilibrium with small amounts of dimer. However, the active form of CAPS bound to PC12 cell membranes or to liposomes containing PI(4,5)P2 and Q-SNARE proteins was mainly dimer. CAPS dimer formation required its C2 domain based on mutation or deletion studies. Moreover, C2 domain mutations or deletions resulted in a loss of CAPS function in regulated vesicle exocytosis, indicating that dimerization is essential for CAPS function. Comparison of the CAPS C2 domain to a structurally defined Munc13-1 C2A domain dimer revealed conserved residues involved in CAPS dimerization. We conclude that CAPS functions as a C2 domain-mediated dimer in regulated vesicle exocytosis. The unique tandem C2-PH domain of CAPS may serve as a PI(4,5)P2-triggered switch for dimerization. CAPS dimerization may be coupled to oligomeric SNARE complex assembly for vesicle docking and priming.
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Affiliation(s)
- Matt Petrie
- From the Department of Biochemistry, Integrated Program in Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Joseph Esquibel
- From the Department of Biochemistry, Program of Molecular and Cellular Pharmacology, and
| | - Greg Kabachinski
- From the Department of Biochemistry, Integrated Program in Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Stephanie Maciuba
- From the Department of Biochemistry, Integrated Program in Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Hirohide Takahashi
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
| | - J Michael Edwardson
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
| | - Thomas F J Martin
- From the Department of Biochemistry, Integrated Program in Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and Program of Molecular and Cellular Pharmacology, and
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17
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Elliott PR, Leske D, Hrdinka M, Bagola K, Fiil BK, McLaughlin SH, Wagstaff J, Volkmar N, Christianson JC, Kessler BM, Freund SMV, Komander D, Gyrd-Hansen M. SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling. Mol Cell 2016; 63:990-1005. [PMID: 27591049 PMCID: PMC5031558 DOI: 10.1016/j.molcel.2016.08.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/14/2016] [Accepted: 07/28/2016] [Indexed: 01/06/2023]
Abstract
The linear ubiquitin chain assembly complex (LUBAC) regulates immune signaling, and its function is regulated by the deubiquitinases OTULIN and CYLD, which associate with the catalytic subunit HOIP. However, the mechanism through which CYLD interacts with HOIP is unclear. We here show that CYLD interacts with HOIP via spermatogenesis-associated protein 2 (SPATA2). SPATA2 interacts with CYLD through its non-canonical PUB domain, which binds the catalytic CYLD USP domain in a CYLD B-box-dependent manner. Significantly, SPATA2 binding activates CYLD-mediated hydrolysis of ubiquitin chains. SPATA2 also harbors a conserved PUB-interacting motif that selectively docks into the HOIP PUB domain. In cells, SPATA2 is recruited to the TNF receptor 1 signaling complex and is required for CYLD recruitment. Loss of SPATA2 increases ubiquitination of LUBAC substrates and results in enhanced NOD2 signaling. Our data reveal SPATA2 as a high-affinity binding partner of CYLD and HOIP, and a regulatory component of LUBAC-mediated NF-κB signaling.
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Affiliation(s)
- Paul R Elliott
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Derek Leske
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Matous Hrdinka
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Katrin Bagola
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Berthe K Fiil
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Stephen H McLaughlin
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jane Wagstaff
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Norbert Volkmar
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - John C Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Stefan M V Freund
- 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.
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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18
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Abstract
Ubiquitin can form eight different linkage types of chains using the intrinsic Met 1 residue or one of the seven intrinsic Lys residues. Each linkage type of ubiquitin chain has a distinct three-dimensional topology, functioning as a tag to attract specific signaling molecules, which are so-called ubiquitin readers, and regulates various biological functions. Ubiquitin chains linked via Met 1 in a head-to-tail manner are called linear ubiquitin chains. Linear ubiquitination plays an important role in the regulation of cellular signaling, including the best-characterized tumor necrosis factor (TNF)-induced canonical nuclear factor-κB (NF-κB) pathway. Linear ubiquitin chains are specifically generated by an E3 ligase complex called the linear ubiquitin chain assembly complex (LUBAC) and hydrolyzed by a deubiquitinase (DUB) called ovarian tumor (OTU) DUB with linear linkage specificity (OTULIN). LUBAC linearly ubiquitinates critical molecules in the TNF pathway, such as NEMO and RIPK1. The linear ubiquitin chains are then recognized by the ubiquitin readers, including NEMO, which control the TNF pathway. Accumulating evidence indicates an importance of the LUBAC complex in the regulation of apoptosis, development, and inflammation in mice. In this article, I focus on the role of linear ubiquitin chains in adaptive immune responses with an emphasis on the TNF-induced signaling pathways.
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Affiliation(s)
- Fumiyo Ikeda
- Institute of Molecular Biotechnology (IMBA), Vienna, Austria
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19
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Mutually Exclusive Roles of SHARPIN in Integrin Inactivation and NF-κB Signaling. PLoS One 2015; 10:e0143423. [PMID: 26600301 PMCID: PMC4658161 DOI: 10.1371/journal.pone.0143423] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/04/2015] [Indexed: 01/30/2023] Open
Abstract
SHANK-associated RH domain interactor (SHARPIN) inhibits integrins through interaction with the integrin α-subunit. In addition, SHARPIN enhances nuclear factor-kappaB (NF-κB) activity as a component of the linear ubiquitin chain assembly complex (LUBAC). However, it is currently unclear how regulation of these seemingly different roles is coordinated. Here, we show that SHARPIN binds integrin and LUBAC in a mutually exclusive manner. We map the integrin binding site on SHARPIN to the ubiquitin-like (UBL) domain, the same domain implicated in SHARPIN interaction with LUBAC component RNF31 (ring finger protein 31), and identify two SHARPIN residues (V267, L276) required for both integrin and RNF31 regulation. Accordingly, the integrin α-tail is capable of competing with RNF31 for SHARPIN binding in vitro. Importantly, the full SHARPIN RNF31-binding site contains residues (F263A/I272A) that are dispensable for SHARPIN-integrin interaction. Importantly, disrupting SHARPIN interaction with integrin or RNF31 abolishes SHARPIN-mediated regulation of integrin or NF-κB activity, respectively. Altogether these data suggest that the roles of SHARPIN in inhibiting integrin activity and supporting linear ubiquitination are (molecularly) distinct.
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20
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De Melo J, Tang D. Elevation of SIPL1 (SHARPIN) Increases Breast Cancer Risk. PLoS One 2015; 10:e0127546. [PMID: 25992689 PMCID: PMC4438068 DOI: 10.1371/journal.pone.0127546] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 04/16/2015] [Indexed: 12/31/2022] Open
Abstract
SIPL1 (Sharpin) or Sharpin plays a role in tumorigenesis. However, its involvement in breast cancer tumorigenesis remains largely unknown. To investigate this issue, we have systemically analyzed SIPL1 gene amplification and expression data available from Oncomine datasets, which were derived from 17 studies and contained approximately 20,000 genes, 3438 breast cancer cases, and 228 normal individuals. We found a SIPL1 gene amplification in invasive ductal breast cancers compared to normal breast tissues and a significant elevation of SIPL1 mRNA in breast cancers in comparison to non-tumor breast tissues. These results collectively reveal that increases in SIPL1 expression occur during breast cancer tumorigenesis. To further investigate this association, we observed increases in the SIPL1 gene and mRNA in the breast cancer subtypes of estrogen receptor (ER)+, progesterone receptor (PR)+, HER2+, or triple negative. Additionally, a gain of the SIPL1 gene correlated with breast cancer grade and the levels of SIPL1 mRNA associated with both breast cancer stages and grades. Elevation of SIPL1 gene copy and mRNA is linked to a decrease in patient survival, especially for those with PR+, ER+, or HER2- breast cancers. These results are supported by our analysis of SIPL1 protein expression using a tissue microarray containing 224 breast cancer cases, in which higher levels of SIPL1 relate to ER+ and PR+ tumors and AKT activation. Furthermore, we were able to show that progesterone significantly reduced SIPL1 mRNA and protein expression in MCF7 cells. As progesterone enhances breast cancer tumorigenesis in a context dependent manner, inhibition of SIPL1 expression may contribute to progesterone's non-tumorigenic function which might be countered by SIPL1 upregulation. Taken together, we demonstrate a positive correlation of SIPL1 with BC tumorigenesis.
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Affiliation(s)
- Jason De Melo
- Division of Nephrology, Department of Medicine, McMaster University, Ontario, Canada
- Father Sean O’Sullivan Research Institute, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph’s Hospital, Hamilton, Ontario, Canada
| | - Damu Tang
- Division of Nephrology, Department of Medicine, McMaster University, Ontario, Canada
- Father Sean O’Sullivan Research Institute, Ontario, Canada
- The Hamilton Center for Kidney Research, St. Joseph’s Hospital, Hamilton, Ontario, Canada
- * E-mail:
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21
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De Melo J, Lin X, He L, Wei F, Major P, Tang D. SIPL1-facilitated PTEN ubiquitination contributes to its association with PTEN. Cell Signal 2014; 26:2749-56. [DOI: 10.1016/j.cellsig.2014.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 08/17/2014] [Indexed: 11/16/2022]
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22
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Corradini BR, Iamashita P, Tampellini E, Farfel JM, Grinberg LT, Moreira-Filho CA. Complex network-driven view of genomic mechanisms underlying Parkinson's disease: analyses in dorsal motor vagal nucleus, locus coeruleus, and substantia nigra. BIOMED RESEARCH INTERNATIONAL 2014; 2014:543673. [PMID: 25525598 PMCID: PMC4261556 DOI: 10.1155/2014/543673] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/15/2014] [Indexed: 12/16/2022]
Abstract
Parkinson's disease (PD)—classically characterized by severe loss of dopaminergic neurons in the substantia nigra pars compacta—has a caudal-rostral progression, beginning in the dorsal motor vagal nucleus and, in a less extent, in the olfactory system, progressing to the midbrain and eventually to the basal forebrain and the neocortex. About 90% of the cases are idiopathic. To study the molecular mechanisms involved in idiopathic PD we conducted a comparative study of transcriptional interaction networks in the dorsal motor vagal nucleus (VA), locus coeruleus (LC), and substantia nigra (SN) of idiopathic PD in Braak stages 4-5 (PD) and disease-free controls (CT) using postmortem samples. Gene coexpression networks (GCNs) for each brain region (patients and controls) were obtained to identify highly connected relevant genes (hubs) and densely interconnected gene sets (modules). GCN analyses showed differences in topology and module composition between CT and PD networks for each anatomic region. In CT networks, VA, LC, and SN hub modules are predominantly associated with neuroprotection and homeostasis in the ageing brain, whereas in the patient's group, for the three brain regions, hub modules are mostly related to stress response and neuron survival/degeneration mechanisms.
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Affiliation(s)
- Beatriz Raposo Corradini
- Department of Pediatrics, Faculdade de Medicina da USP (FMUSP), Avenida Dr. Enéas Carvalho Aguiar 647, 5 Andar, 05403-900 São Paulo, SP, Brazil
| | - Priscila Iamashita
- Department of Pediatrics, Faculdade de Medicina da USP (FMUSP), Avenida Dr. Enéas Carvalho Aguiar 647, 5 Andar, 05403-900 São Paulo, SP, Brazil
| | - Edilaine Tampellini
- Brazilian Aging Brain Study Group (BEHEEC), LIM 22, FMUSP, 01246-903 São Paulo, SP, Brazil
- Hospital Israelita Albert Einstein, 05652-900 São Paulo, SP, Brazil
| | - José Marcelo Farfel
- Hospital Israelita Albert Einstein, 05652-900 São Paulo, SP, Brazil
- Division of Geriatrics, FMUSP, 01246-903 São Paulo, SP, Brazil
| | - Lea Tenenholz Grinberg
- Brazilian Aging Brain Study Group (BEHEEC), LIM 22, FMUSP, 01246-903 São Paulo, SP, Brazil
- Department of Pathology, FMUSP, 01246-903 São Paulo, SP, Brazil
- Department of Neurology and Pathology, University of California, San Francisco, CA 94143, USA
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da USP (FMUSP), Avenida Dr. Enéas Carvalho Aguiar 647, 5 Andar, 05403-900 São Paulo, SP, Brazil
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23
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Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/471836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Advances in several biology-oriented initiatives such as genome sequencing and structural genomics, along with the progress made through traditional biological and biochemical research, have opened up a unique opportunity to better understand the molecular effects of human diseases. Human DNA can vary significantly from person to person and determines an individual’s physical characteristics and their susceptibility to diseases. Armed with an individual’s DNA sequence, researchers and physicians can check for defects known to be associated with certain diseases by utilizing various databases. However, for unclassified DNA mutations or in order to reveal molecular mechanism behind the effects, the mutations have to be mapped onto the corresponding networks and macromolecular structures and then analyzed to reveal their effect on the wild type properties of biological processes involved. Predicting the effect of DNA mutations on individual’s health is typically referred to as personalized or companion diagnostics. Furthermore, once the molecular mechanism of the mutations is revealed, the patient should be given drugs which are the most appropriate for the individual genome, referred to as pharmacogenomics. Altogether, the shift in focus in medicine towards more genomic-oriented practices is the foundation of personalized medicine. The progress made in these rapidly developing fields is outlined.
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24
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Elliott PR, Nielsen SV, Marco-Casanova P, Fiil BK, Keusekotten K, Mailand N, Freund SMV, Gyrd-Hansen M, Komander D. Molecular basis and regulation of OTULIN-LUBAC interaction. Mol Cell 2014; 54:335-48. [PMID: 24726323 PMCID: PMC4017264 DOI: 10.1016/j.molcel.2014.03.018] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/23/2014] [Accepted: 02/25/2014] [Indexed: 01/08/2023]
Abstract
The linear ubiquitin (Ub) chain assembly complex (LUBAC) generates Met1-linked “linear” Ub chains that regulate the activation of the nuclear factor κB (NFκB) transcription factor and other processes. We recently discovered OTULIN as a deubiquitinase that specifically cleaves Met1-linked polyUb. Now, we show that OTULIN binds via a conserved PUB-interacting motif (PIM) to the PUB domain of the LUBAC component HOIP. Crystal structures and nuclear magnetic resonance experiments reveal the molecular basis for the high-affinity interaction and explain why OTULIN binds the HOIP PUB domain specifically. Analysis of LUBAC-induced NFκB signaling suggests that OTULIN needs to be present on LUBAC in order to restrict Met1-polyUb signaling. Moreover, LUBAC-OTULIN complex formation is regulated by OTULIN phosphorylation in the PIM. Phosphorylation of OTULIN prevents HOIP binding, whereas unphosphorylated OTULIN is part of the endogenous LUBAC complex. Our work exemplifies how coordination of ubiquitin assembly and disassembly activities in protein complexes regulates individual Ub linkage types. OTULIN binds the HOIP PUB domain via a conserved N-terminal PUB-interacting motif Structural studies reveal specificity determinants for the binary interaction Loss of HOIP-OTULIN interaction causes deregulated accumulation of Met1-polyUb OTULIN binding to LUBAC is regulated by phosphorylation
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Affiliation(s)
- Paul R Elliott
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sofie V Nielsen
- Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Paola Marco-Casanova
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Berthe Katrine Fiil
- Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kirstin Keusekotten
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Niels Mailand
- Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stefan M V Freund
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Mads Gyrd-Hansen
- Department of Disease Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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Tokunaga F. Linear ubiquitination-mediated NF-κB regulation and its related disorders. J Biochem 2013; 154:313-23. [PMID: 23969028 DOI: 10.1093/jb/mvt079] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ubiquitination is a post-translational modification involved in the regulation of a broad variety of cellular functions, such as protein degradation and signal transduction, including nuclear factor-κB (NF-κB) signalling. NF-κB is crucial for inflammatory and immune responses, and aberrant NF-κB signalling is implicated in multiple disorders. We found that linear ubiquitin chain assembly complex (LUBAC), composed of HOIL-1L, HOIP and SHARPIN, generates a novel type of Met1 (M1)-linked linear polyubiquitin chain and specifically regulates the canonical NF-κB pathway. Moreover, specific deubiquitinases, such as CYLD, A20 (TNFAIP3) and OTULIN/gumby, inhibit LUBAC-induced NF-κB activation by different molecular mechanisms, and several M1-linked ubiquitin-specific binding domains have been structurally defined. LUBAC and these linear ubiquitination-regulating factors contribute to immune and inflammatory processes and apoptosis. Functional impairments of these factors are correlated with multiple disorders, including autoinflammation, immunodeficiencies, dermatitis, B-cell lymphomas and Parkinson's disease. This review summarizes the molecular basis and the pathophysiological implications of the linear ubiquitination-mediated NF-κB activation pathway regulation by LUBAC.
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Affiliation(s)
- Fuminori Tokunaga
- Laboratory of Molecular Cell Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8912, Japan
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Rieser E, Cordier SM, Walczak H. Linear ubiquitination: a newly discovered regulator of cell signalling. Trends Biochem Sci 2013; 38:94-102. [DOI: 10.1016/j.tibs.2012.11.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 11/14/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
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Stieglitz B, Rittinger K, Haire LF. Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:816-9. [PMID: 22750873 PMCID: PMC3388930 DOI: 10.1107/s1744309112022208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/16/2012] [Indexed: 12/05/2022]
Abstract
An N-terminal fragment of human SHARPIN was recombinantly expressed in Escherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 61.55, c = 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively.
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Affiliation(s)
- Benjamin Stieglitz
- Division of Molecular Structure, MRC – National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, England
| | - Katrin Rittinger
- Division of Molecular Structure, MRC – National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, England
| | - Lesley F. Haire
- Division of Molecular Structure, MRC – National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, England
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