1
|
Duan CY, Li Y, Zhi HY, Tian Y, Huang ZY, Chen SP, Zhang Y, Liu Q, Zhou L, Jiang XG, Ullah K, Guo Q, Liu ZH, Xu Y, Han JH, Hou J, O'Connor DP, Xu G. E3 ubiquitin ligase UBR5 modulates circadian rhythm by facilitating the ubiquitination and degradation of the key clock transcription factor BMAL1. Acta Pharmacol Sin 2024; 45:1793-1808. [PMID: 38740904 PMCID: PMC11336169 DOI: 10.1038/s41401-024-01290-z] [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: 01/01/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
The circadian clock is the inner rhythm of life activities and is controlled by a self-sustained and endogenous molecular clock, which maintains a ~ 24 h internal oscillation. As the core element of the circadian clock, BMAL1 is susceptible to degradation through the ubiquitin-proteasome system (UPS). Nevertheless, scant information is available regarding the UPS enzymes that intricately modulate both the stability and transcriptional activity of BMAL1, affecting the cellular circadian rhythm. In this work, we identify and validate UBR5 as a new E3 ubiquitin ligase that interacts with BMAL1 by using affinity purification, mass spectrometry, and biochemical experiments. UBR5 overexpression induced BMAL1 ubiquitination, leading to diminished stability and reduced protein level of BMAL1, thereby attenuating its transcriptional activity. Consistent with this, UBR5 knockdown increases the BMAL1 protein. Domain mapping discloses that the C-terminus of BMAL1 interacts with the N-terminal domains of UBR5. Similarly, cell-line-based experiments discover that HYD, the UBR5 homolog in Drosophila, could interact with and downregulate CYCLE, the BMAL1 homolog in Drosophila. PER2-luciferase bioluminescence real-time reporting assay in a mammalian cell line and behavioral experiments in Drosophila reveal that UBR5 or hyd knockdown significantly reduces the period of the circadian clock. Therefore, our work discovers a new ubiquitin ligase UBR5 that regulates BMAL1 stability and circadian rhythm and elucidates the underlying molecular mechanism. This work provides an additional layer of complexity to the regulatory network of the circadian clock at the post-translational modification level, offering potential insights into the modulation of the dysregulated circadian rhythm.
Collapse
Affiliation(s)
- Chun-Yan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, 123 St Stephen's Green, Dublin 2, D02 YN77, Dublin, Ireland
| | - Yue Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Hao-Yu Zhi
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Yao Tian
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, 2 Sipailou Road, Nanjing, 210096, China
| | - Zheng-Yun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, 215123, China
| | - Su-Ping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Xiao-Gang Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Kifayat Ullah
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Qing Guo
- Department of Human Anatomy and Cytoneurobiology, Medical School of Soochow University, Suzhou, 215123, China
| | - Zhao-Hui Liu
- Department of Human Anatomy and Cytoneurobiology, Medical School of Soochow University, Suzhou, 215123, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, 215123, China
| | - Jun-Hai Han
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, 2 Sipailou Road, Nanjing, 210096, China
| | - Jiajie Hou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Darran P O'Connor
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, 123 St Stephen's Green, Dublin 2, D02 YN77, Dublin, Ireland
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, China.
| |
Collapse
|
2
|
Kotewicz KM, Zhang M, Kim S, Martin MS, Roy Chowdhury A, Tai A, Scheck RA, Isberg RR. Sde proteins coordinate ubiquitin utilization and phosphoribosylation to establish and maintain the Legionella replication vacuole. Nat Commun 2024; 15:7479. [PMID: 39214970 PMCID: PMC11364549 DOI: 10.1038/s41467-024-51272-2] [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: 08/26/2023] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
The Legionella pneumophila Sde family of translocated proteins promotes host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity is tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, prevents binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb results in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decays quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
Collapse
Affiliation(s)
- Kristin M Kotewicz
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Mengyun Zhang
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Seongok Kim
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Department of Food Science & Biotechnology, Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul, South Korea
| | | | - Atish Roy Chowdhury
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Albert Tai
- Department of Immunology, Tufts University School of Medicine, Boston, MA, USA
| | | | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
| |
Collapse
|
3
|
Wang Y, Niu K, Shi Y, Zhou F, Li X, Li Y, Chen T, Zhang Y. A review: targeting UBR5 domains to mediate emerging roles and mechanisms - chance or necessity? Int J Surg 2024; 110:4947-4964. [PMID: 38701508 PMCID: PMC11326040 DOI: 10.1097/js9.0000000000001541] [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: 02/06/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024]
Abstract
Ubiquitinases are known to catalyze ubiquitin chains on target proteins to regulate various physiological functions like cell proliferation, autophagy, apoptosis, and cell cycle progression. As a member of E3 ligase, ubiquitin protein ligase E3 component n-recognin 5 (UBR5) belongs to the HECT E3 ligase and has been reported to be correlated with various pathophysiological processes. In this review, the authors give a comprehensive insight into the structure and function of UBR5. The authors discuss the specific domains of UBR5 and explore their biological functions separately. Furthermore, the authors describe the involvement of UBR5 in different pathophysiological conditions, including immune response, virus infection, DNA damage response, and protein quality control. Moreover, the authors provide a thorough summary of the important roles and regulatory mechanisms of UBR5 in cancers and other diseases. On the whole, investigating the domains and functions of UBR5, elucidating the underlying mechanisms of UBR5 with various substrates in detail may provide new theoretical basis for the treatment of diseases, including cancers, which could improve future studies to construct novel UBR5-targeted therapy strategies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People’s Republic of China
| |
Collapse
|
4
|
Kotewicz KM, Zhang M, Kim S, Martin MS, Chowdhury AR, Tai A, Scheck RA, Isberg RR. Sde Proteins Coordinate Ubiquitin Utilization and Phosphoribosylation to Establish and Maintain the Legionella Replication Vacuole. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.553534. [PMID: 38645023 PMCID: PMC11030226 DOI: 10.1101/2023.09.07.553534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The Legionella pneumophila Sde family of translocated proteins promotes host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity is tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, prevents binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb results in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decays quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
Collapse
|
5
|
Hu B, Chen S. The role of UBR5 in tumor proliferation and oncotherapy. Gene 2024; 906:148258. [PMID: 38331119 DOI: 10.1016/j.gene.2024.148258] [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: 12/16/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Ubiquitin (Ub) protein ligase E3 component n-recognin 5 (UBR5), as a crucial Ub ligase, plays a pivotal role in the field of cell biology, attracting significant attention for its functions in regulating protein degradation and signaling pathways. This review delves into the fundamental characteristics and structure of UBR5. UBR5, through ubiquitination, regulates various key proteins, directly or indirectly participating in cell cycle control, thereby exerting a direct impact on the proliferation of tumor cells. Meanwhile, we comprehensively review the expression levels of UBR5 in different types of tumors and its relationship with tumor development, providing key clues for the role of UBR5 in cancer. Furthermore, we summarize the current research status of UBR5 in cancer treatment. Through literature review, we find that UBR5 may play a crucial role in the sensitivity of tumor cells to radiotherapy chemotherapy, and other anti-tumor treatment, providing new insights for optimizing cancer treatment strategies. Finally, we discuss the challenges faced by UBR5 in cancer treatment, and looks forward to the future research directions. With the continuous breakthroughs in technology and in-depth research, we hope to further study the biological functions of UBR5 and lay the foundation for its anti-tumor treatment.
Collapse
Affiliation(s)
- Bin Hu
- Department of Geriatrics, Beilun District People's Hospital, Ningbo 315800, China
| | - Shiyuan Chen
- Department of Geriatrics, Beilun District People's Hospital, Ningbo 315800, China.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Nawarathnage S, Tseng YJ, Soleimani S, Smith T, Pedroza Romo MJ, Abiodun WO, Egbert CM, Madhusanka D, Bunn D, Woods B, Tsubaki E, Stewart C, Brown S, Doukov T, Andersen JL, Moody JD. Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. Structure 2023; 31:1589-1603.e6. [PMID: 37776857 PMCID: PMC10843481 DOI: 10.1016/j.str.2023.09.001] [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: 06/14/2023] [Revised: 08/11/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1 ubiquitin-associated (UBA) domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. No experimentally determined molecular structure of this unusual UBA domain is available. We fused the UBA domain to the 1TEL variant of the translocation ETS leukemia protein sterile alpha motif (TELSAM) crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and crystallize at protein concentrations as low as 0.2 mg/mL. Our studies support a mechanism of 1TEL fusion crystallization and show that 1TEL fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
Collapse
Affiliation(s)
| | - Yi Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Maria J Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Wisdom O Abiodun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christina M Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA
| | - Deshan Madhusanka
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA
| | - Derick Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Bridger Woods
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Evan Tsubaki
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA.
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| |
Collapse
|
8
|
Isberg R, Kotewicz K, Zheng M, Kim S, Tai A. Sde Proteins Coordinate Ubiquitin Utilization and Phosphoribosylation to Promote Establishment and Maintenance of the Legionella Replication Vacuole. RESEARCH SQUARE 2023:rs.3.rs-3269310. [PMID: 37790456 PMCID: PMC10543313 DOI: 10.21203/rs.3.rs-3269310/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Legionella pneumophilaSde family of translocated proteins promote host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity was tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, caused an absolute block in binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb resulted in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decayed quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
Collapse
|
9
|
Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
Collapse
Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| |
Collapse
|
10
|
Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Słabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thomä NH, Ebert BL. UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability. Mol Cell 2023; 83:2753-2767.e10. [PMID: 37478846 PMCID: PMC11134608 DOI: 10.1016/j.molcel.2023.06.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.
Collapse
Affiliation(s)
- Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yen-Der Li
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jared Brown
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brittany Sandoval
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Justine C Rutter
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pius Galli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
| | - Colby R Sandate
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jevon A Cutler
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charles Zou
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Paul M C Park
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan Sievers
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlie Hatton
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Ener
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Brandon D Regalado
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Micah T Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeonghyeon Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Zon
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zinan Zhang
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter G Miller
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Roger Belizaire
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam S Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rafael Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott A Armstrong
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Benjamin L Ebert
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
| |
Collapse
|
11
|
Nawarathnage S, Tseng YJ, Soleimani S, Smith T, Romo MJP, Abiodun WO, Egbert CM, Madhusanka D, Bunn D, Woods B, Tsubaki E, Stewart C, Brown S, Doukov T, Andersen JL, Moody JD. Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544429. [PMID: 37398013 PMCID: PMC10312729 DOI: 10.1101/2023.06.14.544429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
Collapse
Affiliation(s)
- Supeshala Nawarathnage
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Yi Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Maria J Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Wisdom Oshireku Abiodun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Christina M. Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Deshan Madhusanka
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Derick Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Bridger Woods
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Evan Tsubaki
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, California, United States of America
| | - Joshua L. Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - James D. Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| |
Collapse
|
12
|
Wang F, He Q, Zhan W, Yu Z, Finkin-Groner E, Ma X, Lin G, Li H. Structure of the human UBR5 E3 ubiquitin ligase. Structure 2023; 31:541-552.e4. [PMID: 37040767 PMCID: PMC10403316 DOI: 10.1016/j.str.2023.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
The human UBR5 is a single polypeptide chain homology to E6AP C terminus (HECT)-type E3 ubiquitin ligase essential for embryonic development in mammals. Dysregulated UBR5 functions like an oncoprotein to promote cancer growth and metastasis. Here, we report that UBR5 assembles into a dimer and a tetramer. Our cryoelectron microscopy (cryo-EM) structures reveal that two crescent-shaped UBR5 monomers assemble head to tail to form the dimer, and two dimers bind face to face to form the cage-like tetramer with all four catalytic HECT domains facing the central cavity. Importantly, the N-terminal region of one subunit and the HECT of the other form an "intermolecular jaw" in the dimer. We show the jaw-lining residues are important for function, suggesting that the intermolecular jaw functions to recruit ubiquitin-loaded E2 to UBR5. Further work is needed to understand how oligomerization regulates UBR5 ligase activity. This work provides a framework for structure-based anticancer drug development and contributes to a growing appreciation of E3 ligase diversity.
Collapse
Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Ziqi Yu
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Efrat Finkin-Groner
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th Street, New York, NY 10021, USA
| | - Xiaojing Ma
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
| |
Collapse
|
13
|
Sap KA, Geijtenbeek KW, Schipper-Krom S, Guler AT, Reits EA. Ubiquitin-modifying enzymes in Huntington's disease. Front Mol Biosci 2023; 10:1107323. [PMID: 36926679 PMCID: PMC10013475 DOI: 10.3389/fmolb.2023.1107323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the N-terminus of the HTT gene. The CAG repeat expansion translates into a polyglutamine expansion in the mutant HTT (mHTT) protein, resulting in intracellular aggregation and neurotoxicity. Lowering the mHTT protein by reducing synthesis or improving degradation would delay or prevent the onset of HD, and the ubiquitin-proteasome system (UPS) could be an important pathway to clear the mHTT proteins prior to aggregation. The UPS is not impaired in HD, and proteasomes can degrade mHTT entirely when HTT is targeted for degradation. However, the mHTT protein is differently ubiquitinated when compared to wild-type HTT (wtHTT), suggesting that the polyQ expansion affects interaction with (de) ubiquitinating enzymes and subsequent targeting for degradation. The soluble mHTT protein is associated with several ubiquitin-modifying enzymes, and various ubiquitin-modifying enzymes have been identified that are linked to Huntington's disease, either by improving mHTT turnover or affecting overall homeostasis. Here we describe their potential mechanism of action toward improved mHTT targeting towards the proteostasis machinery.
Collapse
Affiliation(s)
- Karen A Sap
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Karlijne W Geijtenbeek
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Arzu Tugce Guler
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric A Reits
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
14
|
Mikhalev A, Nottoli M, Stamm B. Linearly scaling computation of ddPCM solvation energy and forces using the fast multipole method. J Chem Phys 2022; 157:114103. [PMID: 36137796 DOI: 10.1063/5.0104536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This paper proposes the first linear scaling implementation for the domain decomposition approach of the polarizable continuum model (ddPCM) for the computation of the solvation energy and forces. The ddPCM-equation consists of a (non-local) integral equation on the van der Waals or solvent accessible surface of the solute's cavity resulting in a dense solution matrix, and, in turn, one matrix-vector multiplication has a quadratic arithmetic complexity with respect to the number of atoms of the solute molecule. The use of spherical harmonics as basis functions makes it natural to employ the fast multipole method (FMM) in order to provide an asymptotically linear scaling method. In this paper, we employ the FMM in a non-uniform manner with a clusterization based on a recursive inertial bisection. We present some numerical tests illustrating the accuracy and scaling of our implementation.
Collapse
Affiliation(s)
- A Mikhalev
- Department of Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - M Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - B Stamm
- Institute of Applied Analysis and Numerical Simulations, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| |
Collapse
|
15
|
Huang Y, Wan Z, Tang Y, Xu J, Laboret B, Nallamothu S, Yang C, Liu B, Lu RO, Lu B, Feng J, Cao J, Hayflick S, Wu Z, Zhou B. Pantothenate kinase 2 interacts with PINK1 to regulate mitochondrial quality control via acetyl-CoA metabolism. Nat Commun 2022; 13:2412. [PMID: 35504872 PMCID: PMC9065001 DOI: 10.1038/s41467-022-30178-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/20/2022] [Indexed: 12/26/2022] Open
Abstract
Human neurodegenerative disorders often exhibit similar pathologies, suggesting a shared aetiology. Key pathological features of Parkinson's disease (PD) are also observed in other neurodegenerative diseases. Pantothenate Kinase-Associated Neurodegeneration (PKAN) is caused by mutations in the human PANK2 gene, which catalyzes the initial step of de novo CoA synthesis. Here, we show that fumble (fbl), the human PANK2 homolog in Drosophila, interacts with PINK1 genetically. fbl and PINK1 mutants display similar mitochondrial abnormalities, and overexpression of mitochondrial Fbl rescues PINK1 loss-of-function (LOF) defects. Dietary vitamin B5 derivatives effectively rescue CoA/acetyl-CoA levels and mitochondrial function, reversing the PINK1 deficiency phenotype. Mechanistically, Fbl regulates Ref(2)P (p62/SQSTM1 homolog) by acetylation to promote mitophagy, whereas PINK1 regulates fbl translation by anchoring mRNA molecules to the outer mitochondrial membrane. In conclusion, Fbl (or PANK2) acts downstream of PINK1, regulating CoA/acetyl-CoA metabolism to promote mitophagy, uncovering a potential therapeutic intervention strategy in PD treatment.
Collapse
Affiliation(s)
- Yunpeng Huang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Zhihui Wan
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Department of Laboratory Medicine, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, 100026, China
| | - Yinglu Tang
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Junxuan Xu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bretton Laboret
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Sree Nallamothu
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Chenyu Yang
- Department of Statistical Science, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Boxiang Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rongze Olivia Lu
- Department of Neurosurgery, Dell Medical School, University of Texas Austin, Austin, TX, 78712, USA
- Department of Neurological Surgery, Brain Tumor Center, University of California San Francisco, California, CA, 94143, USA
| | - Bingwei Lu
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Juan Feng
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Jing Cao
- Department of Statistical Science, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Susan Hayflick
- Department of Molecular & Medical Genetics, Oregon Health and Science University, Portland, OR, 97201, USA
| | - Zhihao Wu
- Department of Biological Sciences, Dedman College of Humanities and Sciences, Southern Methodist University, Dallas, TX, 75275, USA.
| | - Bing Zhou
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| |
Collapse
|
16
|
Galimova IA, Dorogova NV, Fedorova SA. Functions of E3 Ubiquitin Ligase Hyd in Drosophila Tissues. Mol Biol 2021. [DOI: 10.1134/s0026893321020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Pluska L, Jarosch E, Zauber H, Kniss A, Waltho A, Bagola K, von Delbrück M, Löhr F, Schulman BA, Selbach M, Dötsch V, Sommer T. The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63-branched ubiquitin chains. EMBO J 2021; 40:e106094. [PMID: 33576509 PMCID: PMC7957398 DOI: 10.15252/embj.2020106094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/23/2022] Open
Abstract
The assembly of a specific polymeric ubiquitin chain on a target protein is a key event in the regulation of numerous cellular processes. Yet, the mechanisms that govern the selective synthesis of particular polyubiquitin signals remain enigmatic. The homologous ubiquitin-conjugating (E2) enzymes Ubc1 (budding yeast) and Ube2K (mammals) exclusively generate polyubiquitin linked through lysine 48 (K48). Uniquely among E2 enzymes, Ubc1 and Ube2K harbor a ubiquitin-binding UBA domain with unknown function. We found that this UBA domain preferentially interacts with ubiquitin chains linked through lysine 63 (K63). Based on structural modeling, in vitro ubiquitination experiments, and NMR studies, we propose that the UBA domain aligns Ubc1 with K63-linked polyubiquitin and facilitates the selective assembly of K48/K63-branched ubiquitin conjugates. Genetic and proteomics experiments link the activity of the UBA domain, and hence the formation of this unusual ubiquitin chain topology, to the maintenance of cellular proteostasis.
Collapse
Affiliation(s)
- Lukas Pluska
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Ernst Jarosch
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Henrik Zauber
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Andreas Kniss
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Anita Waltho
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Katrin Bagola
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | | | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Brenda A Schulman
- Department of Molecular Machines and SignalingMax Planck Institute of BiochemistryMartinsriedGermany
| | - Matthias Selbach
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Charité – Universitätsmedizin BerlinBerlinGermany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - Thomas Sommer
- Max‐Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Institute for BiologyHumboldt‐Universität zu BerlinBerlinGermany
| |
Collapse
|
18
|
Singh S, Ng J, Sivaraman J. Exploring the "Other" subfamily of HECT E3-ligases for therapeutic intervention. Pharmacol Ther 2021; 224:107809. [PMID: 33607149 DOI: 10.1016/j.pharmthera.2021.107809] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/13/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
The HECT E3 ligase family regulates key cellular signaling pathways, with its 28 members divided into three subfamilies: NEDD4 subfamily (9 members), HERC subfamily (6 members) and "Other" subfamily (13 members). Here, we focus on the less-explored "Other" subfamily and discuss the recent findings pertaining to their biological roles. The N-terminal regions preceding the conserved HECT domains are significantly diverse in length and sequence composition, and are mostly unstructured, except for short regions that incorporate known substrate-binding domains. In some of the better-characterized "Other" members (e.g., HUWE1, AREL1 and UBE3C), structure analysis shows that the extended region (~ aa 50) adjacent to the HECT domain affects the stability and activity of the protein. The enzymatic activity is also influenced by interactions with different adaptor proteins and inter/intramolecular interactions. Primarily, the "Other" subfamily members assemble atypical ubiquitin linkages, with some cooperating with E3 ligases from the other subfamilies to form branched ubiquitin chains on substrates. Viruses and pathogenic bacteria target and hijack the activities of "Other" subfamily members to evade host immune responses and cause diseases. As such, these HECT E3 ligases have emerged as potential candidates for therapeutic drug development.
Collapse
Affiliation(s)
- Sunil Singh
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore
| | - Joel Ng
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore.
| |
Collapse
|
19
|
Wang M, Dai W, Ke Z, Li Y. Functional roles of E3 ubiquitin ligases in gastric cancer. Oncol Lett 2020; 20:22. [PMID: 32774495 PMCID: PMC7405480 DOI: 10.3892/ol.2020.11883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
To date, >650 E3 ubiquitin ligases have been described in humans, including >600 really interesting new genes (RINGs), 28 homologous to E6-associated protein C-terminus (HECTs) and several RING-in-between-RINGs. They are considered key regulators and therapeutic targets of many types of human cancers, including gastric cancer (GC). Among them, some RING and HECT E3 ligases are closely related to the proliferation, infiltration and prognosis of GC. During the past few years, abnormal expressions and functions of many E3 ligases have been identified in GC. However, the functional roles of E3 ligases in GC have not been fully elucidated. The present article focuses on the functional roles of E3 ligases related to the proteasome in GC. In this comprehensive review, the latest research progress on E3 ligases involved in GC and elaborate their structure, classification, functional roles and therapeutic value in GC was summarized. Finally, 30 E3 ligases that serve essential roles in regulating the development of GC were described. Some of these ligases may serve as oncogenes or tumor suppressors in GC, whereas the pathological mechanism of others needs further study; for example, constitutive photomorphogenic 1. In conclusion, the present review demonstrated that E3 ligases are crucial tumor regulatory factors and potential therapeutic targets in GC. Therefore, more studies should focus on the therapeutic targeting of E3 ligases in GC.
Collapse
Affiliation(s)
- Mingliang Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Wei Dai
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Zhangyan Ke
- Department of Geriatric Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Yongxiang Li
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| |
Collapse
|
20
|
Shahul Hameed D, van Tilburg GBA, Merkx R, Flierman D, Wienk H, El Oualid F, Hofmann K, Boelens R, Ovaa H. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Front Chem 2020; 7:921. [PMID: 32039147 PMCID: PMC6987245 DOI: 10.3389/fchem.2019.00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination is a process in which a protein is modified by the covalent attachment of the C-terminal carboxylic acid of ubiquitin (Ub) to the ε-amine of lysine or N-terminal methionine residue of a substrate protein or another Ub molecule. Each of the seven internal lysine residues and the N-terminal methionine residue of Ub can be linked to the C-terminus of another Ub moiety to form 8 distinct Ub linkages and the resulting differences in linkage types elicit different Ub signaling pathways. Cellular responses are triggered when proteins containing ubiquitin-binding domains (UBDs) recognize and bind to specific polyUb linkage types. To get more insight into the differences between polyUb chains, all of the seven lysine-linked di-ubiquitin molecules (diUbs) were prepared and used as a model to study their structural conformations in solution using NMR spectroscopy. We report the synthesis of diUb molecules, fully 15N-labeled on the distal (N-terminal) Ub moiety and revealed their structural orientation with respect to the proximal Ub. As expected, the diUb molecules exist in different conformations in solution, with multiple conformations known to exist for K6-, K48-, and K63-linked diUb molecules. These multiple conformations allow structural flexibility in binding with UBDs thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interaction is the recognition of K6 polyubiquitin by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using our synthetic 15N-labeled diUbs, we establish here how a C-terminally extended UBA domain of UBXN1 confers specificity to K6 diUb while the non-extended version of the domain does not show any linkage preference. We show that the two distinct conformations of K6 diUb that exist in solution converge into a single conformation upon binding to this extended form of the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in Ub signaling. The isotopically labeled diUb compounds described here and the use of NMR to study their interactions with relevant partner molecules will help accelerate our understanding of Ub signaling pathways.
Collapse
Affiliation(s)
- Dharjath Shahul Hameed
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Gabrielle B A van Tilburg
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Remco Merkx
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Flierman
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Farid El Oualid
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,UbiQ Bio BV, Amsterdam, Netherlands
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| |
Collapse
|
21
|
Choi J, Busino L. E3 ubiquitin ligases in B-cell malignancies. Cell Immunol 2019; 340:103905. [PMID: 30827673 PMCID: PMC6584052 DOI: 10.1016/j.cellimm.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/05/2018] [Accepted: 02/19/2019] [Indexed: 12/21/2022]
Abstract
Ubiquitylation is a post-translational modification (PTM) that controls various cellular signaling pathways. It is orchestrated by a three-step enzymatic cascade know as the ubiquitin proteasome system (UPS). E3 ligases dictate the specificity to the substrates, primarily leading to proteasome-dependent degradation. Deregulation of the UPS components by various mechanisms contributes to the pathogenesis of cancer. This review focuses on E3 ligase-substrates pairings that are implicated in B-cell malignancies. Understanding the molecular mechanism of specific E3 ubiquitin ligases will present potential opportunities for the development of targeted therapeutic approaches.
Collapse
Affiliation(s)
- Jaewoo Choi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
22
|
Shen Q, Qiu Z, Wu W, Zheng J, Jia Z. Characterization of interaction and ubiquitination of phosphoenolpyruvate carboxykinase by E3 ligase UBR5. Biol Open 2018; 7:bio.037366. [PMID: 30552140 PMCID: PMC6310884 DOI: 10.1242/bio.037366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phosphoenolpyruvate carboxykinase (PEPCK1) is ubiquitinated by E3 ubiquitin ligase UBR5, which was thought to be facilitated by the acetylation of Lys70, Lys71 and Lys594 in PEPCK1. Here, we made a series of UBR5 HECT domain truncation variants and, through pull-down assay, showed that the N-terminal lobe of the UBR5 HECT domain is largely responsible for interacting with PEPCK1. We mutated all three lysine residues thought to be acetylated in PEPCK1 but were surprised to observe no loss of binding to UBR5 HECT domain. Furthermore, two PEPCK1 truncation variants (74-622 aa and 10-560 aa) lacking these lysine residues were still able to bind with UBR5 and ubiquitinated in HEK293T cells. To discover the ubiquitination site(s) of PEPCK1, which is currently unknown, the Lys residues of PEPCK1 were mutated to Ala and the ubiquitination level of the PEPCK1 mutants was assessed. Results revealed at least two ubiquitination sites (Lys243 and Lys342), which represent the first time that ubiquitination sites of PEPCK1 have been identified. Our pull-down experiments further show that the lack of ubiquitination of PEPCK1 Lys243Ala and Lys342Ala mutants is not due to their binding to UBR5, which remained unchanged. Taken together, our work has provided new insights into UBR5 mediated ubiquitination of PEPCK1. Summary: Identification of the recruit function of the N-terminal lobe of the UBR5 HECT domain and ubiquitination site(s) of PEPCK1.
Collapse
Affiliation(s)
- Qingya Shen
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhiyu Qiu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wenping Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zongchao Jia
- Department of Biochemical and Molecular Sciences, Queen's University, Kingston, Ontario, K7L 3N6, Canada
| |
Collapse
|
23
|
Shearer RF, Frikstad KAM, McKenna J, McCloy RA, Deng N, Burgess A, Stokke T, Patzke S, Saunders DN. The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia. Mol Biol Cell 2018; 29:1542-1554. [PMID: 29742019 PMCID: PMC6080653 DOI: 10.1091/mbc.e17-04-0248] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Primary cilia are crucial for signal transduction in a variety of pathways, including hedgehog and Wnt. Disruption of primary cilia formation (ciliogenesis) is linked to numerous developmental disorders (known as ciliopathies) and diseases, including cancer. The ubiquitin-proteasome system (UPS) component UBR5 was previously identified as a putative positive regulator of ciliogenesis in a functional genomics screen. UBR5 is an E3 ubiquitin ligase that is frequently deregulated in tumors, but its biological role in cancer is largely uncharacterized, partly due to a lack of understanding of interacting proteins and pathways. We validated the effect of UBR5 depletion on primary cilia formation using a robust model of ciliogenesis, and identified CSPP1, a centrosomal and ciliary protein required for cilia formation, as a UBR5-interacting protein. We show that UBR5 ubiquitylates CSPP1, and that UBR5 is required for cytoplasmic organization of CSPP1-comprising centriolar satellites in centrosomal periphery, suggesting that UBR5-mediated ubiquitylation of CSPP1 or associated centriolar satellite constituents is one underlying requirement for cilia expression. Hence, we have established a key role for UBR5 in ciliogenesis that may have important implications in understanding cancer pathophysiology.
Collapse
Affiliation(s)
- Robert F Shearer
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Kari-Anne Myrum Frikstad
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - Jessie McKenna
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Rachael A McCloy
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia
| | - Niantao Deng
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia
| | - Andrew Burgess
- Garvan Institute of Medical Research, Kinghorn Cancer Centre, Darlinghurst 2010, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia
| | - Trond Stokke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - Sebastian Patzke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0310 Oslo, Norway
| | - Darren N Saunders
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| |
Collapse
|
24
|
Du J, Strieter ER. A fluorescence polarization-based competition assay for measuring interactions between unlabeled ubiquitin chains and UCH37•RPN13. Anal Biochem 2018; 550:84-89. [PMID: 29698671 DOI: 10.1016/j.ab.2018.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/18/2018] [Indexed: 01/19/2023]
Abstract
Ubiquitin chains regulate distinct signaling events through cooperative interactions with effector proteins and deubiquitinases. Measuring the strength of these interactions is often challenging; either large amounts of material are required or one of the binding partners must be labeled for detection. We sought to develop a label-free method for measuring binding of ubiquitin chains to the proteasome-associated deubiquitinase UCH37 and its binding partner RPN13. The method we describe here is based on a fluorescence polarization competition (FPcomp) assay in which fluorescent monoubiquitin is competed off the UCH37•RPN13 complex by the addition of unlabeled ubiquitin chains. We show that the UCH37•RPN13 complex displays higher affinity toward chains with more than two ubiquitin subunits. Removing the ubiquitin-binding PRU domain of RPN13 does not change affinities. These results suggest UCH37•RPN13 acts to selectively recruit proteins modified with long chains (>2 subunits) to the proteasome for degradation. We also demonstrate that the FPcomp assay is suitable for high-throughput screening, which is important considering both UCH37 and RPN13 are potential targets for cancer therapy.
Collapse
Affiliation(s)
- Jiale Du
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
| |
Collapse
|
25
|
Lorenz S. Structural mechanisms of HECT-type ubiquitin ligases. Biol Chem 2018; 399:127-145. [PMID: 29016349 DOI: 10.1515/hsz-2017-0184] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022]
Abstract
Ubiquitin ligases (E3 enzymes) transfer ubiquitin from ubiquitin-conjugating (E2) enzymes to target proteins. By determining the selection of target proteins, modification sites on those target proteins, and the types of ubiquitin modifications that are formed, E3 enzymes are key specificity factors in ubiquitin signaling. Here, I summarize our knowledge of the structural mechanisms in the HECT E3 subfamily, many members of which play important roles in human disease. I discuss interactions of the conserved HECT domain with E2 enzymes, ubiquitin and target proteins, as well as macromolecular interactions with regulatory functions. While we understand individual steps in the catalytic cycle of HECT E3 enzymes on a structural level, this review also highlights key aspects that have yet to be elucidated. For instance, it remains unclear how diverse target proteins are presented to the catalytic center and how certain HECT E3 enzymes achieve specificity in ubiquitin linkage formation. The structural and functional properties of the N-terminal regions of HECT E3 enzymes that likely act as signaling hubs are also largely unknown. Structural insights into these aspects may open up routes for a therapeutic intervention with specific HECT E3 functions in distinct pathophysiological settings.
Collapse
Affiliation(s)
- Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| |
Collapse
|
26
|
K63 ubiquitylation triggers proteasomal degradation by seeding branched ubiquitin chains. Proc Natl Acad Sci U S A 2018; 115:E1401-E1408. [PMID: 29378950 DOI: 10.1073/pnas.1716673115] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Different polyubiquitin chain linkages direct substrates toward distinct cellular pathways. K63-linked ubiquitylation is known to regulate proteasome-independent events such as signal transduction, but its function in the context of heterogeneous ubiquitin chains remains unclear. Here, we report that K63 ubiquitylation plays a critical role in proteasome-mediated substrate degradation by serving as a "seed" for K48/K63 branched ubiquitin chains. Quantitative analysis revealed that K48/K63 branched linkages preferentially associate with proteasomes in cells. We found that ITCH-dependent K63 ubiquitylation of the proapoptotic regulator TXNIP triggered subsequent assembly of K48/K63 branched chains by recruiting ubiquitin-interacting ligases such as UBR5, leading to TXNIP degradation. These results reveal a role for K63 chains as a substrate-specific mark for proteasomal degradation involved in regulating cell fate. Our findings provide insight into how cellular interpretation of the ubiquitin code is altered by combinations of ubiquitin linkages.
Collapse
|
27
|
|
28
|
Kinsella E, Dora N, Mellis D, Lettice L, Deveney P, Hill R, Ditzel M. Use of a Conditional Ubr5 Mutant Allele to Investigate the Role of an N-End Rule Ubiquitin-Protein Ligase in Hedgehog Signalling and Embryonic Limb Development. PLoS One 2016; 11:e0157079. [PMID: 27299863 PMCID: PMC4907512 DOI: 10.1371/journal.pone.0157079] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 05/24/2016] [Indexed: 01/16/2023] Open
Abstract
Hedgehog (Hh) signalling is a potent regulator of cell fate and function. While much is known about the events within a Hh-stimulated cell, far less is known about the regulation of Hh-ligand production. Drosophila Hyperplastic Discs (Hyd), a ubiquitin-protein ligase, represents one of the few non-transcription factors that independently regulates both hh mRNA expression and pathway activity. Using a murine embryonic stem cell system, we revealed that shRNAi of the mammalian homologue of hyd, Ubr5, effectively prevented retinoic-acid-induced Sonic hedgehog (Shh) expression. We next investigated the UBR5:Hh signalling relationship in vivo by generating and validating a mouse bearing a conditional Ubr5 loss-of-function allele. Conditionally deleting Ubr5 in the early embryonic limb-bud mesenchyme resulted in a transient decrease in Indian hedgehog ligand expression and decreased Hh pathway activity, around E13.5. Although Ubr5-deficient limbs and digits were, on average, shorter than control limbs, the effects were not statistically significant. Hence, while loss of UBR5 perturbed Hedgehog signalling in the developing limb, there were no obvious morphological defects. In summary, we report the first conditional Ubr5 mutant mouse and provide evidence for a role for UBR5 in influencing Hh signalling, but are uncertain to whether the effects on Hedgehog signaling were direct (cell autonomous) or indirect (non-cell-autonomous). Elaboration of the cellular/molecular mechanism(s) involved may help our understanding on diseases and developmental disorders associated with aberrant Hh signalling.
Collapse
Affiliation(s)
- Elaine Kinsella
- Edinburgh CRUK Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Natalie Dora
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - David Mellis
- Edinburgh CRUK Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Laura Lettice
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Paul Deveney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Robert Hill
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Mark Ditzel
- Edinburgh CRUK Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| |
Collapse
|
29
|
Shearer RF, Iconomou M, Watts CKW, Saunders DN. Functional Roles of the E3 Ubiquitin Ligase UBR5 in Cancer. Mol Cancer Res 2015; 13:1523-32. [PMID: 26464214 DOI: 10.1158/1541-7786.mcr-15-0383] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
Abstract
The Ubiquitin-Proteasome System (UPS) is an important regulator of cell signaling and proteostasis, which are essential to a variety of cellular processes. The UPS is disrupted in many diseases including cancer, and targeting the UPS for cancer therapy is gaining wide interest. E3 ubiquitin ligases occupy a key position in the hierarchical UPS enzymatic cascade, largely responsible for determining substrate specificity and ubiquitin (Ub) chain topology. The E3 ligase UBR5 (aka EDD1) is emerging as a key regulator of the UPS in cancer and development. UBR5 expression is deregulated in many cancer types and UBR5 is frequently mutated in mantle cell lymphoma. UBR5 is highly conserved in metazoans, has unique structural features, and has been implicated in regulation of DNA damage response, metabolism, transcription, and apoptosis. Hence, UBR5 is a key regulator of cell signaling relevant to broad areas of cancer biology. However, the mechanism by which UBR5 may contribute to tumor initiation and progression remains poorly defined. This review synthesizes emerging insights from genetics, biochemistry, and cell biology to inform our understanding of UBR5 in cancer. These molecular insights indicate a role for UBR5 in integrating/coordinating various cellular signaling pathways. Finally, we discuss outstanding questions in UBR5 biology and highlight the need to systematically characterize substrates, and address limitations in current animal models, to better define the role of UBR5 in cancer.
Collapse
Affiliation(s)
- Robert F Shearer
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Mary Iconomou
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Colin K W Watts
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Darren N Saunders
- Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, Australia. School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia.
| |
Collapse
|
30
|
Moncrieff S, Moncan M, Scialpi F, Ditzel M. Regulation of hedgehog Ligand Expression by the N-End Rule Ubiquitin-Protein Ligase Hyperplastic Discs and the Drosophila GSK3β Homologue, Shaggy. PLoS One 2015; 10:e0136760. [PMID: 26334301 PMCID: PMC4559392 DOI: 10.1371/journal.pone.0136760] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/07/2015] [Indexed: 12/11/2022] Open
Abstract
Hedgehog (Hh) morphogen signalling plays an essential role in tissue development and homeostasis. While much is known about the Hh signal transduction pathway, far less is known about the molecules that regulate the expression of the hedgehog (hh) ligand itself. Here we reveal that Shaggy (Sgg), the Drosophila melanogaster orthologue of GSK3β, and the N-end Rule Ubiquitin-protein ligase Hyperplastic Discs (Hyd) act together to co-ordinate Hedgehog signalling through regulating hh ligand expression and Cubitus interruptus (Ci) expression. Increased hh and Ci expression within hyd mutant clones was effectively suppressed by sgg RNAi, placing sgg downstream of hyd. Functionally, sgg RNAi also rescued the adult hyd mutant head phenotype. Consistent with the genetic interactions, we found Hyd to physically interact with Sgg and Ci. Taken together we propose that Hyd and Sgg function to co-ordinate hh ligand and Ci expression, which in turn influences important developmental signalling pathways during imaginal disc development. These findings are important as tight temporal/spatial regulation of hh ligand expression underlies its important roles in animal development and tissue homeostasis. When deregulated, hh ligand family misexpression underlies numerous human diseases (e.g., colorectal, lung, pancreatic and haematological cancers) and developmental defects (e.g., cyclopia and polydactyly). In summary, our Drosophila-based findings highlight an apical role for Hyd and Sgg in initiating Hedgehog signalling, which could also be evolutionarily conserved in mammals.
Collapse
Affiliation(s)
- Sophie Moncrieff
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Matthieu Moncan
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Flavia Scialpi
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
| | - Mark Ditzel
- MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Edinburgh CRUK Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom
- * E-mail:
| |
Collapse
|
31
|
Muñoz-Escobar J, Matta-Camacho E, Kozlov G, Gehring K. The MLLE domain of the ubiquitin ligase UBR5 binds to its catalytic domain to regulate substrate binding. J Biol Chem 2015. [PMID: 26224628 DOI: 10.1074/jbc.m115.672246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
E3 ubiquitin ligases catalyze the transfer of ubiquitin from an E2-conjugating enzyme to a substrate. UBR5, homologous to the E6AP C terminus (HECT)-type E3 ligase, mediates the ubiquitination of proteins involved in translation regulation, DNA damage response, and gluconeogenesis. In addition, UBR5 functions in a ligase-independent manner by prompting protein/protein interactions without ubiquitination of the binding partner. Despite recent functional studies, the mechanisms involved in substrate recognition and selective ubiquitination of its binding partners remain elusive. The C terminus of UBR5 harbors the HECT catalytic domain and an adjacent MLLE domain. MLLE domains mediate protein/protein interactions through the binding of a conserved peptide motif, termed PAM2. Here, we characterize the binding properties of the UBR5 MLLE domain to PAM2 peptides from Paip1 and GW182. The crystal structure with a Paip1 PAM2 peptide reveals the network of hydrophobic and ionic interactions that drive binding. In addition, we identify a novel interaction of the MLLE domain with the adjacent HECT domain mediated by a PAM2-like sequence. Our results confirm the role of the MLLE domain of UBR5 in substrate recruitment and suggest a potential role in regulating UBR5 ligase activity.
Collapse
Affiliation(s)
- Juliana Muñoz-Escobar
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Edna Matta-Camacho
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Guennadi Kozlov
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Kalle Gehring
- From the Department of Biochemistry, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G 0B1, Canada
| |
Collapse
|
32
|
McDonald WJ, Thomas LN, Koirala S, Too CKL. Progestin-inducible EDD E3 ubiquitin ligase binds to α4 phosphoprotein to regulate ubiquitination and degradation of protein phosphatase PP2Ac. Mol Cell Endocrinol 2014; 382:254-261. [PMID: 24145130 DOI: 10.1016/j.mce.2013.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/20/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
Abstract
Mammalian α4 phosphoprotein binds to the protein phosphatase 2A catalytic subunit (PP2Ac) to regulate PP2A activity, and to poly(A)-binding protein (PABP) and progestin-inducible EDD E3 ubiquitin ligase. This study showed induction of the EDD protein by progesterone, 17β-estradiol and prolactin in breast cancer cells. Co-immunoprecipitation analyses, using lysates of COS-1 cells transfected with α4-deletion constructs, showed the α4 N-terminus binding to endogenous PP2Ac and PABP, and the C-terminus to EDD. Monoubiquitinated α4 in MCF-7 cells was unaffected by EDD-targeting siRNA (siEDD) nor by non-targetting siNT, thus, EDD does not ubiquitinate α4. PP2Ac is polyubiquitinated, and 36-kDa PP2Ac only was detected in siEDD- or siNT-transfected cells. However, treatment with proteasomal inhibitor MG132 showed polyubiquitinated-PP2Ac molecules (∼65-250kDa) abundantly in siNT controls but low in siEDD-transfectants, implicating PP2Ac as an EDD substrate. Finally, progesterone induction of EDD in MCF-7 cells correlated with decreased PP2Ac levels, further implicating hormone-inducible EDD in PP2Ac turnover.
Collapse
Affiliation(s)
- William J McDonald
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Lynn N Thomas
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Samir Koirala
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Catherine K L Too
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Obstetrics & Gynaecology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| |
Collapse
|
33
|
Bouvier B. Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations. Phys Chem Chem Phys 2014; 16:48-60. [DOI: 10.1039/c3cp52436a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
34
|
A functional genomic approach reveals the transcriptional role of EDD in the expression and function of angiogenesis regulator ACVRL1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1309-19. [PMID: 24189493 DOI: 10.1016/j.bbagrm.2013.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 10/18/2013] [Accepted: 10/28/2013] [Indexed: 11/22/2022]
Abstract
EDD (E3 isolated by differential display) was initially isolated as a progestin-regulated gene in breast cancer cells, and represents the human ortholog of the Drosophila melanogaster hyperplastic discs gene (hyd). It encodes a highly conserved and predominantly nuclear ubiquitin E3 ligase of the HECT family, with potential multifunctional roles in development and tumorigenesis. In this study, we further examined the largely uncharacterized role of EDD in transcriptional regulation by uncovering the spectrum of its direct target genes at a genome-wide level. Use of a systematic approach that integrates gene expression and chromatin binding profiling identified several candidate EDD-target genes, one of which is ACVRL1, a TGF-β receptor with functional implications in blood vessel development. Further characterization revealed a negative regulation of ACVRL1 gene expression by EDD that is exerted at the promoter. Consistent with the aberrant upregulation of ACVRL1 and downstream Smad signaling, abrogation of EDD led to deregulated vessel development and endothelial cell motility. Collectively, these results extended the known cellular roles of EDD to critical functions in transcriptional regulation as well as angiogenesis, and may provide mechanistic explanations for EDD's tumorigenic and developmental roles.
Collapse
|
35
|
Jung H, Kim BG, Han WH, Lee JH, Cho JY, Park WS, Maurice MM, Han JK, Lee MJ, Finley D, Jho EH. Deubiquitination of Dishevelled by Usp14 is required for Wnt signaling. Oncogenesis 2013; 2:e64. [PMID: 23958854 PMCID: PMC3759127 DOI: 10.1038/oncsis.2013.28] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 07/13/2013] [Indexed: 12/14/2022] Open
Abstract
Dishevelled (Dvl) is a key regulator of Wnt signaling both in the canonical and non-canonical pathways. Here we report the identification of a regulatory domain of ubiquitination (RDU) in the C-terminus of Dvl. Mutations in the RDU resulted in accumulation of polyubiquitinated forms of Dvl, which were mainly K63 linked. Small interfering RNA-based screening identified Usp14 as a mediator of Dvl deubiquitination. Genetic and chemical suppression of Usp14 activity caused an increase in Dvl polyubiquitination and significantly impaired downstream Wnt signaling. These data suggest that Usp14 functions as a positive regulator of the Wnt signaling pathway. Consistently, tissue microarray analysis of colon cancer revealed a strong correlation between the levels of Usp14 and β-catenin, which suggests an oncogenic role for Usp14 via enhancement of Wnt/β-catenin signaling.
Collapse
Affiliation(s)
- H Jung
- Department of Life Science, The University of Seoul, Seoul, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Matta-Camacho E, Kozlov G, Menade M, Gehring K. Structure of the HECT C-lobe of the UBR5 E3 ubiquitin ligase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1158-63. [PMID: 23027739 PMCID: PMC3497971 DOI: 10.1107/s1744309112036937] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/27/2012] [Indexed: 01/12/2023]
Abstract
UBR5 ubiquitin ligase (also known as EDD, Rat100 or hHYD) is a member of the E3 protein family of HECT (homologous to E6-AP C-terminus) ligases as it contains a C-terminal HECT domain. In ubiquitination cascades involving E3s of the HECT class, ubiquitin is transferred from an associated E2 ubiquitin-conjugating enzyme to the acceptor cysteine of the HECT domain, which consists of structurally distinct N- and C-lobes connected by a flexible linker. Here, the high-resolution crystal structure of the C-lobe of the HECT domain of human UBR5 is presented. The structure reveals important features that are unique compared with other HECT domains. In particular, a distinct four-residue insert in the second helix elongates this helix, resulting in a strikingly different orientation of the preceding loop. This protruding loop is likely to contribute to specificity towards the E2 ubiquitin-conjugating enzyme UBCH4, which is an important functional partner of UBR5. Ubiquitination assays showed that the C-lobe of UBR5 is able to form a thioester-linked E3-ubiquitin complex, although it does not physically interact with UBCH4 in NMR experiments. This study contributes to a better understanding of UBR5 ubiquitination activity.
Collapse
Affiliation(s)
- Edna Matta-Camacho
- Groupe de Recherche axé sur la Structure des Protéines, Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Guennadi Kozlov
- Groupe de Recherche axé sur la Structure des Protéines, Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Marie Menade
- Groupe de Recherche axé sur la Structure des Protéines, Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Kalle Gehring
- Groupe de Recherche axé sur la Structure des Protéines, Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| |
Collapse
|
37
|
Odagiri S, Tanji K, Mori F, Kakita A, Takahashi H, Kamitani T, Wakabayashi K. Immunohistochemical analysis of Marinesco bodies, using antibodies against proteins implicated in the ubiquitin-proteasome system, autophagy and aggresome formation. Neuropathology 2011; 32:261-6. [PMID: 22118216 DOI: 10.1111/j.1440-1789.2011.01267.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Marinesco bodies (MBs) are spherical eosinophilic intranuclear inclusions in pigmented neurons in the substantia nigra and locus ceruleus. Previous immunohistochemical studies have shown that MBs are positive for ubiquitin, p62 and SUMO-1, suggesting the involvement of ubiquitination and related proteins in the formation or disaggregation of MBs. However, the involvement is not thoroughly understood. Therefore, we immunohistochemically examined the midbrain from five control subjects ranged from 53 to 84 years old. MBs were positive for various proteins implicated in the ubiquitin-proteasome system (ubiquitin, p62, EDD1, NEDD8, NUB1, SUMO-1 and SUMO-2), aggresome formation (HDAC6) and autophagy (ubiquitin, p62, LC3, GABARAP and GATE-16). These findings suggest that proteins related to ubiquitination, proteasomal degradation and autophagy are involved in the formation or disaggregation of MBs.
Collapse
Affiliation(s)
- Saori Odagiri
- Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan.
| | | | | | | | | | | | | |
Collapse
|
38
|
Su H, Meng S, Lu Y, Trombly MI, Chen J, Lin C, Turk A, Wang X. Mammalian hyperplastic discs homolog EDD regulates miRNA-mediated gene silencing. Mol Cell 2011; 43:97-109. [PMID: 21726813 DOI: 10.1016/j.molcel.2011.06.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 03/16/2011] [Accepted: 06/10/2011] [Indexed: 01/10/2023]
Abstract
MicroRNAs (miRNAs) regulate gene expression through translation repression and mRNA destabilization. However, the molecular mechanisms of miRNA silencing are still not well defined. Using a genetic screen in mouse embryonic stem (ES) cells, we identify mammalian hyperplastic discs protein EDD, a known E3 ubiquitin ligase, as a key component of the miRNA silencing pathway. ES cells deficient for EDD are defective in miRNA function and exhibit growth defects. We demonstrate that E3 ubiquitin ligase activity is dispensable for EDD function in miRNA silencing. Instead, EDD interacts with GW182 family proteins in the Argonaute-miRNA complexes. The PABC domain of EDD is essential for its silencing function. Through the PABC domain, EDD participates in miRNA silencing by recruiting downstream effectors. Among the PABC-interactors, DDX6 and Tob1/2 are both required and sufficient for silencing mRNA targets. Taken together, these data demonstrate a critical function for EDD in miRNA silencing.
Collapse
Affiliation(s)
- Hong Su
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Jahr N, Fiedler E, Günther R, Hofmann HJ, Berger S. NH exchange in point mutants of human ubiquitin. Int J Biol Macromol 2011; 49:154-60. [DOI: 10.1016/j.ijbiomac.2011.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 04/12/2011] [Accepted: 04/13/2011] [Indexed: 11/16/2022]
|
40
|
Garner TP, Long J, Layfield R, Searle MS. Impact of p62/SQSTM1 UBA domain mutations linked to Paget's disease of bone on ubiquitin recognition. Biochemistry 2011; 50:4665-74. [PMID: 21517082 DOI: 10.1021/bi200079n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The scaffold protein p62/SQSTM1 acts as a hub in regulating a diverse range of signaling pathways which are dependent upon a functional ubiquitin-binding C-terminal UBA domain. Mutations linked to Paget's disease of bone (PDB) commonly cluster within the UBA domain. The p62 UBA domain is unique in forming a highly stable dimer which regulates ubiquitin recognition by using overlapping surface patches in both dimerization and ubiquitin binding, making the two association events competitive. NMR structural analysis and biophysical methods show that some PDB mutations modulated the ubiquitin binding affinity by both direct and indirect mechanisms that affect UBA structural integrity, dimer stability, and contacts at the UBA-ubiquitin interface. In other cases, common PDB mutations (P392L in particular) result in no significant change in ubiquitin binding affinity for the UBA domain in isolation; however, all PDB UBA mutations lead to loss of function with respect to ubiquitin binding in the context of full-length p62, suggesting a more complex underlying mechanism.
Collapse
Affiliation(s)
- Thomas P Garner
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham, U.K
| | | | | | | |
Collapse
|
41
|
Ai Y, Wang J, Johnson RE, Haracska L, Prakash L, Zhuang Z. A novel ubiquitin binding mode in the S. cerevisiae translesion synthesis DNA polymerase η. MOLECULAR BIOSYSTEMS 2011; 7:1874-82. [PMID: 21483899 DOI: 10.1039/c0mb00355g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ubiquitin binding zinc finger (UBZ) domain in the C-terminal portion of Polη has been found to interact with ubiquitin. However, the affinity between the Polη UBZ and ubiquitin was shown to be low with a previously reported K(d) of 73-81 μM. This low-affinity binding between Polη UBZ and ubiquitin has been difficult to reconcile with its presumed role in translesion synthesis as suggested by genetic and cell biology studies. In this work, we constructed a minimal S. cerevisiae Polη UBZ domain and probed the Polη UBZ-ubiquitin interaction using a surface plasmon resonance (SPR) technique. Our quantitative binding data between the wild-type or mutant Polη UBZ and ubiquitin revealed an interesting divergence between the Polη UBZ from S. cerevisiae and humans. Moreover, we found that the C-terminal portion of yeast Polη (amino acid 515-632) binds ubiquitin with a much higher affinity than the minimal UBZ domain. Further, distinct ubiquitin-binding kinetics were observed for the C-terminal portion of Polη and the isolated UBZ domain. This observation raised the interesting possibility that the Polη C-terminal portion binds ubiquitin in a novel mode that affords higher affinity. Our findings have broader implication in understanding the generally weak interaction between the known ubiquitin-binding domains and ubiquitin.
Collapse
Affiliation(s)
- Yongxing Ai
- Department of Chemistry and Biochemistry, 214A Drake Hall, University of Delaware, Newark, DE 19716, USA
| | | | | | | | | | | |
Collapse
|
42
|
Huang KY, Amodeo GA, Tong L, McDermott A. The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch. Protein Sci 2011; 20:630-9. [PMID: 21432937 PMCID: PMC3064841 DOI: 10.1002/pro.584] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new crystal structure of human ubiquitin is reported at 1.8 Å resolution. Compared with the other known crystal structure or the solution NMR structure of monomeric human ubiquitin, this new structure is similar in its overall fold but differs with respect to the conformation of the backbone in a surface-exposed region. The conformation reported here resembles conformations previously seen in complex with deubiquinating enzymes, wherein the Asp52/Gly53 main chain and Glu24 side chain move. This movement exposes the backbone carbonyl of Asp52 to the exterior of the molecule, making it possible to engage in hydrogen-bond contacts with neighboring molecules, rather than in an internal hydrogen bond with the backbone of Glu24. This particular crystal form of ubiquitin has been used in a large number of solid state NMR studies. The structure described here elucidates the origin of many of the chemical shift differences comparing solution and solid state studies.
Collapse
Affiliation(s)
- Kuo Ying Huang
- Department of Chemistry, Columbia UniversityNew York, New York 10027
| | - Gabriele A Amodeo
- Department of Biological Science, Columbia UniversityNew York, New York 10027
| | - Liang Tong
- Department of Biological Science, Columbia UniversityNew York, New York 10027
| | - Ann McDermott
- Department of Chemistry, Columbia UniversityNew York, New York 10027,*Correspondence to: Ann McDermott, Columbia University, Department of Chemistry, MC3113, New York, NY 10027. E-mail:
| |
Collapse
|
43
|
The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet 2010; 6:e1001182. [PMID: 21060858 PMCID: PMC2965745 DOI: 10.1371/journal.pgen.1001182] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2010] [Accepted: 09/28/2010] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive sequences, including transposons and retroviruses. This silencing is stable between cell generations as cytosine methylation is maintained epigenetically through DNA replication. The Arabidopsis thaliana Dnmt3 cytosine methyltransferase ortholog DOMAINS rearranged methyltransferase2 (DRM2) is required for establishment of small interfering RNA (siRNA) directed DNA methylation. In mammals PIWI proteins and piRNA act in a convergently evolved RNA-directed DNA methylation system that is required to repress transposon expression in the germ line. De novo methylation may also be independent of RNA interference and small RNAs, as in Neurospora crassa. Here we identify a clade of catalytically mutated DRM2 paralogs in flowering plant genomes, which in A.thaliana we term domains rearranged methyltransferase3 (DRM3). Despite being catalytically mutated, DRM3 is required for normal maintenance of non-CG DNA methylation, establishment of RNA-directed DNA methylation triggered by repeat sequences and accumulation of repeat-associated small RNAs. Although the mammalian catalytically inactive Dnmt3L paralogs act in an analogous manner, phylogenetic analysis indicates that the DRM and Dnmt3 protein families diverged independently in plants and animals. We also show by site-directed mutagenesis that both the DRM2 N-terminal UBA domains and C-terminal methyltransferase domain are required for normal RNA-directed DNA methylation, supporting an essential targeting function for the UBA domains. These results suggest that plant and mammalian RNA-directed DNA methylation systems consist of a combination of ancestral and convergent features.
Collapse
|
44
|
Ko S, Kang GB, Song SM, Lee JG, Shin DY, Yun JH, Sheng Y, Cheong C, Jeon YH, Jung YK, Arrowsmith CH, Avvakumov GV, Dhe-Paganon S, Yoo YJ, Eom SH, Lee W. Structural basis of E2-25K/UBB+1 interaction leading to proteasome inhibition and neurotoxicity. J Biol Chem 2010; 285:36070-80. [PMID: 20826778 DOI: 10.1074/jbc.m110.145219] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
E2-25K/Hip2 is an unusual ubiquitin-conjugating enzyme that interacts with the frameshift mutant of ubiquitin B (UBB(+1)) and has been identified as a crucial factor regulating amyloid-β neurotoxicity. To study the structural basis of the neurotoxicity mediated by the E2-25K-UBB(+1) interaction, we determined the three-dimensional structures of UBB(+1), E2-25K and the E2-25K/ubiquitin, and E2-25K/UBB(+1) complex. The structures revealed that ubiquitin or UBB(+1) is bound to E2-25K via the enzyme MGF motif and residues in α9 of the enzyme. Polyubiquitylation assays together with analyses of various E2-25K mutants showed that disrupting UBB(+1) binding markedly diminishes synthesis of neurotoxic UBB(+1)-anchored polyubiquitin. These results suggest that the interaction between E2-25K and UBB(+1) is critical for the synthesis and accumulation of UBB(+1)-anchored polyubiquitin, which results in proteasomal inhibition and neuronal cell death.
Collapse
Affiliation(s)
- Sunggeon Ko
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Pasikowski P, Cydzik M, Kluczyk A, Stefanowicz P, Szewczuk Z. Ubiquitin fragments: their known biological activities and putative roles. Biomol Concepts 2010; 1:67-83. [PMID: 25961987 DOI: 10.1515/bmc.2010.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ubiquitin (Ub) is involved in many key processes of cell biology. Identification of compounds that could interfere in the ubiquitination process is of importance. It could be expected that peptides derived from the Ub-binding regions might be able to interact with Ub receptors themselves and modify an ability of the Ub receptors interactions. This review summarizes current knowledge about known Ub-derived peptides and discusses putative activity of unexplored Ub fragments. Among identified biologically active Ub-derived peptides, its decapeptide fragment of the LEDGRTLSDY sequence was found to exhibit strong immunosuppressive effects on the cellular and humoral immune responses, comparable to that of cyclosporine. Some of the Ub fragments possess strong antibacterial and antifungal potency. In the search for new peptides that could interfere in the interaction of Ub with other proteins, we investigated the pentapeptide Ub sequences present in non-ubiquitin proteins. Based on examination of the Swiss-Prot database, we postulated that sequences of some Ub fragments often exist in other protein molecules. However, some of those motives are represented more frequently than others and could be involved in regulation of cellular processes related to Ub.
Collapse
|
46
|
Perica T, Chothia C. Ubiquitin--molecular mechanisms for recognition of different structures. Curr Opin Struct Biol 2010; 20:367-76. [PMID: 20456943 DOI: 10.1016/j.sbi.2010.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 03/24/2010] [Accepted: 03/25/2010] [Indexed: 11/15/2022]
Abstract
The role of ubiquitin in many of the known cellular processes, not just protein degradation, is based on its unique ability to bind a range of proteins that are structurally and functionally different. To understand how ubiquitin can bind to proteins with different structures, we review the extent of the conservation and variation that occur in the structures of two free ubiquitins and ubiquitins in 16 complexes that have been determined at high resolution (1.2-2A). Around 80% of the atomic groups in these structures have positions that differ less than 1A. This conserved core provides a rigid platform for flexible loop regions, 39 residues with side chains that can take up different conformations, and a flexible six-residue region at the C-terminus. In most cases the ability of ubiquitin to bind different structures is limited in part by a central set of residues that largely conserve their conformations. The accommodation of differences in binding proteins is enabled by changes in the flexible surface side chains, loop movements, different specific interactions, water molecules in the interface and the flexible C-terminus.
Collapse
Affiliation(s)
- Tina Perica
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 OQH, UK.
| | | |
Collapse
|
47
|
Kozlov G, Safaee N, Rosenauer A, Gehring K. Structural basis of binding of P-body-associated proteins GW182 and ataxin-2 by the Mlle domain of poly(A)-binding protein. J Biol Chem 2010; 285:13599-606. [PMID: 20181956 DOI: 10.1074/jbc.m109.089540] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Poly(A)-binding protein (PABPC1) is involved in multiple aspects of mRNA processing and translation. It is a component of RNA stress granules and binds the RNA-induced silencing complex to promote degradation of silenced mRNAs. Here, we report the crystal structures of the C-terminal Mlle (or PABC) domain in complex with peptides from GW182 (TNRC6C) and Ataxin-2. The structures reveal overlapping binding sites but with unexpected diversity in the peptide conformation and residues involved in binding. The mutagenesis and binding studies show low to submicromolar binding affinity with overlapping but distinct specificity determinants. These results rationalize the role of the Mlle domain of PABPC1 in microRNA-mediated mRNA deadenylation and suggest a more general function in the assembly of cytoplasmic RNA granules.
Collapse
Affiliation(s)
- Guennadi Kozlov
- Department of Biochemistry and Groupe de Recherche axé sur la Structure des Protéines, McGill University, Montréal, Québec H3G1Y6, Canada
| | | | | | | |
Collapse
|
48
|
Song J, Park JK, Lee JJ, Choi YS, Ryu KS, Kim JH, Kim E, Lee KJ, Jeon YH, Kim EE. Structure and interaction of ubiquitin-associated domain of human Fas-associated factor 1. Protein Sci 2010; 18:2265-76. [PMID: 19722279 DOI: 10.1002/pro.237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fas-associated factor (FAF)-1 is a multidomain protein that was first identified as a member of the Fas death-inducing signaling complex, but later found to be involved in various biological processes. Although the exact mechanisms are not clear, FAF1 seems to play an important role in cancer, asbestos-induced mesotheliomas, and Parkinson's disease. It interacts with polyubiquitinated proteins, Hsp70, and p97/VCP (valosin-containing protein), in addition to the proteins of the Fas-signaling pathway. We have determined the crystal structure of the ubiquitin-associated domain of human FAF1 (hFAF1-UBA) and examined its interaction with ubiquitin and ubiquitin-like proteins using nuclear magnetic resonance. hFAF1-UBA revealed a canonical three-helical bundle that selectively binds to mono- and di-ubiquitin (Lys48-linked), but not to SUMO-1 (small ubiquitin-related modifier 1) or NEDD8 (neural precursor cell expressed, developmentally down-regulated 8). The interaction between hFAF1-UBA and di-ubiquitin involves hydrophobic interaction accompanied by a transition in the di-ubiquitin conformation. These results provide structural insight into the mechanism of polyubiquitin recognition by hFAF1-UBA.
Collapse
Affiliation(s)
- Jinsue Song
- Magnetic Resonance Team, Korea Basic Science Institute, 804-1 Yangchung-Ri, Ochang, Chungbuk, Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Dimerisation of the UBA domain of p62 inhibits ubiquitin binding and regulates NF-kappaB signalling. J Mol Biol 2009; 396:178-94. [PMID: 19931284 DOI: 10.1016/j.jmb.2009.11.032] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 11/11/2009] [Accepted: 11/12/2009] [Indexed: 11/24/2022]
Abstract
The ubiquitin (Ub)-binding p62 scaffold protein (encoded by the SQSTM1 gene) regulates a diverse range of signalling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors and is an important regulator of macroautophagy. Mutations within the gene encoding p62 are commonly found in patients with Paget's disease of bone and largely cluster within the C-terminal ubiquitin-associated (UBA) domain, impairing its ability to bind Ub, resulting in dysregulated NF-kappaB signalling. However, precisely how Ub-binding is regulated at the molecular level is unclear. NMR relaxation dispersion experiments, coupled with concentration-dependent NMR, CD, isothermal titration calorimetry and fluorescence kinetic measurements, reveal that the p62 UBA domain forms a highly stable dimer (K(dim) approximately 4-12 microM at 298 K). NMR analysis shows that the dimer interface partially occludes the Ub-binding surface, particularly at the C-terminus of helix 3, making UBA dimerisation and Ub-binding mutually exclusive processes. Somewhat unusually, the monomeric UBA appears to be the biologically active form and the dimer appears to be the inactive one. Engineered point mutations in loop 1 (E409K and G410K) are shown to destabilise the dimer interface, lead to a higher proportion of the bound monomer and, in NF-kappaB luciferase reporter assays, are associated with reduced NF-kappaB activity compared with wt-p62.
Collapse
|
50
|
Matta-Camacho E, Kozlov G, Trempe JF, Gehring K. Atypical Binding of the Swa2p UBA Domain to Ubiquitin. J Mol Biol 2009; 386:569-77. [DOI: 10.1016/j.jmb.2008.09.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 09/30/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
|