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Suranjika S, Barla P, Sharma N, Dey N. A review on ubiquitin ligases: Orchestrators of plant resilience in adversity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112180. [PMID: 38964613 DOI: 10.1016/j.plantsci.2024.112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Ubiquitin- proteasome system (UPS) is universally present in plants and animals, mediating many cellular processes needed for growth and development. Plants constantly defend themselves against endogenous and exogenous stimuli such as hormonal signaling, biotic stresses such as viruses, fungi, nematodes, and abiotic stresses like drought, heat, and salinity by developing complex regulatory mechanisms. Ubiquitination is a regulatory mechanism involving selective elimination and stabilization of regulatory proteins through the UPS system where E3 ligases play a central role; they can bind to the targets in a substrate-specific manner, followed by poly-ubiquitylation, and subsequent protein degradation by 26 S proteasome. Increasing evidence suggests different types of E3 ligases play important roles in plant development and stress adaptation. Herein, we summarize recent advances in understanding the regulatory roles of different E3 ligases and primarily focus on protein ubiquitination in plant-environment interactions. It also highlights the diversity and complexity of these metabolic pathways that enable plant to survive under challenging conditions. This reader-friendly review provides a comprehensive overview of E3 ligases and their substrates associated with abiotic and biotic stresses that could be utilized for future crop improvement.
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Affiliation(s)
- Sandhya Suranjika
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India; Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), KIIT Road, Patia, Bhubaneswar, Odisha, India
| | - Preeti Barla
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Namisha Sharma
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India.
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2
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Naryzhny S. Puzzle of Proteoform Variety-Where Is a Key? Proteomes 2024; 12:15. [PMID: 38804277 PMCID: PMC11130821 DOI: 10.3390/proteomes12020015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.
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Affiliation(s)
- Stanislav Naryzhny
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad Region, Gatchina 188300, Russia
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3
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Chen X, Zhang W, Han X, Li X, Xia L, Wu Y, Zhou Y. TMED3 stabilizes SMAD2 by counteracting NEDD4-mediated ubiquitination to promote ovarian cancer. Mol Carcinog 2024; 63:803-816. [PMID: 38411267 DOI: 10.1002/mc.23689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 02/28/2024]
Abstract
Ovarian cancer is a major cause of death among cancer patients. Recent research has shown that the transmembrane emp24 domain (TMED) protein family plays a role in the progression of various types of cancer. In this study, we investigated the expression of TMED3 in ovarian cancer tumors compared to nontumor tissues using immunohistochemical staining. We found that TMED3 was overexpressed in ovarian cancer tumors, and its high expression was associated with poor disease-free and overall survival. To understand the functional implications of TMED3 overexpression in ovarian cancer, we conducted experiments to knockdown TMED3 using short hairpin RNA (shRNA). We observed that TMED3 knockdown resulted in reduced cell viability and migration, as well as increased cell apoptosis. Additionally, in subcutaneous xenograft models in BALB-c nude mice, TMED3 knockdown inhibited tumor growth. Further investigation revealed that SMAD family member 2 (SMAD2) was a downstream target of TMED3, driving ovarian cancer progression. TMED3 stabilized SMAD2 by inhibiting the E3 ligase NEDD4-mediated ubiquitination of SMAD2. To confirm the importance of SMAD2 in TMED3-mediated ovarian cancer, we performed functional rescue experiments and found that SMAD2 played a critical role in this process. Moreover, we discovered that the PI3K-AKT pathway was involved in the promoting effects of TMED3 overexpression on ovarian cancer cells. Overall, our study identifies TMED3 as a prognostic indicator and tumor promoter in ovarian cancer. Its function is likely mediated through the regulation of the SMAD2 and PI3K-AKT signaling pathway. These findings contribute to our understanding of the molecular mechanisms underlying ovarian cancer progression and provide potential targets for therapeutic intervention.
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Affiliation(s)
- Xiaojun Chen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Zhang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaotian Han
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoqi Li
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lingfang Xia
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yong Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yang Zhou
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Huang R, Nie W, Mi L, Yao C, Zhu H. EIF3B stabilizes PCNA by counteracting SYVN1-mediated ubiquitination to serve as a promotor in cholangiocarcinoma. Aging (Albany NY) 2024; 16:7311-7330. [PMID: 38687509 PMCID: PMC11087095 DOI: 10.18632/aging.205759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024]
Abstract
Cholangiocarcinoma, a prevalent hepatic malignancy, exhibits a progressively rising incidence. While Eukaryotic translation initiation factor 3 subunit B (EIF3B) has been implicated in the occurrence and development of various cancers, its specific roles in cholangiocarcinoma remain unexplored. Immunohistochemical (IHC) analysis was employed to detect EIF3B/PCNA expression in cholangiocarcinoma. Cells were manipulated using short hairpin RNA (shRNA)-mediated lentiviruses or overexpression plasmids. Statistical significance was assessed using the Student's t-test and one-way ANOVA, with P < 0.05 considered statistically significant. EIF3B exhibited robust expression in cholangiocarcinoma, demonstrating a significant correlation with the pathological grade of cholangiocarcinoma patients. Furthermore, modulation of EIF3B expression, either depletion or elevation, demonstrated the ability to inhibit or enhance cholangiocarcinoma cell survival and migration in vitro. Mechanistically, we identified Proliferating Cell Nuclear Antigen (PCNA) as a downstream gene of EIF3B, driving cholangiocarcinoma. EIF3B stabilized PCNA by inhibiting PCNA ubiquitination, a process mediated by E3 ligase SYVN1. Similar to EIF3B, PCNA levels were also abundant in cholangiocarcinoma, and knocking down PCNA impeded cholangiocarcinoma development. Intriguingly, silencing PCNA attenuated the promotion induced by EIF3B overexpression. Furthermore, the elevated P21 protein level in shEIF3B RBE cells was partially attenuated after UC2288 (P21 signaling pathway inhibitor) treatment. Our findings underscored the potential of EIF3B as a therapeutic target for cholangiocarcinoma. Unraveling its functions holds promise for the development of more specific and effective targeted therapy strategies.
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Affiliation(s)
- Ranglang Huang
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of the Central South University, Changsha 400013, Hunan, P.R. China
| | - Wanpin Nie
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of the Central South University, Changsha 400013, Hunan, P.R. China
| | - Liangliang Mi
- Department of Hepatobiliary and Pancreatic Surgery, The Third Xiangya Hospital of the Central South University, Changsha 400013, Hunan, P.R. China
| | - Chenjiao Yao
- Department of General Medicine, Third Xiangya Hospital, Central South University, Changsha 400013, Hunan, P.R. China
| | - Haixia Zhu
- Department of General Medicine, Third Xiangya Hospital, Central South University, Changsha 400013, Hunan, P.R. China
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5
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Zhang F, Huang C. GSG2 promotes thyroid cancer via stabilizing AURKB and activating AKT pathway. Aging (Albany NY) 2024; 16:5091-5107. [PMID: 38441546 PMCID: PMC11006493 DOI: 10.18632/aging.205605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 01/29/2024] [Indexed: 04/06/2024]
Abstract
Thyroid cancer stands out as the most prevalent endocrine cancer, with its incidence on a global rise. While numerous studies have delved into the roles of GSG2 in the progression of various malignancies, its involvement in thyroid cancer remains relatively unexplored. Therefore, this study was initiated to assess the functional importance of GSG2 in human thyroid cancer development. Our findings revealed a notable upregulation of GSG2 in both thyroid cancer tissues and cell lines, demonstrating a significant correlation with the pathological stage and patients' prognosis. Depletion of GSG2 in thyroid cancer cells resulted in suppressed malignant cell development and inhibited tumor outgrowth. Crucially, our investigation identified AURKB as a downstream gene of GSG2. GSG2 exhibited its regulatory role by stabilizing AURKB, countering SMURF1-mediated ubiquitination of AURKB. Furthermore, overexpressing AURKB restored the functional consequences of GSG2 depletion in thyroid cancer cells. Additionally, we proposed the involvement of the AKT pathway in GSG2-mediated regulation of thyroid cancer. Intriguingly, the reversal of cell phenotype alterations in GSG2-depleted cells following an AKT activator underscored the potential link between GSG2 and the AKT pathway. At the molecular level, GSG2 knockdown downregulated p-AKT, an effect partially restored after AKT activator treatment. In summary, our study concluded that GSG2 played a pivotal role in thyroid carcinogenesis, underscoring its potential as a therapeutic target for thyroid cancer.
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Affiliation(s)
- Fenghua Zhang
- Department of Thyroid and Breast Surgery, Hebei General Hospital, Shijiazhuang 050051, Hebei Province, China
| | - Chiming Huang
- Thyroid Hernia Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Yuexiu, Guangzhou 510182, Guangdong Province, China
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Liu Q, Maqbool A, Mirkin FG, Singh Y, Stevenson CEM, Lawson DM, Kamoun S, Huang W, Hogenhout SA. Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation. Proc Natl Acad Sci U S A 2023; 120:e2310664120. [PMID: 38039272 DOI: 10.1073/pnas.2310664120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 12/03/2023] Open
Abstract
In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously identified that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05-Rpn10vWA complex at 2.17 Å resolution and of the SAP05-SPL5ZnF complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a remarkable bimodular architecture with two distinct nonoverlapping surfaces, a "loop surface" with three protruding loops that form electrostatic interactions with ZnF, and a "sheet surface" featuring two β-sheets, loops, and α-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical ubiquitin-proteasome proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of TPD technologies.
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Affiliation(s)
- Qun Liu
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Abbas Maqbool
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Federico G Mirkin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Yeshveer Singh
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Weijie Huang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 20032, China
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Qiao H, Xu Q, Xu Y, Zhao Y, He N, Tang J, Zhao J, Liu Y. Molecular chaperones in stroke-induced immunosuppression. Neural Regen Res 2023; 18:2638-2644. [PMID: 37449602 DOI: 10.4103/1673-5374.373678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Stroke-induced immunosuppression is a process that leads to peripheral suppression of the immune system after a stroke and belongs to the central nervous system injury-induced immunosuppressive syndrome. Stroke-induced immunosuppression leads to increased susceptibility to post-stroke infections, such as urinary tract infections and stroke-associated pneumonia, worsening prognosis. Molecular chaperones are a large class of proteins that are able to maintain proteostasis by directing the folding of nascent polypeptide chains, refolding misfolded proteins, and targeting misfolded proteins for degradation. Various molecular chaperones have been shown to play roles in stroke-induced immunosuppression by modulating the activity of other molecular chaperones, cochaperones, and their associated pathways. This review summarizes the role of molecular chaperones in stroke-induced immunosuppression and discusses new approaches to restore host immune defense after stroke.
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Affiliation(s)
- Haoduo Qiao
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
| | - Qing Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
| | - Yunfei Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
| | - Yao Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
| | - Nina He
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
| | - Jie Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Jie Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
| | - Ying Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University; Department of Pathophysiology, Xiangya School of Medicine, Central South University; Sepsis Translational Medicine Key Laboratory of Hunan Province; National Medicine Functional Experimental Teaching Center, Changsha, Hunan Province, China
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8
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Qi N, Yan J, Lei P, Kang W, Liu X, Xuan Y, Fan H, Wang Y, Yang N, Chen L, Duan Y, Zhu X. Transcriptome Analysis of GmPUB20A Overexpressing and RNA-Interferencing Transgenic Hairy Roots Reveals Underlying Negative Role in Soybean Resistance to Cyst Nematode. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18059-18073. [PMID: 37948664 DOI: 10.1021/acs.jafc.3c05617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Ubiquitination genes are key components of plant responses to biotic stress. GmPUB20A, a ubiquitination gene, plays a negative role in soybean resistance to soybean cyst nematode (SCN). In this study, we employed high-throughput sequencing to investigate transcriptional changes in GmPUB20A overexpressing and RNA-interfering transgenic hairy roots. Totally, 7661 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that DEGs were significantly enriched in disease resistance and signal transduction pathways. In addition, silencing Glyma.15G021600 and Glyma.09G284700 by siRNA, the total number of nematodes was decreased by 33.48% and 27.47% than control plants, respectively. Further, GUS activity and reactive oxygen species (ROS) assays revealed that GmPUB20A, Glyma.15G021600, and Glyma.09G284700 respond to SCN parasitism and interfere with the accumulation of ROS in plant roots, respectively. Collectively, our study provides insights into the molecular mechanism of GmPUB20A in soybean resistance to SCN.
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Affiliation(s)
- Nawei Qi
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Jichen Yan
- Institute of Plant Protection, Liaoning Academy of Agriculture Sciences, Shenyang 100161, China
| | - Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Wenshu Kang
- College of Environment, Shenyang University, Shenyang 110044, China
| | - Xiaoyu Liu
- College of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ning Yang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
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Liu Y, Xiong Y. HADHA promotes ovarian cancer outgrowth via up-regulating CDK1. Cancer Cell Int 2023; 23:283. [PMID: 37986001 PMCID: PMC10658966 DOI: 10.1186/s12935-023-03120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Ovarian cancer, a prevalent cause of cancer-related mortality among gynecological cancers, still lacks a clear understanding of its pathogenesis. In this study, our objective was to investigate the functional roles and pathogenic mechanisms of HADHA in ovarian cancer. METHODS We utilized an ovarian cancer tissue microarray and three ovarian cancer cell lines (HO-8910, A2780, and SK-OV-3) for our analysis. Lentiviral-mediated short hairpin RNA (shRNA) was employed to interfere with HADHA expression in ovarian cancer cells. Various cellular events associated with tumor development were assessed using techniques such as Celigo cell counting assay, wound healing assay, Transwell assay, and flow cytometry analysis. Additionally, xenograft tumor models were developed to visualize the impacts of HADHA/CDK1 on ovarian cancer progression. RESULTS Our data revealed significant HADHA overexpression in both ovarian cancer tissues and cell lines. Patients with elevated HADHA levels tended to experience poor survival outcomes. Moreover, HADHA upregulation correlated with several pathological parameters, including pathological stage, tumor size, tumor infiltrate, metastasis, and recurrence. Loss-of-function experiments targeting HADHA demonstrated that its suppression in ovarian cancer cells hindered cell growth and migration, while promoting apoptosis. To elucidate the underlying mechanism by which HADHA regulates ovarian cancer, we identified CDK1 as a target of HADHA. HADHA upregulated CDK1 expression by inhibiting its ubiquitination-dependent proteasomal degradation. Significantly, the overexpression of CDK1 reversed the impaired cell development caused by HADHA depletion, both in vitro and in vivo. CONCLUSION Our study highlights the involvement of HADHA in ovarian cancer tumorigenesis and suggests its potential as a promising prognostic marker in ovarian cancer. Through its regulation of CDK1, HADHA influences critical cellular processes in ovarian cancer, providing insights into its pathogenic mechanism.
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Affiliation(s)
- Yinglan Liu
- Department of Obsdetrics and Gynecology, First Affiliated Hospital of Harbin Medical University, No.23, Youzheng Road, Harbin city, 150001, Heilongjiang Province, China
| | - Ying Xiong
- Department of Gynecology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, No.651, Dongfengdong Road, Guangzhou, 5100160, Guangdong Province, China.
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10
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Chandran A, Oliver HJ, Rochet JC. Role of NFE2L1 in the Regulation of Proteostasis: Implications for Aging and Neurodegenerative Diseases. BIOLOGY 2023; 12:1169. [PMID: 37759569 PMCID: PMC10525699 DOI: 10.3390/biology12091169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
A hallmark of aging and neurodegenerative diseases is a disruption of proteome homeostasis ("proteostasis") that is caused to a considerable extent by a decrease in the efficiency of protein degradation systems. The ubiquitin proteasome system (UPS) is the major cellular pathway involved in the clearance of small, short-lived proteins, including amyloidogenic proteins that form aggregates in neurodegenerative diseases. Age-dependent decreases in proteasome subunit expression coupled with the inhibition of proteasome function by aggregated UPS substrates result in a feedforward loop that accelerates disease progression. Nuclear factor erythroid 2- like 1 (NFE2L1) is a transcription factor primarily responsible for the proteasome inhibitor-induced "bounce-back effect" regulating the expression of proteasome subunits. NFE2L1 is localized to the endoplasmic reticulum (ER), where it is rapidly degraded under basal conditions by the ER-associated degradation (ERAD) pathway. Under conditions leading to proteasome impairment, NFE2L1 is cleaved and transported to the nucleus, where it binds to antioxidant response elements (AREs) in the promoter region of proteasome subunit genes, thereby stimulating their transcription. In this review, we summarize the role of UPS impairment in aging and neurodegenerative disease etiology and consider the potential benefit of enhancing NFE2L1 function as a strategy to upregulate proteasome function and alleviate pathology in neurodegenerative diseases.
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Affiliation(s)
- Aswathy Chandran
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Haley Jane Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
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11
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Collins MA, Avery R, Albert FW. Substrate-specific effects of natural genetic variation on proteasome activity. PLoS Genet 2023; 19:e1010734. [PMID: 37126494 PMCID: PMC10174532 DOI: 10.1371/journal.pgen.1010734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 05/11/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome's 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation.
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Affiliation(s)
- Mahlon A. Collins
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Randi Avery
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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Chen CL, Tseng PC, Chao YP, Shen TJ, Jhan MK, Wang YT, Nguyen TT, Lin CF. Polypeptide antibiotic actinomycin D induces Mcl-1 uncanonical downregulation in lung cancer cell apoptosis. Life Sci 2023; 321:121615. [PMID: 37001403 DOI: 10.1016/j.lfs.2023.121615] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 03/31/2023]
Abstract
AIMS Actinomycin (Act) D, a polypeptide antibiotic, is used clinically to inhibit the growth of malignant tumors. Act D binds to DNA at the transcription initiation complex to prevent the elongation of RNA. Act D causes DNA damage, growth inhibition, and cell death. Myeloid cell leukemia (Mcl-1) is an anti-apoptotic Bcl-2 family member protein, and the present study explored the effects and molecular mechanism of Act D-induced Mcl-1 downregulation. MAIN METHODS Human adenocarcinoma A549 cells were used to check the cytotoxic signaling pathways of Act D, particularly in apoptotic mechanism, in a cell-based study approach. Specific blockers targeting the apoptotic factors were examined for their possible roles. KEY FINDINGS We found that Act D caused cell growth inhibition and apoptosis. Propidium iodide-based flow cytometric analysis and immunostaining confirmed cell apoptosis. Treatment with Act D caused DNA damage, followed by p53-independent cell death. Western blotting showed a significant decrease in Mcl-1 expression, mitochondrial transmembrane potential loss, and caspase-9/caspase-3 cascade activation. The proteasome inhibitor MG132 reversed Act D-induced Mcl-1 downregulation. However, pharmacological inhibition of glycogen synthase kinase-3, p53 expression, ER stress, autophagy, and vesicle acidification, which are Mcl-1-regulating signaling pathways, did not rescue these effects. Notably, Cullin-Ring E3 ligase partially mediated Mcl-1 downregulation. Administration of transforming growth factor-β induced mesenchymal cell differentiation, but Act D still decreased Mcl-1 and caused cell apoptosis. SIGNIFICANCE All of these data show a potential pro-apoptotic effect for Act D by facilitating Mcl-1 uncanonical downregulation.
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13
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SGOL2 promotes prostate cancer progression by inhibiting RAB1A ubiquitination. Aging (Albany NY) 2022; 14:10050-10066. [PMID: 36566018 PMCID: PMC9831743 DOI: 10.18632/aging.204443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer is the most prevalent genitourinary malignant cancer in men worldwide. Patients with prostate cancer who progress to castration-resistant prostate cancer (CRPC) or metastatic CRPC have significantly poorer survival. Advanced prostate cancer is a clinical challenge due to the lack of effective treatment strategies. In the field of oncology, SGOL2 was an emerging and differentially expressed molecule, which enhanced the proliferation of cell populations in vitro in our studies. Mass spectrum and Co-IP validated the interaction of SGOL2 and RAB1A in a protein-protein manner. We further investigated the role of SGOL2 in the regulatory mechanism of RAB1A in prostate cancer cell lines. Furthermore, SGOL2 regulated RAB1A expression by inhibiting its ubiquitination. Rescue Experiments demonstrated that SGOL2 promoted prostate cancer cell proliferation and migration by upregulating RAB1A expression. Finally, we found that SGOL2 and RAB1A may regulate the tumor microenvironment (TME) in prostate cancer. In conclusion, our findings concluded that SGOL2 stabilized RAB1A expression to promote prostate cancer development. Both of them were of great importance in TME modulation.
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14
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Fang P, Han Y, Qu Y, Wang X, Zhang Y, Zhang W, Zhang N, Li G, Ma W. EIF3B stabilizes PTGS2 expression by counteracting MDM2-mediated ubiquitination to promote the development and progression of malignant melanoma. Cancer Sci 2022; 113:4181-4192. [PMID: 36050601 DOI: 10.1111/cas.15543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022] Open
Abstract
Malignant melanoma (MM) is a neoplasm that develops from human melanocytes. It was reported that eukaryotic translation initiation factor 3 subunit B (EIF3B) is associated with multiple types of cancers, but its role in MM has not been reported. In the present study, we found that EIF3B was abundantly expressed in MM and was strongly related to lymphatic metastasis and pathological stage of MM patients. In addition, EIF3B depletion could block the progression of MM in vitro and in vivo. In contrast, EIF3B overexpression increased cell proliferation and migration in melanoma cells. More importantly, we identified that EIF3B's driver role in MM was mediated by PTGS2. In detail, we found that EIF3B stabilized PTGS2 expression by inhibiting PTGS2 ubiquitination, which is mediated by the E3 ligase MDM2. Moreover, like EIF3B, silencing PTGS2 could suppress MM development, and more interestingly, it could reverse the situation caused by overexpression of EIF3B in vitro and in vivo. Furthermore, the proliferation and migration inhibited by silencing of EIF3B were also partially recovered by overexpression of PTGS2. Overall, our findings revealed the potential of EIF3B as a therapeutic target for MM. Identification of EIF3B's function in MM may pave the way for future development of more specific and more effective targeted therapy strategies against MM.
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Affiliation(s)
- Pengli Fang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yikai Han
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanhong Qu
- Oncology Department of Laiyang People's Hospital, Laiyang, China
| | - Xin Wang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yong Zhang
- Department of Cancer Biotherapy Center, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Wei Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Na Zhang
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangshuai Li
- Department of Plastic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wang Ma
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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15
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Wang J, Sun X, Wang J, Zhang K, Yuan Y, Guo Y, Yao L, Li X, Shen L. NDRG2 inhibits pyruvate carboxylase-mediated anaplerosis and combines with glutamine blockade to inhibit the proliferation of glioma cells. Am J Cancer Res 2022; 12:3729-3744. [PMID: 36119843 PMCID: PMC9442009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023] Open
Abstract
Due to the rapid proliferation, cancer cells have increased anabolic biosynthesis, which requires anaplerosis to replenish precursor intermediates. The major anaplerotic sources are pyruvate and glutamine, which require the catalysis of pyruvate carboxylase (PC) and glutaminase (GLS) respectively. In GLS-suppressed cancer cells, the PC-mediated pathway for anaplerosis is crucial to maintain cell growth and proliferation. Here, we investigated the regulatory role and molecular mechanism of N-myc downstream-regulated gene 2 (NDRG2) in PC and PC-mediated anaplerosis. NDRG2 interacted with PC and induced the degradation of PC in glutamine-deprived cells. NDRG2 also inhibited the activity of PC and PC-mediated anaplerosis. As a result, NDRG2 significantly inhibited the malignant growth and proliferation of glioma cells in combination with a glutamine antagonist. In addition, NDRG2 more significantly inhibited the protein level of PC in isocitrate dehydrogenase 1 (R132H)-mutant glioma cells than in wild-type glioma cells. These findings indicate that the molecular mechanism of NDRG2 inhibits PC-mediated anaplerosis and collaborates with glutamine antagonist to inhibit the malignant proliferation of glioma cells, thus providing a theoretical and experimental basis for targeting anaplerosis in glioma therapy.
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Affiliation(s)
- Jiancai Wang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
- Department of Neurosurgery, PLA 982 HospitalTangshan 063099, Hebei, China
| | - Xiang Sun
- Department of Special Diagnosis, School of Stomatology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Jiayuan Wang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
- Department of Pathogenic Biology, Medical College, Yan’an UniversityYan’an 716000, Shaanxi, China
| | - Kun Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
- Department of Medical Genetics, Medical College, Yan’an UniversityYan’an 716000, Shaanxi, China
| | - Yiyi Yuan
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Yan Guo
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Libo Yao
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Xia Li
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
| | - Lan Shen
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical UniversityXi’an 710032, Shaanxi, China
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16
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Logan A, Nagy Z, Barnes NM, Belli A, Di Pietro V, Tavazzi B, Lazzarino G, Lazzarino G, Bruce L, Persson LI. A phase II open label clinical study of the safety, tolerability and efficacy of ILB® for Amyotrophic Lateral Sclerosis. PLoS One 2022; 17:e0267183. [PMID: 35613082 PMCID: PMC9132272 DOI: 10.1371/journal.pone.0267183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/04/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Amyotrophic lateral sclerosis (ALS) is an invariably lethal progressive disease, causing degeneration of neurons and muscle. No current treatment halts or reverses disease advance. This single arm, open label, clinical trial in patients with ALS investigated the safety and tolerability of a novel modified low molecular weight dextran sulphate (LMW-DS, named ILB®) previously proven safe for use in healthy volunteers and shown to exert potent neurotrophic effects in pre-clinical studies. Secondary endpoints relate to efficacy and exploratory biomarkers. Methods Thirteen patients with ALS were treated with 5 weekly subcutaneous injections of ILB®. Safety and efficacy outcome measures were recorded weekly during treatment and at regular intervals for a further 70 days. Functional and laboratory biomarkers were assessed before, during and after treatment. Results No deaths, serious adverse events or participant withdrawals occurred during or after ILB® treatment and no significant drug-related changes in blood safety markers were evident, demonstrating safety and tolerability of the drug in this cohort of patients with ALS. The PK of ILB® in patients with ALS was similar to that seen in healthy controls. The ILB® injection elicited a transient elevation of plasma Hepatocyte Growth Factor, a neurotrophic and myogenic growth factor. Following the ILB® injections patients reported increased vitality, decreased spasticity and increased mobility. The ALSFRS-R rating improved from 36.31 ± 6.66 to 38.77 ± 6.44 and the Norris rating also improved from 70.61 ± 13.91 to 77.85 ± 14.24 by Day 36. The improvement of functions was associated with a decrease in muscle atrophy biomarkers. These therapeutic benefits decreased 3–4 weeks after the last dosage. Conclusions This pilot clinical study demonstrates safety and tolerability of ILB® in patients with ALS. The exploratory biomarker and functional measures must be cautiously interpreted but suggest clinical benefit and have a bearing on the mechanism of action of ILB®. The results support the drug’s potential as the first disease modifying treatment for patients with ALS. Trial registration EudraCT 2017-005065-47.
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Affiliation(s)
- Ann Logan
- Axolotl Consulting Ltd, Droitwich, United Kingdom
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- * E-mail:
| | - Zsuzsanna Nagy
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nicholas M. Barnes
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Antonio Belli
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Barbara Tavazzi
- Department of Basic Biotechnological Sciences, Intensive and Perioperative Clinics, Catholic University of Rome, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giuseppe Lazzarino
- Department of Biomedical and Biotechnological Sciences, Division of Medical Biochemistry, University of Catania, Catania, Italy
| | - Giacomo Lazzarino
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | | | - Lennart I. Persson
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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17
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Lospinoso Severini L, Bufalieri F, Infante P, Di Marcotullio L. Proteolysis-Targeting Chimera (PROTAC): Is the Technology Looking at the Treatment of Brain Tumors? Front Cell Dev Biol 2022; 10:854352. [PMID: 35242765 PMCID: PMC8886235 DOI: 10.3389/fcell.2022.854352] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Post-translational modifications, such as ubiquitylation, need to be tightly controlled to guarantee the accurate localization and activity of proteins. Ubiquitylation is a dynamic process primarily responsible for proteasome-mediated degradation of substrate proteins and crucial for both normal homeostasis and disease. Alterations in ubiquitylation lead to the upregulation of oncoproteins and/or downregulation of tumor suppressors, thus concurring in tumorigenesis. PROteolysis-TArgeting Chimera (PROTAC) is an innovative strategy that takes advantage by the cell’s own Ubiquitin-Proteasome System (UPS). Each PROTAC molecule is composed by a ligand that recruits the target protein of interest (POI), a ligand specific for an E3 ubiquitin ligase enzyme, and a linker that connects these units. Upon binding to the POI, the PROTAC recruits the E3 inducing ubiquitylation-dependent proteasome degradation of the POI. To date, PROTAC technology has entered in clinical trials for several human cancers. Here, we will discuss the advantages and limitations of PROTACs development and safety considerations for their clinical application. Furthermore, we will review the potential of PROTAC strategy as therapeutic option in brain tumor, focusing on glioblastoma.
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Affiliation(s)
| | - Francesca Bufalieri
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Paola Infante
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, University of Rome La Sapienza, Rome, Italy
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18
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Reboud-Ravaux M. [The proteasome - structural aspects and inhibitors: a second life for a validated drug target]. Biol Aujourdhui 2021; 215:1-23. [PMID: 34397372 DOI: 10.1051/jbio/2021005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 02/06/2023]
Abstract
The proteasome is the central component of the adaptable ubiquitin proteasome system (UPS) discovered in the 1980's. It sustains protein homeostasis (proteostasis) under a large variety of physiological and pathological conditions. Its dysregulation has been often associated to various human diseases. Its potential regulation by modulators has emerged as promising avenue to develop treatments of various pathologies. The FDA approval in 2003 of the proteasome inhibitor bortezomib to treat multiple myeloma, then mantle lymphoma in 2006, has considerably increased the clinical interest of proteasome inhibition. Second-generation proteasome inhibitors (carfilzomib and ixazomib) have been approved to overcome bortezomib resistance and improved toxicity profile and route of administration. Selective inhibition of immunoproteasome is a promising approach towards the development of immunomodulatory drugs. The design of these drugs relies greatly on the elucidation of high-resolution structures of the targeted proteasomes. The ATPase-dependent 26S proteasome (2.4 MDa) consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of catalytic sites. In recent years, due to technical advances especially in atomic cryo-electron microscopy, significant progress has been made in the understanding of 26S proteasome structure and its dynamics. Stepwise conformational changes of the 19S particle induced by ATP hydrolysis lead to substrate translocation, 20S pore opening and processive protein degradation by the 20S proteolytic subunits (2β1, 2β2 and 2β5). A large variety of structurally different inhibitors, both natural products or synthetic compounds targeting immuno- and constitutive proteasomes, has been discovered. The latest advances in this drug discovery are presented. Knowledge about structures, inhibition mechanism and detailed biological regulations of proteasomes can guide strategies for the development of next-generation inhibitors to treat human diseases, especially cancers, immune disorders and pathogen infections. Proteasome activators are also potentially applicable to the reduction of proteotoxic stresses in neurodegeneration and aging.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
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19
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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20
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Madeira C, Costa PM. Proteomics in systems toxicology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:55-91. [PMID: 34340774 DOI: 10.1016/bs.apcsb.2021.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.
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Affiliation(s)
- Carolina Madeira
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal
| | - Pedro M Costa
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal.
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21
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Chin-Fatt A, Saberianfar R, Menassa R. A Rationally Designed Bovine IgA Fc Scaffold Enhances in planta Accumulation of a V HH-Fc Fusion Without Compromising Binding to Enterohemorrhagic E. coli. FRONTIERS IN PLANT SCIENCE 2021; 12:651262. [PMID: 33936135 PMCID: PMC8079772 DOI: 10.3389/fpls.2021.651262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
We previously isolated a single domain antibody (VHH) that binds Enterohemorrhagic Escherichia coli (EHEC) with the end-goal being the enteromucosal passive immunization of cattle herds. To improve the yield of a chimeric fusion of the VHH with an IgA Fc, we employed two rational design strategies, supercharging and introducing de novo disulfide bonds, on the bovine IgA Fc component of the chimera. After mutagenizing the Fc, we screened for accumulation levels after transient transformation in Nicotiana benthamiana leaves. We identified and characterized five supercharging and one disulfide mutant, termed '(5 + 1)Fc', that improve accumulation in comparison to the native Fc. Combining all these mutations is associated with a 32-fold increase of accumulation for the Fc alone, from 23.9 mg/kg fresh weight (FW) to 599.5 mg/kg FW, as well as a twenty-fold increase when fused to a VHH that binds EHEC, from 12.5 mg/kg FW tissue to 236.2 mg/kg FW. Co-expression of native or mutated VHH-Fc with bovine joining chain (JC) and bovine secretory component (SC) followed by co-immunoprecipitation suggests that the stabilizing mutations do not interfere with the capacity of VHH-Fc to assemble with JC and FC into a secretory IgA. Both the native and the mutated VHH-Fc similarly neutralized the ability of four of the seven most prevalent EHEC strains (O157:H7, O26:H11, O111:Hnm, O145:Hnm, O45:H2, O121:H19 and O103:H2), to adhere to HEp-2 cells as visualized by immunofluorescence microscopy and quantified by fluorometry. These results collectively suggest that supercharging and disulfide bond tethering on a Fc chain can effectively improve accumulation of a VHH-Fc fusion without impacting VHH functionality.
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Affiliation(s)
- Adam Chin-Fatt
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Reza Saberianfar
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Rima Menassa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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22
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Wen F, Sun X, Sun C, Dong Z, Jia G, Bao W, Yu H, Yang C. TAGLN Is Downregulated by TRAF6-Mediated Proteasomal Degradation in Prostate Cancer Cells. Mol Cancer Res 2021; 19:1113-1122. [PMID: 33771884 DOI: 10.1158/1541-7786.mcr-20-0513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/02/2020] [Accepted: 03/23/2021] [Indexed: 11/16/2022]
Abstract
Transgelin (TAGLN, also named SM22) is an actin-associated protein and affects dynamics of actin filaments. Deregulation of TAGLN contributes to the development of different cancers, and it is commonly considered to be a tumor suppressor. TAGLN is usually downregulated in prostate cancer; however, the detailed functions of TAGLN in prostate cancer and how TAGLN is regulated remains unclear. In this study, we confirmed that TAGLN is downregulated in prostate cancer tissues and demonstrated that the downregulation of TAGLN occurs through proteasomal degradation. Next, we found that the expression level of TAGLN is inversely correlated with TRAF6. We screened more than 20 E2-E3 pairs by in vitro ubiquitination assay and found that the E2A-TRAF6 pair catalyzed mono ubiquitination of TAGLN. We then identified the ubiquitination sites of TAGLN to be on K89 or K108 residues and demonstrated that ubiquitination of TAGLN on K89/K108 are important for TRAF6-mediated proteasomal degradation. Furthermore, we investigated the function of TAGLN in prostate cancer cells. We found that ablation of TAGLN promoted prostate cancer cell proliferation and suppressed their migration via activation of NF-κB and Myc signaling pathways. Overall, our study provided new insights into the mechanisms underlying TAGLN expression and activity in prostate cancer. IMPLICATIONS: E3 ligase TRAF6 mediate mono-ubiquitination and degradation of TAGLN, which leads to activation of NF-κB and Myc signaling pathways in prostate cancer cells.
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Affiliation(s)
- Fuping Wen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaochen Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chenxia Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhenyang Dong
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gaozhen Jia
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wei Bao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haolan Yu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China.,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chenghua Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China. .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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23
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Peng H, Cassel J, McCracken DS, Prokop JW, Sementino E, Cheung M, Collop PR, Polo A, Joshi S, Mandell JP, Ayyanathan K, Hinds D, Malkowicz SB, Harbour JW, Bowcock AM, Salvino J, Kennedy EJ, Testa JR, Rauscher FJ. Kinetic Characterization of ASXL1/2-Mediated Allosteric Regulation of the BAP1 Deubiquitinase. Mol Cancer Res 2021; 19:1099-1112. [PMID: 33731362 DOI: 10.1158/1541-7786.mcr-20-0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/22/2020] [Accepted: 03/11/2021] [Indexed: 11/16/2022]
Abstract
BAP1 is an ubiquitin hydrolase whose deubiquitinase activity is mediated by polycomb group-like protein ASXL2. Cancer-related BAP1 mutations/deletions lead to loss-of-function by targeting the catalytic ubiquitin C-terminal hydrolase (UCH) or UCH37-like domain (ULD) domains of BAP1, and the latter disrupts binding to ASXL2, an obligate partner for BAP1 enzymatic activity. However, the biochemical and biophysical properties of domains involved in forming the enzymatically active complex are unknown. Here, we report the molecular dynamics, kinetics, and stoichiometry of these interactions. We demonstrate that interactions between BAP1 and ASXL2 are direct, specific, and stable to biochemical and biophysical manipulations as detected by isothermal titration calorimetry (ITC), GST association, and optical biosensor assays. Association of the ASXL2-AB box greatly stimulates BAP1 activity. A stable ternary complex is formed, comprised of the BAP1-UCH, BAP1-ULD, and ASXL2-AB domains. Stoichiometric analysis revealed that one molecule of the ULD domain directly interacts with one molecule of the AB box. Real-time kinetic analysis of the ULD/AB protein complex to the BAP1-UCH domain, based on surface plasmon resonance, indicated that formation of the ULD/AB complex with the UCH domain is a single-step event with fast association and slow dissociation rates. In vitro experiments validated in cells that the ASXL-AB box directly regulates BAP1 activity. IMPLICATIONS: Collectively, these data elucidate molecular interactions between specific protein domains regulating BAP1 deubiquitinase activity, thus establishing a foundation for small-molecule approaches to reactivate latent wild-type BAP1 catalytic activity in BAP1-mutant cancers.
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Affiliation(s)
| | - Joel Cassel
- The Wistar Institute, Philadelphia, Pennsylvania
| | - Daniel S McCracken
- The Wistar Institute, Philadelphia, Pennsylvania.,Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | | | | | - Paul R Collop
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
| | | | - Surbhi Joshi
- The Wistar Institute, Philadelphia, Pennsylvania
| | | | | | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan
| | - S Bruce Malkowicz
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Anne M Bowcock
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia
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Banford S, McCorvie TJ, Pey AL, Timson DJ. Galactosemia: Towards Pharmacological Chaperones. J Pers Med 2021; 11:jpm11020106. [PMID: 33562227 PMCID: PMC7914515 DOI: 10.3390/jpm11020106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Galactosemia is a rare inherited metabolic disease resulting from mutations in the four genes which encode enzymes involved in the metabolism of galactose. The current therapy, the removal of galactose from the diet, is inadequate. Consequently, many patients suffer lifelong physical and cognitive disability. The phenotype varies from almost asymptomatic to life-threatening disability. The fundamental biochemical cause of the disease is a decrease in enzymatic activity due to failure of the affected protein to fold and/or function correctly. Many novel therapies have been proposed for the treatment of galactosemia. Often, these are designed to treat the symptoms and not the fundamental cause. Pharmacological chaperones (PC) (small molecules which correct the folding of misfolded proteins) represent an exciting potential therapy for galactosemia. In theory, they would restore enzyme function, thus preventing downstream pathological consequences. In practice, no PCs have been identified for potential application in galactosemia. Here, we review the biochemical basis of the disease, identify opportunities for the application of PCs and describe how these might be discovered. We will conclude by considering some of the clinical issues which will affect the future use of PCs in the treatment of galactosemia.
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Affiliation(s)
- Samantha Banford
- South Eastern Health and Social Care Trust, Downpatrick BT30 6RL, UK;
| | - Thomas J. McCorvie
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton BN2 4GJ, UK
- Correspondence:
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25
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Toro A, Anselmino N, Solari C, Francia M, Oses C, Sanchis P, Bizzotto J, Vazquez Echegaray C, Petrone MV, Levi V, Vazquez E, Guberman A. Novel Interplay between p53 and HO-1 in Embryonic Stem Cells. Cells 2020; 10:cells10010035. [PMID: 33383653 PMCID: PMC7823265 DOI: 10.3390/cells10010035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023] Open
Abstract
Stem cells genome safeguarding requires strict oxidative stress control. Heme oxygenase-1 (HO-1) and p53 are relevant components of the cellular defense system. p53 controls cellular response to multiple types of harmful stimulus, including oxidative stress. Otherwise, besides having a protective role, HO-1 is also involved in embryo development and in embryonic stem (ES) cells differentiation. Although both proteins have been extensively studied, little is known about their relationship in stem cells. The aim of this work is to explore HO-1-p53 interplay in ES cells. We studied HO-1 expression in p53 knockout (KO) ES cells and we found that they have higher HO-1 protein levels but similar HO-1 mRNA levels than the wild type (WT) ES cell line. Furthermore, cycloheximide treatment increased HO-1 abundance in p53 KO cells suggesting that p53 modulates HO-1 protein stability. Notably, H2O2 treatment did not induce HO-1 expression in p53 KO ES cells. Finally, SOD2 protein levels are also increased while Sod2 transcripts are not in KO cells, further suggesting that the p53 null phenotype is associated with a reinforcement of the antioxidant machinery. Our results demonstrate the existence of a connection between p53 and HO-1 in ES cells, highlighting the relationship between these stress defense pathways.
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Affiliation(s)
- Ayelén Toro
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Nicolás Anselmino
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Claudia Solari
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Marcos Francia
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Camila Oses
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Pablo Sanchis
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Juan Bizzotto
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Camila Vazquez Echegaray
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - María Victoria Petrone
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Valeria Levi
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
| | - Elba Vazquez
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Correspondence: (E.V.); (A.G.); Tel.: +54-91144087796 (E.V.); +54-115-285-8683 (A.G.)
| | - Alejandra Guberman
- CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina; (A.T.); (N.A.); (C.S.); (M.F.); (C.O.); (P.S.); (J.B.); (C.V.E.); (M.V.P.); (V.L.)
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Correspondence: (E.V.); (A.G.); Tel.: +54-91144087796 (E.V.); +54-115-285-8683 (A.G.)
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Wang N, Liu Y, Cai Y, Tang J, Li Y, Gai J. The soybean U-box gene GmPUB6 regulates drought tolerance in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:284-296. [PMID: 32795910 DOI: 10.1016/j.plaphy.2020.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 06/15/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
The plant U-box (PUB) proteins function as E3 ligases to poly-ubiquitinate the target proteins for their degradation or post-translational modification. PUBs also play important roles in regulation of diverse biological processes, including plant response to environmental stresses. In this study, the functional characterization of a soybean PUB gene, GmPUB6, was performed. GmPUB6 was mainly localized to peroxisome, and showed E3 ubiquitin ligase activity. The transcript levels of GmPUB6 in soybean leaves and roots were induced by abscisic acid (ABA), high salinity and polyethylene glycol (PEG) treatment. Comparing with the wild-type (WT) plants, overexpression of GmPUB6 in Arabidopsis thaliana decreased plant survival rate after drought stress, reduced seed germination rate and root elongation under mannitol (osmotic) stress, and suppressed ABA- or mannitol-mediated stomatal closure. In addition, under dehydration stress, the relative expression levels of seven stress responsive genes, including ABI1, DREB2A, KIN2, RAB18, RD20, RD29A and RD29B, were lower in GmPUB6-overexpressed plants than WT. Taken together, these results suggest that GmPUB6 functions as a negative regulator in drought tolerance, and plays an important role in osmotic stress and ABA signaling pathways, which might be the possible mechanism of PUB6 participating in drought stress response.
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Affiliation(s)
- Ning Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Yandang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanyuan Cai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiajun Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
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27
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Carmi G, Tagore S, Gorohovski A, Sivan A, Raviv-Shay D, Frenkel-Morgenstern M. Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks. Sci Rep 2020; 10:15628. [PMID: 32973219 PMCID: PMC7519090 DOI: 10.1038/s41598-020-71976-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
In contrast to fossorial and above-ground organisms, subterranean species have adapted to the extreme stresses of living underground. We analyzed the predicted protein–protein interactions (PPIs) of all gene products, including those of stress-response genes, among nine subterranean, ten fossorial, and 13 aboveground species. We considered 10,314 unique orthologous protein families and constructed 5,879,879 PPIs in all organisms using ChiPPI. We found strong association between PPI network modulation and adaptation to specific habitats, noting that mutations in genes and changes in protein sequences were not linked directly with niche adaptation in the organisms sampled. Thus, orthologous hypoxia, heat-shock, and circadian clock proteins were found to cluster according to habitat, based on PPIs rather than on sequence similarities. Curiously, "ordered" domains were preserved in aboveground species, while "disordered" domains were conserved in subterranean organisms, and confirmed for proteins in DistProt database. Furthermore, proteins with disordered regions were found to adopt significantly less optimal codon usage in subterranean species than in fossorial and above-ground species. These findings reveal design principles of protein networks by means of alterations in protein domains, thus providing insight into deep mechanisms of evolutionary adaptation, generally, and particularly of species to underground living and other confined habitats.
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Affiliation(s)
- Gon Carmi
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, 13195, Safed, Israel
| | - Somnath Tagore
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, 13195, Safed, Israel.,Department of Systems Biology, Columbia University Medical Center, Herbert Irving Cancer Research Center, New York, USA
| | - Alessandro Gorohovski
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, 13195, Safed, Israel
| | - Aviad Sivan
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, 13195, Safed, Israel
| | - Dorith Raviv-Shay
- The Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold St, 13195, Safed, Israel
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28
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Proteolysis targeting chimeras (PROTACs) in cancer therapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:189. [PMID: 32933565 PMCID: PMC7493969 DOI: 10.1186/s13046-020-01672-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022]
Abstract
Exploitation of the protein degradation machinery as a therapeutic strategy to degrade oncogenic proteins is experiencing revolutionary advances with the development of proteolysis targeting chimeras (PROTACs). PROTACs are heterobifunctional structures consisting of a ligand that binds a protein to be degraded and a ligand for an E3 ubiquitin ligase. The bridging between the protein of interest and the E3 ligase mediated by the PROTAC facilitates ubiquitination of the protein and its proteasomal degradation. In this review we discuss the molecular medicine behind PROTAC mechanism of action, with special emphasis on recent developments and their potential translation to the clinical setting.
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29
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Donohue TM, Osna NA, Kharbanda KK, Thomes PG. Lysosome and proteasome dysfunction in alcohol-induced liver injury. LIVER RESEARCH 2019. [DOI: 10.1016/j.livres.2019.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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30
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Abstract
The proteasome degrades most cellular proteins in a controlled and tightly regulated manner and thereby controls many processes, including cell cycle, transcription, signalling, trafficking and protein quality control. Proteasomal degradation is vital in all cells and organisms, and dysfunction or failure of proteasomal degradation is associated with diverse human diseases, including cancer and neurodegeneration. Target selection is an important and well-established way to control protein degradation. In addition, mounting evidence indicates that cells adjust proteasome-mediated degradation to their needs by regulating proteasome abundance through the coordinated expression of proteasome subunits and assembly chaperones. Central to the regulation of proteasome assembly is TOR complex 1 (TORC1), which is the master regulator of cell growth and stress. This Review discusses how proteasome assembly and the regulation of proteasomal degradation are integrated with cellular physiology, including the interplay between the proteasome and autophagy pathways. Understanding these mechanisms has potential implications for disease therapy, as the misregulation of proteasome function contributes to human diseases such as cancer and neurodegeneration.
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31
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Eldeeb MA, Siva-Piragasam R, Ragheb MA, Esmaili M, Salla M, Fahlman RP. A molecular toolbox for studying protein degradation in mammalian cells. J Neurochem 2019; 151:520-533. [PMID: 31357232 DOI: 10.1111/jnc.14838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022]
Abstract
Protein degradation is a crucial regulatory process in maintaining cellular proteostasis. The selective degradation of intracellular proteins controls diverse cellular and biochemical processes in all kingdoms of life. Targeted protein degradation is implicated in controlling the levels of regulatory proteins as well as eliminating misfolded and any otherwise abnormal proteins. Deregulation of protein degradation is concomitant with the progression of various neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. Thus, methods of measuring metabolic half-lives of proteins greatly influence our understanding of the diverse functions of proteins in mammalian cells including neuronal cells. Historically, protein degradation rates have been studied via exploiting methods that estimate overall protein degradation or focus on few individual proteins. Notably, with the recent technical advances and developments in proteomic and imaging techniques, it is now possible to measure degradation rates of a large repertoire of defined proteins and analyze the degradation profile in a detailed spatio-temporal manner, with the aim of determining proteome-wide protein stabilities upon different physiological conditions. Herein, we discuss some of the classical and novel methods for determining protein degradation rates highlighting the crucial role of some state of art approaches in deciphering the global impact of dynamic nature of targeted degradation of cellular proteins. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed Salla
- Department of Biological Sciences, Lebanese International University, Bekaa, Lebanon
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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32
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The PSMA8 subunit of the spermatoproteasome is essential for proper meiotic exit and mouse fertility. PLoS Genet 2019; 15:e1008316. [PMID: 31437213 PMCID: PMC6726247 DOI: 10.1371/journal.pgen.1008316] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 09/04/2019] [Accepted: 07/17/2019] [Indexed: 01/01/2023] Open
Abstract
The ubiquitin proteasome system regulates meiotic recombination in yeast through its association with the synaptonemal complex, a ‘zipper’-like structure that holds homologous chromosome pairs in synapsis during meiotic prophase I. In mammals, the proteasome activator subunit PA200 targets acetylated histones for degradation during somatic DNA double strand break repair and during histone replacement during spermiogenesis. We investigated the role of the testis-specific proteasomal subunit α4s (PSMA8) during spermatogenesis, and found that PSMA8 was localized to and dependent on the central region of the synaptonemal complex. Accordingly, synapsis-deficient mice show delocalization of PSMA8. Moreover, though Psma8-deficient mice are proficient in meiotic homologous recombination, there are alterations in the proteostasis of several key meiotic players that, in addition to the known substrate acetylated histones, have been shown by a proteomic approach to interact with PSMA8, such as SYCP3, SYCP1, CDK1 and TRIP13. These alterations lead to an accumulation of spermatocytes in metaphase I and II which either enter massively into apoptosis or give rise to a low number of aberrant round spermatids that apoptose before histone replacement takes place. Proteins within the cells that are unnecessary or damaged are degraded by a large protein complex named the proteasome. The proteins to be degraded are marked by a small protein called ubiquitin. The addition of a small modification (acetyl group) to some proteins also promotes their degradation by the proteasome. Proteasomal degradation of proteins is an essential mechanism for many developmental programs including gametogenesis, a process whereby a diploid cell produces a haploid cell or gamete (sperm or egg). The mechanism by which this genome reduction occurs is called meiosis. Here, we report the study of a protein, named PSMA8 that is specific for the testis proteasome in vertebrates. Using the mouse as a model, we show that loss of PSMA8 leads to infertility in males. By co-immunoprecipitation-coupled mass spectroscopy we identified a large list of novel PSMA8 interacting proteins. We focused our functional analysis on several key meiotic proteins which were accumulated such as SYCP3, SYCP1, CDK1 and TRIP13 in addition to the known substrate of the spermatoproteasome, the acetylated histones. We suggest that the altered accumulation of these important proteins causes a disequilibrium of the meiotic division that produces apoptotic spermatocytes in metaphase I and II and also early spermatids that die soon after reaching this stage.
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33
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Yong L, Ma Y, Liang C, He G, Zhao Z, Yang C, Hai B, Pan X, Liu Z, Liu X. Oleandrin sensitizes human osteosarcoma cells to cisplatin by preventing degradation of the copper transporter 1. Phytother Res 2019; 33:1837-1850. [PMID: 31050072 DOI: 10.1002/ptr.6373] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Lei Yong
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Yunlong Ma
- The Center for Pain MedicinePeking University Third Hospital Beijing 100191 China
| | - Chen Liang
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Guanping He
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Zhigang Zhao
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Chenlong Yang
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Bao Hai
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Xiaoyu Pan
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Zhongjun Liu
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
| | - Xiaoguang Liu
- Department of OrthopedicsPeking University Third Hospital Beijing 100191 China
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34
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Yan S, Wu G. Proteases HtrA and HtrB for α-amylase secreted from Bacillus subtilis in secretion stress. Cell Stress Chaperones 2019; 24:493-502. [PMID: 31001739 PMCID: PMC6527527 DOI: 10.1007/s12192-019-00985-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 01/16/2023] Open
Abstract
HtrA and HtrB are two important proteases across species. In biotechnological industries, they are related to degradation of secreted heterologous proteins from bacteria, especially in the case of overproduction of α-amylases in Bacillus subtilis. Induction of HtrA and HtrB synthesis follows the overproduction of α-amylases in B. subtilis. This is different from the order usually observed in B. subtilis, i.e., the production of proteases is prior to the secretion of proteins. This discrepancy suggests three possibilities: (i) HtrA and HtrB are constantly synthesized from the end of the exponential phase, and then are synthesized more abundantly due to secretion stress; (ii) There is a hysteresis mechanism that holds HtrA and HtrB back from their large amount of secretion before the overproduction of α-amylases; (iii) Heterologous amylases could be a stress to B. subtilis leading to a general response to stress. In this review, we analyze the literature to explore these three possibilities. The first possibility is attributed to the regulatory pathway of CssR-CssS. The second possibility is because sigma factor σD plays a role in the overproduction of α-amylases and is subpopulation dependent with the switch between "ON" and "OFF" states that is fundamental for a bistable system and a hysteresis mechanism. Thus, sigma factor σD helps to hold HtrA and HtrB back from massive secretion before the overproduction of α-amylases. The third possibility is that several sigma factors promote the secretion of proteases at the end of the exponential phase of growth under the condition that heterologous amylases are considered as a stress.
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Affiliation(s)
- Shaomin Yan
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
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35
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Caputi FF, Rullo L, Stamatakos S, Candeletti S, Romualdi P. Interplay between the Endogenous Opioid System and Proteasome Complex: Beyond Signaling. Int J Mol Sci 2019; 20:ijms20061441. [PMID: 30901925 PMCID: PMC6470665 DOI: 10.3390/ijms20061441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023] Open
Abstract
Intracellular signaling mechanisms underlying the opioid system regulation of nociception, neurotransmitters release, stress responses, depression, and the modulation of reward circuitry have been investigated from different points of view. The presence of the ubiquitin proteasome system (UPS) in the synaptic terminations suggest a potential role of ubiquitin-dependent mechanisms in the control of the membrane occupancy by G protein-coupled receptors (GPCRs), including those belonging to the opioid family. In this review, we focused our attention on the role played by the ubiquitination processes and by UPS in the modulation of opioid receptor signaling and in pathological conditions involving the endogenous opioid system. The collective evidence here reported highlights the potential usefulness of proteasome inhibitors in neuropathic pain, addictive behavior, and analgesia since these molecules can reduce pain behavioral signs, heroin self-administration, and the development of morphine analgesic tolerance. Moreover, the complex mechanisms involved in the effects induced by opioid agonists binding to their receptors include the ubiquitination process as a post-translational modification which plays a relevant role in receptor trafficking and degradation. Hence, UPS modulation may offer novel opportunities to control the balance between therapeutic versus adverse effects evoked by opioid receptor activation, thus, representing a promising druggable target.
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Affiliation(s)
- Francesca Felicia Caputi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
| | - Laura Rullo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
| | - Serena Stamatakos
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
| | - Sanzio Candeletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
| | - Patrizia Romualdi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
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36
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LPLUNC1 stabilises PHB1 by counteracting TRIM21-mediated ubiquitination to inhibit NF-κB activity in nasopharyngeal carcinoma. Oncogene 2019; 38:5062-5075. [PMID: 30886235 PMCID: PMC6756001 DOI: 10.1038/s41388-019-0778-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/22/2022]
Abstract
Long-palate, lung and nasal epithelium clone 1 (LPLUNC1) is a tumour suppressor gene in nasopharyngeal carcinoma (NPC), and low expression of LPLUNC1 is associated with poor prognosis. Our previous study showed that LPLUNC1 upregulates Prohibitin 1 (PHB1), a pleiotropic protein that functions as a tumour suppressor gene in various cancers. Low expression of PHB1 was also found to be associated with the poor prognosis of NPC patients. However, the mechanisms by which LPLUNC1 upregulates PHB1 and the potential role of PHB1 in NPC are unclear. Here, we found that LPLUNC1 stabilised PHB1 by inhibiting PHB1 ubiquitination, which is mediated by E3 ligase TRIM21. LPLUNC1 competitively impaired the binding of PHB1 to TRIM21 due to its stronger binding affinity to PHB1, suppressing the ubiquitination of PHB1. Therefore, our study indicates that PHB1 acted as a tumour suppressor gene by inhibiting NF-κB activity. Depletion of PHB1 significantly attenuated the anti-tumour effects of LPLUNC1 in NPC cells, and the inhibitory effect of LPLUNC1 on NF-κB activity was thus reversed. Together, our findings revealed a novel mechanism underlying the anticancer effect of LPLUNC1 and clarified that PHB1 may represent a novel, promising candidate tumour suppressor gene in NPC, with potential therapeutic target value.
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37
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Martinelli AHS, Lopes FC, John EBO, Carlini CR, Ligabue-Braun R. Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies. Int J Mol Sci 2019; 20:ijms20061322. [PMID: 30875980 PMCID: PMC6471803 DOI: 10.3390/ijms20061322] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.
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Affiliation(s)
- Anne H S Martinelli
- Department of Molecular Biology and Biotechnology & Department of Biophysics, Biosciences Institute-IB, (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Fernanda C Lopes
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Elisa B O John
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Célia R Carlini
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 91410-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Department of Pharmaceutical Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre CEP 90050-170, RS, Brazil.
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38
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Liu J, Zeinert R, Francis L, Chien P. Lon recognition of the replication initiator DnaA requires a bipartite degron. Mol Microbiol 2018; 111:176-186. [PMID: 30288816 DOI: 10.1111/mmi.14146] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2018] [Indexed: 12/17/2022]
Abstract
DnaA initiates chromosome replication in bacteria. In Caulobacter crescentus, the Lon protease degrades DnaA to coordinate replication with nutrient availability and to halt the cell cycle during acute stress. Here, we characterize the mechanism of DnaA recognition by Lon. We find that the folded state of DnaA appears crucial for its degradation, in contrast to the well-known role of Lon in degrading misfolded proteins. We fail to identify a single degradation motif (degron) sufficient for DnaA degradation, rather we show that both the ATPase domain and a species-specific N-terminal motif are important for productive Lon degradation of full-length DnaA. Mutations in either of these determinants disrupt DnaA degradation in vitro and in vivo. However, analysis of truncation products reveals that appending other extensions to the ATPase domain is sufficient to trigger degradation, suggesting plasticity in Lon recognition. Our final working model is that Lon engages DnaA through at least two elements, one of which anchors DnaA to Lon and the other acting as an initiation site for degradation.
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Affiliation(s)
- Jing Liu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, 01002, USA.,Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, MA, 01002, USA
| | - Rilee Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, 01002, USA.,Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, MA, 01002, USA
| | - Laura Francis
- Department of Biology, University of Massachusetts Amherst, MA, 01002, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, MA, 01002, USA.,Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, MA, 01002, USA
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39
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Mesa-Torres N, Betancor-Fernández I, Oppici E, Cellini B, Salido E, Pey AL. Evolutionary Divergent Suppressor Mutations in Conformational Diseases. Genes (Basel) 2018; 9:E352. [PMID: 30011855 PMCID: PMC6071075 DOI: 10.3390/genes9070352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 12/26/2022] Open
Abstract
Neutral and adaptive mutations are key players in the evolutionary dynamics of proteins at molecular, cellular and organismal levels. Conversely, largely destabilizing mutations are rarely tolerated by evolution, although their occurrence in diverse human populations has important roles in the pathogenesis of conformational diseases. We have recently proposed that divergence at certain sites from the consensus (amino acid) state during mammalian evolution may have rendered some human proteins more vulnerable towards disease-associated mutations, primarily by decreasing their conformational stability. We herein extend and refine this hypothesis discussing results from phylogenetic and structural analyses, structure-based energy calculations and structure-function studies at molecular and cellular levels. As proof-of-principle, we focus on different mammalian orthologues of the NQO1 (NAD(P)H:quinone oxidoreductase 1) and AGT (alanine:glyoxylate aminotransferase) proteins. We discuss the different loss-of-function pathogenic mechanisms associated with diseases involving the two enzymes, including enzyme inactivation, accelerated degradation, intracellular mistargeting, and aggregation. Last, we take into account the potentially higher robustness of mammalian orthologues containing certain consensus amino acids as suppressors of human disease, and their relation with different intracellular post-translational modifications and protein quality control capacities, to be discussed as sources of phenotypic variability between human and mammalian models of disease and as tools for improving current therapeutic approaches.
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Affiliation(s)
- Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
| | - Isabel Betancor-Fernández
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy.
| | - Eduardo Salido
- Hospital Universitario de Canarias, Center for Rare Diseases (CIBERER), University of La Laguna, 38320 Tenerife, Spain.
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, 18010 Granada, Spain.
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40
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Inobe T, Tsukamoto M, Nozaki M. Proteasome-mediated protein degradation is enhanced by fusion ubiquitin with unstructured degron. Biochem Biophys Res Commun 2018; 501:948-954. [PMID: 29777695 DOI: 10.1016/j.bbrc.2018.05.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 11/28/2022]
Abstract
Methods to induce proteasomal degradation of unwanted proteins are valuable in biomedical studies and thus receive increasing attention. For efficient degradation, the proteasome requires both a ubiquitin tag, which delivers substrates to the proteasome, and an unstructured region, where the proteasome engages the substrate for unfolding and degradation. We fused two degron components into a single molecule to create a fusion protein comprising ubiquitin and Rpn4-derived unstructured region. We demonstrated that the fusion protein retained its function to polyubiquitinate target proteins, thereby inducing more efficient proteasomal target degradation than wild-type ubiquitin in vitro and in cells. These results provide novel strategies for robust degradation enhancement of polyubiquitinated proteins.
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Affiliation(s)
- Tomonao Inobe
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan; Graduate School of Innovative Life Sciences, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan.
| | - Masayuki Tsukamoto
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
| | - Miyuki Nozaki
- Department of Life Sciences and Bioengineering, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan
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41
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Abstract
The ubiquitin-proteasome system (UPS) controls cellular functions by maintenance of a functional proteome and degradation of key regulatory proteins. Central to the UPS is the proteasome that adjusts the abundance of numerous proteins, thereby safeguarding their activity or initiating regulatory events. Here, we demonstrate that the essential Saccharomyces cerevisiae protein Yjr141w/Ipa1 (Important for cleavage and PolyAdenylation) belongs to the HECT_2 (homologous to E6-AP carboxyl terminus_2) family. We found that five cysteine residues within the HECT_2 family signature and the C-terminus are essential for Ipa1 activity. Furthermore, Ipa1 interacts with several ubiquitin-conjugating enzymes in vivo and localizes to the cytosol and nucleus. Importantly, Ipa1 has an impact on proteasome activity, which is indicated by the activation of the Rpn4 regulon as well as by decreased turnover of destabilized proteasome substrates in an IPA1 mutant. These changes in proteasome activity might be connected to reduced maturation or modification of proteasomal core particle proteins. Our results highlight the influence of Ipa1 on the UPS. The conservation within the HECT_2 family and the connection of the human HECT_2 family member to an age-related degeneration disease might suggest that HECT_2 family members share a conserved function linked to proteasome activity.
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42
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Eising S, van der Linden NGA, Kleinpenning F, Bonger KM. Vinylboronic Acids as Efficient Bioorthogonal Reactants for Tetrazine Labeling in Living Cells. Bioconjug Chem 2018; 29:982-986. [PMID: 29438611 PMCID: PMC5942871 DOI: 10.1021/acs.bioconjchem.7b00796] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Bioorthogonal chemistry
can be used for the selective modification
of biomolecules without interfering with any other functionality present
in the cell. The tetrazine ligation is very suitable as a bioorthogonal
reaction because of its selectivity and high reaction rates with several
alkenes and alkynes. Recently, we described vinylboronic acids (VBAs)
as novel hydrophilic bioorthogonal moieties that react efficiently
with dipyridyl-s-tetrazines and used them for protein
modification in cell lysate. It is not clear, however, whether VBAs
are suitable for labeling experiments in living cells because of the
possible coordination with, for example, vicinal carbohydrate diols.
Here, we evaluated VBAs as bioorthogonal reactants for labeling of
proteins in living cells using an irreversible inhibitor of the proteasome
and compared the reactivity to that of an inhibitor containing norbornene,
a widely used reactant for the tetrazine ligation. No large differences
were observed between the VBA and norbornene probes in a two-step
labeling approach with a cell-penetrable fluorescent tetrazine, indicating
that the VBA gives little or no side reactions with diols and can
be used efficiently for protein labeling in living cells.
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Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Nicole G A van der Linden
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Fleur Kleinpenning
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Kimberly M Bonger
- Department of Biomolecular Chemistry, Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
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43
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Mi Y, Wang W, Lu J, Zhang C, Wang Y, Ying H, Sun K. Proteasome-mediated degradation of collagen III by cortisol in amnion fibroblasts. J Mol Endocrinol 2018; 60:45-54. [PMID: 29191827 DOI: 10.1530/jme-17-0215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022]
Abstract
Rupture of fetal membranes (ROM) can initiate parturition at both term and preterm. Collagen III in the compact layer of the amnion contributes to the tensile strength of fetal membranes. However, the upstream signals triggering collagen III degradation remain mostly elusive. In this study, we investigated the role of cortisol regenerated by 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) in collagen III degradation in human amnion fibroblasts with an aim to seek novel targets for the prevention of preterm premature ROM (pPROM)-elicited preterm birth. Human amnion tissue and cultured amnion tissue explants and amnion fibroblasts were used to study the regulation of collagen III, which is composed of three identical 3α 1 chains (COL3A1), by cortisol. Cortisol decreased COL3A1 protein but not mRNA abundance in a concentration-dependent manner. Cortisone also decreased COL3A1 protein, which was blocked by 11β-HSD1 inhibition. The reduction in COL3A1 protein by cortisol was not affected by a transcription inhibitor but was further enhanced by a translation inhibitor. Autophagic pathway inhibitor chloroquine or siRNA-mediated knock-down of ATG7, an essential protein for autophagy, failed to block cortisol-induced reduction in COL3A1 protein abundance, whereas proteasome pathway inhibitors MG132 and bortezomib significantly attenuated cortisol-induced reduction in COL3A1 protein abundance. Moreover, cortisol increased COL3A1 ubiquitination and the reduction of COL3A1 protein by cortisol was blocked by PYR-41, a ubiquitin-activating enzyme inhibitor. Conclusively, cortisol regenerated in amnion fibroblasts may be associated with ROM at parturition by reducing collagen III protein abundance through a ubiquitin-proteasome pathway.
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Affiliation(s)
- Yabing Mi
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Wangsheng Wang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Jiangwen Lu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Chuyue Zhang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
| | - Yawei Wang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Hao Ying
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Kang Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
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Hickey CM, Xie Y, Hochstrasser M. DNA binding by the MATα2 transcription factor controls its access to alternative ubiquitin-modification pathways. Mol Biol Cell 2018; 29:542-556. [PMID: 29298839 PMCID: PMC6004586 DOI: 10.1091/mbc.e17-10-0589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 11/16/2022] Open
Abstract
Like many transcription factors, the yeast protein MATalpha2 (α2) undergoes rapid proteolysis via the ubiquitin-proteasome system (UPS). At least two ubiquitylation pathways regulate α2 degradation: one pathway utilizes the ubiquitin ligase (E3) Doa10 and the other the heterodimeric E3 Slx5/Slx8. Doa10 is a transmembrane protein of the endoplasmic reticulum/inner nuclear membrane, whereas Slx5/Slx8 localizes to the nucleus and binds DNA nonspecifically. While a single protein can often be ubiquitylated by multiple pathways, the reasons for this “division of labor” are not well understood. Here we show that α2 mutants with impaired DNA binding become inaccessible to the Slx5/Slx8 pathway but are still rapidly degraded through efficient shunting to the Doa10 pathway. These results are consistent with the distinct localization of these E3s. We also characterized a novel class of DNA binding-defective α2 variants whose degradation is strongly impaired. Our genetic data suggest that this is due to a gain-of-function interaction that limits their access to Doa10. Together, these results suggest multiple ubiquitin-ligation mechanisms may have evolved to promote rapid destruction of a transcription factor that resides in distinct cellular subcompartments under different conditions. Moreover, gain-of-function mutations, which also occur with oncogenic forms of human transcription factors such as p53, may derail this fail-safe system.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
| | - Yang Xie
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520
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45
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Betancor-Fernández I, Timson DJ, Salido E, Pey AL. Natural (and Unnatural) Small Molecules as Pharmacological Chaperones and Inhibitors in Cancer. Handb Exp Pharmacol 2018; 245:155-190. [PMID: 28993836 DOI: 10.1007/164_2017_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations causing single amino acid exchanges can dramatically affect protein stability and function, leading to disease. In this chapter, we will focus on several representative cases in which such mutations affect protein stability and function leading to cancer. Mutations in BRAF and p53 have been extensively characterized as paradigms of loss-of-function/gain-of-function mechanisms found in a remarkably large fraction of tumours. Loss of RB1 is strongly associated with cancer progression, although the molecular mechanisms by which missense mutations affect protein function and stability are not well known. Polymorphisms in NQO1 represent a remarkable example of the relationships between intracellular destabilization and inactivation due to dynamic alterations in protein ensembles leading to loss of function. We will review the function of these proteins and their dysfunction in cancer and then describe in some detail the effects of the most relevant cancer-associated single amino exchanges using a translational perspective, from the viewpoints of molecular genetics and pathology, protein biochemistry and biophysics, structural, and cell biology. This will allow us to introduce several representative examples of natural and synthetic small molecules applied and developed to overcome functional, stability, and regulatory alterations due to cancer-associated amino acid exchanges, which hold the promise for using them as potential pharmacological cancer therapies.
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Affiliation(s)
- Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, 18071, Spain.
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46
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Peng H, Prokop J, Karar J, Park K, Cao L, Harbour JW, Bowcock AM, Malkowicz SB, Cheung M, Testa JR, Rauscher FJ. Familial and Somatic BAP1 Mutations Inactivate ASXL1/2-Mediated Allosteric Regulation of BAP1 Deubiquitinase by Targeting Multiple Independent Domains. Cancer Res 2017; 78:1200-1213. [PMID: 29284740 DOI: 10.1158/0008-5472.can-17-2876] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/16/2017] [Accepted: 12/19/2017] [Indexed: 11/16/2022]
Abstract
Deleterious mutations of the ubiquitin carboxy-terminal hydrolase BAP1 found in cancers are predicted to encode inactive truncated proteins, suggesting that loss of enzyme function is a primary tumorigenic mechanism. However, many tumors exhibit missense mutations or in-frame deletions or insertions, often outside the functionally critical UCH domain in this tumor suppressor protein. Thus, precisely how these mutations inactivate BAP1 is unknown. Here, we show how these mutations affect BAP1 interactions with the Polycomb group-like protein, ASXL2, using combinations of computational modeling technology, molecular biology, and in vitro reconstitution biochemistry. We found that the BAP1-ASXL2 interaction is direct and high affinity, occurring through the ASXH domain of ASXL2, an obligate partner for BAP1 enzymatic activity. The ASXH domain was the minimal domain for binding the BAP1 ULD domain, and mutations on the surfaces of predicted helices of ASXH abolished BAP1 association and stimulation of BAP1 enzymatic activity. The BAP1-UCH, BAP1-ULD, and ASXH domains formed a cooperative stable ternary complex required for deubiquitination. We defined four classes of alterations in BAP1 outside the UCH domain, each failing to productively recruit ASXH to the wild-type BAP1 catalytic site via the ULD, resulting in loss of BAP1 ubiquitin hydrolase activity. Our results indicate that many BAP1 mutations act allosterically to inhibit ASXH binding, thereby leading to loss of enzyme activity. Small-molecule approaches to reactivate latent wild-type UCH activity of these mutants might be therapeutically viable.Significance: Combined computational and biochemical approaches demonstrate that the BAP1-ASXL2 interaction is direct and high affinity and that many BAP1 mutations act allosterically to inhibit BAP1-ASXL2 binding. Cancer Res; 78(5); 1200-13. ©2017 AACR.
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Affiliation(s)
| | - Jeremy Prokop
- HudsonAlpha Genome Sequencing Center, Huntsville, Alabama
| | | | - Kyewon Park
- Wistar Institute, Philadelphia, Pennsylvania
| | - Li Cao
- Washington University in St Louis, St. Louis, Missouri
| | | | - Anne M Bowcock
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - S Bruce Malkowicz
- University of Pennsylvania and Veterans Affairs Medical Center Philadelphia, Philadelphia, Pennsylvania
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47
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Eldridge MJG, Sanchez-Garrido J, Hoben GF, Goddard PJ, Shenoy AR. The Atypical Ubiquitin E2 Conjugase UBE2L3 Is an Indirect Caspase-1 Target and Controls IL-1β Secretion by Inflammasomes. Cell Rep 2017; 18:1285-1297. [PMID: 28147281 PMCID: PMC5300903 DOI: 10.1016/j.celrep.2017.01.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
Caspase-1 activation by inflammasome signaling scaffolds initiates inflammation and antimicrobial responses. Caspase-1 proteolytically converts newly induced pro-interleukin 1 beta (IL-1β) into its mature form and directs its secretion, triggering pyroptosis and release of non-substrate alarmins such as interleukin 1 alpha (IL-1α) and HMGB1. While some caspase-1 substrates involved in these events are known, the identities and roles of non-proteolytic targets remain unknown. Here, we use unbiased proteomics to show that the UBE2L3 ubiquitin conjugase is an indirect target of caspase-1. Caspase-1, but not caspase-4, controls pyroptosis- and ubiquitin-independent proteasomal degradation of UBE2L3 upon canonical and non-canonical inflammasome activation by sterile danger signals and bacterial infection. Mechanistically, UBE2L3 acts post-translationally to promote K48-ubiquitylation and turnover of pro-IL-1β and dampen mature-IL-1β production. UBE2L3 depletion increases pro-IL-1β levels and mature-IL-1β secretion by inflammasomes. These findings regarding UBE2L3 as a molecular rheostat have implications for IL-1-driven pathology in hereditary fever syndromes and in autoinflammatory conditions associated with UBE2L3 polymorphisms. Caspase-1 inflammasomes induce loss of UBE2L3 in macrophages and dendritic cells UBE2L3 loss is proteasome-dependent, ubiquitin- and pyroptosis-independent UBE2L3 participates in K48 ubiquitylation and proteasomal turnover of pro-IL-1β UBE2L3 modulates levels of pro-IL-1β available for processing by caspase-1
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Affiliation(s)
- Matthew J G Eldridge
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gil Ferreira Hoben
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Philippa J Goddard
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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48
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Oh JH, Chen SJ, Varshavsky A. A reference-based protein degradation assay without global translation inhibitors. J Biol Chem 2017; 292:21457-21465. [PMID: 29122887 DOI: 10.1074/jbc.m117.814236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/05/2017] [Indexed: 11/06/2022] Open
Abstract
Although it is widely appreciated that the use of global translation inhibitors, such as cycloheximide, in protein degradation assays may result in artefacts, these inhibitors continue to be employed, owing to the absence of robust alternatives. We describe here the promoter reference technique (PRT), an assay for protein degradation with two advantageous features: a reference protein and a gene-specific inhibition of translation. In PRT assays, one measures, during a chase, the ratio of a test protein to a long-lived reference protein, a dihydrofolate reductase (DHFR). The test protein and DHFR are coexpressed, in the yeast Saccharomyces cerevisiae, on a low-copy plasmid from two identical P TDH3 promoters containing additional, previously developed DNA elements. Once transcribed, these elements form 5'-RNA aptamers that bind to the added tetracycline, which represses translation of aptamer-containing mRNAs. The selectivity of repression avoids a global inhibition of translation. This selectivity is particularly important if a component of a relevant proteolytic pathway (e.g. a specific ubiquitin ligase) is itself short-lived. We applied PRT to the Pro/N-end rule pathway, whose substrates include the short-lived Mdh2 malate dehydrogenase. Mdh2 is targeted for degradation by the Gid4 subunit of the GID ubiquitin ligase. Gid4 is also a metabolically unstable protein. Through analyses of short-lived Mdh2 as a target of short-lived Gid4, we illustrate the advantages of PRT over degradation assays that lack a reference and/or involve cycloheximide. In sum, PRT avoids the use of global translation inhibitors during a chase and also provides a "built-in" reference protein.
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Affiliation(s)
- Jang-Hyun Oh
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Shun-Jia Chen
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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49
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Marastoni M, Trapella C, Scotti A, Fantinati A, Ferretti V, Marzola E, Eleonora G, Gavioli R, Preti D. Naphthoquinone amino acid derivatives, synthesis and biological activity as proteasome inhibitors. J Enzyme Inhib Med Chem 2017; 32:865-877. [PMID: 28657369 PMCID: PMC6445160 DOI: 10.1080/14756366.2017.1334649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The ubiquitin-proteasome system has been largely investigated for its key role in protein degradation mechanisms that regulate both apoptosis and cell division. Because of their antitumour activity, different classes of proteasome inhibitors have been identified to date. Some of these compounds are currently employed in the clinical treatment of several types of cancer among which multiple myeloma. Here, we describe the design, chemistry, biological activity and modelling studies of a large series of amino acid derivatives linked to a naphthoquinone pharmacophoric group through variable spacers. Some analogues showed interesting inhibitory potency for the β1 and β5 subunits of the proteasome with IC50 values in the sub-µm range.
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Affiliation(s)
- Mauro Marastoni
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Claudio Trapella
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Alessandra Scotti
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Anna Fantinati
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Valeria Ferretti
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Erika Marzola
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Gallerani Eleonora
- b Department of Life Sciences and Biotechnology , University of Ferrara , Ferrara , Italy
| | - Riccardo Gavioli
- b Department of Life Sciences and Biotechnology , University of Ferrara , Ferrara , Italy
| | - Delia Preti
- a Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
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50
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Boselli M, Lee BH, Robert J, Prado MA, Min SW, Cheng C, Silva MC, Seong C, Elsasser S, Hatle KM, Gahman TC, Gygi SP, Haggarty SJ, Gan L, King RW, Finley D. An inhibitor of the proteasomal deubiquitinating enzyme USP14 induces tau elimination in cultured neurons. J Biol Chem 2017; 292:19209-19225. [PMID: 28972160 DOI: 10.1074/jbc.m117.815126] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is responsible for most selective protein degradation in eukaryotes and regulates numerous cellular processes, including cell cycle control and protein quality control. A component of this system, the deubiquitinating enzyme USP14, associates with the proteasome where it can rescue substrates from degradation by removal of the ubiquitin tag. We previously found that a small-molecule inhibitor of USP14, known as IU1, can increase the rate of degradation of a subset of proteasome substrates. We report here the synthesis and characterization of 87 variants of IU1, which resulted in the identification of a 10-fold more potent USP14 inhibitor that retains specificity for USP14. The capacity of this compound, IU1-47, to enhance protein degradation in cells was tested using as a reporter the microtubule-associated protein tau, which has been implicated in many neurodegenerative diseases. Using primary neuronal cultures, IU1-47 was found to accelerate the rate of degradation of wild-type tau, the pathological tau mutants P301L and P301S, and the A152T tau variant. We also report that a specific residue in tau, lysine 174, is critical for the IU1-47-mediated tau degradation by the proteasome. Finally, we show that IU1-47 stimulates autophagic flux in primary neurons. In summary, these findings provide a powerful research tool for investigating the complex biology of USP14.
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Affiliation(s)
- Monica Boselli
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Byung-Hoon Lee
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, 42988 Daegu, Korea
| | - Jessica Robert
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Sang-Won Min
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Chialin Cheng
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - M Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Changhyun Seong
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.,Regeneron Pharmaceuticals, Tarrytown, New York 10591, and
| | - Suzanne Elsasser
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ketki M Hatle
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, California 92093
| | - Steven P Gygi
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114
| | - Li Gan
- the Department of Neurology, Gladstone Institute of Neurological Diseases, University of California, San Francisco, California 94158
| | - Randall W King
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
| | - Daniel Finley
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115,
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