51
|
Wang HT, Hur S. Substrate recognition by TRIM and TRIM-like proteins in innate immunity. Semin Cell Dev Biol 2021; 111:76-85. [PMID: 33092958 PMCID: PMC7572318 DOI: 10.1016/j.semcdb.2020.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022]
Abstract
TRIM (Tripartite motif) and TRIM-like proteins have emerged as an important class of E3 ligases in innate immunity. Their functions range from activation or regulation of innate immune signaling pathway to direct detection and restriction of pathogens. Despite the importance, molecular mechanisms for many TRIM/TRIM-like proteins remain poorly characterized, in part due to challenges of identifying their substrates. In this review, we discuss several TRIM/TRIM-like proteins in RNA sensing pathways and viral restriction functions. We focus on those containing PRY-SPRY, the domain most frequently used for substrate recognition, and discuss emerging mechanisms that are commonly utilized by several TRIM/TRIM-like proteins to tightly control their interaction with the substrates.
Collapse
Affiliation(s)
- Hai-Tao Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
52
|
Zhu G, Harischandra DS, Ghaisas S, Zhang P, Prall W, Huang L, Maghames C, Guo L, Luna E, Mack KL, Torrente MP, Luk KC, Shorter J, Yang X. TRIM11 Prevents and Reverses Protein Aggregation and Rescues a Mouse Model of Parkinson's Disease. Cell Rep 2020; 33:108418. [PMID: 33264628 PMCID: PMC7906527 DOI: 10.1016/j.celrep.2020.108418] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 07/15/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022] Open
Abstract
Neurodegenerative diseases are characterized by the formation and propagation of protein aggregates, especially amyloid fibrils. However, what normally suppresses protein misfolding and aggregation in metazoan cells remains incompletely understood. Here, we show that TRIM11, a member of the metazoan tripartite motif (TRIM) family, both prevents the formation of protein aggregates and dissolves pre-existing protein deposits, including amyloid fibrils. These molecular chaperone and disaggregase activities are ATP independent. They enhance folding and solubility of normal proteins and cooperate with TRIM11 SUMO ligase activity to degrade aberrant proteins. TRIM11 abrogates α-synuclein fibrillization and restores viability in cell models of Parkinson's disease (PD). Intracranial adeno-associated viral delivery of TRIM11 mitigates α-synuclein-mediated pathology, neurodegeneration, and motor impairments in a PD mouse model. Other TRIMs can also function as ATP-independent molecular chaperones and disaggregases. Thus, we define TRIMs as a potent and multifunctional protein quality-control system in metazoa, which might be applied to treat neurodegenerative diseases.
Collapse
Affiliation(s)
- Guixin Zhu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dilshan S Harischandra
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shivani Ghaisas
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pengfei Zhang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wil Prall
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liangqian Huang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chantal Maghames
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lili Guo
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esteban Luna
- Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Korrie L Mack
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariana P Torrente
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelvin C Luk
- Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
53
|
Xu N, Luo X, Wu W, Xing Y, Liang Y, Liu Y, Zou H, Wei HL, Liu J. A Plant Lectin Receptor-like Kinase Phosphorylates the Bacterial Effector AvrPtoB to Dampen Its Virulence in Arabidopsis. MOLECULAR PLANT 2020; 13:1499-1512. [PMID: 32977056 DOI: 10.1016/j.molp.2020.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/27/2020] [Accepted: 09/19/2020] [Indexed: 05/19/2023]
Abstract
Plasma membrane-localized receptor-like kinases (RLKs) perceive conserved pathogen-associated molecular patterns (PAMPs) in plants, leading to PAMP-triggered immunity (PTI). The Arabidopsis thaliana lectin RLK LecRK-IX.2 has been shown to regulate the bacterial flagellin-derived peptide flg22-induced PTI. Here, we discover that Pseudomonas syringae effector AvrPtoB targets LecRK-IX.2 for degradation, which subsequently suppresses LecRK-IX.2-mediated PTI and disease resistance. However, LecRK-IX.2 can interact with and phosphorylate AvrPtoB at serine site 335 (S335). AvrPtoB self-associates in vitro and in vivo, and the association appears to be essential for its E3 ligase activity in ubiquitinating substrate in plants. Phosphorylation of S335 disrupts the self-association and as a result, phosphomimetic AvrPtoBS335D cannot ubiquitinate LecRK-IX.2 efficiently, leading to the compromised virulence of AvrPtoB in suppressing PTI responses. flg22 enhances AvrPtoB S335 phosphorylation by inducing the expression and activating of LecRK-IX.2. Our study demonstrates that host RLKs can modify pathogen effectors to dampen their virulence and undermine their ability in suppressing PTI.
Collapse
Affiliation(s)
- Ning Xu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuming Luo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yingying Xing
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingbo Liang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanzhi Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huasong Zou
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hai-Lei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
54
|
Keown JR, Yang J, Black MM, Goldstone DC. The RING domain of TRIM69 promotes higher-order assembly. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:954-961. [PMID: 33021497 DOI: 10.1107/s2059798320010499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/30/2020] [Indexed: 11/10/2022]
Abstract
Members of the TRIM protein family have been shown to inhibit a range of viral infections. Recently, TRIM69 was identified as a potent inhibitor of Vesicular stomatitis Indiana virus infection, with its inhibition being dependent upon multimerization. Using SEC-MALLS analysis, it is demonstrated that the assembly of TRIM69 is mediated through the RING domain and not the Bbox domain as has been shown for other TRIM proteins. Using X-ray crystallography, the structure of the TRIM69 RING domain has been determined to a resolution of 2.1 Å, the oligomerization interface has been identified and regions outside the four-helix bundle have been observed to form interactions that are likely to support assembly.
Collapse
Affiliation(s)
- Jeremy R Keown
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Joy Yang
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Moyra M Black
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| |
Collapse
|
55
|
Peris-Moreno D, Taillandier D, Polge C. MuRF1/TRIM63, Master Regulator of Muscle Mass. Int J Mol Sci 2020; 21:ijms21186663. [PMID: 32933049 PMCID: PMC7555135 DOI: 10.3390/ijms21186663] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The E3 ubiquitin ligase MuRF1/TRIM63 was identified 20 years ago and suspected to play important roles during skeletal muscle atrophy. Since then, numerous studies have been conducted to decipher the roles, molecular mechanisms and regulation of this enzyme. This revealed that MuRF1 is an important player in the skeletal muscle atrophy process occurring during catabolic states, making MuRF1 a prime candidate for pharmacological treatments against muscle wasting. Indeed, muscle wasting is an associated event of several diseases (e.g., cancer, sepsis, diabetes, renal failure, etc.) and negatively impacts the prognosis of patients, which has stimulated the search for MuRF1 inhibitory molecules. However, studies on MuRF1 cardiac functions revealed that MuRF1 is also cardioprotective, revealing a yin and yang role of MuRF1, being detrimental in skeletal muscle and beneficial in the heart. This review discusses data obtained on MuRF1, both in skeletal and cardiac muscles, over the past 20 years, regarding the structure, the regulation, the location and the different functions identified, and the first inhibitors reported, and aim to draw the picture of what is known about MuRF1. The review also discusses important MuRF1 characteristics to consider for the design of future drugs to maintain skeletal muscle mass in patients with different pathologies.
Collapse
|
56
|
Zhang L, Afolabi LO, Wan X, Li Y, Chen L. Emerging Roles of Tripartite Motif-Containing Family Proteins (TRIMs) in Eliminating Misfolded Proteins. Front Cell Dev Biol 2020; 8:802. [PMID: 32984318 PMCID: PMC7479839 DOI: 10.3389/fcell.2020.00802] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022] Open
Abstract
Protein quality control (PQC) is pivotal for eukaryotic cells to eliminate misfolded proteins and maintain cellular homeostasis. A decreased or increased capacity of PQC is associated with various diseases, e.g., neurodegenerative diseases and cancers. Recently, increasing evidences have suggested that tripartite motif-containing family proteins (TRIMs) are the key players in PQC regulation. Most TRIMs are E3 ubiquitin ligases, such as TRIM11/19/25, which, through the ubiquitination modifications, can contribute to effectively remove the cellular misfolded proteins or protein aggregates via the UPS pathway. In this review, we summarized the participation of TRIM members in misfolded protein elimination through distinct pathways, including the ubiquitin-proteasome system (UPS), autophagy system, and ER-associated degradation (ERAD).
Collapse
Affiliation(s)
- Litian Zhang
- Shenzhen Laboratory of Tumor Cell Biology, Center for Antibody Drug Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lukman O Afolabi
- Shenzhen Laboratory of Tumor Cell Biology, Center for Antibody Drug Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaochun Wan
- Shenzhen Laboratory of Tumor Cell Biology, Center for Antibody Drug Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yang Li
- Shenzhen Laboratory of Tumor Cell Biology, Center for Antibody Drug Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Chen
- Shenzhen Laboratory of Tumor Cell Biology, Center for Antibody Drug Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| |
Collapse
|
57
|
Affiliation(s)
- Jingwei Zeng
- University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Leo C. James
- The Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
58
|
Sun N, Jiang L, Ye M, Wang Y, Wang G, Wan X, Zhao Y, Wen X, Liang L, Ma S, Liu L, Bu Z, Chen H, Li C. TRIM35 mediates protection against influenza infection by activating TRAF3 and degrading viral PB2. Protein Cell 2020; 11:894-914. [PMID: 32562145 PMCID: PMC7719147 DOI: 10.1007/s13238-020-00734-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 12/25/2022] Open
Abstract
Tripartite motif (TRIM) family proteins are important effectors of innate immunity against viral infections. Here we identified TRIM35 as a regulator of TRAF3 activation. Deficiency in or inhibition of TRIM35 suppressed the production of type I interferon (IFN) in response to viral infection. Trim35-deficient mice were more susceptible to influenza A virus (IAV) infection than were wild-type mice. TRIM35 promoted the RIG-I-mediated signaling by catalyzing Lys63-linked polyubiquitination of TRAF3 and the subsequent formation of a signaling complex with VISA and TBK1. IAV PB2 polymerase countered the innate antiviral immune response by impeding the Lys63-linked polyubiquitination and activation of TRAF3. TRIM35 mediated Lys48-linked polyubiquitination and proteasomal degradation of IAV PB2, thereby antagonizing its suppression of TRAF3 activation. Our in vitro and in vivo findings thus reveal novel roles of TRIM35, through catalyzing Lys63- or Lys48-linked polyubiquitination, in RIG-I antiviral immunity and mechanism of defense against IAV infection.
Collapse
Affiliation(s)
- Nan Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Li Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Miaomiao Ye
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yihan Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guangwen Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiaopeng Wan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yuhui Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xia Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Libin Liang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Shujie Ma
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Liling Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| |
Collapse
|
59
|
Lin Z, Lin X, Zhu L, Huang J, Huang Y. TRIM2 directly deubiquitinates and stabilizes Snail1 protein, mediating proliferation and metastasis of lung adenocarcinoma. Cancer Cell Int 2020; 20:228. [PMID: 32536816 PMCID: PMC7288537 DOI: 10.1186/s12935-020-01316-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023] Open
Abstract
Background Lung adenocarcinoma has surpassed lung squamous cell carcinoma as the most common type of non-small cell lung cancer. In this study, we had tested the biological role of TRIM2 in lung adenocarcinoma. Methods TRIM2 abundance in clinical tissues and six cell lines were examined with quantitative real-time PCR test (qRT-PCR) and western blot. TRIM2 overexpression treated H322 cells and TRIM2 knockdown treated A549 cells were used to study cell proliferation, migration, colony formation, invasion, and the expression of epithelial mesenchymal transformation (EMT) biomarkers. Moreover, ubiquitination related Snail1 degradation were studied with qRT-PCR and western blot. The relationships between TRIM2 and Snail1 were investigated with western blot, co-immunoprecipitation, migration, and invasion. Results TRIM2 was highly expressed in lung adenocarcinoma tissues. TRIM2 overexpression and knockdown treatments could affect cell proliferation, colony formation, migration, invasion, and the expression of EMT associated biomarkers. Moreover, TRIM2 can regulate the ubiquitination related Snail1 degradation. In addition, TRIM2 can regulate Snail1 degradation in lung adenocarcinoma via ubiquitination pathway. TRIM2 could promote the proliferation, migration, and invasion of lung adenocarcinoma. Meanwhile, TRIM2 can deubiquitinate and stabilize Snail1 protein, which play important role in the function of lung adenocarcinoma. Conclusion A high TRIM2 expression could be detected in lung adenocarcinoma tissues and cells. TRIM2 could aggravate cell proliferation, invasion, and migration in colorectal cancer by regulating Snail1 ubiquitylation degradation. Our results could provide detailed information for further studies in lung adenocarcinoma.
Collapse
Affiliation(s)
- Zhaoxian Lin
- Department of Thoracic Surgery, Fujian Provincial Hospital, No. 134 East Street, Gulou District, Fuzhou, 350001 Fujian China
| | - Xing Lin
- Department of Thoracic Surgery, Fujian Provincial Hospital, No. 134 East Street, Gulou District, Fuzhou, 350001 Fujian China
| | - Lihuan Zhu
- Department of Thoracic Surgery, Fujian Provincial Hospital, No. 134 East Street, Gulou District, Fuzhou, 350001 Fujian China
| | - Jianyuan Huang
- Department of Thoracic Surgery, Fujian Provincial Hospital, No. 134 East Street, Gulou District, Fuzhou, 350001 Fujian China
| | - Yangyun Huang
- Department of Thoracic Surgery, Fujian Provincial Hospital, No. 134 East Street, Gulou District, Fuzhou, 350001 Fujian China
| |
Collapse
|
60
|
Zhang JR, Li XX, Hu WN, Li CY. Emerging Role of TRIM Family Proteins in Cardiovascular Disease. Cardiology 2020; 145:390-400. [PMID: 32305978 DOI: 10.1159/000506150] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/23/2020] [Indexed: 11/19/2022]
Abstract
Ubiquitination is one of the basic mechanisms of cell protein homeostasis and degradation and is accomplished by 3 enzymes, E1, E2, and E3. Tripartite motif-containing proteins (TRIMs) constitute the largest subfamily of RING E3 ligases, with >70 current members in humans and mice. These members are involved in multiple biological processes, including growth, differentiation, and apoptosis as well as disease and tumorigenesis. Accumulating evidence has shown that many TRIM proteins are associated with various cardiac processes and pathologies, such as heart development, signal transduction, protein degradation, autophagy mediation, ion channel regulation, congenital heart disease, and cardiomyopathies. In this review, we provide an overview of the TRIM family and discuss its involvement in the regulation of cardiac proteostasis and pathophysiology and its potential therapeutic implications.
Collapse
Affiliation(s)
- Jing-Rui Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Xin-Xin Li
- Department of Respiratory Medicine, Tangshan People's Hospital, Tangshan, China
| | - Wan-Ning Hu
- Department of Cardiology, Laboratory of Molecular Biology, Tangshan Gongren Hospital, Tangshan, China,
| | - Chang-Yi Li
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.,Department of Cardiology, Laboratory of Molecular Biology, Tangshan Gongren Hospital, Tangshan, China
| |
Collapse
|
61
|
Mu T, Zhao X, Zhu Y, Fan H, Tang H. The E3 Ubiquitin Ligase TRIM21 Promotes HBV DNA Polymerase Degradation. Viruses 2020; 12:v12030346. [PMID: 32245233 PMCID: PMC7150939 DOI: 10.3390/v12030346] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/26/2022] Open
Abstract
The tripartite motif (TRIM) protein family is an E3 ubiquitin ligase family. Recent reports have indicated that some TRIM proteins have antiviral functions, especially against retroviruses. However, most studies mainly focus on the relationship between TRIM21 and interferon or other antiviral effectors. The effect of TRIM21 on virus-encoded proteins remains unclear. In this study, we screened candidate interacting proteins of HBV DNA polymerase (Pol) by FLAG affinity purification and mass spectrometry assay and identified TRIM21 as its regulator. We used a coimmunoprecipitation (co-IP) assay to demonstrate that TRIM21 interacted with the TP domain of HBV DNA Pol. In addition, TRIM21 promoted the ubiquitination and degradation of HBV DNA Pol using its RING domain, which has E3 ubiquitin ligase activity. Lys260 and Lys283 of HBV DNA Pol were identified as targets for ubiquitination mediated by TRIM21. Finally, we uncovered that TRIM21 degrades HBV DNA Pol to restrict HBV DNA replication, and its SPRY domain is critical for this activity. Taken together, our results indicate that TRIM21 suppresses HBV DNA replication mainly by promoting the ubiquitination of HBV DNA Pol, which may provide a new potential target for the treatment of HBV.
Collapse
Affiliation(s)
| | | | | | | | - Hua Tang
- Correspondence: ; Tel./Fax: +86-22-2354-2503
| |
Collapse
|
62
|
Garcia-Barcena C, Osinalde N, Ramirez J, Mayor U. How to Inactivate Human Ubiquitin E3 Ligases by Mutation. Front Cell Dev Biol 2020; 8:39. [PMID: 32117970 PMCID: PMC7010608 DOI: 10.3389/fcell.2020.00039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
E3 ubiquitin ligases are the ultimate enzymes involved in the transfer of ubiquitin to substrate proteins, a process that determines the fate of the modified protein. Numerous diseases are caused by defects in the ubiquitin-proteasome machinery, including when the activity of a given E3 ligase is hampered. Thus, inactivation of E3 ligases and the resulting effects at molecular or cellular level have been the focus of many studies during the last few years. For this purpose, site-specific mutation of key residues involved in either protein interaction, substrate recognition or ubiquitin transfer have been reported to successfully inactivate E3 ligases. Nevertheless, it is not always trivial to predict which mutation(s) will block the catalytic activity of a ligase. Here we review over 250 site-specific inactivating mutations that have been carried out in 120 human E3 ubiquitin ligases. We foresee that the information gathered here will be helpful for the design of future experimental strategies.
Collapse
Affiliation(s)
- Cristina Garcia-Barcena
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Ikerbasque - Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
63
|
Liu Y, Tao S, Liao L, Li Y, Li H, Li Z, Lin L, Wan X, Yang X, Chen L. TRIM25 promotes the cell survival and growth of hepatocellular carcinoma through targeting Keap1-Nrf2 pathway. Nat Commun 2020; 11:348. [PMID: 31953436 PMCID: PMC6969153 DOI: 10.1038/s41467-019-14190-2] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/18/2019] [Indexed: 12/20/2022] Open
Abstract
Tumor cells often exhibit augmented capacity to maintain endoplasmic reticulum (ER) homeostasis under adverse conditions, yet the underlying mechanisms are not well defined. Here, through the evaluation of all human TRIM proteins, we find that TRIM25 is significantly induced upon ER stress. Upregulation of TRIM25 ameliorates oxidative stress, promotes ER-associated degradation (ERAD), and reduces IRE1 signaling in the UPR pathway. In contrast, depletion of TRIM25 leads to ER stress and attenuates tumor cell growth in vitro and in vivo. Mechanistically, TRIM25 directly targets Keap1 by ubiquitination and degradation. This leads to Nrf2 activation, which bolsters anti-oxidant defense and cell survival. TRIM25 expression is positively associated with Nrf2 expression and negatively with Keap1 expression in hepatocellular carcinoma (HCC) xenografts and specimens. Moreover, high TRIM25 expression correlates with poor patient survival in HCC. These findings reveal TRIM25 as a regulator of ER homeostasis and a potential target for tumor therapy. The unfolded protein response allows tumour cells to adapt to ER stress, and aberrant activation of Nrf2 confers cancer progression. Here, the authors show that TRIM25 is induced during ER stress and promotes tumour cell survival by targeting Keap1 for degradation, leading to Nrf2 activation.
Collapse
Affiliation(s)
- Yanfeng Liu
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China.,Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Shishi Tao
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Lijuan Liao
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Yang Li
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Hongchang Li
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Zhihuan Li
- Dongguan Enlife Stem Cell Biotechnology Institute, Zheshang Building, #430 Dongguan Ave., Dongguan, Guangdong, 523000, China
| | - Lilong Lin
- Dongguan Enlife Stem Cell Biotechnology Institute, Zheshang Building, #430 Dongguan Ave., Dongguan, Guangdong, 523000, China
| | - Xiaochun Wan
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Liang Chen
- Shenzhen Laboratory of Tumor Cell Biology, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China.
| |
Collapse
|
64
|
Yang W, Gu Z, Zhang H, Hu H. To TRIM the Immunity: From Innate to Adaptive Immunity. Front Immunol 2020; 11:02157. [PMID: 33117334 PMCID: PMC7578260 DOI: 10.3389/fimmu.2020.02157] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/07/2020] [Indexed: 02/05/2023] Open
Abstract
The tripartite motif (TRIM) proteins have been intensively studied as essential modulators in various biological processes, especially in regulating a wide range of signaling pathways involved in immune responses. Most TRIM proteins have E3 ubiquitin ligase activity, mediating polyubiquitination of target proteins. Emerging evidence demonstrates that TRIM proteins play important roles in innate immunity by regulating pattern recognition receptors, vital adaptor proteins, kinases, and transcription factors in innate immune signaling pathways. Additionally, the critical roles of TRIM proteins in adaptive immunity, especially in T cell development and activation, are increasingly appreciated. In this review, we aim to summarize the studies on TRIMs in both innate and adaptive immunity, focusing on their E3 ubiquitin ligase functions in pattern recognition receptor signaling pathways and T cell functions, shedding light on the developing new strategies for modulating innate and adaptive immune responses against invading pathogens and avoiding autoimmunity.
Collapse
Affiliation(s)
| | | | | | - Hongbo Hu
- *Correspondence: Huiyuan Zhang, ; Hongbo Hu,
| |
Collapse
|
65
|
Kueck T, Bloyet LM, Cassella E, Zang T, Schmidt F, Brusic V, Tekes G, Pornillos O, Whelan SPJ, Bieniasz PD. Vesicular Stomatitis Virus Transcription Is Inhibited by TRIM69 in the Interferon-Induced Antiviral State. J Virol 2019; 93:e01372-19. [PMID: 31578292 PMCID: PMC6880163 DOI: 10.1128/jvi.01372-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/24/2019] [Indexed: 12/23/2022] Open
Abstract
Interferons (IFNs) induce the expression of interferon-stimulated genes (ISGs), many of which are responsible for the cellular antiviral state in which the replication of numerous viruses is blocked. How the majority of individual ISGs inhibit the replication of particular viruses is unknown. We conducted a loss-of-function screen to identify genes required for the activity of alpha interferon (IFN-α) against vesicular stomatitis virus, Indiana serotype (VSVIND), a prototype negative-strand RNA virus. Our screen revealed that TRIM69, a member of the tripartite motif (TRIM) family of proteins, is a VSVIND inhibitor. TRIM69 potently inhibited VSVIND replication through a previously undescribed transcriptional inhibition mechanism. Specifically, TRIM69 physically associates with the VSVIND phosphoprotein (P), requiring a specific peptide target sequence encoded therein. P is a cofactor for the viral polymerase and is required for viral RNA synthesis, as well as the assembly of replication compartments. By targeting P, TRIM69 inhibits pioneer transcription of the incoming virion-associated minus-strand RNA, thereby preventing the synthesis of viral mRNAs, and consequently impedes all downstream events in the VSVIND replication cycle. Unlike some TRIM proteins, TRIM69 does not inhibit viral replication by inducing degradation of target viral proteins. Rather, higher-order TRIM69 multimerization is required for its antiviral activity, suggesting that TRIM69 functions by sequestration or anatomical disruption of the viral machinery required for VSVIND RNA synthesis.IMPORTANCE Interferons are important antiviral cytokines that work by inducing hundreds of host genes whose products inhibit the replication of many viruses. While the antiviral activity of interferon has long been known, the identities and mechanisms of action of most interferon-induced antiviral proteins remain to be discovered. We identified gene products that are important for the antiviral activity of interferon against vesicular stomatitis virus (VSV), a model virus that whose genome consists of a single RNA molecule with negative-sense polarity. We found that a particular antiviral protein, TRIM69, functions by a previously undescribed molecular mechanism. Specifically, TRIM69 interacts with and inhibits the function of a particular phosphoprotein (P) component of the viral transcription machinery, preventing the synthesis of viral messenger RNAs.
Collapse
Affiliation(s)
- Tonya Kueck
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Louis-Marie Bloyet
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Elena Cassella
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Trinity Zang
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
| | - Vesna Brusic
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gergely Tekes
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Sean P J Whelan
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| |
Collapse
|
66
|
The E3 ubiquitin ligase TRIM7 suppressed hepatocellular carcinoma progression by directly targeting Src protein. Cell Death Differ 2019; 27:1819-1831. [PMID: 31802035 DOI: 10.1038/s41418-019-0464-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant Src kinase activity is known to be involved in a variety of human malignancies, whereas the regulatory mechanism of Src has not been completely clarified. Here, we demonstrated that tripartite motif containing 7 (TRIM7) directly interacted with Src, induced Lys48-linked polyubiquitination of Src and reduced the abundance of Src protein in hepatocellular carcinoma (HCC) cells. We further identified TRIM7 as a tumor suppressor in HCC cells through its negative modulation of the Src-mTORC1-S6K1 axis in vivo and in vitro in several HCC models. Moreover, we verified the dysregulated expression of TRIM7 in clinical liver cancer tissues and its negative correlation with Src protein in clinical HCC specimens. Overall, we demonstrated that TRIM7 suppressed HCC progression through its direct negative regulation of Src and modulation of the Src-mTORC1-S6K1 axis; thus, we provided a novel insight into the development of HCC and defined a promising therapeutic strategy for cancers with overactive Src by modulating TRIM7.
Collapse
|
67
|
Jaworska AM, Wlodarczyk NA, Mackiewicz A, Czerwinska P. The role of TRIM family proteins in the regulation of cancer stem cell self-renewal. Stem Cells 2019; 38:165-173. [PMID: 31664748 PMCID: PMC7027504 DOI: 10.1002/stem.3109] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/08/2019] [Indexed: 12/29/2022]
Abstract
The tripartite-motif (TRIM) family of proteins represents one of the largest classes of putative single protein RING-finger E3 ubiquitin ligases. The members of this family are characterized by an N-terminal TRIM motif containing one RING-finger domain, one or two zinc-finger domains called B boxes (B1 box and B2 box), and a coiled-coil region. The TRIM motif can be found in isolation or in combination with a variety of C-terminal domains, and based on C-terminus, TRIM proteins are classified into 11 distinct groups. Because of the complex nature of TRIM proteins, they are implicated in a variety of cellular functions and biological processes, including regulation of cell proliferation, cell division and developmental processes, cancer transformation, regulation of cell metabolism, autophagocytosis, modification of chromatin status, regulation of gene transcription, post-translational modifications, and interactions with pathogens. Here, we demonstrate the specific activities of TRIM family proteins that contribute to the cancer stem cell phenotype. A growing body of evidence demonstrates that several TRIM members guarantee the acquisition of stem cell properties and the ability to sustain stem-like phenotype by cancer cells using distinct mechanisms. For other members, further work is needed to understand their full contribution to stem cell self-renewal. Identification of TRIM proteins that possess the potential to serve as therapeutic targets may result in the development of new therapeutic strategies. Finally, these strategies may result in the disruption of the machinery of stemness acquisition, which may prevent tumor growth, progression, and overcome the resistance to anticancer therapies.
Collapse
Affiliation(s)
- Anna Maria Jaworska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Nikola Agata Wlodarczyk
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland
| | - Patrycja Czerwinska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland
| |
Collapse
|
68
|
Zheng SC, Chang XJ, Li WD, Wang H, Guo LM, Wang KJ, Liu HP. A novel RING finger protein CqRNF152-like with self-ubiquitination activity inhibits white spot syndrome virus infection in a crustacean Cherax quadricarinatus. FISH & SHELLFISH IMMUNOLOGY 2019; 94:934-943. [PMID: 31600596 DOI: 10.1016/j.fsi.2019.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/29/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
Really Interesting New Gene (RING) finger proteins are highly conserved molecules that participate in a variety of biological processes such as regulation of development, apoptosis and antiviral immunity in vertebrates. However, the functions of RING finger proteins are still poorly understood in crustaceans. Previously, we found that the transcript of a homolog of RING finger protein 152 (CqRNF152-like) was up-regulated in a differentially expressed transcriptome library of the haematopietic tissue (Hpt) cells from red claw crayfish Cherax quadricarinatus upon white spot syndrome virus (WSSV) infection, which is one of the most devastating viral diseases for crustaceans like shrimp and crayfish. The full-length cDNA sequence of CqRNF152-like was then identified with 975 bp, including an ORF of 685 bp that encoded a 195 amino acids protein, a 5'- UTR of 180 bp, and a 3'-UTR with a poly (A) tail of 207 bp. The conserved domain prediction showed that CqRNF152-like contained a conserved RING-finger domain. Gene expression analysis showed that CqRNF152-like was distributed in all tissues examined and the transcript is significantly up-regulated after WSSV challenge both in vivo in Hpt tissue and in vitro in cultured Hpt cells. Furthermore, the transcripts of both an immediate early gene ie1 and a late envelope protein gene vp28 of WSSV were clearly increased in the Hpt tissues, hemocytes and cultured Hpt cells after gene silencing of CqRNF152-like, which were further proved to be significantly decreased after overloading of recombinant CqRNF152-like protein in Hpt cell cultures. Meanwhile, CqRNF152-like was found to bind with WSSV envelope protein VP28 by proteins pull-down assay. Similar to most of RNF proteins, CqRNF152-like protein sequence contained a conserved RING-finger domain and showed self-ubiquitination activity in a RING finger domain dependent manner. Taken together, CqRNF152-like is likely to function as an antiviral molecular against WSSV infection through interaction with the envelope protein VP28 in a crustacean C. quadricarinatus. This is the first report that a RING finger protein with directly antiviral functions via interaction with viral protein and self-ubiquitination activity in crustacean, which sheds new light on the molecular mechanism of WSSV infection and the control of white spot disease.
Collapse
Affiliation(s)
- Shu-Cheng Zheng
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xue-Jiao Chang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Wei-Dong Li
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hao Wang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Li-Mei Guo
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China.
| |
Collapse
|
69
|
Kiss L, Zeng J, Dickson CF, Mallery DL, Yang JC, McLaughlin SH, Boland A, Neuhaus D, James LC. A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases. Nat Commun 2019; 10:4502. [PMID: 31582740 PMCID: PMC6776665 DOI: 10.1038/s41467-019-12388-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/30/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosolic antibody receptor TRIM21 possesses unique ubiquitination activity that drives broad-spectrum anti-pathogen targeting and underpins the protein depletion technology Trim-Away. This activity is dependent on formation of self-anchored, K63-linked ubiquitin chains by the heterodimeric E2 enzyme Ube2N/Ube2V2. Here we reveal how TRIM21 facilitates ubiquitin transfer and differentiates this E2 from other closely related enzymes. A tri-ionic motif provides optimally distributed anchor points that allow TRIM21 to wrap an Ube2N~Ub complex around its RING domain, locking the closed conformation and promoting ubiquitin discharge. Mutation of these anchor points inhibits ubiquitination with Ube2N/Ube2V2, viral neutralization and immune signalling. We show that the same mechanism is employed by the anti-HIV restriction factor TRIM5 and identify spatially conserved ionic anchor points in other Ube2N-recruiting RING E3s. The tri-ionic motif is exclusively required for Ube2N but not Ube2D1 activity and provides a generic E2-specific catalysis mechanism for RING E3s.
Collapse
Affiliation(s)
- Leo Kiss
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jingwei Zeng
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Claire F Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- University of New South Wales, Sydney, NSW, Australia
| | - Donna L Mallery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Ji-Chun Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Andreas Boland
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland
| | - David Neuhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Leo C James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| |
Collapse
|
70
|
Zhang H, Deng Y, Liang L, Shen L, Zhu J, Wang Y, Zhang J, Zhang Z. Knockdown Of TRIM31 Enhances Colorectal Cancer Radiosensitivity By Inducing DNA Damage And Activating Apoptosis. Onco Targets Ther 2019; 12:8179-8188. [PMID: 31632068 PMCID: PMC6781640 DOI: 10.2147/ott.s215769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/19/2019] [Indexed: 12/28/2022] Open
Abstract
Purpose Biomarkers that predict radiosensitivity are essential for personalized radiotherapy. We performed microarray analysis for rectal cancer patients between those with good response and poor response to preoperative radiotherapy and found that patients with lower expression of tripartite motif-containing protein 31 (TRIM31) showed a better response. In this study, we confirmed the effects of TRIM31 on radiosensitivity by knockdown of TRIM31 in colorectal cancer cells. Methods and materials Human colorectal cancer cell lines HT-29 and SW480, which are TRIM31 stably knocked-down, were used for analysis. We studied the level of DNA damage and the change of relative proteins after irradiation in TRIM31-knockdown cells. Flow cytometry was used to test for apoptosis, cell cycle stage, and reactive oxygen species (ROS) levels after irradiation. Cell survival was measured by cloning assay. Proteins related to DNA damage were evaluated by Western blotting. Results The percentage of apoptotic cells and the levels of ROS were elevated, and the survival fraction was reduced in TRIM31-knockdown cells. The expression levels of the DNA damage proteins phosphorylated ataxia-telangiectasia mutation (P-ATM), DNA protein kinases (DNA-PKs), and γ-H2AX were higher in TRIM31-knockdown cells. Conclusion Knockdown of TRIM31 increases DNA damage and radiosensitivity in colorectal cancer cells.
Collapse
Affiliation(s)
- Hui Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Yun Deng
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China.,Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China
| | - Liping Liang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Lijun Shen
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Ji Zhu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Yaqi Wang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Jing Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People's Republic of China
| |
Collapse
|
71
|
Fonti G, Marcaida MJ, Bryan LC, Träger S, Kalantzi AS, Helleboid PYJ, Demurtas D, Tully MD, Grudinin S, Trono D, Fierz B, Dal Peraro M. KAP1 is an antiparallel dimer with a functional asymmetry. Life Sci Alliance 2019; 2:2/4/e201900349. [PMID: 31427381 PMCID: PMC6701479 DOI: 10.26508/lsa.201900349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 01/10/2023] Open
Abstract
This study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1. KAP1 (KRAB domain–associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 small ubiquitin modifier ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering data, integrative modeling, and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with an asymmetry at the C-terminal domains. This conformation is consistent with the finding that the Really Interesting New Gene (RING) domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
Collapse
Affiliation(s)
- Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Louise C Bryan
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra S Kalantzi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pierre-Yves Jl Helleboid
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Davide Demurtas
- Interdisciplinary Centre for Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mark D Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Sergei Grudinin
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Inria, Grenoble Institut Polytechnique de Grenoble, Laboratoire Jean Kuntzmann, Grenoble, France
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
72
|
Stoll GA, Oda SI, Chong ZS, Yu M, McLaughlin SH, Modis Y. Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing. Proc Natl Acad Sci U S A 2019; 116:15042-15051. [PMID: 31289231 PMCID: PMC6660772 DOI: 10.1073/pnas.1901318116] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Transcription of transposable elements is tightly regulated to prevent genome damage. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, inducing the assembly of an epigenetic silencing complex, with chromatin remodeling activities that repress transcription of the targeted retrotransposon and adjacent genes. Our biophysical and structural data show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevent higher-order oligomerization without significant loss of retrotransposon silencing activity, indicating that, in contrast to other TRIM-family proteins, self-assembly is not essential for KAP1 function. The crystal structure of the KAP1 TRIM dimer identifies the KRAB domain binding site in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 TRIM responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing.
Collapse
Affiliation(s)
- Guido A Stoll
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology (MRC-LMB), CB2 0QH Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, CB2 0AW Cambridge, United Kingdom
| | - Shun-Ichiro Oda
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology (MRC-LMB), CB2 0QH Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, CB2 0AW Cambridge, United Kingdom
| | - Zheng-Shan Chong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology (MRC-LMB), CB2 0QH Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, CB2 0AW Cambridge, United Kingdom
| | - Minmin Yu
- X-ray Crystallography Facility, MRC-LMB, CB2 0QH Cambridge, United Kingdom
| | | | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council Laboratory of Molecular Biology (MRC-LMB), CB2 0QH Cambridge, United Kingdom;
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, CB2 0AW Cambridge, United Kingdom
| |
Collapse
|
73
|
Stevens M, Franke B, Skorupka KA, Cafiso DS, Pornillos O, Mayans O, Norman DG. Exploration of the TRIM Fold of MuRF1 Using EPR Reveals a Canonical Antiparallel Structure and Extended COS-Box. J Mol Biol 2019; 431:2900-2909. [PMID: 31125568 PMCID: PMC6599887 DOI: 10.1016/j.jmb.2019.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/07/2019] [Accepted: 05/14/2019] [Indexed: 12/15/2022]
Abstract
MuRF1 (TRIM63) is a RING-type E3 ubiquitin ligase with a predicted tripartite TRIM fold. TRIM proteins rely upon the correct placement of an N-terminal RING domain, with respect to C-terminal, specific substrate-binding domains. The TRIM domain organization is orchestrated by a central helical domain that forms an antiparallel coiled-coil motif and mediates the dimerization of the fold. MuRF1 has a reduced TRIM composition characterized by a lack of specific substrate binding domains, but contains in its helical domain a conserved sequence motif termed COS-box that has been speculated to fold independently into an α-hairpin. These characteristics had led to question whether MuRF1 adopts a canonical TRIM fold. Using a combination of electron paramagnetic resonance, on spin-labeled protein, and disulfide crosslinking, we show that TRIM63 follows the structural conservation of the TRIM dimerization domain, observed in other proteins. We also show that the COS-box motif folds back onto the dimerization coiled-coil motif, predictably forming a four-helical bundle at the center of the protein and emulating the architecture of canonical TRIMs.
Collapse
Affiliation(s)
- Michael Stevens
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
| | - Barbara Franke
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Katarzyna A Skorupka
- Department of Molecular Physiology and Biological Physics, University of Virginia, 22908 Charlottesville, VA, USA
| | - David S Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, 22908 Charlottesville, VA, USA
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom.
| |
Collapse
|
74
|
Wang H, Nada MH, Tanaka Y, Sakuraba S, Morita CT. Critical Roles for Coiled-Coil Dimers of Butyrophilin 3A1 in the Sensing of Prenyl Pyrophosphates by Human Vγ2Vδ2 T Cells. THE JOURNAL OF IMMUNOLOGY 2019; 203:607-626. [PMID: 31227581 DOI: 10.4049/jimmunol.1801252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/23/2019] [Indexed: 12/25/2022]
Abstract
Vγ2Vδ2 T cells play important roles in human immunity to pathogens and tumors. Their TCRs respond to the sensing of isoprenoid metabolites, such as (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate and isopentenyl pyrophosphate, by butyrophilin (BTN) 3A1. BTN3A1 is an Ig superfamily protein with extracellular IgV/IgC domains and intracellular B30.2 domains that bind prenyl pyrophosphates. We have proposed that intracellular α helices form a coiled-coil dimer that functions as a spacer for the B30.2 domains. To test this, five pairs of anchor residues were mutated to glycine to destabilize the coiled-coil dimer. Despite maintaining surface expression, BTN3A1 mutagenesis either abrogated or decreased stimulation by (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate. BTN3A2 and BTN3A3 proteins and orthologs in alpacas and dolphins are also predicted to have similar coiled-coil dimers. A second short coiled-coil region dimerizes the B30.2 domains. Molecular dynamics simulations predict that mutation of a conserved tryptophan residue in this region will destabilize the dimer, explaining the loss of stimulation by BTN3A1 proteins with this mutation. The juxtamembrane regions of other BTN/BTN-like proteins with B30.2 domains are similarly predicted to assume α helices, with many predicted to form coiled-coil dimers. An exon at the end of this region and the exon encoding the dimerization region for B30.2 domains are highly conserved. We propose that coiled-coil dimers function as rod-like helical molecular spacers to position B30.2 domains, as interaction sites for other proteins, and as dimerization regions to allow sensing by B30.2 domains. In these ways, the coiled-coil domains of BTN3A1 play critical roles for its function.
Collapse
Affiliation(s)
- Hong Wang
- Division of Immunology, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242.,Department of Veterans Affairs, Iowa City Health Care System, Iowa City, IA 52246
| | - Mohanad H Nada
- Division of Immunology, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242.,Department of Veterans Affairs, Iowa City Health Care System, Iowa City, IA 52246.,College of Medicine, Tikrit University, Tiktit, 34001, Iraq
| | - Yoshimasa Tanaka
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan.,Hyogo College of Medicine, Nishinomiya, Hyogo 663-8501, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; and
| | - Craig T Morita
- Division of Immunology, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242; .,Department of Veterans Affairs, Iowa City Health Care System, Iowa City, IA 52246.,Interdisciplinary Graduate Program in Immunology, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| |
Collapse
|
75
|
Anandapadamanaban M, Kyriakidis NC, Csizmók V, Wallenhammar A, Espinosa AC, Ahlner A, Round AR, Trewhella J, Moche M, Wahren-Herlenius M, Sunnerhagen M. E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2. J Biol Chem 2019; 294:11404-11419. [PMID: 31160341 DOI: 10.1074/jbc.ra119.008485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/28/2019] [Indexed: 12/23/2022] Open
Abstract
The E3 ubiquitin-protein ligase TRIM21, of the RING-containing tripartite motif (TRIM) protein family, is a major autoantigen in autoimmune diseases and a modulator of innate immune signaling. Together with ubiquitin-conjugating enzyme E2 E1 (UBE2E1), TRIM21 acts both as an E3 ligase and as a substrate in autoubiquitination. We here report a 2.82-Å crystal structure of the human TRIM21 RING domain in complex with the human E2-conjugating UBE2E1 enzyme, in which a ubiquitin-targeted TRIM21 substrate lysine was captured in the UBE2E1 active site. The structure revealed that the direction of lysine entry is similar to that described for human proliferating cell nuclear antigen (PCNA), a small ubiquitin-like modifier (SUMO)-targeted substrate, and thus differs from the canonical SUMO-targeted substrate entry. In agreement, we found that critical UBE2E1 residues involved in the capture of the TRIM21 substrate lysine are conserved in ubiquitin-conjugating E2s, whereas residues critical for SUMOylation are not conserved. We noted that coordination of the acceptor lysine leads to remodeling of amino acid side-chain interactions between the UBE2E1 active site and the E2-E3 direct interface, including the so-called "linchpin" residue conserved in RING E3s and required for ubiquitination. The findings of our work support the notion that substrate lysine activation of an E2-E3-connecting allosteric path may trigger catalytic activity and contribute to the understanding of specific lysine targeting by ubiquitin-conjugating E2s.
Collapse
Affiliation(s)
| | - Nikolaos C Kyriakidis
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden.,Escuela de Medicina, Facultad de Ciencias de la Salud, Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas (UDLA), Quito, EC170504 Ecuador
| | - Veronika Csizmók
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Amélie Wallenhammar
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Alexander C Espinosa
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Alexandra Ahlner
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Adam R Round
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Jill Trewhella
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden.,School of Life and Environmental Sciences (SoLES), The University of Sydney, New South Wales 2006, Australia
| | - Martin Moche
- Department of Medical Biochemistry and Biophysics, Protein Science Facility, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| |
Collapse
|
76
|
A Dissection of Oligomerization by the TRIM28 Tripartite Motif and the Interaction with Members of the Krab-ZFP Family. J Mol Biol 2019; 431:2511-2527. [PMID: 31078555 DOI: 10.1016/j.jmb.2019.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 01/15/2023]
Abstract
TRIM28 (also known as KAP1 or TIF1β) is the universal co-repressor of the Krüppel-associated box-containing zinc finger proteins (Krab-ZFPs), the largest family of transcription factors in mammals. During early embryogenesis, TRIM28 mediates the transcriptional silencing of many endogenous retroviral elements and genomic imprinted sites. Silencing is initiated by the recruitment of TRIM28 to a target locus by members of the Krab-ZFP. Subsequently, TRIM28 functions as a scaffold protein to recruit chromatin modifying effectors featuring SETDB1, HP1 and the NuRD complex. Although many protein partners involved in silencing have been identified, the molecular basis of the protein interactions that mediate silencing remains largely unclear. In the present study, we identified the first Bbox domain (T28_B1 135-203) as a molecular interface responsible for the formation of higher-order oligomers of TRIM28. The structure of this domain reveals a new interface on the surface of the Bbox domain. Mutants disrupting the interface disrupt the formation of oligomers but have no observed effect on transcriptional silencing defining a single TRIM28 dimer as the functional unit for silencing. Using assembly-deficient mutants, we employed small-angle X-ray scattering and biophysical techniques to characterize binding to member of the Krab-ZFP family. This allows us to narrow and define the binding interface to the center of the coiled-coil region (residues 294-321) of TRIM28 and define mutants that abolish binding to the Krab-ZFP proteins.
Collapse
|
77
|
Liu C, Shan Z, Diao J, Wen W, Wang W. Crystal structure of the coiled‐coil domain of
Drosophila
TRIM protein Brat. Proteins 2019; 87:706-710. [DOI: 10.1002/prot.25691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Chunhua Liu
- Department of ChemistryInstitutes of Biomedical Sciences and Multiscale Research Institute of Complex System, Fudan University Shanghai People's Republic of China
| | - Zelin Shan
- Department of NeurosurgeryHuashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Shanghai Medical College of Fudan University Shanghai People's Republic of China
- Department of Systems Biology for MedicineSchool of Basic Medical Sciences, Shanghai Medical College of Fudan University Shanghai People's Republic of China
| | - Jianqiao Diao
- Department of ChemistryInstitutes of Biomedical Sciences and Multiscale Research Institute of Complex System, Fudan University Shanghai People's Republic of China
| | - Wenyu Wen
- Department of NeurosurgeryHuashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Shanghai Medical College of Fudan University Shanghai People's Republic of China
- Department of Systems Biology for MedicineSchool of Basic Medical Sciences, Shanghai Medical College of Fudan University Shanghai People's Republic of China
| | - Wenning Wang
- Department of ChemistryInstitutes of Biomedical Sciences and Multiscale Research Institute of Complex System, Fudan University Shanghai People's Republic of China
| |
Collapse
|
78
|
Liu W, Kuang M, Zhang Z, Lu Y, Liu X. Molecular Characterization and Expression Analysis of ftr01, ftr42, and ftr58 in Zebrafish (Danio rerio). Virol Sin 2019; 34:434-443. [PMID: 30989427 DOI: 10.1007/s12250-019-00112-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 02/21/2019] [Indexed: 11/30/2022] Open
Abstract
Tripartite motif (TRIM) proteins were shown to play an important role in innate antiviral immunity. FinTRIM (ftr) is a new subset of TRIM genes that do not possess obvious orthologs in higher vertebrates. However, little is known about its function. In this study, we used bioinformatic analysis to examine the phylogenetic relationships and conserved domains of zebrafish (Danio rerio) ftr01, ftr42, and ftr58, as well as qualitative real-time PCR to examine their expression patterns in zebrafish embryonic fibroblast (ZF4) cells and zebrafish tissues. Sequence analysis showed that the three finTRIMs are highly conserved, and all contain a RING domain, B-box domain, and SPRY-PRY domain. In addition, ftr42 and ftr58 had one coiled-coil domain (CCD), whereas ftr01 had two CCDs. Tissue expression analysis revealed that the mRNA level of ftr01 was the highest in the liver, whereas those of ftr42 and ftr58 were the highest in the gill; the expression of these finTRIMs was clearly upregulated not in the eyes, but in the liver, spleen, kidney, gill, and brain of zebrafish following spring viremia of carp virus (SVCV) infection. Similarly, the expression of these three finTRIM genes also increased in ZF4 cells after SVCV infection. Our study revealed that ftr01, ftr42, and ftr58 may play an important role in antiviral immune responses, and these findings validate the need for more in-depth research on the finTRIM family in the future.
Collapse
Affiliation(s)
- Wanmeng Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China.,Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
| | - Ming Kuang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China.,Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China
| | - Ze Zhang
- School of Life Sciences, Beijing Normal University, Beijing, 100875, China.,National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing, 102206, China
| | - Yuanan Lu
- Department of Public Health Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Xueqin Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China. .,Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan, 430070, China.
| |
Collapse
|
79
|
TRIM46 Organizes Microtubule Fasciculation in the Axon Initial Segment. J Neurosci 2019; 39:4864-4873. [PMID: 30967428 DOI: 10.1523/jneurosci.3105-18.2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
Selective cargo transport into axons and dendrites over the microtubule network is essential for neuron polarization. The axon initial segment (AIS) separates the axon from the somatodendritic compartment and controls the microtubule-dependent transport into the axon. Interestingly, the AIS has a characteristic microtubule organization; it contains bundles of closely spaced microtubules with electron dense cross-bridges, referred to as microtubule fascicles. The microtubule binding protein TRIM46 localizes to the AIS and when overexpressed in non-neuronal cells forms microtubule arrays that closely resemble AIS fascicles in neurons. However, the precise role of TRIM46 in microtubule fasciculation in neurons has not been studied. Here we developed a novel correlative light and electron microscopy approach to study AIS microtubule organization. We show that in cultured rat hippocampal neurons of both sexes, TRIM46 levels steadily increase at the AIS during early neuronal differentiation and at the same time closely spaced microtubules form, whereas the fasciculated microtubules appear at later developmental stages. Moreover, we localized TRIM46 to the electron dense cross-bridges and show that depletion of TRIM46 causes loss of cross-bridges and increased microtubule spacing. These data indicate that TRIM46 has an essential role in organizing microtubule fascicles in the AIS.SIGNIFICANCE STATEMENT The axon initial segment (AIS) is a specialized region at the proximal axon where the action potential is initiated. In addition the AIS separates the axon from the somatodendritic compartment, where it controls protein transport to establish and maintain neuron polarity. Cargo vesicles destined for the axon recognize specialized microtubule tracks that enter the AIS. Interestingly the microtubules entering the AIS form crosslinked bundles, called microtubule fascicules. Recently we found that the microtubule-binding protein TRIM46 localizes to the AIS, where it may organize the AIS microtubules. In the present study we developed a novel correlative light and electron microscopy approach to study the AIS microtubules during neuron development and identified an essential role for TRIM46 in microtubule fasciculation.
Collapse
|
80
|
Cao H, Fang Y, Liang Q, Wang J, Luo B, Zeng G, Zhang T, Jing X, Wang X. TRIM2 is a novel promoter of human colorectal cancer. Scand J Gastroenterol 2019; 54:210-218. [PMID: 30916596 DOI: 10.1080/00365521.2019.1575463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/13/2019] [Accepted: 01/19/2019] [Indexed: 02/04/2023]
Abstract
OBJECTIVES The incidence of colorectal cancer (CRC) is increasing year by year and appears to be younger, due to the low early diagnosis rate and metastasis. It is difficult to remedy by conventional treatment. Here, we reported that tripartite motif containing protein 2 (TRIM2) could promote tumor growth, invasion and metastasis of CRC via a mechanism that involved EMT both in vitro and in vivo. METHODS First, we used immunohistochemistry to detect TRIM2 expression. Next, TCGA database was applied to the coorelation between TRIM2 and CRC progression. Then, the plasmids and lentivirus particles were used to manipulate TRIM2 expression in SW620 or HT29 cells. The assays of proliferation, adhesion, magration and invasion were employed to detect the migration and invasion ability of CRC cells. Finally, a tail injection of CRC cells was used to identify the role of TRIM2 in tumor metastasis. RESULTS TRIM2 expression was significantly higher in CRC tissues than in non-cancerous tissues and was significantly associated with some clinicopathological factors. Forced overexpression of TRIM2 promoted CRC cell proliferation, migration and invasion in vitro, while opposing results were observed when TRIM2 was depleted by short hairpin RNA. TRIM2 expression had reversely correlated with YAP signaling, which was a novel pathway way referred to tumorigenesis. Furthermore, animal metastasis models confirmed that the in vivo results were consistent with the outcomes in vitro. TRIM2 conducts its function during CRC cell metastasis by epithelial-mesenchymal transition (EMT). These results indicate that TRIM2 is a novel promoter of human colorectal cancer.
Collapse
Affiliation(s)
- Hua Cao
- a Emergency Department , Shanghai Tenth People's Hospital , Shanghai , China
| | - Yi Fang
- a Emergency Department , Shanghai Tenth People's Hospital , Shanghai , China
| | - Qiwen Liang
- b Emergency Department , First Affiliated Hospital of Naval Military Medical University , Shanghai , China
| | - Jianzhong Wang
- a Emergency Department , Shanghai Tenth People's Hospital , Shanghai , China
| | - Bijun Luo
- a Emergency Department , Shanghai Tenth People's Hospital , Shanghai , China
| | - Guanghao Zeng
- a Emergency Department , Shanghai Tenth People's Hospital , Shanghai , China
| | - Tingting Zhang
- a Emergency Department , Shanghai Tenth People's Hospital , Shanghai , China
| | - Xiaoqian Jing
- c Department of Surgery, Ruijin Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , China
| | - Xiongjun Wang
- d Precise Genome Engineering Center, School of Life Sciences , Guangzhou University , Guangzhou , China
| |
Collapse
|
81
|
Wu J, Guo NZ, Cui LL, Wang W, Xiong CQ, Zhang XY. Correlation between tripartite motif-containing protein 44 protein expression and the prognosis of postoperative patients exhibiting skin squamous cell carcinoma. Medicine (Baltimore) 2018; 97:e13021. [PMID: 30383661 PMCID: PMC6221647 DOI: 10.1097/md.0000000000013021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Tripartite motif-containing protein 44 (TRIM44) plays an important role in the development and progression of some human cancers; however, its role in skin squamous cell carcinoma (SCC) remains unknown. The aim of the present study was to investigate TRIM44 expression and clinicopathological significance of TRIM44 in SCC.Immunohistochemistry (IHC) technique, reverse transcriptase-polymerase chain reaction (RT-PCR) and western blot were performed to evaluate differences in TRIM44 protein expression in SCC and normal skin tissues.IHC showed that the positive rate of TRIM44 staining in SCC tissues 26.00% (9/30), while the positive rate of normal control group was 83.33% (25/30). The positive rate of TRIM44 staining in SCC tissues is significantly lower than normal skin tissue (P <.01). RT-PCR showed that the positive rates of TRIM44 mRNA expression in SCC tissues were 16.67% (5/30), but the positive rate of normal control group was 86.67% (26/30). TRIM44 mRNA expression in SCC group was significantly lower than that in the normal group (P <.01). Kaplan-Meier survival analysis showed that low expression was associated with poor overall survival in SCC patients (P =.004). Multi-factor survival analysis indicated that both low TRIM44 expression and tumor stage were independent factors affecting the overall survival of patients with SCC (P =.038 and P =.001, respectively). Low expression of TRIM44 in SCC was associated with staging (P =.009 and P =.008, respectively) and metastasis (P =.003 and P =.004, respectively).The levels of TRIM44 protein and TRIM44 mRNA in SCC are both lowly expressed which is strongly associated with tumor staging, metastasis, and poor survival. And it also is an independent factor affecting the overall survival of patients with SCC.
Collapse
Affiliation(s)
- Jian Wu
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City, Yancheng
| | - Nai-Zhou Guo
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City, Yancheng
| | - Lei-lei Cui
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City, Yancheng
| | - Wei Wang
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City, Yancheng
| | - Cun-quan Xiong
- College of pharmacy, Jiangsu Vocational College Medicine, Yancheng, Jiangsu, China
| | - Xue-yan Zhang
- College of pharmacy, Jiangsu Vocational College Medicine, Yancheng, Jiangsu, China
| |
Collapse
|
82
|
The Human CMV IE1 Protein: An Offender of PML Nuclear Bodies. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2018; 223:77-94. [PMID: 28528440 DOI: 10.1007/978-3-319-53168-7_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PML nuclear bodies (PML-NBs) are SUMOylation-dependent, highly complex protein assemblies that accumulate in the interchromosomal territories of the cell nucleus. Research of the last two decades revealed that many viruses have evolved effector proteins that modify PML-NBs. This correlates with antagonization of individual PML-NB components which act as host cell restriction factors. The multifunctional immediate-early protein IE1 of human cytomegalovirus directly interacts with the PML protein resulting in a disruption of the dot-like structure of PML-NBs. This review summarizes recent advances on the functional consequences of PML-NB modification by IE1. In particular, we describe that PML exerts a novel co-regulatory role during the interferon response which is abrogated by IE1. Via binding to PML, IE1 is able to compromise both intrinsic antiviral defense mechanisms and classical innate immune responses. These interactions of IE1 with innate host defenses are crucial for the onset of lytic replication and, consequently, may represent promising targets for antiviral strategies.
Collapse
|
83
|
Gushchina LV, Kwiatkowski TA, Bhattacharya S, Weisleder NL. Conserved structural and functional aspects of the tripartite motif gene family point towards therapeutic applications in multiple diseases. Pharmacol Ther 2018; 185:12-25. [PMID: 29097306 PMCID: PMC5721676 DOI: 10.1016/j.pharmthera.2017.10.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The tripartite motif (TRIM) gene family is a highly conserved group of E3 ubiquitin ligase proteins that can establish substrate specificity for the ubiquitin-proteasome complex and also have proteasome-independent functions. While several family members were studied previously, it is relatively recent that over 80 genes, based on sequence homology, were grouped to establish the TRIM gene family. Functional studies of various TRIM genes linked these proteins to modulation of inflammatory responses showing that they can contribute to a wide variety of disease states including cardiovascular, neurological and musculoskeletal diseases, as well as various forms of cancer. Given the fundamental role of the ubiquitin-proteasome complex in protein turnover and the importance of this regulation in most aspects of cellular physiology, it is not surprising that TRIM proteins display a wide spectrum of functions in a variety of cellular processes. This broad range of function and the highly conserved primary amino acid sequence of family members, particularly in the canonical TRIM E3 ubiquitin ligase domain, complicates the development of therapeutics that specifically target these proteins. A more comprehensive understanding of the structure and function of TRIM proteins will help guide therapeutic development for a number of different diseases. This review summarizes the structural organization of TRIM proteins, their domain architecture, common and unique post-translational modifications within the family, and potential binding partners and targets. Further discussion is provided on efforts to target TRIM proteins as therapeutic agents and how our increasing understanding of the nature of TRIM proteins can guide discovery of other therapeutics in the future.
Collapse
Affiliation(s)
- Liubov V Gushchina
- Department of Physiology & Cell Biology, The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Thomas A Kwiatkowski
- Department of Physiology & Cell Biology, The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Sayak Bhattacharya
- Department of Physiology & Cell Biology, The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Noah L Weisleder
- Department of Physiology & Cell Biology, The Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
| |
Collapse
|
84
|
de Moura TR, Mozaffari-Jovin S, Szabó CZK, Schmitzová J, Dybkov O, Cretu C, Kachala M, Svergun D, Urlaub H, Lührmann R, Pena V. Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors. Mol Cell 2018; 69:979-992.e6. [DOI: 10.1016/j.molcel.2018.02.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 11/22/2017] [Accepted: 02/15/2018] [Indexed: 01/24/2023]
|
85
|
Wang S, Kollipara RK, Humphries CG, Ma SH, Hutchinson R, Li R, Siddiqui J, Tomlins SA, Raj GV, Kittler R. The ubiquitin ligase TRIM25 targets ERG for degradation in prostate cancer. Oncotarget 2018; 7:64921-64931. [PMID: 27626314 PMCID: PMC5323126 DOI: 10.18632/oncotarget.11915] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/02/2016] [Indexed: 11/25/2022] Open
Abstract
Ets related gene (ERG) is a transcription factor that is overexpressed in 40% of prostate tumors due to a gene fusion between ERG and TMPRSS2. Because ERG functions as a driver of prostate carcinogenesis, understanding the mechanisms that influence its turnover may provide new molecular handles to target the protein. Previously, we found that ERG undergoes ubiquitination and then is deubiquitinated by USP9X in prostate cancer cells to prevent its proteasomal degradation. Here, we identify Tripartite motif-containing protein 25 (TRIM25) as the E3 ubiquitin ligase that ubiquitinates the protein prior to its degradation. TRIM25 binds full-length ERG, and it also binds the N-terminally truncated variants of ERG that are expressed in tumors with TMPRSS2-ERG fusions. We demonstrate that TRIM25 polyubiquitinates ERG in vitro and that inactivation of TRIM25 resulted in reduced polyubiquitination and stabilization of ERG. TRIM25 mRNA and protein expression was increased in ERG rearrangement-positive prostate cancer specimens, and we provide evidence that ERG upregulates TRIM25 expression. Thus, overexpression of ERG in prostate cancer may cause an increase in TRIM25 activity, which is mitigated by the expression of the deubiquitinase USP9X, which is required to stabilize ERG.
Collapse
Affiliation(s)
- Shan Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Caroline G Humphries
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shi-Hong Ma
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Ryan Hutchinson
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Rui Li
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Javed Siddiqui
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Scott A Tomlins
- Department of Pathology, Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.,Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
| |
Collapse
|
86
|
Choudhury NR, Heikel G, Trubitsyna M, Kubik P, Nowak JS, Webb S, Granneman S, Spanos C, Rappsilber J, Castello A, Michlewski G. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. BMC Biol 2017; 15:105. [PMID: 29117863 PMCID: PMC5678581 DOI: 10.1186/s12915-017-0444-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND TRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. However, there is scarce knowledge about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. RESULTS Here, we reveal that the RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain. Using CLIP-seq and SILAC-based co-immunoprecipitation assays, we uncover TRIM25's endogenous RNA targets and protein binding partners. We demonstrate that TRIM25 controls the levels of Zinc Finger Antiviral Protein (ZAP). Finally, we show that the RNA-binding activity of TRIM25 is important for its ubiquitin ligase activity towards itself (autoubiquitination) and its physiologically relevant target ZAP. CONCLUSIONS Our results suggest that many other proteins with the PRY/SPRY domain could have yet uncharacterized RNA-binding potential. Together, our data reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor in their enzymatic activity.
Collapse
Affiliation(s)
- Nila Roy Choudhury
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Gregory Heikel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Maryia Trubitsyna
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Roger Land Building, Edinburgh, EH9 3FF, UK
| | - Peter Kubik
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Jakub Stanislaw Nowak
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Sander Granneman
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, CH Waddington Building, Edinburgh, EH9 3BF, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, 13353, Berlin, Germany
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Gracjan Michlewski
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK.
| |
Collapse
|
87
|
Meyerson NR, Zhou L, Guo YR, Zhao C, Tao YJ, Krug RM, Sawyer SL. Nuclear TRIM25 Specifically Targets Influenza Virus Ribonucleoproteins to Block the Onset of RNA Chain Elongation. Cell Host Microbe 2017; 22:627-638.e7. [PMID: 29107643 PMCID: PMC6309188 DOI: 10.1016/j.chom.2017.10.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 07/21/2017] [Accepted: 09/26/2017] [Indexed: 11/20/2022]
Abstract
TRIM25 is an E3 ubiquitin ligase that activates RIG-I to promote the antiviral interferon response. The NS1 protein from all strains of influenza A virus binds TRIM25, although not all virus strains block the interferon response, suggesting alternative mechanisms for TRIM25 action. Here we present a nuclear role for TRIM25 in specifically restricting influenza A virus replication. TRIM25 inhibits viral RNA synthesis through a direct mechanism that is independent of its ubiquitin ligase activity and the interferon pathway. This activity can be inhibited by the viral NS1 protein. TRIM25 inhibition of viral RNA synthesis results from its binding to viral ribonucleoproteins (vRNPs), the structures containing individual viral RNA segments, the viral polymerase, and multiple viral nucleoproteins. TRIM25 binding does not inhibit initiation of capped-RNA-primed viral mRNA synthesis by the viral polymerase. Rather, the onset of RNA chain elongation is inhibited because TRIM25 prohibits the movement of RNA into the polymerase complex.
Collapse
Affiliation(s)
- Nicholas R Meyerson
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Ligang Zhou
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
| | - Yusong R Guo
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Chen Zhao
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA
| | - Yizhi J Tao
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robert M Krug
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, University of Texas at Austin, Austin, TX 78712, USA.
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80303, USA.
| |
Collapse
|
88
|
Roganowicz MD, Komurlu S, Mukherjee S, Plewka J, Alam SL, Skorupka KA, Wan Y, Dawidowski D, Cafiso DS, Ganser-Pornillos BK, Campbell EM, Pornillos O. TRIM5α SPRY/coiled-coil interactions optimize avid retroviral capsid recognition. PLoS Pathog 2017; 13:e1006686. [PMID: 29040325 PMCID: PMC5667893 DOI: 10.1371/journal.ppat.1006686] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 11/02/2017] [Accepted: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
Restriction factors are important components of intrinsic cellular defense mechanisms against viral pathogens. TRIM5α is a restriction factor that intercepts the incoming capsid cores of retroviruses such as HIV and provides an effective species-specific barrier to retroviral infection. The TRIM5α SPRY domain directly binds the capsid with only very weak, millimolar-level affinity, and productive capsid recognition therefore requires both TRIM5α dimerization and assembly of the dimers into a multivalent hexagonal lattice to promote avid binding. Here, we explore the important unresolved question of whether the SPRY domains are flexibly linked to the TRIM lattice or more precisely positioned to maximize avidity. Biochemical and biophysical experiments indicate that the linker segment connecting the SPRY domain to the coiled-coil domain adopts an α-helical fold, and that this helical portion mediates interactions between the two domains. Targeted mutations were generated to disrupt the putative packing interface without affecting dimerization or higher-order assembly, and we identified mutant proteins that were nevertheless deficient in capsid binding in vitro and restriction activity in cells. Our studies therefore support a model wherein substantial avidity gains during assembly-mediated capsid recognition by TRIM5α come in part from tailored spacing of tethered recognition domains.
Collapse
Affiliation(s)
- Marcin D. Roganowicz
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Sevnur Komurlu
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Santanu Mukherjee
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Jacek Plewka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Steven L. Alam
- Department of Biochemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Katarzyna A. Skorupka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Yueping Wan
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Damian Dawidowski
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - David S. Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Edward M. Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- * E-mail:
| |
Collapse
|
89
|
The TRIMendous Role of TRIMs in Virus-Host Interactions. Vaccines (Basel) 2017; 5:vaccines5030023. [PMID: 28829373 PMCID: PMC5620554 DOI: 10.3390/vaccines5030023] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/09/2017] [Accepted: 08/17/2017] [Indexed: 12/23/2022] Open
Abstract
The innate antiviral response is integral in protecting the host against virus infection. Many proteins regulate these signaling pathways including ubiquitin enzymes. The ubiquitin-activating (E1), -conjugating (E2), and -ligating (E3) enzymes work together to link ubiquitin, a small protein, onto other ubiquitin molecules or target proteins to mediate various effector functions. The tripartite motif (TRIM) protein family is a group of E3 ligases implicated in the regulation of a variety of cellular functions including cell cycle progression, autophagy, and innate immunity. Many antiviral signaling pathways, including type-I interferon and NF-κB, are TRIM-regulated, thus influencing the course of infection. Additionally, several TRIMs directly restrict viral replication either through proteasome-mediated degradation of viral proteins or by interfering with different steps of the viral replication cycle. In addition, new studies suggest that TRIMs can exert their effector functions via the synthesis of unconventional polyubiquitin chains, including unanchored (non-covalently attached) polyubiquitin chains. TRIM-conferred viral inhibition has selected for viruses that encode direct and indirect TRIM antagonists. Furthermore, new evidence suggests that the same antagonists encoded by viruses may hijack TRIM proteins to directly promote virus replication. Here, we describe numerous virus–TRIM interactions and novel roles of TRIMs during virus infections.
Collapse
|
90
|
Liu XJ, Yang B, Huang SN, Wu CC, Li XJ, Cheng S, Jiang X, Hu F, Ming YZ, Nevels M, Britt WJ, Rayner S, Tang Q, Zeng WB, Zhao F, Luo MH. Human cytomegalovirus IE1 downregulates Hes1 in neural progenitor cells as a potential E3 ubiquitin ligase. PLoS Pathog 2017; 13:e1006542. [PMID: 28750047 PMCID: PMC5549770 DOI: 10.1371/journal.ppat.1006542] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/08/2017] [Accepted: 07/19/2017] [Indexed: 01/12/2023] Open
Abstract
Congenital human cytomegalovirus (HCMV) infection is the leading cause of neurological disabilities in children worldwide, but the mechanisms underlying these disorders are far from well-defined. HCMV infection has been shown to dysregulate the Notch signaling pathway in human neural progenitor cells (NPCs). As an important downstream effector of Notch signaling, the transcriptional regulator Hairy and Enhancer of Split 1 (Hes1) is essential for governing NPC fate and fetal brain development. In the present study, we report that HCMV infection downregulates Hes1 protein levels in infected NPCs. The HCMV 72-kDa immediate-early 1 protein (IE1) is involved in Hes1 degradation by assembling a ubiquitination complex and promoting Hes1 ubiquitination as a potential E3 ubiquitin ligase, followed by proteasomal degradation of Hes1. Sp100A, an important component of PML nuclear bodies, is identified to be another target of IE1-mediated ubiquitination. A C-terminal acidic region in IE1, spanning amino acids 451 to 475, is required for IE1/Hes1 physical interaction and IE1-mediated Hes1 ubiquitination, but is dispensable for IE1/Sp100A interaction and ubiquitination. Our study suggests a novel mechanism linking downregulation of Hes1 protein to neurodevelopmental disorders caused by HCMV infection. Our findings also complement the current knowledge of herpesviruses by identifying IE1 as the first potential HCMV-encoded E3 ubiquitin ligase. Congenital human cytomegalovirus (HCMV) infection is the leading cause of neurological disabilities in children, but the underlying pathogenesis of this infection remains unclear. Hes1, an important effector of Notch signaling, governs the fate of neural progenitor cells (NPCs) and fetal brain development. Here we demonstrate that: (1) HCMV infection results in loss of Hes1 protein in NPCs; (2) the HCMV immediate-early 1 protein (IE1) mediates Hes1 protein downregulation through direct interaction, which requires amino acids 451–475; (3) IE1 assembles a Hes1 ubiquitination complex and mediates Hes1 ubiquitination; and (4) IE1 also assembles an Sp100A ubiquitination complex and mediates Sp100A ubiquitination, but does not require amino acids 451–475. These results suggest that HCMV IE1 is a potential E3 ubiquitin ligase. Downregulation of Hes1 by HCMV infection and IE1 implies a novel mechanism linking Hes1 depletion to virus-induced neuropathogenesis.
Collapse
Affiliation(s)
- Xi-Juan Liu
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Yang
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Sheng-Nan Huang
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Cong-Cong Wu
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Jun Li
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shuang Cheng
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xuan Jiang
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, China
| | - Fei Hu
- Wuhan Brain Hospital, Ministry of Transportation, Wuhan, Hubei, China
| | - Ying-Zi Ming
- The Third Xiangya Hospital, South Central University, Changsha, Hunan, China
| | - Michael Nevels
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife, United Kingdom
| | - William J. Britt
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, Alabama, United States of America
| | - Simon Rayner
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- Department of Medical Genetics, Oslo University Hospital & University of Oslo, Oslo, Norway
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Howard University, Washington DC, United States of America
| | - Wen-Bo Zeng
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail: (WBZ); (FZ); (MHL)
| | - Fei Zhao
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail: (WBZ); (FZ); (MHL)
| | - Min-Hua Luo
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children Medical Center, Guangzhou, China
- * E-mail: (WBZ); (FZ); (MHL)
| |
Collapse
|
91
|
Dawidziak DM, Sanchez JG, Wagner JM, Ganser-Pornillos BK, Pornillos O. Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase. Proteins 2017; 85:1957-1961. [PMID: 28681414 DOI: 10.1002/prot.25348] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/03/2017] [Indexed: 01/02/2023]
Abstract
Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2-ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.
Collapse
Affiliation(s)
- Daria M Dawidziak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Jacint G Sanchez
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Jonathan M Wagner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia
| |
Collapse
|
92
|
Hao L, Du B, Xi X. TRIM59 is a novel potential prognostic biomarker in patients with non-small cell lung cancer: A research based on bioinformatics analysis. Oncol Lett 2017; 14:2153-2164. [PMID: 28789440 PMCID: PMC5530082 DOI: 10.3892/ol.2017.6467] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 06/14/2017] [Indexed: 12/28/2022] Open
Abstract
Lung cancer is the leading cause of cancer-associated mortality worldwide and its prognosis is poor. Few effective biomarkers for non-small cell lung cancer (NSCLC) have been translated into the clinical practice aiming to assist in the treatment plan design and prognosis evaluation. The aim of the present study was to identify novel potential prognostic biomarkers for NSCLC. Tripartite motif 59 (TRIM59) was identified from a microarray dataset of matched-samples and was verified as an aberrantly upregulated gene in NSCLC tissue. The expression level of TRIM59 in NSCLC subtypes was observed to be significantly increased in large cell lung carcinoma and squamous cell carcinoma as compared with that in adenocarcinoma. Its expression correlated with several clinicopathological features, including gender, smoking habits, and unfavorable tumor node and pathological stages. Notably, TRIM59 demonstrated a negative correlation with survival time and its overexpression indicated a poor prognosis in NSCLC. Furthermore, univariate and multivariate Cox's regression analyses indicated that TRIM59 was an independent prognostic factor in tumor tissue as compared with age, gender, tumor stage, node stage, and metastasis. Gene set enrichment analysis and protein-protein interaction network construction revealed that TRIM59 was associated with oncogenic mammalian target of rapamycin (MTOR) and eukaryotic initiation factor 4E (EIF4E) signaling through ubiquitin C binding. In conclusion, it was revealed that TRIM59 is a novel prognostic biomarker modulating oncogenic MTOR and EIF4E signaling pathways in NSCLC. These findings provided a novel insight into the clinical application of TRIM59. Therefore, TRIM59 may serve as an independent predictor for prognosis and a potential therapeutic target for NSCLC.
Collapse
Affiliation(s)
- Ling Hao
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Boyu Du
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Xueyan Xi
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| |
Collapse
|
93
|
Abstract
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation. In this review, we summarize the current progress in structure-function studies of ubiquitin ligases as well as exciting new discoveries of novel classes of E3s and diverse substrate recognition mechanisms. Our increased understanding of ubiquitin ligase function and regulation has provided the rationale for developing E3-targeting therapeutics for the treatment of human diseases.
Collapse
Affiliation(s)
- Ning Zheng
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| | - Nitzan Shabek
- Howard Hughes Medical Institute and Department of Pharmacology, University of Washington, Seattle, Washington 98195; ,
| |
Collapse
|
94
|
Watanabe M, Hatakeyama S. TRIM proteins and diseases. J Biochem 2017; 161:135-144. [PMID: 28069866 DOI: 10.1093/jb/mvw087] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 12/20/2022] Open
Abstract
Ubiquitination is one of the posttranslational modifications that regulates a number of intracellular events including signal transduction, protein quality control, transcription, cell cycle, apoptosis and development. The ubiquitin system functions as a garbage machine to degrade target proteins and as a regulator for several signalling pathways. Biochemical reaction of ubiquitination requires several enzymes including E1, E2 and E3, and E3 ubiquitin ligases play roles as receptors for recognizing target proteins. Most of the tripartite motif (TRIM) proteins are E3 ubiquitin ligases. Recent studies have shown that some TRIM proteins function as important regulators for a variety of diseases including cancer, inflammatory diseases, infectious diseases, neuropsychiatric disorders, chromosomal abnormalities and developmental diseases. In this review, we summarize the involvement of TRIM proteins in the aetiology of various diseases.
Collapse
Affiliation(s)
- Masashi Watanabe
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| |
Collapse
|
95
|
Zhang Y, Wu HK, Lv F, Xiao RP. MG53: Biological Function and Potential as a Therapeutic Target. Mol Pharmacol 2017; 92:211-218. [DOI: 10.1124/mol.117.108241] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/12/2017] [Indexed: 01/11/2023] Open
|
96
|
Structural determinants of TRIM protein function. Biochem Soc Trans 2017; 45:183-191. [DOI: 10.1042/bst20160325] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/14/2016] [Accepted: 10/24/2016] [Indexed: 01/04/2023]
Abstract
Tripartite motif (TRIM) proteins constitute one of the largest subfamilies of Really Interesting New Gene (RING) E3 ubiquitin ligases and contribute to the regulation of numerous cellular activities, including innate immune responses. The conserved TRIM harbours a RING domain that imparts E3 ligase activity to TRIM family proteins, whilst a variable C-terminal region can mediate recognition of substrate proteins. The knowledge of the structure of these multidomain proteins and the functional interplay between their constituent domains is paramount to understanding their cellular roles. To date, available structural information on TRIM proteins is still largely restricted to subdomains of many TRIMs in isolation. Nevertheless, applying a combination of structural, biophysical and biochemical approaches has recently allowed important progress to be made towards providing a better understanding of the molecular features that underlie the function of TRIM family proteins and has uncovered an unexpected diversity in the link between self-association and catalytic activity.
Collapse
|
97
|
The Human Cytomegalovirus IE1 Protein Antagonizes PML Nuclear Body-Mediated Intrinsic Immunity via the Inhibition of PML De Novo SUMOylation. J Virol 2017; 91:JVI.02049-16. [PMID: 27903803 DOI: 10.1128/jvi.02049-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
PML nuclear bodies (NBs) are accumulations of cellular proteins embedded in a scaffold-like structure built by SUMO-modified PML/TRIM19. PML and other NB proteins act as cellular restriction factors against human cytomegalovirus (HCMV); however, this intrinsic defense is counteracted by the immediate early protein 1 (IE1) of HCMV. IE1 directly interacts with the PML coiled-coil domain via its globular core region and disrupts NB foci by inducing a loss of PML SUMOylation. Here, we demonstrate that IE1 acts via abrogating the de novo SUMOylation of PML. In order to overcome reversible SUMOylation dynamics, we made use of a cell-based assay that combines inducible IE1 expression with a SUMO mutant resistant to SUMO proteases. Interestingly, we observed that IE1 expression did not affect preSUMOylated PML; however, it clearly prevented de novo SUMO conjugation. Consistent results were obtained by in vitro SUMOylation assays, demonstrating that IE1 alone is sufficient for this effect. Furthermore, IE1 acts in a selective manner, since K160 was identified as the main target lysine. This is strengthened by the fact that IE1 also prevents As2O3-mediated hyperSUMOylation of K160, thereby blocking PML degradation. Since IE1 did not interfere with coiled-coil-mediated PML dimerization, we propose that IE1 affects PML autoSUMOylation either by directly abrogating PML E3 ligase function or by preventing access to SUMO sites. Thus, our data suggest a novel mechanism for how a viral protein counteracts a cellular restriction factor by selectively preventing the de novo SUMOylation at specific lysine residues without affecting global protein SUMOylation. IMPORTANCE The human cytomegalovirus IE1 protein acts as an important antagonist of a cellular restriction mechanism that is mediated by subnuclear structures termed PML nuclear bodies. This function of IE1 is required for efficient viral replication and thus constitutes a potential target for antiviral strategies. In this paper, we further elucidate the molecular mechanism for how IE1 antagonizes PML NBs. We show that tight binding of IE1 to PML interferes with the de novo SUMOylation of a distinct lysine residue that is also the target of stress-mediated hyperSUMOylation of PML. This is of importance since it represents a novel mechanism used by a viral antagonist of intrinsic immunity. Furthermore, it highlights the possibility of developing small molecules that specifically abrogate this PML-antagonistic activity of IE1 and thus inhibit viral replication.
Collapse
|
98
|
Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA. Nat Commun 2017; 8:14004. [PMID: 28084320 PMCID: PMC5241803 DOI: 10.1038/ncomms14004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/21/2016] [Indexed: 12/25/2022] Open
Abstract
The hallmark of Salmonella Typhimurium infection is an acute intestinal inflammatory response, which is mediated through the action of secreted bacterial effector proteins. The pro-inflammatory Salmonella effector SopA is a HECT-like E3 ligase, which was previously proposed to activate host RING ligases TRIM56 and TRIM65. Here we elucidate an inhibitory mechanism of TRIM56 and TRIM65 targeting by SopA. We present the crystal structure of SopA in complex with the RING domain of human TRIM56, revealing the atomic details of their interaction and the basis for SopA selectivity towards TRIM56 and TRIM65. Structure-guided biochemical analysis shows that SopA inhibits TRIM56 E3 ligase activity by occluding the E2-interacting surface of TRIM56. We further demonstrate that SopA ubiquitinates TRIM56 and TRIM65, resulting in their proteasomal degradation during infection. Our results provide the basis for how a bacterial HECT ligase blocks host RING ligases and exemplifies the multivalent power of bacterial effectors during infection.
Collapse
|
99
|
Huang B, Baek SH. Trim13 Potentiates Toll-Like Receptor 2-Mediated Nuclear Factor κB Activation via K29-Linked Polyubiquitination of Tumor Necrosis Factor Receptor-Associated Factor 6. Mol Pharmacol 2017; 91:307-316. [PMID: 28087809 DOI: 10.1124/mol.116.106716] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/03/2017] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a versatile post-translational modification involved in nuclear factor-κB (NF-κB) activation of Toll-like receptor (TLR) signaling. Here, we demonstrated that Trim13, an E3 ubiquitin ligase, is up-regulated in macrophages upon stimulation with TLR2 ligand. Knockdown of Trim13 attenuated TLR2-mediated production of cytokines/chemokines and formation of foam cells as well as activation of NF-κB. Trim13 interacts with tumor necrosis factor receptor-associated factor 6 (TRAF6) and potentiates NF-κB activity via ubiquitination of TRAF6. Overexpression of inactive mutant (C10/13A) or really interesting new gene (RING) deletion mutant of Trim13 did not potentiate ubiquitination of TRAF6 or activation of NF-κB. These results suggest that the effects of Trim13 are dependent on its E3 ligase activity. Trim13 used K29-linked polyubiquitin chains for TRAF6 ubiquitination to promote NF-κB activity and thus potentiated activation of TLR2-mediated immune responses. Our data identify Trim13 as a positive regulator of NF-κB activation and suggest that K29-linked polyubiquitination is a specific ubiquitin-linked pattern involved in the control of TLR2 signaling.
Collapse
Affiliation(s)
- Bin Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, Yeungnam University, Daegu, South Korea
| | - Suk-Hwan Baek
- Department of Biochemistry and Molecular Biology, College of Medicine, Yeungnam University, Daegu, South Korea
| |
Collapse
|
100
|
Sanchez JG, Chiang JJ, Sparrer KMJ, Alam SL, Chi M, Roganowicz MD, Sankaran B, Gack MU, Pornillos O. Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway. Cell Rep 2016; 16:1315-1325. [PMID: 27425606 PMCID: PMC5076470 DOI: 10.1016/j.celrep.2016.06.070] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 05/11/2016] [Accepted: 06/16/2016] [Indexed: 12/25/2022] Open
Abstract
Antiviral response pathways induce interferon by higher-order assembly of signaling complexes called signalosomes. Assembly of the RIG-I signalosome is regulated by K63-linked polyubiquitin chains, which are synthesized by the E3 ubiquitin ligase, TRIM25. We have previously shown that the TRIM25 coiled-coil domain is a stable, antiparallel dimer that positions two catalytic RING domains on opposite ends of an elongated rod. We now show that the RING domain is a separate self-association motif that engages ubiquitin-conjugated E2 enzymes as a dimer. RING dimerization is required for catalysis, TRIM25-mediated RIG-I ubiquitination, interferon induction, and antiviral activity. We also provide evidence that RING dimerization and E3 ligase activity are promoted by binding of the TRIM25 SPRY domain to the RIG-I effector domain. These results indicate that TRIM25 actively participates in higher-order assembly of the RIG-I signalosome and helps to fine-tune the efficiency of the RIG-I-mediated antiviral response.
Collapse
Affiliation(s)
- Jacint G Sanchez
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Steven L Alam
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Chi
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Marcin D Roganowicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michaela U Gack
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
| |
Collapse
|