1
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Huq TS, Luo J, Fakih R, Sauvé V, Gehring K. Naturally occurring hyperactive variants of human parkin. Commun Biol 2024; 7:961. [PMID: 39117722 PMCID: PMC11310320 DOI: 10.1038/s42003-024-06656-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the world. Although most cases are sporadic and occur later in life, 10-15% of cases are genetic. Loss-of-function mutations in the ring-between-ring E3 ubiquitin ligase parkin, encoded by the PRKN gene, cause autosomal recessive forms of early onset PD. Together with the kinase PINK1, parkin forms a mitochondrial quality control pathway that tags damaged mitochondria for clearance. Under basal conditions, parkin is inhibited and compounds that increase its activity have been proposed as a therapy for PD. Recently, several naturally occurring hyperactive parkin variants were identified, which increased mitophagy in cultured cells. Here, we validate the hyperactivities of these variants in vitro and compare the levels of activity of the variants to those of the wild-type and the well-characterized hyperactive variant, W403A. We also study the effects of mutating the parkin ACT (activating element) on parkin activity in vitro. This work advances our understanding of the pathogenicity of parkin variants and is an important first step in the design of molecules to increase parkin activity.
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Affiliation(s)
- Tahrima Saiha Huq
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
- North South University, Dhaka, Bangladesh
| | - Jean Luo
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
- Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Rayan Fakih
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Véronique Sauvé
- Department of Biochemistry, McGill University, Montréal, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montréal, Canada.
- Centre de recherche en biologie structurale, McGill University, Montréal, Canada.
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2
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Connelly EM, Rintala-Dempsey AC, Gundogdu M, Freeman EA, Koszela J, Aguirre JD, Zhu G, Kämäräinen O, Tadayon R, Walden H, Shaw GS. Capturing the catalytic intermediates of parkin ubiquitination. Proc Natl Acad Sci U S A 2024; 121:e2403114121. [PMID: 39078678 DOI: 10.1073/pnas.2403114121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024] Open
Abstract
Parkin is an E3 ubiquitin ligase implicated in early-onset forms of Parkinson's disease. It catalyzes a transthiolation reaction by accepting ubiquitin (Ub) from an E2 conjugating enzyme, forming a short-lived thioester intermediate, and transfers Ub to mitochondrial membrane substrates to signal mitophagy. A major impediment to the development of Parkinsonism therapeutics is the lack of structural and mechanistic detail for the essential, short-lived transthiolation intermediate. It is not known how Ub is recognized by the catalytic Rcat domain in parkin that enables Ub transfer from an E2~Ub conjugate to the catalytic site and the structure of the transthiolation complex is undetermined. Here, we capture the catalytic intermediate for the Rcat domain of parkin in complex with ubiquitin (Rcat-Ub) and determine its structure using NMR-based chemical shift perturbation experiments. We show that a previously unidentified α-helical region near the Rcat domain is unmasked as a recognition motif for Ub and guides the C-terminus of Ub toward the parkin catalytic site. Further, we apply a combination of guided AlphaFold modeling, chemical cross-linking, and single turnover assays to establish and validate a model of full-length parkin in complex with UbcH7, its donor Ub, and phosphoubiquitin, trapped in the process of transthiolation. Identification of this catalytic intermediate and orientation of Ub with respect to the Rcat domain provides important structural insights into Ub transfer by this E3 ligase and explains how the previously enigmatic Parkinson's pathogenic mutation T415N alters parkin activity.
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Affiliation(s)
- Elizabeth M Connelly
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Anne C Rintala-Dempsey
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Mehmet Gundogdu
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - E Aisha Freeman
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Joanna Koszela
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jacob D Aguirre
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Grace Zhu
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Outi Kämäräinen
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Roya Tadayon
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Helen Walden
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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3
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Yoshida Y, Takahashi T, Ishii N, Matsuo I, Takahashi S, Inoue H, Endo A, Tsuchiya H, Okada M, Ando C, Suzuki T, Dohmae N, Saeki Y, Tanaka K, Suzuki T. Sugar-mediated non-canonical ubiquitination impairs Nrf1/NFE2L1 activation. Mol Cell 2024:S1097-2765(24)00589-6. [PMID: 39116872 DOI: 10.1016/j.molcel.2024.07.013] [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: 10/10/2023] [Revised: 05/22/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
Proteasome is essential for cell survival, and proteasome inhibition induces proteasomal gene transcription via the activated endoplasmic-reticulum-associated transcription factor nuclear factor erythroid 2-like 1 (Nrf1/NFE2L1). Nrf1 activation requires proteolytic cleavage by DDI2 and N-glycan removal by NGLY1. We previously showed that Nrf1 ubiquitination by SKP1-CUL1-F-box (SCF)FBS2/FBXO6, an N-glycan-recognizing E3 ubiquitin ligase, impairs its activation, although the molecular mechanism remained elusive. Here, we show that SCFFBS2 cooperates with the RING-between-RING (RBR)-type E3 ligase ARIH1 to ubiquitinate Nrf1 through oxyester bonds in human cells. Endo-β-N-acetylglucosaminidase (ENGASE) generates asparagine-linked N-acetyl glucosamine (N-GlcNAc) residues from N-glycans, and N-GlcNAc residues on Nrf1 served as acceptor sites for SCFFBS2-ARIH1-mediated ubiquitination. We reconstituted the polyubiquitination of N-GlcNAc and serine/threonine residues on glycopeptides and found that the RBR-specific E2 enzyme UBE2L3 is required for the assembly of atypical ubiquitin chains on Nrf1. The atypical ubiquitin chains inhibited DDI2-mediated activation. The present results identify an unconventional ubiquitination pathway that inhibits Nrf1 activation.
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Affiliation(s)
- Yukiko Yoshida
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tsuyoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Nozomi Ishii
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Satoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Haruka Inoue
- Graduate School of Science and Technology, Gunma University, 1-5 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hikaru Tsuchiya
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Meari Okada
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Chikara Ando
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan; Division of Protein Metabolism, The Institute of Medical Science, The University of Tokyo, Shirokanedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Takeda-CiRA Joint Program (T-CiRA), 2-26-1, Muraokahigashi, Fujisawa, Kanagawa 251-8555, Japan.
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4
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Chen Y, Dai R, Cheng M, Wang W, Liu C, Cao Z, Ge Y, Wang Y, Zhang L. Status and role of the ubiquitin-proteasome system in renal fibrosis. Biomed Pharmacother 2024; 178:117210. [PMID: 39059348 DOI: 10.1016/j.biopha.2024.117210] [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: 05/11/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024] Open
Abstract
The ubiquitin-proteasome system (UPS) is a basic regulatory mechanism in cells that is essential for maintaining cell homeostasis, stimulating signal transduction, and determining cell fate. These biological processes require coordinated signaling cascades across members of the UPS to achieve substrate ubiquitination and deubiquitination. The role of the UPS in fibrotic diseases has attracted widespread attention, and the aberrant expression of UPS members affects the fibrosis process. In this review, we provide an overview of the UPS and its relevance for fibrotic diseases. Moreover, for the first time, we explore in detail how the UPS promotes or inhibits renal fibrosis by regulating biological processes such as signaling pathways, inflammation, oxidative stress, and the cell cycle, emphasizing the status and role of the UPS in renal fibrosis. Further research on this system may reveal new strategies for preventing renal fibrosis.
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Affiliation(s)
- Yizhen Chen
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Rong Dai
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Meng Cheng
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Weili Wang
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Chuanjiao Liu
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Zeping Cao
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Yong Ge
- First Clinical Medical College, Anhui University of Chinese Medicine, Hefei, China
| | - Yiping Wang
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
| | - Lei Zhang
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
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5
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Horn-Ghetko D, Hopf LVM, Tripathi-Giesgen I, Du J, Kostrhon S, Vu DT, Beier V, Steigenberger B, Prabu JR, Stier L, Bruss EM, Mann M, Xiong Y, Schulman BA. Noncanonical assembly, neddylation and chimeric cullin-RING/RBR ubiquitylation by the 1.8 MDa CUL9 E3 ligase complex. Nat Struct Mol Biol 2024; 31:1083-1094. [PMID: 38605244 PMCID: PMC11257990 DOI: 10.1038/s41594-024-01257-y] [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: 08/30/2023] [Accepted: 02/26/2024] [Indexed: 04/13/2024]
Abstract
Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also called ROC1), of interest due to its tumor suppressive interaction with TP53, uniquely encompasses both cullin-RING and RBR domains. Here, cryo-EM, biochemistry and cellular assays elucidate a 1.8-MDa hexameric human CUL9-RBX1 assembly. Within one dimeric subcomplex, an E2-bound RBR domain is activated by neddylation of its own cullin domain and positioning from the adjacent CUL9-RBX1 in trans. Our data show CUL9 as unique among RBX1-bound cullins in dependence on the metazoan-specific UBE2F neddylation enzyme, while the RBR domain protects it from deneddylation. Substrates are recruited to various upstream domains, while ubiquitylation relies on both CUL9's neddylated cullin and RBR domains achieving self-assembled and chimeric cullin-RING/RBR E3 ligase activity.
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Affiliation(s)
- Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Linus V M Hopf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Kostrhon
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Viola Beier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Elias M Bruss
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Yue Xiong
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Cullgen Inc., San Diego, CA, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Chemistry, TUM School of Natural Sciences, Garching, Germany.
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6
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Miao Y, Wang S, Zhang J, Liu H, Zhang C, Jin S, Bai D. Strategic advancement of E3 ubiquitin ligase in the management of hepatocellular carcinoma. Med Oncol 2024; 41:178. [PMID: 38888684 DOI: 10.1007/s12032-024-02411-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
Hepatocellular carcinoma (HCC) presents a significant global health challenge due to its high incidence, poor prognosis, and limited treatment options. As a pivotal regulator of protein stability, E3 ubiquitin ligase plays a crucial role in tumorigenesis and development. This review provides an overview of the latest research on the involvement of E3 ubiquitin ligase in hepatocellular carcinoma and elucidates its significance in hepatocellular carcinoma cell proliferation, invasion, and evasion from immune surveillance. Special attention is given to the functions of RING, HECT, and RBR E3 ubiquitin ligases and their association with hepatocellular carcinoma progression. By dissecting the molecular mechanisms and regulatory networks governed by E3 ubiquitin ligase, several potential therapeutic strategies are proposed: including the development of specific inhibitors targeting E3 ligases; augmentation of their tumor suppressor activity through drug or gene therapy; utilization of E3 ubiquitin ligase to modulate immune checkpoint proteins for improved efficacy of immunotherapy; combination strategies integrating traditional therapies with E3 ubiquitin ligase inhibitors; as well as biomarker development based on E3 ubiquitin ligase activity. Furthermore, this review discusses the prospect of overcoming drug resistance in hepatocellular carcinoma treatment through these novel approaches. Overall, this review establishes a theoretical foundation and offers fresh insights into harnessing the potential of E3 ubiquitin ligase for treating hepatocellular carcinoma while highlighting future research directions that pave the way for clinical translation studies and new drug discoveries.
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Affiliation(s)
- Yangyang Miao
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China
| | - Shunyi Wang
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China
| | - Jiahao Zhang
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China
- Dalian Medical University, Dalian, 116000, China
| | - Huanxiang Liu
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China
| | - Chi Zhang
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China.
| | - Shengjie Jin
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China.
| | - Dousheng Bai
- Department of Hepatobiliary Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, 98 West Nantong Rd, Yangzhou, 225000, Jiangsu, China.
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7
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Koszela J, Rintala-Dempsey A, Salzano G, Pimenta V, Kamarainen O, Gabrielsen M, Parui AL, Shaw GS, Walden H. A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597144. [PMID: 38895334 PMCID: PMC11185606 DOI: 10.1101/2024.06.03.597144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mutations in the gene encoding for the E3 ubiquitin ligase Parkin have been linked to early-onset Parkinson's disease. Besides many other cellular roles, Parkin is involved in clearance of damaged mitochondria via mitophagy - a process of particular importance in dopaminergic neurons. Upon mitochondrial damage, Parkin accumulates at the outer mitochondrial membrane and is activated, leading to ubiquitination of many mitochondrial substrates and recruitment of mitophagy effectors. While the activation mechanisms of autoinhibited Parkin have been extensively studied, it remains unknown how Parkin recognises its substrates for ubiquitination, and no substrate interaction site in Parkin has been reported. Here, we identify a conserved region in the flexible linker between the Ubl and RING0 domains of Parkin, which is indispensable for Parkin interaction with the mitochondrial GTPase Miro1. Our results explain the preferential targeting and ubiquitination of Miro1 by Parkin and provide a biochemical explanation for the presence of Parkin at the mitochondrial membrane prior to activation induced by mitochondrial damage. Our findings are important for understanding mitochondrial homeostasis and may inspire new therapeutic avenues for Parkinson's disease.
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Affiliation(s)
- Joanna Koszela
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Anne Rintala-Dempsey
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | | | - Viveka Pimenta
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Outi Kamarainen
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Mads Gabrielsen
- Integrated Protein Analysis, Shared Research Facilities, University of Glasgow, Glasgow, UK
| | - Aasna L Parui
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Helen Walden
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
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8
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Clausen L, Okarmus J, Voutsinos V, Meyer M, Lindorff-Larsen K, Hartmann-Petersen R. PRKN-linked familial Parkinson's disease: cellular and molecular mechanisms of disease-linked variants. Cell Mol Life Sci 2024; 81:223. [PMID: 38767677 PMCID: PMC11106057 DOI: 10.1007/s00018-024-05262-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.
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Affiliation(s)
- Lene Clausen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
| | - Vasileios Voutsinos
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000, Odense, Denmark
- Department of Clinical Research, BRIDGE, Brain Research Inter Disciplinary Guided Excellence, University of Southern Denmark, 5230, Odense, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark.
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9
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Sandoval A, Duran P, Corzo-López A, Fernández-Gallardo M, Muñoz-Herrera D, Leyva-Leyva M, González-Ramírez R, Felix R. The role of voltage-gated calcium channels in the pathogenesis of Parkinson's disease. Int J Neurosci 2024; 134:452-461. [PMID: 35993158 DOI: 10.1080/00207454.2022.2115905] [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: 12/02/2021] [Revised: 06/07/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Aim: Voltage-gated calcium (CaV) channels play an essential role in maintaining calcium homeostasis and regulating numerous physiological processes in neurons. Therefore, dysregulation of calcium signaling is relevant in many neurological disorders, including Parkinson's disease (PD). This review aims to introduce the role of CaV channels in PD and discuss some novel aspects of channel regulation and its impact on the molecular pathophysiology of the disease. Methods: an exhaustive search of the literature in the field was carried out using the PubMed database of The National Center for Biotechnology Information. Systematic searches were performed from the initial date of publication to May 2022. Results: Although α-synuclein aggregates are the main feature of PD, L-type calcium (CaV1) channels seem to play an essential role in the pathogenesis of PD. Changes in the functional expression of CaV1.3 channels alter Calcium homeostasis and contribute to the degeneration of dopaminergic neurons. Furthermore, recent studies suggest that CaV channel trafficking towards the cell membrane depends on the activity of the ubiquitin-proteasome system (UPS). In PD, there is an increase in the expression of L-type channels associated with a decrease in the expression of Parkin, an E3 enzyme of the UPS. Therefore, a link between Parkin and CaV channels could play a fundamental role in the pathogenesis of PD and, as such, could be a potentially attractive target for therapeutic intervention. Conclusion: The study of alterations in the functional expression of CaV channels will provide a framework to understand better the neurodegenerative processes that occur in PD and a possible path toward identifying new therapeutic targets to treat this condition.
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Affiliation(s)
- Alejandro Sandoval
- School of Medicine FES Iztacala, National Autonomous University of Mexico (UNAM), Tlalnepantla, Mexico
| | - Paz Duran
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Alejandra Corzo-López
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | | | - David Muñoz-Herrera
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
| | - Margarita Leyva-Leyva
- Department of Molecular Biology and Histocompatibility, "Dr. Manuel Gea González" General Hospital, Mexico City, Mexico
| | - Ricardo González-Ramírez
- Department of Molecular Biology and Histocompatibility, "Dr. Manuel Gea González" General Hospital, Mexico City, Mexico
| | - Ricardo Felix
- Department of Cell Biology, Centre for Research and Advanced Studies (Cinvestav), Mexico City, Mexico
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10
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Zhou Y, Zhang Q, Zhao Z, Hu X, You Q, Jiang Z. Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives. Eur J Med Chem 2024; 269:116270. [PMID: 38490062 DOI: 10.1016/j.ejmech.2024.116270] [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: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.
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Affiliation(s)
- Yangguo Zhou
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziquan Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiuqi Hu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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11
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Abdul Rehman SA, Cazzaniga C, Di Nisio E, Antico O, Knebel A, Johnson C, Şahin AT, Ibrahim PEGF, Lamoliatte F, Negri R, Muqit MMK, De Cesare V. Discovery and characterization of noncanonical E2-conjugating enzymes. SCIENCE ADVANCES 2024; 10:eadh0123. [PMID: 38536929 PMCID: PMC10971424 DOI: 10.1126/sciadv.adh0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/20/2024] [Indexed: 04/10/2024]
Abstract
E2-conjugating enzymes (E2s) play a central role in the enzymatic cascade that leads to the attachment of ubiquitin to a substrate. This process, termed ubiquitylation, is required to maintain cellular homeostasis and affects almost all cellular process. By interacting with multiple E3 ligases, E2s dictate the ubiquitylation landscape within the cell. Since its discovery, ubiquitylation has been regarded as a posttranslational modification that specifically targets lysine side chains (canonical ubiquitylation). We used Matrix-Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry to identify and characterize a family of E2s that are instead able to conjugate ubiquitin to serine and/or threonine. We used structural modeling and prediction tools to identify the key activity determinants that these E2s use to interact with ubiquitin as well as their substrates. Our results unveil the missing E2s necessary for noncanonical ubiquitylation, underscoring the adaptability and versatility of ubiquitin modifications.
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Chiara Cazzaniga
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Elena Di Nisio
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Clare Johnson
- MRCPPU Reagents and Services, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Alp T Şahin
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow St, Dundee DD1 5EH, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Rodolfo Negri
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, via dei Sardi, 70 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli 4, 00185 Rome, Italy
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
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12
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Islam NN, Weber CA, Coban M, Cocker LT, Fiesel FC, Springer W, Caulfield TR. In Silico Investigation of Parkin-Activating Mutations Using Simulations and Network Modeling. Biomolecules 2024; 14:365. [PMID: 38540783 PMCID: PMC10968616 DOI: 10.3390/biom14030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/05/2024] Open
Abstract
Complete loss-of-function mutations in the PRKN gene are a major cause of early-onset Parkinson's disease (PD). PRKN encodes the Parkin protein, an E3 ubiquitin ligase that works in conjunction with the ubiquitin kinase PINK1 in a distinct quality control pathway to tag damaged mitochondria for autophagic clearance, i.e., mitophagy. According to previous structural investigations, Parkin protein is typically kept in an inactive conformation via several intramolecular, auto-inhibitory interactions. Here, we performed molecular dynamics simulations (MDS) to provide insights into conformational changes occurring during the de-repression of Parkin and the gain of catalytic activity. We analyzed four different Parkin-activating mutations that are predicted to disrupt certain aspects of its auto-inhibition. All four variants showed greater conformational motions compared to wild-type protein, as well as differences in distances between domain interfaces and solvent-accessible surface area, which are thought to play critical roles as Parkin gains catalytic activity. Our findings reveal that the studied variants exert a notable influence on Parkin activation as they alter the opening of its closed inactive structure, a finding that is supported by recent structure- and cell-based studies. These findings not only helped further characterize the hyperactive variants but overall improved our understanding of Parkin's catalytic activity and nominated targets within Parkin's structure for potential therapeutic designs.
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Affiliation(s)
- Naeyma N. Islam
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Caleb A. Weber
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Matt Coban
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Liam T. Cocker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA; (N.N.I.); (C.A.W.); (M.C.); (F.C.F.)
- Department of Neurosurgery, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
- Department of Biochemistry & Molecular Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
- Department of Computational Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
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13
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Zhou L, Liu R, Pathak H, Wang X, Jeong GH, Kumari P, Kumar M, Yin J. Ubiquitin Ligase Parkin Regulates the Stability of SARS-CoV-2 Main Protease and Suppresses Viral Replication. ACS Infect Dis 2024; 10:879-889. [PMID: 38386664 PMCID: PMC10928718 DOI: 10.1021/acsinfecdis.3c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
The highly infectious coronavirus SARS-CoV-2 relies on the viral main protease (Mpro, also known as 3CLpro or Nsp5) to proteolytically process the polyproteins encoded by the viral genome for the release of functional units in the host cells to initiate viral replication. Mpro also interacts with host proteins of the innate immune pathways, such as IRF3 and STAT1, to suppress their activities and facilitate virus survival and proliferation. To identify the host mechanism for regulating Mpro, we screened various classes of E3 ubiquitin ligases and found that Parkin of the RING-between-RING family can induce the ubiquitination and degradation of Mpro in the cell. Furthermore, when the cells undergo mitophagy, the PINK1 kinase activates Parkin and enhances the ubiquitination of Mpro. We also found that elevated expression of Parkin in the cells significantly decreased the replication of SARS-CoV-2 virus. Interestingly, SARS-CoV-2 infection downregulates Parkin expression in the mouse lung tissues compared to healthy controls. These results suggest an antiviral role of Parkin as a ubiquitin ligase targeting Mpro and the potential for exploiting the virus-host interaction mediated by Parkin to treat SARS-CoV-2 infection.
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Affiliation(s)
- Li Zhou
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ruochuan Liu
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Heather Pathak
- Department
of Biology and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Xiaoyu Wang
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Geon H. Jeong
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Pratima Kumari
- Department
of Biology and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mukesh Kumar
- Department
of Biology and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jun Yin
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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14
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Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G. Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol Cell 2024; 84:839-853.e12. [PMID: 38242129 PMCID: PMC10939898 DOI: 10.1016/j.molcel.2023.12.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation.
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Affiliation(s)
- Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Debiao Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | | | | | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Cancer Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
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15
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Wu Z, Huang Y, Liu K, Min J. N/C-degron pathways and inhibitor development for PROTAC applications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:194952. [PMID: 37263341 DOI: 10.1016/j.bbagrm.2023.194952] [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: 04/23/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
Ubiquitination is a fascinating post-translational modification that has received continuous attention since its discovery. In this review, we first provide a concise overview of the E3 ubiquitin ligases, delving into classification, characteristics and mechanisms of ubiquitination. We then specifically examine the ubiquitination pathways mediated by the N/C-degrons, discussing their unique features and substrate recognition mechanisms. Finally, we offer insights into the current state of development pertaining to inhibitors that target the N/C-degron pathways, as well as the promising advances in the field of PROTAC (PROteolysis TArgeting Chimeras). Overall, this review offers a comprehensive understanding of the rapidly-evolving field of ubiquitin biology.
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Affiliation(s)
- Zhibin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yunyuan Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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16
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Weinberg J, Whitcomb E, Bohm A, Chekkilla UK, Taylor A. The E3 ligase SMURF1 stabilizes p27 via UbcH7 catalyzed K29-linked ubiquitin chains to promote cell migration SMURF1-UbcH7 K29 ubiquitination of p27 and cell migration. J Biol Chem 2024; 300:105693. [PMID: 38301893 PMCID: PMC10897894 DOI: 10.1016/j.jbc.2024.105693] [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: 09/08/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
Ubiquitination is a key regulator of protein stability and function. The multifunctional protein p27 is known to be degraded by the proteasome following K48-linked ubiquitination. However, we recently reported that when the ubiquitin-conjugating enzyme UbcH7 (UBE2L3) is overexpressed, p27 is stabilized, and cell cycle is arrested in multiple diverse cell types including eye lens, retina, HEK-293, and HELA cells. However, the ubiquitin ligase associated with this stabilization of p27 remained a mystery. Starting with an in vitro ubiquitination screen, we identified RSP5 as the yeast E3 ligase partner of UbcH7 in the ubiquitination of p27. Screening of the homologous human NEDD4 family of E3 ligases revealed that SMURF1 but not its close homolog SMURF2, stabilizes p27 in cells. We found that SMURF1 ubiquitinates p27 with K29O but not K29R or K63O ubiquitin in vitro, demonstrating a strong preference for K29 chain formation. Consistent with SMURF1/UbcH7 stabilization of p27, we also found that SMURF1, UbcH7, and p27 promote cell migration, whereas knockdown of SMURF1 or UbcH7 reduces cell migration. We further demonstrated the colocalization of SMURF1/p27 and UbcH7/p27 at the leading edge of migrating cells. In sum, these results indicate that SMURF1 and UbcH7 work together to produce K29-linked ubiquitin chains on p27, resulting in the stabilization of p27 and promoting its cell-cycle independent function of regulating cell migration.
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Affiliation(s)
- Jasper Weinberg
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Elizabeth Whitcomb
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Andrew Bohm
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Uday Kumar Chekkilla
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University
| | - Allen Taylor
- Laboratory for Nutrition and Vision Research Human Nutrition Research Center on Aging Tufts University.
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17
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Traynor R, Moran J, Stevens M, Antico O, Knebel A, Behrouz B, Merchant K, Hastie CJ, Davies P, Muqit MMK, De Cesare V. Design and high-throughput implementation of MALDI-TOF/MS-based assays for Parkin E3 ligase activity. CELL REPORTS METHODS 2024; 4:100712. [PMID: 38382522 PMCID: PMC10921019 DOI: 10.1016/j.crmeth.2024.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Parkinson's disease (PD) is a progressive neurological disorder that manifests clinically as alterations in movement as well as multiple non-motor symptoms including but not limited to cognitive and autonomic abnormalities. Loss-of-function mutations in the gene encoding the ubiquitin E3 ligase Parkin are causal for familial and juvenile PD. Among several therapeutic approaches being explored to treat or improve the prognosis of patients with PD, the use of small molecules able to reinstate or boost Parkin activity represents a potential pharmacological treatment strategy. A major barrier is the lack of high-throughput platforms for the robust and accurate quantification of Parkin activity in vitro. Here, we present two different and complementary Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF/MS)-based approaches for the quantification of Parkin E3 ligase activity in vitro. Both approaches are scalable for high-throughput primary screening to facilitate the identification of Parkin modulators.
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Affiliation(s)
- Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Michael Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Bahareh Behrouz
- Vincere Biosciences, Inc., 245 Main St. Fl 2, Cambridge, MA 02142, USA
| | - Kalpana Merchant
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, School of Life Sciences, University of Dundee, Dow St., Dundee DD1 5EH, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow St, Dundee DD1 5EH, Scotland, UK.
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18
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Hehl LA, Horn-Ghetko D, Prabu JR, Vollrath R, Vu DT, Pérez Berrocal DA, Mulder MPC, van der Heden van Noort GJ, Schulman BA. Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5. Nat Chem Biol 2024; 20:190-200. [PMID: 37620400 PMCID: PMC10830417 DOI: 10.1038/s41589-023-01414-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023]
Abstract
Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
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Affiliation(s)
- Laura A Hehl
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ronnald Vollrath
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David A Pérez Berrocal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Brenda A Schulman
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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19
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Barnsby-Greer L, Mabbitt PD, Dery MA, Squair DR, Wood NT, Lamoliatte F, Lange SM, Virdee S. UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4. Nat Struct Mol Biol 2024; 31:351-363. [PMID: 38182926 PMCID: PMC10873205 DOI: 10.1038/s41594-023-01192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 11/27/2023] [Indexed: 01/07/2024]
Abstract
UBR4 is a 574 kDa E3 ligase (E3) of the N-degron pathway with roles in neurodevelopment, age-associated muscular atrophy and cancer. The catalytic module that carries out ubiquitin (Ub) transfer remains unknown. Here we identify and characterize a distinct E3 module within human UBR4 consisting of a 'hemiRING' zinc finger, a helical-rich UBR zinc-finger interacting (UZI) subdomain, and an N-terminal region that can serve as an affinity factor for the E2 conjugating enzyme (E2). The structure of an E2-E3 complex provides atomic-level insight into the specificity determinants of the hemiRING toward the cognate E2s UBE2A/UBE2B. Via an allosteric mechanism, the UZI subdomain modestly activates the Ub-loaded E2 (E2∼Ub). We propose attenuated activation is complemented by the intrinsically high lysine reactivity of UBE2A, and their cooperation imparts a reactivity profile important for substrate specificity and optimal degradation kinetics. These findings reveal the mechanistic underpinnings of a neuronal N-degron E3, its specific recruitment of UBE2A, and highlight the underappreciated architectural diversity of cross-brace domains with Ub E3 activity.
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Affiliation(s)
- Lucy Barnsby-Greer
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Peter D Mabbitt
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
- Scion, Rotorua, New Zealand
| | - Marc-Andre Dery
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Daniel R Squair
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK.
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20
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Basu B, Kal S, Karmakar S, Basu M, Ghosh MK. E3 ubiquitin ligases in lung cancer: Emerging insights and therapeutic opportunities. Life Sci 2024; 336:122333. [PMID: 38061537 DOI: 10.1016/j.lfs.2023.122333] [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: 10/11/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
Aim In this review, we have attempted to provide the readers with an updated account of the role of a family of proteins known as E3 ligases in different aspects of lung cancer progression, along with insights into the deregulation of expression of these proteins during lung cancer. A detailed account of the therapeutic strategies involving E3 ligases that have been developed or currently under development has also been provided in this review. MATERIALS AND METHODS: The review article employs extensive literature search, along with differential gene expression analysis of lung cancer associated E3 ligases using the DESeq2 package in R, and the Gene Expression Profiling Interactive Analysis (GEPIA) database (http://gepia.cancer-pku.cn/). Protein expression analysis of CPTAC lung cancer samples was carried out using the UALCAN webtool (https://ualcan.path.uab.edu/index.html). Assessment of patient overall survival (OS) in response to high and low expression of selected E3 ligases was performed using the online Kaplan-Meier plotter (https://kmplot.com/analysis/index.php?p=background). KEY FINDINGS: SIGNIFICANCE: The review provides an in-depth understanding of the role of E3 ligases in lung cancer progression and an up-to-date account of the different therapeutic strategies targeting oncogenic E3 ligases for improved lung cancer management.
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Affiliation(s)
- Bhaskar Basu
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Satadeepa Kal
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Subhajit Karmakar
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Malini Basu
- Department of Microbiology, Dhruba Chand Halder College, Dakshin Barasat, South 24 Parganas, PIN -743372, India
| | - Mrinal K Ghosh
- Cancer Biology and Inflammatory Disorder Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB), TRUE Campus, CN-6, Sector-V, Salt Lake, Kolkata- 700091 & 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India.
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21
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Banerjee S, Varga JK, Kumar M, Zoltsman G, Rotem-Bamberger S, Cohen-Kfir E, Isupov MN, Rosenzweig R, Schueler-Furman O, Wiener R. Structural study of UFL1-UFC1 interaction uncovers the role of UFL1 N-terminal helix in ufmylation. EMBO Rep 2023; 24:e56920. [PMID: 37988244 DOI: 10.15252/embr.202356920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023] Open
Abstract
Ufmylation plays a crucial role in various cellular processes including DNA damage response, protein translation, and ER homeostasis. To date, little is known about how the enzymes responsible for ufmylation coordinate their action. Here, we study the details of UFL1 (E3) activity, its binding to UFC1 (E2), and its relation to UBA5 (E1), using a combination of structural modeling, X-ray crystallography, NMR, and biochemical assays. Guided by Alphafold2 models, we generate an active UFL1 fusion construct that includes its partner DDRGK1 and solve the crystal structure of this critical interaction. This fusion construct also unveiled the importance of the UFL1 N-terminal helix for binding to UFC1. The binding site suggested by our UFL1-UFC1 model reveals a conserved interface, and competition between UFL1 and UBA5 for binding to UFC1. This competition changes in the favor of UFL1 following UFM1 charging of UFC1. Altogether, our study reveals a novel, terminal helix-mediated regulatory mechanism, which coordinates the cascade of E1-E2-E3-mediated transfer of UFM1 to its substrate and provides new leads to target this modification.
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Affiliation(s)
- Sayanika Banerjee
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Julia K Varga
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manoj Kumar
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Guy Zoltsman
- Department of Chemical and Structural Biology, Weizmann Institute of Sciences, Rehovot, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, UK
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Sciences, Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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22
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Purser N, Tripathi-Giesgen I, Li J, Scott DC, Horn-Ghetko D, Baek K, Schulman BA, Alpi AF, Kleiger G. Catalysis of non-canonical protein ubiquitylation by the ARIH1 ubiquitin ligase. Biochem J 2023; 480:1817-1831. [PMID: 37870100 PMCID: PMC10657180 DOI: 10.1042/bcj20230373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Protein ubiquitylation typically involves isopeptide bond formation between the C-terminus of ubiquitin to the side-chain amino group on Lys residues. However, several ubiquitin ligases (E3s) have recently been identified that ubiquitylate proteins on non-Lys residues. For instance, HOIL-1 belongs to the RING-in-between RING (RBR) class of E3s and has an established role in Ser ubiquitylation. Given the homology between HOIL-1 and ARIH1, an RBR E3 that functions with the large superfamily of cullin-RING E3 ligases (CRLs), a biochemical investigation was undertaken, showing ARIH1 catalyzes Ser ubiquitylation to CRL-bound substrates. However, the efficiency of ubiquitylation was exquisitely dependent on the location and chemical environment of the Ser residue within the primary structure of the substrate. Comprehensive mutagenesis of the ARIH1 Rcat domain identified residues whose mutation severely impacted both oxyester and isopeptide bond formation at the preferred site for Ser ubiquitylation while only modestly affecting Lys ubiquitylation at the physiological site. The results reveal dual isopeptide and oxyester protein ubiquitylation activities of ARIH1 and set the stage for physiological investigations into this function of emerging importance.
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Affiliation(s)
- Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Daniel C. Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Arno F. Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
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23
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Sakamaki JI, Mizushima N. Ubiquitination of non-protein substrates. Trends Cell Biol 2023; 33:991-1003. [PMID: 37120410 DOI: 10.1016/j.tcb.2023.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/01/2023]
Abstract
The covalent attachment of ubiquitin is a common regulatory mechanism in various proteins. Although it has long been thought that the substrates of ubiquitination are limited to proteins, recent studies have changed this view: ubiquitin can be conjugated to lipids, sugars, and nucleotides. Ubiquitin is linked to these substrates by the action of different classes of ubiquitin ligases that have distinct catalytic mechanisms. Ubiquitination of non-protein substrates likely serves as a signal for the recruitment of other proteins to bring about specific effects. These discoveries have expanded the concept of ubiquitination and have advanced our insight into the biology and chemistry of this well-established modification process. In this review we describe the molecular mechanisms and roles of non-protein ubiquitination and discuss the current limitations.
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Affiliation(s)
- Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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24
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Jeong Y, Oh AR, Jung YH, Gi H, Kim YU, Kim K. Targeting E3 ubiquitin ligases and their adaptors as a therapeutic strategy for metabolic diseases. Exp Mol Med 2023; 55:2097-2104. [PMID: 37779139 PMCID: PMC10618535 DOI: 10.1038/s12276-023-01087-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 10/03/2023] Open
Abstract
Posttranslational modification of proteins via ubiquitination determines their activation, translocation, dysregulation, or degradation. This process targets a large number of cellular proteins, affecting all biological pathways involved in the cell cycle, development, growth, and differentiation. Thus, aberrant regulation of ubiquitination is likely associated with several diseases, including various types of metabolic diseases. Among the ubiquitin enzymes, E3 ubiquitin ligases are regarded as the most influential ubiquitin enzymes due to their ability to selectively bind and recruit target substrates for ubiquitination. Continued research on the regulatory mechanisms of E3 ligases and their adaptors in metabolic diseases will further stimulate the discovery of new targets and accelerate the development of therapeutic options for metabolic diseases. In this review, based on recent discoveries, we summarize new insights into the roles of E3 ubiquitin ligases and their adaptors in the pathogenesis of metabolic diseases by highlighting recent evidence obtained in both human and animal model studies.
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Affiliation(s)
- Yelin Jeong
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - Ah-Reum Oh
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - Young Hoon Jung
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - HyunJoon Gi
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - Young Un Kim
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea
| | - KyeongJin Kim
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea.
- Program in Biomedical Science & Engineering, Inha University, Incheon, Republic of Korea.
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon, 22212, Republic of Korea.
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25
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Mishra V, Crespo-Puig A, McCarthy C, Masonou T, Glegola-Madejska I, Dejoux A, Dow G, Eldridge MJG, Marinelli LH, Meng M, Wang S, Bennison DJ, Morrison R, Shenoy AR. IL-1β turnover by the UBE2L3 ubiquitin conjugating enzyme and HECT E3 ligases limits inflammation. Nat Commun 2023; 14:4385. [PMID: 37474493 PMCID: PMC10359330 DOI: 10.1038/s41467-023-40054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/10/2023] [Indexed: 07/22/2023] Open
Abstract
The cytokine interleukin-1β (IL-1β) has pivotal roles in antimicrobial immunity, but also incites inflammatory disease. Bioactive IL-1β is released following proteolytic maturation of the pro-IL-1β precursor by caspase-1. UBE2L3, a ubiquitin conjugating enzyme, promotes pro-IL-1β ubiquitylation and proteasomal disposal. However, actions of UBE2L3 in vivo and its ubiquitin ligase partners in this process are unknown. Here we report that deletion of Ube2l3 in mice reduces pro-IL-1β turnover in macrophages, leading to excessive mature IL-1β production, neutrophilic inflammation and disease following inflammasome activation. An unbiased RNAi screen identified TRIP12 and AREL1 E3 ligases of the Homologous to E6 C-terminus (HECT) family in adding destabilising K27-, K29- and K33- poly-ubiquitin chains on pro-IL-1β. We show that precursor abundance determines mature IL-1β production, and UBE2L3, TRIP12 and AREL1 limit inflammation by shrinking the cellular pool of pro-IL-1β. Our study uncovers fundamental processes governing IL-1β homeostasis and provides molecular insights that could be exploited to mitigate its adverse actions in disease.
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Affiliation(s)
- Vishwas Mishra
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Anna Crespo-Puig
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Callum McCarthy
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Tereza Masonou
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Izabela Glegola-Madejska
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Alice Dejoux
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Gabriella Dow
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Matthew J G Eldridge
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Luciano H Marinelli
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Meihan Meng
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Shijie Wang
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Daniel J Bennison
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Rebecca Morrison
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Avinash R Shenoy
- Medical Research Council Centre for Molecular Bacteriology & Infection, Department of Infectious Disease, Imperial College London, London, UK.
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26
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Wang Y, Liu P, Cai Y, Li Y, Tang C, Zhu N, Wang P, Zhang S, Wu J. PbrBZR1 interacts with PbrARI2.3 to mediate brassinosteroid-regulated pollen tube growth during self-incompatibility signaling in pear. PLANT PHYSIOLOGY 2023; 192:2356-2373. [PMID: 37010117 PMCID: PMC10315279 DOI: 10.1093/plphys/kiad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
S-RNase-mediated self-incompatibility (SI) prevents self-fertilization and promotes outbreeding to ensure genetic diversity in many flowering plants, including pear (Pyrus sp.). Brassinosteroids (BRs) have well-documented functions in cell elongation, but their molecular mechanisms in pollen tube growth, especially in the SI response, remain elusive. Here, exogenously applied brassinolide (BL), an active BR, countered incompatible pollen tube growth inhibition during the SI response in pear. Antisense repression of BRASSINAZOLE-RESISTANT1 (PbrBZR1), a critical component of BR signaling, blocked the positive effect of BL on pollen tube elongation. Further analyses revealed that PbrBZR1 binds to the promoter of EXPANSIN-LIKE A3 (PbrEXLA3) to activate its expression. PbrEXLA3 encodes an expansin that promotes pollen tube elongation in pear. The stability of dephosphorylated PbrBZR1 was substantially reduced in incompatible pollen tubes, where it is targeted by ARIADNE2.3 (PbrARI2.3), an E3 ubiquitin ligase that is strongly expressed in pollen. Our results show that during the SI response, PbrARI2.3 accumulates and negatively regulates pollen tube growth by accelerating the degradation of PbrBZR1 via the 26S proteasome pathway. Together, our results show that an ubiquitin-mediated modification participates in BR signaling in pollen and reveal the molecular mechanism by which BRs regulate S-RNase-based SI.
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Affiliation(s)
- Yicheng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Panpan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiling Cai
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Li
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Tang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Nan Zhu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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27
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Sanati M, Afshari AR, Ahmadi SS, Moallem SA, Sahebkar A. Modulation of the ubiquitin-proteasome system by phytochemicals: Therapeutic implications in malignancies with an emphasis on brain tumors. Biofactors 2023; 49:782-819. [PMID: 37162294 DOI: 10.1002/biof.1958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/20/2023] [Indexed: 05/11/2023]
Abstract
Regarding the multimechanistic nature of cancers, current chemo- or radiotherapies often fail to eradicate disease pathology, and frequent relapses or resistance to therapies occur. Brain malignancies, particularly glioblastomas, are difficult-to-treat cancers due to their highly malignant and multidimensional biology. Unfortunately, patients suffering from malignant tumors often experience poor prognoses and short survival periods. Thus far, significant efforts have been conducted to discover novel and more effective modalities. To that end, modulation of the ubiquitin-proteasome system (UPS) has attracted tremendous interest since it affects the homeostasis of proteins critically engaged in various cell functions, for example, cell metabolism, survival, proliferation, and differentiation. With their safe and multimodal actions, phytochemicals are among the promising therapeutic tools capable of turning the operation of various UPS elements. The present review, along with an updated outline of the role of UPS dysregulation in multiple cancers, provided a detailed discussion on the impact of phytochemicals on the UPS function in malignancies, especially brain tumors.
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Affiliation(s)
- Mehdi Sanati
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran
- Experimental and Animal Study Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Amir R Afshari
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
- Department of Physiology and Pharmacology, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Seyed Sajad Ahmadi
- Department of Ophthalmology, Khatam-Ol-Anbia Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Adel Moallem
- Department of Pharmacology and Toxicology, College of Pharmacy, Al-Zahraa University for Women, Karbala, Iraq
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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28
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Stevens MU, Croteau N, Eldeeb MA, Antico O, Zeng ZW, Toth R, Durcan TM, Springer W, Fon EA, Muqit MM, Trempe JF. Structure-based design and characterization of Parkin-activating mutations. Life Sci Alliance 2023; 6:e202201419. [PMID: 36941054 PMCID: PMC10027901 DOI: 10.26508/lsa.202201419] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
Autosomal recessive mutations in the Parkin gene cause Parkinson's disease. Parkin encodes an ubiquitin E3 ligase that functions together with the kinase PINK1 in a mitochondrial quality control pathway. Parkin exists in an inactive conformation mediated by autoinhibitory domain interfaces. Thus, Parkin has become a target for the development of therapeutics that activate its ligase activity. Yet, the extent to which different regions of Parkin can be targeted for activation remained unknown. Here, we have used a rational structure-based approach to design new activating mutations in both human and rat Parkin across interdomain interfaces. Out of 31 mutations tested, we identified 11 activating mutations that all cluster near the RING0:RING2 or REP:RING1 interfaces. The activity of these mutants correlates with reduced thermal stability. Furthermore, three mutations V393D, A401D, and W403A rescue a Parkin S65A mutant, defective in mitophagy, in cell-based studies. Overall our data extend previous analysis of Parkin activation mutants and suggests that small molecules that would mimic RING0:RING2 or REP:RING1 destabilisation offer therapeutic potential for Parkinson's disease patients harbouring select Parkin mutations.
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Affiliation(s)
- Michael U Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nathalie Croteau
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structurale, Montpellier, France
| | - Mohamed A Eldeeb
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zhi Wei Zeng
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas M Durcan
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience PhD Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Edward A Fon
- McGill Parkinson Program, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Miratul Mk Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montréal, Canada
- Centre de Recherche en Biologie Structurale, Montpellier, France
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29
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De Cesare V. MALDI-TOF Mass Spectrometry for interrogating ubiquitin enzymes. Front Mol Biosci 2023; 10:1184934. [PMID: 37234921 PMCID: PMC10206504 DOI: 10.3389/fmolb.2023.1184934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
The attachment of ubiquitin to a substrate (ubiquitination or ubiquitylation) impacts its lifetime and regulates its function within the cell. Several classes of enzymes oversee the attachment of ubiquitin to the substrate: an E1 activating enzyme that makes ubiquitin chemically susceptible prior to the following stages of conjugation and ligation, respectively mediated by E2 conjugating enzymes (E2s) and E3 ligases (E3s). Around 40 E2s and more than 600 E3s are encoded in the human genome, and their combinatorial and cooperative behaviour dictate the tight specificity necessary for the regulation of thousands of substrates. The removal of ubiquitin is orchestrated by a network of about 100 deubiquitylating enzymes (DUBs). Many cellular processes are tightly controlled by ubiquitylation, which is essential in maintaining cellular homeostasis. Because of the fundamental role(s) of ubiquitylation, there is an interest in better understanding the function and specificity of the ubiquitin machinery. Since 2014, an expanding array of Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) Mass Spectrometry (MS) assays have been developed to systematically characterise the activity of a variety of ubiquitin enzymes in vitro. Here we recapitulate how MALDI-TOF MS aided the in vitro characterization of ubiquitin enzymes and the discovery of new and unexpected of E2s and DUBs functions. Given the versatility of the MALDI-TOF MS approach, we foreseen the use of this technology to further expand our understanding of ubiquitin and ubiquitin-like enzymes.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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Trempe JF, Gehring K. Structural mechanisms of mitochondrial quality control mediated by PINK1 and parkin. J Mol Biol 2023:168090. [PMID: 37054910 DOI: 10.1016/j.jmb.2023.168090] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease and represents a looming public health crisis as the global population ages. While the etiology of the more common, idiopathic form of the disease remains unknown, the last ten years have seen a breakthrough in our understanding of the genetic forms related to two proteins that regulate a quality control system for the removal of damaged or non-functional mitochondria. Here, we review the structure of these proteins, PINK1, a protein kinase, and parkin, a ubiquitin ligase with an emphasis on the molecular mechanisms responsible for their recognition of dysfunctional mitochondria and control of the subsequent ubiquitination cascade. Recent atomic structures have revealed the basis of PINK1 substrate specificity and the conformational changes responsible for activation of PINK1 and parkin catalytic activity. Progress in understanding the molecular basis of mitochondrial quality control promises to open new avenues for therapeutic interventions in PD.
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Affiliation(s)
- Jean-François Trempe
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Centre de Recherche en Biologie Structurale
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31
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Mauro D, Manou-Stathopoulou S, Rivellese F, Sciacca E, Goldmann K, Tsang V, Lucey-Clayton I, Pagani S, Alam F, Pyne D, Rajakariar R, Gordon PA, Whiteford J, Bombardieri M, Pitzalis C, Lewis MJ. UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus. J Autoimmun 2023; 136:103023. [PMID: 37001433 DOI: 10.1016/j.jaut.2023.103023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023]
Abstract
Both TLR7 and NF-κB hyperactivity are known to contribute to pathogenesis in Systemic Lupus Erythematosus (SLE), driving a pro-interferon response, autoreactive B cell expansion and autoantibody production. UBE2L3 is an SLE susceptibility gene which drives plasmablast/plasma cell expansion in SLE, but its role in TLR7 signalling has not been elucidated. We aimed to investigate the role of UBE2L3 in TLR7-mediated NF-κB activation, and the effect of UBE2L3 inhibition by Dimethyl Fumarate (DMF) on SLE B cell differentiation in vitro. Our data demonstrate that UBE2L3 is critical for activation of NF-κB downstream of TLR7 stimulation, via interaction with LUBAC. DMF, which directly inhibits UBE2L3, significantly inhibited TLR7-induced NF-κB activation, differentiation of memory B cells and plasmablasts, and autoantibody secretion in SLE. DMF also downregulated interferon signature genes and plasma cell transcriptional programmes. These results demonstrate that UBE2L3 inhibition could potentially be used as a therapy in SLE through repurposing of DMF, thus preventing TLR7-driven autoreactive B cell maturation.
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32
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Kaur A, Gladu EM, Wright KM, Webb JA, Massiah MA. B-box1 Domain of MID1 Interacts with the Ube2D1 E2 Enzyme Differently Than RING E3 Ligases. Biochemistry 2023; 62:1012-1025. [PMID: 36820504 DOI: 10.1021/acs.biochem.2c00693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The MID1 TRIM protein is important for ventral midline development in vertebrates, and mutations of its B-box1 domain result in several birth defects. The B-box1 domain of the human MID1 protein binds two zinc atoms and adopt a similar ββα-RING structure. This domain is required for the efficient ubiquitination of protein phosphatase 2A, alpha4, and fused kinase. Considering the structural similarity, the MID1 B-box1 domain exhibits mono-autoubiquitination activity, in contrast to poly-autoubiquitination observed for RING E3 ligases. To understand its mechanism of action, the interaction of the B-box1 domain with Ube2D1 (UbcH5a, E2), a preferred E2 ligase, is investigated. Using isothermal titration calorimetry, the MID1 RING and B-box1 domains were observed to have similar binding affinities with the Ube2D1 protein. However, NMR 15N-1H Heteronuclear Single Quantum Coherence titration, 15N relaxation data, and High Ambiguity Driven protein-protein DOCKing (HADDOCK) calculations show the B-box1 domain binding on a surface distinct from where RING domains bind. The novel binding interaction shows the B-box1 domain partially overlapping the noncovalent Ube2D1 and a ubiquitin binding site that is necessary for poly-autoubiquitination activity. The B-box1 domain also displaces the ubiquitin from the Ube2D1 protein. These studies reveal a novel binding interaction between the zinc-binding ββα-fold B-box1 domain and the Ube2D enzyme family and that this difference in binding, compared to RING E3 ligases, provides a rationale for its auto-monoubiquitination E3 ligase activity.
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Affiliation(s)
- Anupreet Kaur
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Erin M Gladu
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Katharine M Wright
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Jessica A Webb
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
| | - Michael A Massiah
- Department of Chemistry, George Washington University, 800 22nd St NW, Washington, D.C. 20052, United States
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Connelly EM, Frankel KS, Shaw GS. Parkin and mitochondrial signalling. Cell Signal 2023; 106:110631. [PMID: 36803775 DOI: 10.1016/j.cellsig.2023.110631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Aging, toxic chemicals and changes to the cellular environment are sources of oxidative damage to mitochondria which contribute to neurodegenerative conditions including Parkinson's disease. To counteract this, cells have developed signalling mechanisms to identify and remove select proteins and unhealthy mitochondria to maintain homeostasis. Two important proteins that work in concert to control mitochondrial damage are the protein kinase PINK1 and the E3 ligase parkin. In response to oxidative stress, PINK1 phosphorylates ubiquitin present on proteins at the mitochondrial surface. This signals the translocation of parkin, accelerates further phosphorylation, and stimulates ubiquitination of outer mitochondrial membrane proteins such as Miro1/2 and Mfn1/2. The ubiquitination of these proteins is the key step needed to target them for degradation via the 26S proteasomal machinery or eliminate the entire organelle through mitophagy. This review highlights the signalling mechanisms used by PINK1 and parkin and presents several outstanding questions yet to be resolved.
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Affiliation(s)
- Elizabeth M Connelly
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karling S Frankel
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada.
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Delegkou GN, Birkou M, Fragkaki N, Toro T, Marousis KD, Episkopou V, Spyroulias GA. E2 Partner Tunes the Ubiquitylation Specificity of Arkadia E3 Ubiquitin Ligase. Cancers (Basel) 2023; 15:1040. [PMID: 36831384 PMCID: PMC9954413 DOI: 10.3390/cancers15041040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Arkadia (RNF111) is a positive regulator of the TGF-β signaling that mediates the proteasome-dependent degradation of negative factors of the pathway. It is classified as an E3 ubiquitin ligase and a SUMO-targeted ubiquitin ligase (STUBL), implicated in various pathological conditions including cancer and fibrosis. The enzymatic (ligase) activity of Arkadia is located at its C-terminus and involves the RING domain. Notably, E3 ligases require E2 enzymes to perform ubiquitylation. However, little is known about the cooperation of Arkadia with various E2 enzymes and the type of ubiquitylation that they mediate. In the present work, we study the interaction of Arkadia with the E2 partners UbcH5B and UbcH13, as well as UbcH7. Through NMR spectroscopy, we found that the E2-Arkadia interaction surface is similar in all pairs examined. Nonetheless, the requirements and factors that determine an enzymatically active E2-Arkadia complex differ in each case. Furthermore, we revealed that the cooperation of Arkadia with different E2s results in either monoubiquitylation or polyubiquitin chain formation via K63, K48, or K11 linkages, which can determine the fate of the substrate and lead to distinct biological outcomes.
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Affiliation(s)
| | - Maria Birkou
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Nefeli Fragkaki
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Tamara Toro
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | | | - Vasso Episkopou
- Department of Brain Sciences, Imperial College, London W12 0NN, UK
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35
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Li J, Yang D, Li Z, Zhao M, Wang D, Sun Z, Wen P, Dai Y, Gou F, Ji Y, Zhao D, Yang L. PINK1/Parkin-mediated mitophagy in neurodegenerative diseases. Ageing Res Rev 2023; 84:101817. [PMID: 36503124 DOI: 10.1016/j.arr.2022.101817] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Mitochondria play key roles in bioenergetics, metabolism, and signaling; therefore, stable mitochondrial function is essential for cell survival, particularly in energy-intensive neuronal cells. In neurodegenerative diseases, damaged mitochondria accumulate in neurons causing associated bioenergetics deficiency, impaired cell signaling, defective cytoplasmic calcium buffering, and other pathological changes. Mitochondrial quality control is an important mechanism to ensure the maintenance of mitochondrial health, homeostasis, and mitophagy, the latter of which is a pathway that delivers defective mitochondria to the lysosome for degradation. Defective mitophagy is thought to be responsible for the accumulation of damaged mitochondria, which leads to cellular dysfunction and/or death in neurodegenerative diseases. PINK1/Parkin mainly regulates ubiquitin-dependent mitophagy, which is crucial for many aspects of mitochondrial physiology, particularly the initiation of autophagic mechanisms. Therefore, in the present review, we summarize the current knowledge of the conventional mitophagy pathway, focusing on the molecular mechanisms underlying mitophagy dysregulation in prion disease and other age-related neurodegenerative diseases, especially in relation to the PINK1/Parkin pathway. Moreover, we list the inducers of mitophagy that possess neuroprotective effects, in addition to their mechanisms related to the PINK1/Parkin pathway. These mechanisms may provide potential interventions centered on the regulation of mitophagy and offer therapeutic strategies for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Jie Li
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Dongming Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Zhiping Li
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Mengyang Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Dongdong Wang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Zhixin Sun
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Pei Wen
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Yuexin Dai
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Fengting Gou
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Yilan Ji
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Deming Zhao
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Lifeng Yang
- National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China.
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36
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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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37
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Wang XS, Cotton TR, Trevelyan SJ, Richardson LW, Lee WT, Silke J, Lechtenberg BC. The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family. Nat Commun 2023; 14:168. [PMID: 36631489 PMCID: PMC9834252 DOI: 10.1038/s41467-023-35871-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
The RING-between-RING (RBR) E3 ubiquitin ligase family in humans comprises 14 members and is defined by a two-step catalytic mechanism in which ubiquitin is first transferred from an E2 ubiquitin-conjugating enzyme to the RBR active site and then to the substrate. To define the core features of this catalytic mechanism, we here structurally and biochemically characterise the two RBRs HOIL-1 and RNF216. Crystal structures of both enzymes in their RBR/E2-Ub/Ub transthiolation complexes capturing the first catalytic step, together with complementary functional experiments, reveal the defining features of the RBR catalytic mechanism. RBRs catalyse ubiquitination via a conserved transthiolation complex structure that enables efficient E2-to-RBR ubiquitin transfer. Our data also highlight a conserved RBR allosteric activation mechanism by distinct ubiquitin linkages that suggests RBRs employ a feed-forward mechanism. We finally identify that the HOIL-1 RING2 domain contains an unusual Zn2/Cys6 binuclear cluster that is required for catalytic activity and substrate ubiquitination.
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Affiliation(s)
- Xiangyi S Wang
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Thomas R Cotton
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Sarah J Trevelyan
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Lachlan W Richardson
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Wei Ting Lee
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - John Silke
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Bernhard C Lechtenberg
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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38
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Bou Malhab LJ, Alsafar H, Ibrahim S, Rahmani M. PROTACs: Walking through hematological malignancies. Front Pharmacol 2023; 14:1086946. [PMID: 36909156 PMCID: PMC9994433 DOI: 10.3389/fphar.2023.1086946] [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: 11/01/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional small molecules that uses the proteasome ubiquitin system to target proteins of interest and promote their degradation with remarkable selectivity. Importantly, unlike conventional small molecule inhibitors, PROTACs have proven highly effective in targeting undruggable proteins and those bearing mutations. Because of these considerations, PROTACs have increasingly become an emerging technology for the development of novel targeted anticancer therapeutics. Interestingly, many PROTACs have demonstrated a great potency and specificity in degrading several oncogenic drivers. Many of these, following extensive preclinical evaluation, have reached advanced stages of clinical testing in various cancers including hematologic malignancies. In this review, we provide a comprehensive summary of the recent advances in the development of PROTACs as therapeutic strategies in diverse hematological malignancies. A particular attention has been given to clinically relevant PROTACs and those targeting oncogenic mutants that drive resistance to therapies. We also discus limitations, and various considerations to optimize the design for effective PROTACs.
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Affiliation(s)
- Lara J Bou Malhab
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, College of Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Saleh Ibrahim
- Department of Physiology and Immunology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Mohamed Rahmani
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates.,Department of Molecular Biology and Genetics, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
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39
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Genetic code expansion reveals aminoacylated lysine ubiquitination mediated by UBE2W. Nat Struct Mol Biol 2023; 30:62-71. [PMID: 36593310 DOI: 10.1038/s41594-022-00866-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 10/10/2022] [Indexed: 01/03/2023]
Abstract
Protein post-translational modification (PTM) regulates nearly every aspect of cellular processes in eukaryotes. However, the identification of new protein PTMs is very challenging. Here, using genetically encoded unnatural amino acids as chemical probes, we report the identification and validation of a previously unreported form of protein PTM, aminoacylated lysine ubiquitination, in which the modification occurs on the α-amine group of aminoacylated lysine. We identify more than 2,000 ubiquitination sites on all 20 aminoacylated lysines in two human cell lines. The modifications can mediate rapid protein degradation, complementing the canonical lysine ubiquitination-mediated proteome degradation. Furthermore, we demonstrate that the ubiquitin-conjugating enzyme UBE2W acts as a writer of aminoacylated lysine ubiquitination and facilitates the ubiquitination event on proteins. More broadly, the discovery and validation of aminoacylated lysine ubiquitination paves the way for the identification and verification of new protein PTMs with the genetic code expansion strategy.
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40
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Farnung J, Tolmachova KA, Bode JW. Installation of electrophiles onto the C-terminus of recombinant ubiquitin and ubiquitin-like proteins. Chem Sci 2022; 14:121-129. [PMID: 36605735 PMCID: PMC9769091 DOI: 10.1039/d2sc04279g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin and related ubiquitin-like proteins (Ubls) influence a variety of cellular pathways including protein degradation and response to viral infections. The chemical interrogation of these complex enzymatic cascades relies on the use of tailored activity-based probes (ABPs). Herein, we report the preparation of ABPs for ubiquitin, NEDD8, SUMO2 and ISG15 by selective acyl hydrazide modification. Acyl hydrazides of Ubls are readily accessible by direct hydrazinolysis of Ubl-intein fusions. The suppressed pK a and superior nucleophilicity of the acyl hydrazides enables their selective modification at acidic pH with carboxylic acid anhydrides. The modification proceeds rapidly and efficiently, and does not require chromatographic purification or refolding of the probes. We modified Ubl-NHNH2 with various thiol-reactive electrophiles that couple selectively with E2s and DUBs. The ease of modification enables the rapid generation and screening of ubiquitin probes with various C-terminal truncations and warheads for the selection of the most suitable combination for a given E2 or DUB.
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Affiliation(s)
- Jakob Farnung
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH ZürichZürich 8093Switzerland
| | - Kateryna A. Tolmachova
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH ZürichZürich 8093Switzerland
| | - Jeffrey W. Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH ZürichZürich 8093Switzerland
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41
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Hayashida R, Kikuchi R, Imai K, Kojima W, Yamada T, Iijima M, Sesaki H, Tanaka K, Matsuda N, Yamano K. Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid-liquid phase separation-based method. J Biol Chem 2022; 299:102822. [PMID: 36563856 PMCID: PMC9860496 DOI: 10.1016/j.jbc.2022.102822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
RING-between RING (RBR)-type ubiquitin (Ub) ligases (E3s) such as Parkin receive Ub from Ub-conjugating enzymes (E2s) in response to ligase activation. However, the specific E2s that transfer Ub to each RBR-type ligase are largely unknown because of insufficient methods for monitoring their interaction. To address this problem, we have developed a method that detects intracellular interactions between E2s and activated Parkin. Fluorescent homotetramer Azami-Green fused with E2 and oligomeric Ash (Assembly helper) fused with Parkin form a liquid-liquid phase separation (LLPS) in cells only when E2 and Parkin interact. Using this method, we identified multiple E2s interacting with activated Parkin on damaged mitochondria during mitophagy. Combined with in vitro ubiquitination assays and bioinformatics, these findings revealed an underlying consensus sequence for E2 interactions with activated Parkin. Application of this method to other RBR-type E3s including HOIP, HHARI, and TRIAD1 revealed that HOIP forms an LLPS with its substrate NEMO in response to a proinflammatory cytokine and that HHARI and TRIAD1 form a cytosolic LLPS independent of Ub-like protein NEDD8. Since an E2-E3 interaction is a prerequisite for RBR-type E3 activation and subsequent substrate ubiquitination, the method we have established here can be an in-cell tool to elucidate the potentially novel mechanisms involved in RBR-type E3s.
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Affiliation(s)
- Ryota Hayashida
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Reika Kikuchi
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuya Yamada
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan; Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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42
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Tomaskovic I, Gonzalez A, Dikic I. Ubiquitin and Legionella: From bench to bedside. Semin Cell Dev Biol 2022; 132:230-241. [PMID: 35177348 DOI: 10.1016/j.semcdb.2022.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
Legionella pneumophila, a Gram-negative intracellular bacterium, is one of the major causes of Legionnaires' disease, a specific type of atypical pneumonia. Despite intensive research efforts that elucidated many relevant structural, molecular and medical insights into Legionella's pathogenicity, Legionnaires' disease continues to present an ongoing public health concern. Legionella's virulence is based on its ability to simultaneously hijack multiple molecular pathways of the host cell to ensure its fast replication and dissemination. Legionella usurps the host ubiquitin system through multiple effector proteins, using the advantage of both conventional and unconventional (phosphoribosyl-linked) ubiquitination, thus providing optimal conditions for its replication. In this review, we summarize the current understanding of L. pneumophila from medical, biochemical and molecular perspectives. We describe the clinical disease presentation, its diagnostics and treatment, as well as host-pathogen interactions, with the emphasis on the ability of Legionella to target the host ubiquitin system upon infection. Furthermore, the interdisciplinary use of innovative technologies enables better insights into the pathogenesis of Legionnaires' disease and provides new opportunities for its treatment and prevention.
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Affiliation(s)
- Ines Tomaskovic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany.
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43
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Tsefou E, Ketteler R. Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin. Int J Mol Sci 2022; 23:12105. [PMID: 36292958 PMCID: PMC9603086 DOI: 10.3390/ijms232012105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
The quality control of mitochondria is critical for the survival of cells, and defects in the pathways required for this quality control can lead to severe disease. A key quality control mechanism in cells is mitophagy, which functions to remove damaged mitochondria under conditions of various stresses. Defective mitophagy can lead to a number of diseases including neurodegeneration. It has been proposed that an enhancement of mitophagy can improve cell survival, enhance neuronal function in neurodegeneration and extend health and lifespans. In this review, we highlight the role of deubiquitinating enzymes (DUBs) in the regulation of mitophagy. We summarise the current knowledge on DUBs that regulate mitophagy as drug targets and provide a list of small molecule inhibitors that are valuable tools for the further development of therapeutic strategies targeting the mitophagy pathway in neurodegeneration.
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Affiliation(s)
- Eliona Tsefou
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- UCL:Eisai Therapeutic Innovation Group, Translational Research Office, University College London, London W1T 7NF, UK
| | - Robin Ketteler
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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44
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Sengupta M, Pluciennik A, Merry DE. The role of ubiquitination in spinal and bulbar muscular atrophy. Front Mol Neurosci 2022; 15:1020143. [PMID: 36277484 PMCID: PMC9583669 DOI: 10.3389/fnmol.2022.1020143] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Spinal and bulbar muscular atrophy (SBMA) is a neurodegenerative and neuromuscular genetic disease caused by the expansion of a polyglutamine-encoding CAG tract in the androgen receptor (AR) gene. The AR is an important transcriptional regulator of the nuclear hormone receptor superfamily; its levels are regulated in many ways including by ubiquitin-dependent degradation. Ubiquitination is a post-translational modification (PTM) which plays a key role in both AR transcriptional activity and its degradation. Moreover, the ubiquitin-proteasome system (UPS) is a fundamental component of cellular functioning and has been implicated in diseases of protein misfolding and aggregation, including polyglutamine (polyQ) repeat expansion diseases such as Huntington's disease and SBMA. In this review, we discuss the details of the UPS system, its functions and regulation, and the role of AR ubiquitination and UPS components in SBMA. We also discuss aspects of the UPS that may be manipulated for therapeutic effect in SBMA.
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Affiliation(s)
| | | | - Diane E. Merry
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
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45
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Ajoolabady A, Chiong M, Lavandero S, Klionsky DJ, Ren J. Mitophagy in cardiovascular diseases: molecular mechanisms, pathogenesis, and treatment. Trends Mol Med 2022; 28:836-849. [PMID: 35879138 PMCID: PMC9509460 DOI: 10.1016/j.molmed.2022.06.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/18/2022] [Accepted: 06/23/2022] [Indexed: 12/19/2022]
Abstract
With the growing prevalence of cardiovascular disease (CVD), there is an urgent need to explore non-conventional therapeutic measures to alleviate the burden of CVD on global healthcare. Mitochondrial injury plays a cardinal role in the pathogenesis of CVD. Mitochondrial dynamics and mitophagy are essential machineries that govern mitochondrial health in cardiomyocytes in physiological and pathophysiological settings. However, with the onset and progression of CVD, homeostasis of mitophagy is disturbed through largely unknown pathological mechanisms, causing mitochondrial damage and ultimately cardiomyocyte death. In this review we decipher the dual regulatory role of mitophagy in CVD pathogenesis, summarize controversies in mitophagy, and highlight recently identified compounds capable of modulating mitophagy. We share our perspectives on future mitophagy research directions in the context of CVD.
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Affiliation(s)
- Amir Ajoolabady
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Mario Chiong
- Center for Advanced Chronic Diseases (ACCDiS), Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago 8380492, Chile
| | - Sergio Lavandero
- Center for Advanced Chronic Diseases (ACCDiS), Faculty of Chemical and Pharmaceutical Sciences & Faculty of Medicine, University of Chile, Santiago 8380492, Chile; Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX 75390-8573, USA.
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jun Ren
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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46
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Peter JJ, Magnussen HM, DaRosa PA, Millrine D, Matthews SP, Lamoliatte F, Sundaramoorthy R, Kopito RR, Kulathu Y. A non-canonical scaffold-type E3 ligase complex mediates protein UFMylation. EMBO J 2022; 41:e111015. [PMID: 36121123 DOI: 10.15252/embj.2022111015] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
Protein UFMylation, i.e., post-translational modification with ubiquitin-fold modifier 1 (UFM1), is essential for cellular and endoplasmic reticulum homeostasis. Despite its biological importance, we have a poor understanding of how UFM1 is conjugated onto substrates. Here, we use a rebuilding approach to define the minimal requirements of protein UFMylation. We find that the reported cognate E3 ligase UFL1 is inactive on its own and instead requires the adaptor protein UFBP1 to form an active E3 ligase complex. Structure predictions suggest the UFL1/UFBP1 complex to be made up of winged helix (WH) domain repeats. We show that UFL1/UFBP1 utilizes a scaffold-type E3 ligase mechanism that activates the UFM1-conjugating E2 enzyme, UFC1, for aminolysis. Further, we characterize a second adaptor protein CDK5RAP3 that binds to and forms an integral part of the ligase complex. Unexpectedly, we find that CDK5RAP3 inhibits UFL1/UFBP1 ligase activity in vitro. Results from reconstituting ribosome UFMylation suggest that CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26. In summary, our reconstitution approach reveals the biochemical basis of UFMylation and regulatory principles of this atypical E3 ligase complex.
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Affiliation(s)
- Joshua J Peter
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Helge M Magnussen
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - David Millrine
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Stephen P Matthews
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
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47
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Kelsall IR. Non-lysine ubiquitylation: Doing things differently. Front Mol Biosci 2022; 9:1008175. [PMID: 36200073 PMCID: PMC9527308 DOI: 10.3389/fmolb.2022.1008175] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
The post-translational modification of proteins with ubiquitin plays a central role in nearly all aspects of eukaryotic biology. Historically, studies have focused on the conjugation of ubiquitin to lysine residues in substrates, but it is now clear that ubiquitylation can also occur on cysteine, serine, and threonine residues, as well as on the N-terminal amino group of proteins. Paradigm-shifting reports of non-proteinaceous substrates have further extended the reach of ubiquitylation beyond the proteome to include intracellular lipids and sugars. Additionally, results from bacteria have revealed novel ways to ubiquitylate (and deubiquitylate) substrates without the need for any of the enzymatic components of the canonical ubiquitylation cascade. Focusing mainly upon recent findings, this review aims to outline the current understanding of non-lysine ubiquitylation and speculate upon the molecular mechanisms and physiological importance of this non-canonical modification.
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48
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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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49
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Stieglitz B. HHARI in motion reveals an unexpected substrate recognition site for RBR ligases. Structure 2022; 30:1221-1223. [PMID: 36055221 DOI: 10.1016/j.str.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Capturing the enzymatic activity of RBR ligases in molecular detail is challenging due to their inherent dynamic behavior. In this issue of Structure, Reiter and colleagues tackle this problem using a multidisciplinary approach. They show that activation of the ubiquitin ligase HHARI by phosphorylation induces a major conformational rearrangement, which reveals an unexpected substrate binding site.
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Affiliation(s)
- Benjamin Stieglitz
- Department of Biochemistry, School of Biological and Behavioural Sciences, Queen Mary University of London, Blizard Institute, 4 Newark Street, London E1 2AT, UK.
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50
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Reiter KH, Zelter A, Janowska MK, Riffle M, Shulman N, MacLean BX, Tamura K, Chambers MC, MacCoss MJ, Davis TN, Guttman M, Brzovic PS, Klevit RE. Cullin-independent recognition of HHARI substrates by a dynamic RBR catalytic domain. Structure 2022; 30:1269-1284.e6. [PMID: 35716664 PMCID: PMC9444911 DOI: 10.1016/j.str.2022.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/15/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022]
Abstract
RING-between-RING (RBR) E3 ligases mediate ubiquitin transfer through an obligate E3-ubiquitin thioester intermediate prior to substrate ubiquitination. Although RBRs share a conserved catalytic module, substrate recruitment mechanisms remain enigmatic, and the relevant domains have yet to be identified for any member of the class. Here we characterize the interaction between the auto-inhibited RBR, HHARI (AriH1), and its target protein, 4EHP, using a combination of XL-MS, HDX-MS, NMR, and biochemical studies. The results show that (1) a di-aromatic surface on the catalytic HHARI Rcat domain forms a binding platform for substrates and (2) a phosphomimetic mutation on the auto-inhibitory Ariadne domain of HHARI promotes release and reorientation of Rcat for transthiolation and substrate modification. The findings identify a direct binding interaction between a RING-between-RING ligase and its substrate and suggest a general model for RBR substrate recognition.
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Affiliation(s)
- Katherine H Reiter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alex Zelter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Maria K Janowska
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Shulman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kaipo Tamura
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew C Chambers
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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