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Tan P, Cai S, Huang Z, Li M, Liu S, Chen J, Fu W, Zhao L. E3 ubiquitin ligase FBXW11 as a novel inflammatory biomarker is associated with immune infiltration and NF-κB pathway activation in pancreatitis and pancreatic cancer. Cell Signal 2024; 116:111033. [PMID: 38182068 DOI: 10.1016/j.cellsig.2024.111033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
BACKGROUND Pancreatic cancer (pancreatic ductal adenocarcinoma, PDAC) is an aggressive disease with an overall poor prognosis. Pancreatitis is a major risk factor for the development of PDAC. Due to the lack of reliable and accurate biomarkers, the diagnosis, treatment, and prognosis of PDAC face great challenges. It is of great significance to elucidate the pathogenesis of PDAC and explore novel inflammatory biomarkers. METHODS We identified E3 ubiquitin ligases associated with pancreatic inflammation by combining multiple GEO datasets and UbiNet 2.0, and integrating the WGCNA algorithm and Limma R package. A risk score model for PDAC patients was established by using LASSO regression. We investigated the correlation between FBXW11 and immune cell infiltration using CIBERSORT, mMCP-counter, ImmuCellAI-mouse, QUANTISEQ, and TIMER algorithms, based on GEO, ArrayExpress, and TCGA datasets. We used Ubibrowser 2.0 to predict potential substrates for FBXW11. WikiPathway, MSigDB Hallmark, and Elsevier pathway analysis of FBXW11 key substrates were also performed using the EnrichR database. We detected protein expression through IHC, immunofluorescence, and western blot in the cerulein-induced acute pancreatitis mouse model. RESULTS We first identified that FBXW11 exhibited a clear tendency to gradually increase in normal, pancreatitis, and PDAC patients. The validation analysis revealed that the FBXW11 protein exhibited significantly high expression in cerulein-induced acute pancreatitis mice, with its distribution primarily observed in the cytoplasm. Simultaneously, we developed a risk model utilizing the genes associated with FBXW11 to forecast the outcome of patients with PDAC and the likelihood of pancreatitis advancing to pancreatic cancer. Functional analysis showed that FBXW11, as a novel inflammatory biomarker, had a significant positive correlation with macrophage infiltration and the NF-κB signaling pathway. Finally, the western blot assay of the NF-κB signaling pathway in pancreatic tissues demonstrated that high activation of NF-κB was correlated with high expression of FBXW11. CONCLUSIONS Our research not only provides evidence for FBXW11 as a novel inflammatory biomarker but also provides new insights into the research and clinical treatment of pancreatic cancer.
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Affiliation(s)
- Peng Tan
- Department of Cell Biology and Genetics, Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710000, China; Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, Academician (Expert) Workstation of Sichuan Province, Department of General Surgery (Hepatopancreatobiliary surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Shuang Cai
- Department of Cell Biology and Genetics, Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710000, China
| | - Zhiwei Huang
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Mo Li
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Shenglu Liu
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Jiatong Chen
- Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Wenguang Fu
- Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, Academician (Expert) Workstation of Sichuan Province, Department of General Surgery (Hepatopancreatobiliary surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China.; Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Lingyu Zhao
- Department of Cell Biology and Genetics, Institute of Genetics and Developmental Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710000, China.
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Jin B, Moududee SA, Ge D, Zhou P, Wang AR, Liu YZ, You Z. SCF FBXW11 Complex Targets Interleukin-17 Receptor A for Ubiquitin-Proteasome-Mediated Degradation. Biomedicines 2024; 12:755. [PMID: 38672111 PMCID: PMC11047997 DOI: 10.3390/biomedicines12040755] [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: 02/28/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Interleukin-17 (IL-17) is a pro-inflammatory cytokine that participates in innate and adaptive immune responses and plays an important role in host defense, autoimmune diseases, tissue regeneration, metabolic regulation, and tumor progression. Post-translational modifications (PTMs) are crucial for protein function, stability, cellular localization, cellular transduction, and cell death. However, PTMs of IL-17 receptor A (IL-17RA) have not been investigated. Here, we show that human IL-17RA was targeted by F-box and WD repeat domain-containing 11 (FBXW11) for ubiquitination, followed by proteasome-mediated degradation. We used bioinformatics tools and biochemical techniques to determine that FBXW11 ubiquitinated IL-17RA through a lysine 27-linked polyubiquitin chain, targeting IL-17RA for proteasomal degradation. Domain 665-804 of IL-17RA was critical for interaction with FBXW11 and subsequent ubiquitination. Our study demonstrates that FBXW11 regulates IL-17 signaling pathways at the IL-17RA level.
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Affiliation(s)
- Ben Jin
- Southeast Louisiana Veterans Health Care System, New Orleans, LA 70112, USA; (B.J.); (S.A.M.)
- Department of Structural & Cellular Biology, Tulane University, New Orleans, LA 70112, USA
| | - Sayed Ala Moududee
- Southeast Louisiana Veterans Health Care System, New Orleans, LA 70112, USA; (B.J.); (S.A.M.)
- Department of Structural & Cellular Biology, Tulane University, New Orleans, LA 70112, USA
| | - Dongxia Ge
- Department of Orthopaedic Surgery, Tulane University, New Orleans, LA 70112, USA;
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Alun R. Wang
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Yao-Zhong Liu
- Department of Biostatistics and Data Science, Tulane University, New Orleans, LA 70112, USA;
| | - Zongbing You
- Southeast Louisiana Veterans Health Care System, New Orleans, LA 70112, USA; (B.J.); (S.A.M.)
- Department of Structural & Cellular Biology, Tulane University, New Orleans, LA 70112, USA
- Department of Orthopaedic Surgery, Tulane University, New Orleans, LA 70112, USA;
- Tulane Cancer Center and Louisiana Cancer Research Consortium, Tulane University, New Orleans, LA 70112, USA
- Tulane Center for Stem Cell Research and Regenerative Medicine, Tulane University, New Orleans, LA 70112, USA
- Tulane Center for Aging, Tulane University, New Orleans, LA 70112, USA
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3
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McGillivary RM, Starr DA, Luxton GWG. Building and breaking mechanical bridges between the nucleus and cytoskeleton: Regulation of LINC complex assembly and disassembly. Curr Opin Cell Biol 2023; 85:102260. [PMID: 37857179 PMCID: PMC10859145 DOI: 10.1016/j.ceb.2023.102260] [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: 08/04/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
The nucleus is physically coupled to the cytoskeleton through LINC complexes, macromolecular bridges composed of SUN and KASH proteins that span the nuclear envelope. LINC complexes are involved in a wide variety of critical cellular processes. For these processes to occur, cells regulate the composition, assembly, and disassembly of LINC complexes. Here we discuss recent studies on the regulation of the SUN-KASH interaction that forms the core of the LINC complex. These new findings encompass the stages of LINC complex assembly, from the formation of SUN-KASH heterooligomers to higher-order assemblies of LINC complexes. There is also new work on how components of the LINC complex are selectively dismantled, particularly by proteasomal degradation. It is becoming increasingly clear that LINC complexes are subject to multiple layers of regulation.
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Affiliation(s)
| | - Daniel A Starr
- Department of Molecular and Cellular Biology, University of California, Davis, USA.
| | - G W Gant Luxton
- Department of Molecular and Cellular Biology, University of California, Davis, USA.
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4
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Lee S, Carrasquillo Rodríguez JW, Merta H, Bahmanyar S. A membrane-sensing mechanism links lipid metabolism to protein degradation at the nuclear envelope. J Cell Biol 2023; 222:e202304026. [PMID: 37382667 PMCID: PMC10309186 DOI: 10.1083/jcb.202304026] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
Lipid composition determines organelle identity; however, whether the lipid composition of the inner nuclear membrane (INM) domain of the ER contributes to its identity is not known. Here, we show that the INM lipid environment of animal cells is under local control by CTDNEP1, the master regulator of the phosphatidic acid phosphatase lipin 1. Loss of CTDNEP1 reduces association of an INM-specific diacylglycerol (DAG) biosensor and results in a decreased percentage of polyunsaturated containing DAG species. Alterations in DAG metabolism impact the levels of the resident INM protein Sun2, which is under local proteasomal regulation. We identify a lipid-binding amphipathic helix (AH) in the nucleoplasmic domain of Sun2 that prefers membrane packing defects. INM dissociation of the Sun2 AH is linked to its proteasomal degradation. We suggest that direct lipid-protein interactions contribute to sculpting the INM proteome and that INM identity is adaptable to lipid metabolism, which has broad implications on disease mechanisms associated with the nuclear envelope.
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Affiliation(s)
- Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Holly Merta
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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5
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Li J, Xiang R, Li Y, Liao Q, Liu Y. Intrathyroid thymic carcinoma: clinicopathological features and whole exome sequencing analysis. Virchows Arch 2023; 482:813-822. [PMID: 37016248 DOI: 10.1007/s00428-023-03536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
Intrathyroid thymic carcinoma (ITC) is a rare malignant tumour. We present nine cases of ITC that were analysed by immunohistochemical staining, of which five were analysed using whole exome sequencing (WES). These cases included six women and three men with an age range of 31-66 years. The average postoperative follow-up term was 37.8 months (range, 7-95 months), and all patients survived well except for one case with lung metastasis. Microscopically, ITC showed solid islands of tumour cells separated by fibrous connective tissue containing lymphocytes and other inflammatory cells. Tumour cells strongly expressed Ckpan (AE1/AE3), P63, and CD117. And all cases but one were positive for CD5. The median value of Ki-67 was 32% (range 10-60%). We observed partial positivity of Syn and CgA in only one case. ITC shares morphological and immunohistochemical similarities with thymic squamous cell carcinoma. In situ hybridization of EBER showed negative results. All cases were microsatellite stable, and the tumour mutational burden of the 5 cases was all < 1 mutations/Mb. WES showed higher mutation rates for N4BP1 (2/5), and many genetic alterations were related to the NF-kB signalling pathway, which is crucial for insight into the molecular mechanisms of the occurrence and development of ITC.
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Affiliation(s)
- Jiayu Li
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, No.55, Section 4, Renmin South Road, Chengdu, 610041, China
| | - Run Xiang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yunzhu Li
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, No.55, Section 4, Renmin South Road, Chengdu, 610041, China
| | - Qiong Liao
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, No.55, Section 4, Renmin South Road, Chengdu, 610041, China.
| | - Yang Liu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, No.55, Section 4, Renmin South Road, Chengdu, 610041, China.
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6
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Geiger-Schuller K, Eraslan B, Kuksenko O, Dey KK, Jagadeesh KA, Thakore PI, Karayel O, Yung AR, Rajagopalan A, Meireles AM, Yang KD, Amir-Zilberstein L, Delorey T, Phillips D, Raychowdhury R, Moussion C, Price AL, Hacohen N, Doench JG, Uhler C, Rozenblatt-Rosen O, Regev A. Systematically characterizing the roles of E3-ligase family members in inflammatory responses with massively parallel Perturb-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525198. [PMID: 36747789 PMCID: PMC9900845 DOI: 10.1101/2023.01.23.525198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
E3 ligases regulate key processes, but many of their roles remain unknown. Using Perturb-seq, we interrogated the function of 1,130 E3 ligases, partners and substrates in the inflammatory response in primary dendritic cells (DCs). Dozens impacted the balance of DC1, DC2, migratory DC and macrophage states and a gradient of DC maturation. Family members grouped into co-functional modules that were enriched for physical interactions and impacted specific programs through substrate transcription factors. E3s and their adaptors co-regulated the same processes, but partnered with different substrate recognition adaptors to impact distinct aspects of the DC life cycle. Genetic interactions were more prevalent within than between modules, and a deep learning model, comβVAE, predicts the outcome of new combinations by leveraging modularity. The E3 regulatory network was associated with heritable variation and aberrant gene expression in immune cells in human inflammatory diseases. Our study provides a general approach to dissect gene function.
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7
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Fiore APZP, Rodrigues AM, Ribeiro-Filho HV, Manucci AC, de Freitas Ribeiro P, Botelho MCS, Vogel C, Lopes-de-Oliveira PS, Pagano M, Bruni-Cardoso A. Extracellular matrix stiffness regulates degradation of MST2 via SCF βTrCP. Biochim Biophys Acta Gen Subj 2022; 1866:130238. [PMID: 36044955 PMCID: PMC9926743 DOI: 10.1016/j.bbagen.2022.130238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/01/2022] [Accepted: 08/23/2022] [Indexed: 01/28/2023]
Abstract
The Hippo pathway plays central roles in relaying mechanical signals during development and tumorigenesis, but how the proteostasis of the Hippo kinase MST2 is regulated remains unknown. Here, we found that chemical inhibition of proteasomal proteolysis resulted in increased levels of MST2 in human breast epithelial cells. MST2 binds SCFβTrCP E3 ubiquitin ligase and silencing βTrCP resulted in MST2 accumulation. Site-directed mutagenesis combined with computational molecular dynamics studies revealed that βTrCP binds MST2 via a non-canonical degradation motif. Additionally, stiffer extracellular matrix, as well as hyperactivation of integrins resulted in enhanced MST2 degradation mediated by integrin-linked kinase (ILK) and actomyosin stress fibers. Our study uncovers the underlying biochemical mechanisms controlling MST2 degradation and underscores how alterations in the microenvironment rigidity regulate the proteostasis of a central Hippo pathway component.
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Affiliation(s)
- Ana Paula Zen Petisco Fiore
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil; Department of Biology, New York University, New York, NY 10003, USA
| | - Ana Maria Rodrigues
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Helder Veras Ribeiro-Filho
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Antonio Carlos Manucci
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Pedro de Freitas Ribeiro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | | | - Christine Vogel
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alexandre Bruni-Cardoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, Brazil.
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8
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Mannino PJ, Lusk CP. Quality control mechanisms that protect nuclear envelope identity and function. J Biophys Biochem Cytol 2022; 221:213424. [PMID: 36036741 PMCID: PMC9442147 DOI: 10.1083/jcb.202205123] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/22/2022] Open
Abstract
The nuclear envelope (NE) is a specialization of the endoplasmic reticulum with distinct biochemistry that defines inner and outer membranes connected at a pore membrane that houses nuclear pore complexes (NPCs). Quality control mechanisms that maintain the physical integrity and biochemical identity of these membranes are critical to ensure that the NE acts as a selective barrier that also contributes to genome stability and metabolism. As the proteome of the NE is highly integrated, it is challenging to turn over by conventional ubiquitin-proteasome and autophagy mechanisms. Further, removal of entire sections of the NE requires elaborate membrane remodeling that is poorly understood. Nonetheless, recent work has made inroads into discovering specializations of cellular degradative machineries tailored to meeting the unique challenges imposed by the NE. In addition, cells have evolved mechanisms to surveil and repair the NE barrier to protect against the deleterious effects of a breach in NE integrity, in the form of either a ruptured NE or a dysfunctional NPC. Here, we synthesize the most recent work exploring NE quality control mechanisms across eukaryotes.
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9
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Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. Cell Death Differ 2022; 29:1-13. [PMID: 34215846 PMCID: PMC8738747 DOI: 10.1038/s41418-021-00827-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
SKP1-CUL1-F-box (SCF) ubiquitin ligases play fundamental roles in cellular functions. Typically, substrate phosphorylation is required for SCF recognition and subsequent degradation. However, phospho-dependent substrates remain largely unidentified. Here, using quantitative phoshoproteome approach, we performed a system-wide investigation of phospho-dependent SCF substrates. This strategy identified diverse phospho-dependent candidates. Biochemical verification revealed a mechanism by which SCFFBXO22 recognizes the motif XXPpSPXPXX as a conserved phosphodegron to target substrates for destruction. We further demonstrated BAG3, a HSP70 co-chaperone, is a bona fide substrate of SCFFBXO22. FBXO22 mediates BAG3 ubiquitination and degradation that requires ERK-dependent BAG3 phosphorylation at S377. FBXO22 depletion or expression of a stable BAG3 S377A mutant promotes tumor growth via defects in apoptosis and cell cycle progression in vitro and in vivo. In conclusion, our study identified broad phosphorylation-dependent SCF substrates and demonstrated a phosphodegron recognized by FBXO22 and a novel ERK-FBXO22-BAG3 axis involved in tumorigenesis.
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10
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Yao J, Yang J, Yang Z, Wang XP, Yang T, Ji B, Zhang ZY. FBXW11 contributes to stem-cell-like features and liver metastasis through regulating HIC1-mediated SIRT1 transcription in colorectal cancer. Cell Death Dis 2021; 12:930. [PMID: 34642302 PMCID: PMC8511012 DOI: 10.1038/s41419-021-04185-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/02/2021] [Accepted: 09/15/2021] [Indexed: 01/10/2023]
Abstract
Colorectal tumorigenesis is a heterogeneous disease driven by multiple genetic and epigenetic alterations. F-box and WD repeat domain containing 11 (FBXW11) is a member of the F-box protein family that regulates the ubiquitination of key factors associated with tumor growth and aggressiveness. Our study aimed to explore the role of FBXW11 in the development and metastasis of colorectal cancer (CRC). FBXW11 was overexpressed in colorectal tumor tissues and its overexpression was associated with a poor prognosis of CRC patients. The upregulation of FBXW11 not only promoted cell proliferation, invasion, and migration, but also contributed to maintaining stem-cell features in colorectal tumor cells. Further analysis revealed that FBXW11 targeted hypermethylated in cancer 1 (HIC1) and reduced its stability in CRC cells through ubiquitination. Moreover, the expression of sirtuin 1 (SIRT1), a deacetylase in tumor cells was upregulated by FBXW11 via regulating HIC1 expression. The mouse xenograft models of CRC confirmed that FBXW11 knockdown impeded colorectal tumor growth and liver metastasis in vivo. In summary, our study identified FBXW11 as an oncogenic factor that contributed to stem-cell-like properties and liver metastasis in CRC via regulating HIC1-mediated SIRT1 expression. These results provide a rationale for the development of FBXW11-targeting drugs for CRC patients.
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Affiliation(s)
- Jing Yao
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai City, 200233, China
| | - Jun Yang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai City, 200233, China
| | - Zhe Yang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai City, 200233, China
| | - Xin-Ping Wang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai City, 200233, China
| | - Tong Yang
- Department of Internal Medicine, Huzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Huzhou City, Zhejiang Province, 313000, China
| | - Bing Ji
- Department of Internal Medicine, Huzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Huzhou City, Zhejiang Province, 313000, China.
| | - Zheng-Yun Zhang
- Department of Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai City, 200233, China.
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11
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Clinical Correlations of Polycomb Repressive Complex 2 in Different Tumor Types. Cancers (Basel) 2021; 13:cancers13133155. [PMID: 34202528 PMCID: PMC8267669 DOI: 10.3390/cancers13133155] [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: 05/27/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary PRC2 (Polycomb repressive complex 2) is a catalytic multi-subunit complex involved in transcriptional repression through the methylation of lysine 27 at histone 3 (H3K27me1/2/3). Dysregulation of PRC2 has been linked to tumor development and progression. Here, we performed a comprehensive analysis of data in the genomic and transcriptomic (cBioPortal, KMplot) database portals of clinical tumor samples and evaluated clinical correlations of EZH2, SUZ12, and EED. Next, we developed an original Python application enabling the identification of genes cooperating with PRC2 in oncogenic processes for the analysis of the DepMap CRISPR knockout database. Our study identified cancer types that are most likely to be responsive to PRC2 inhibitors. By analyzing co-dependencies with other genes, this analysis also provides indications of prognostic biomarkers and new therapeutic regimens. Abstract PRC2 (Polycomb repressive complex 2) is an evolutionarily conserved protein complex required to maintain transcriptional repression. The core PRC2 complex includes EZH2, SUZ12, and EED proteins and methylates histone H3K27. PRC2 is known to contribute to carcinogenesis and several small molecule inhibitors targeting PRC2 have been developed. The present study aimed to identify the cancer types in which PRC2 targeting drugs could be beneficial. We queried genomic and transcriptomic (cBioPortal, KMplot) database portals of clinical tumor samples to evaluate clinical correlations of PRC2 subunit genes. EZH2, SUZ12, and EED gene amplification was most frequently found in prostate cancer, whereas lymphoid malignancies (DLBCL) frequently showed EZH2 mutations. In both cases, PRC2 alterations were associated with poor prognosis. Moreover, higher expression of PRC2 subunits was correlated with poor survival in renal and liver cancers as well as gliomas. Finally, we generated a Python application to analyze the correlation of EZH2/SUZ12/EED gene knockouts by CRISPR with the alterations detected in the cancer cell lines using DepMap data. As a result, we were able to identify mutations that correlated significantly with tumor cell sensitivity to PRC2 knockout, including SWI/SNF, COMPASS/COMPASS-like subunits and BCL2, warranting the investigation of these genes as potential markers of sensitivity to PRC2-targeting drugs.
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12
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Dong S, Wei J, Bowser RK, Chen BB, Mallampalli RK, Miao J, Ye Q, Tran KC, Zhao Y, Zhao J. SCF FBXW17 E3 ubiquitin ligase regulates FBXL19 stability and cell migration. J Cell Biochem 2021; 122:326-334. [PMID: 33053230 PMCID: PMC7887023 DOI: 10.1002/jcb.29860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/16/2023]
Abstract
The Skp1-Cul1-F-box protein (SCF) E3 ligase complex is one of the largest ubiquitin E3 ligase families. FBXL19, a F-box protein in SCFFBXL19 E3 ligase complex, regulates a variety of cellular responses including cell migration. We have shown that FBXL19 is not stable and its degradation is mediated by the ubiquitin-proteasome system, while the ubiquitin E3 ligase for FBXL19 ubiquitination and degradation has not been identified. In the study, we discovered that a new ubiquitin E3 ligase, SCFFBXW17 , ubiquitinates and induces FBXL19 degradation. Exogenous FBXW17 targets FBXL19 for its ubiquitination and degradation. Lysine 114 in FBXL19 is a potential ubiquitin acceptor site. Acetylation of FBXL19 attenuated SCFFBXW17 -mediated FBXL19 degradation. SCFFBXL19 E3 ligase reduced Rac1 levels and cell migration, while the effects were attenuated by exogenous FBXW17. Downregulation of FBXW17 attenuated lysophosphatidic acid-induced lamellipodia formation and Rac1 accumulation at migration leading edge. Taken together with our previous studies, FBXL19 is degraded by the ubiquitin-proteasome system and its site-specific ubiquitination is mediated by SCFFBXW17 E3 ligase, which promotes cell migration.
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Affiliation(s)
- Su Dong
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Jianxin Wei
- Department of Medicine, The University of Pittsburgh,
Pittsburgh, PA
| | - Rachel K. Bowser
- Department of Medicine, The University of Pittsburgh,
Pittsburgh, PA
| | - Bill B. Chen
- Department of Medicine, The University of Pittsburgh,
Pittsburgh, PA
| | - Rama K. Mallampalli
- Pulmonary, Critical Care & Sleep Medicine Division, The
Ohio State University, Columbus, OH
| | - Jiaxing Miao
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Qinmao Ye
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Kevin C. Tran
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Yutong Zhao
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH,Pulmonary, Critical Care & Sleep Medicine Division, The
Ohio State University, Columbus, OH
| | - Jing Zhao
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH,Pulmonary, Critical Care & Sleep Medicine Division, The
Ohio State University, Columbus, OH,Address correspondence to: Jing Zhao, MD, PhD,
Department of Physiology and Cell Biology, The Ohio State University, 333 10th
Avenue, Graves Hall 2166D, Columbus, OH, United States, 43065. Tel:
614-685-0024;
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13
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Choi J, Lee W, An G, Kim SR. OsCBE1, a Substrate Receptor of Cullin4-Based E3 Ubiquitin Ligase, Functions as a Regulator of Abiotic Stress Response and Productivity in Rice. Int J Mol Sci 2021; 22:ijms22052487. [PMID: 33801226 PMCID: PMC7957871 DOI: 10.3390/ijms22052487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/03/2023] Open
Abstract
Ubiquitination is an important environmental stress response, and E3 ubiquitin ligases play a major role in the process. T-DNA insertion mutants of rice, Oscbe1-1, and Oscbe1-2, were identified through the screening of cold stress tolerance at seedling stage. Oscbe1 mutants showed a significantly higher cold stress tolerance in the fresh weight, chlorophyll content, and photosynthetic efficiency than wild type. Molecular prediction showed that OsCBE1 (Oryza sativa Cullin4-Based E3 ubiquitin ligase1) encoded a novel substrate receptor of Cullin4-based E3 ubiquitin ligase complex (C4E3). Whereas Oscbe1 mutants had fewer panicles and grains than wild type in the paddy field, the overexpression lines of OsCBE1 had more panicles and grains, suggesting that OsCBE1 is involved in the regulation of both abiotic stress response and development. Oscbe1 mutants also showed ABA hypersensitivity during seed germination, suggesting OsCBE1 function for the stress response via ABA signaling. In silico analysis of OsCBE1 activity predicted a CCCH-type transcription factor, OsC3H32, as a putative substrate. Co-IP (Co-immunoprecipitation) study showed that OsCBE1 interacts with OsDDB1, an expected binding component of OsCBE1 and OsC3H32. Additionally, expression of OsOLE16, OsOLE18, and OsBURP5 were negatively related with expression of OsCBE1. These results suggest that OsCBE1 functions as a regulator of the abiotic stress response via CCCH as a member of the C4E3.
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Affiliation(s)
- Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
| | - Wonkyung Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 17104, Korea;
| | - Seong-Ryong Kim
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
- Correspondence:
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14
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Abstract
The KEAP1-NRF2 pathway is the principal protective response to oxidative and electrophilic stresses. Under homeostatic conditions, KEAP1 forms part of an E3 ubiquitin ligase, which tightly regulates the activity of the transcription factor NRF2 by targeting it for ubiquitination and proteasome-dependent degradation. In response to stress, an intricate molecular mechanism facilitated by sensor cysteines within KEAP1 allows NRF2 to escape ubiquitination, accumulate within the cell, and translocate to the nucleus, where it can promote its antioxidant transcription program. Recent advances have revealed that KEAP1 contains multiple stress sensors and inactivation modalities, which together allow diverse cellular inputs, from oxidative stress and cellular metabolites to dysregulated autophagy, to regulate NRF2 activity. This integration of the KEAP1-NRF2 system into multiple cellular signaling and metabolic pathways places NRF2 activation as a critical regulatory node in many disease phenotypes and suggests that the pharmaceutical modulation of NRF2's cytoprotective activity will be beneficial for human health in a broad range of noncommunicable diseases.
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15
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Sjögren syndrome/scleroderma autoantigen 1 is a direct Tankyrase binding partner in cancer cells. Commun Biol 2020; 3:123. [PMID: 32170109 PMCID: PMC7070046 DOI: 10.1038/s42003-020-0851-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Sjögren syndrome/scleroderma autoantigen 1 (SSSCA1) was first described as an auto-antigen over-expressed in Sjögren’s syndrome and in scleroderma patients. SSSCA1 has been linked to mitosis and centromere association and as a potential marker candidate in diverse solid cancers. Here we characterize SSSCA1 for the first time, to our knowledge, at the molecular, structural and subcellular level. We have determined the crystal structure of a zinc finger fold, a zinc ribbon domain type 2 (ZNRD2), at 2.3 Å resolution. We show that the C-terminal domain serves a dual function as it both behaves as the interaction site to Tankyrase 1 (TNKS1) and as a nuclear export signal. We identify TNKS1 as a direct binding partner of SSSCA1, map the binding site to TNKS1 ankyrin repeat cluster 2 (ARC2) and thus define a new binding sequence. We experimentally verify and map a new nuclear export signal sequence in SSSCA1. Perdreau-Dahl et al. systematically characterise Sjögren syndrome/scleroderma autoantigen 1 at the molecular, structural and subcellular level. They show that the C-terminal domain serves a dual function as it both behaves as the interaction site to Tankyrase 1 and as a nuclear export signal.
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16
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Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer. ACTA ACUST UNITED AC 2019; 1:122-135. [DOI: 10.1038/s43018-019-0001-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
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17
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Barfield R, Wang H, Liu Y, Brody JA, Swenson B, Li R, Bartz TM, Sotoodehnia N, Chen YDI, Cade BE, Chen H, Patel SR, Zhu X, Gharib SA, Johnson WC, Rotter JI, Saxena R, Purcell S, Lin X, Redline S, Sofer T. Epigenome-wide association analysis of daytime sleepiness in the Multi-Ethnic Study of Atherosclerosis reveals African-American-specific associations. Sleep 2019; 42:zsz101. [PMID: 31139831 PMCID: PMC6685317 DOI: 10.1093/sleep/zsz101] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
STUDY OBJECTIVES Daytime sleepiness is a consequence of inadequate sleep, sleep-wake control disorder, or other medical conditions. Population variability in prevalence of daytime sleepiness is likely due to genetic and biological factors as well as social and environmental influences. DNA methylation (DNAm) potentially influences multiple health outcomes. Here, we explored the association between DNAm and daytime sleepiness quantified by the Epworth Sleepiness Scale (ESS). METHODS We performed multi-ethnic and ethnic-specific epigenome-wide association studies for DNAm and ESS in the Multi-Ethnic Study of Atherosclerosis (MESA; n = 619) and the Cardiovascular Health Study (n = 483), with cross-study replication and meta-analysis. Genetic variants near ESS-associated DNAm were analyzed for methylation quantitative trait loci and followed with replication of genotype-sleepiness associations in the UK Biobank. RESULTS In MESA only, we detected four DNAm-ESS associations: one across all race/ethnic groups; three in African-Americans (AA) only. Two of the MESA AA associations, in genes KCTD5 and RXRA, nominally replicated in CHS (p-value < 0.05). In the AA meta-analysis, we detected 14 DNAm-ESS associations (FDR q-value < 0.05, top association p-value = 4.26 × 10-8). Three DNAm sites mapped to genes (CPLX3, GFAP, and C7orf50) with biological relevance. We also found evidence for associations with DNAm sites in RAI1, a gene associated with sleep and circadian phenotypes. UK Biobank follow-up analyses detected SNPs in RAI1, RXRA, and CPLX3 with nominal sleepiness associations. CONCLUSIONS We identified methylation sites in multiple genes possibly implicated in daytime sleepiness. Most significant DNAm-ESS associations were specific to AA. Future work is needed to identify mechanisms driving ancestry-specific methylation effects.
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Affiliation(s)
- Richard Barfield
- Department of Epidemiology, University of Washington, Seattle, WA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Heming Wang
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Brenton Swenson
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Institute for Public Health Genetics, University of Washington, Seattle, WA
| | - Ruitong Li
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Institute for Public Health Genetics, University of Washington, Seattle, WA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Yii-der I Chen
- The Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
| | - Han Chen
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Center for Precision Health, School of Public Health & School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX
| | - Sanjay R Patel
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington Medicine Sleep Center, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, WA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, MA
| | - Shaun Purcell
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Psychiatry, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
- Department of Statistics, Harvard University, Cambridge, MA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
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18
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Rayner SL, Morsch M, Molloy MP, Shi B, Chung R, Lee A. Using proteomics to identify ubiquitin ligase-substrate pairs: how novel methods may unveil therapeutic targets for neurodegenerative diseases. Cell Mol Life Sci 2019; 76:2499-2510. [PMID: 30919022 PMCID: PMC11105231 DOI: 10.1007/s00018-019-03082-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/14/2019] [Accepted: 03/20/2019] [Indexed: 12/13/2022]
Abstract
Ubiquitin ligases play an integral role in fine-tuning signaling cascades necessary for normal cell function. Aberrant regulation of ubiquitin ligases has been implicated in several neurodegenerative diseases, generally, due to mutations within the E3 ligase itself. Several proteomic-based methods have recently emerged to facilitate the rapid identification of ligase-substrate pairs-a previously challenging feat due to the transient nature of ligase-substrate interactions. These novel methods complement standard immunoprecipitations (IPs) and include proximity-dependent biotin identification (BioID), ubiquitin ligase-substrate trapping, tandem ubiquitin-binding entities (TUBEs), and a molecular trapping unit known as the NEDDylator. The implementation of these techniques is expected to facilitate the rapid identification of novel substrates of E3 ubiquitin ligases, a process that is likely to enhance our understanding of neurodegenerative diseases and highlight novel therapeutic targets for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Stephanie L Rayner
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Macquarie Park, Sydney, NSW, 2109, Australia
| | - Marco Morsch
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Macquarie Park, Sydney, NSW, 2109, Australia
| | - Mark P Molloy
- Faculty of Medicine and Health, Sydney School of Medicine, Royal North Shore Hospital, Pacific Hwy, St Leonards, Sydney, NSW, 2065, Australia
| | - Bingyang Shi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Macquarie Park, Sydney, NSW, 2109, Australia
| | - Roger Chung
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Macquarie Park, Sydney, NSW, 2109, Australia
| | - Albert Lee
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, Macquarie Park, Sydney, NSW, 2109, Australia.
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19
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Wang W, Zhang X, Niittylä T. OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis. THE PLANT CELL 2019; 31:1446-1465. [PMID: 31023726 PMCID: PMC6635878 DOI: 10.1105/tpc.19.00033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/01/2019] [Accepted: 04/23/2019] [Indexed: 05/19/2023]
Abstract
Currently one-third of the proteins encoded by the Arabidopsis (Arabidopsis thaliana) genome are of unknown function. Some of these unknown proteins are likely to be involved in uncharacterized vital biological processes. Evolutionarily conserved single copy genes in flowering plants have been shown to be enriched in essential housekeeping functions. This together with publicly available gene expression data allows for a focused search for uncharacterized essential genes. Here we identify an essential single copy gene called OPENER (OPNR) in Arabidopsis. We show that OPNR is predominantly expressed in actively dividing cells and performs essential functions in seed development and root meristem maintenance. Cell cycle tracking using 5-ethynyl-2'-deoxyuridine staining and fluorescent cell cycle markers together with the increased size of nucleolus and nucleus in opnr mutants indicate that OPNR is required for cell cycle progression through the S or G2 phases. Intriguingly, OPNR localizes to the nuclear envelope and mitochondria. Furthermore, the nuclear envelope localization of OPNR is dependent on its interaction with nuclear inner membrane Sad1/UNC-84 (SUN) domain proteins SUN1 and SUN2. Taken together our results open a line of investigation into an evolutionarily conserved essential cellular process occurring in both the nuclear envelopes and mitochondria of dividing cells.
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Affiliation(s)
- Wei Wang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Xueyang Zhang
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
| | - Totte Niittylä
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umea, Sweden
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20
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Bakos G, Yu L, Gak IA, Roumeliotis TI, Liakopoulos D, Choudhary JS, Mansfeld J. An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules. Nat Commun 2018; 9:4776. [PMID: 30429481 PMCID: PMC6235928 DOI: 10.1038/s41467-018-07251-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to many biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we present an E2-thioester-driven identification (E2~dID) method for the targeted identification of substrates of specific E2 and E3 enzyme pairs. E2~dID exploits the central position of E2-conjugating enzymes in the ubiquitination cascade and provides in vitro generated biotinylated E2~ubiquitin thioester conjugates as the sole source for ubiquitination in extracts. This enables purification and mass spectrometry-based identification of modified proteins under stringent conditions independently of the biological source of the extract. We demonstrate the sensitivity and specificity of E2-dID by identifying and validating substrates of APC/C in human cells. Finally, we perform E2~dID with SUMO in S. cerevisiae, showing that this approach can be easily adapted to other ubiquitin-like modifiers and experimental models.
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Affiliation(s)
- Gábor Bakos
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Igor A Gak
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany
| | | | - Dimitris Liakopoulos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), CNRS UMR 5237, 34293, Montpellier Cedex 05, France
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307, Dresden, Germany.
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21
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Hepatitis C virus enters liver cells using the CD81 receptor complex proteins calpain-5 and CBLB. PLoS Pathog 2018; 14:e1007111. [PMID: 30024968 PMCID: PMC6053247 DOI: 10.1371/journal.ppat.1007111] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/18/2018] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) and the malaria parasite Plasmodium use the membrane protein CD81 to invade human liver cells. Here we mapped 33 host protein interactions of CD81 in primary human liver and hepatoma cells using high-resolution quantitative proteomics. In the CD81 protein network, we identified five proteins which are HCV entry factors or facilitators including epidermal growth factor receptor (EGFR). Notably, we discovered calpain-5 (CAPN5) and the ubiquitin ligase Casitas B-lineage lymphoma proto-oncogene B (CBLB) to form a complex with CD81 and support HCV entry. CAPN5 and CBLB were required for a post-binding and pre-replication step in the HCV life cycle. Knockout of CAPN5 and CBLB reduced susceptibility to all tested HCV genotypes, but not to other enveloped viruses such as vesicular stomatitis virus and human coronavirus. Furthermore, Plasmodium sporozoites relied on a distinct set of CD81 interaction partners for liver cell entry. Our findings reveal a comprehensive CD81 network in human liver cells and show that HCV and Plasmodium highjack selective CD81 interactions, including CAPN5 and CBLB for HCV, to invade cells. CD81 is a cell membrane protein, which functions as entry factor for hepatitis C virus (HCV) and malaria sporozoites in the human liver. Currently, it remains enigmatic how CD81 guides the entry process of both pathogens and whether it functions in a similar way during liver cell invasion of HCV and malaria parasites. Here, we use high resolution quantitative proteomics to identify CD81 associated host proteins in liver cells. We found that at least 33 proteins form a complex with CD81, 23 of which were not reported as interaction partners before. We further determined that at least five CD81 interactors are HCV host factors, among them calpain-5 (CAPN5) and the ubiquitin ligase Casitas B-lineage lymphoma proto-oncogene B (CBLB). All tested HCV genotypes require CAPN5 and CBLB for full infection, but neither malaria parasites nor other tested enveloped virus rely on CAPN5 or CBLB. Our study maps the liver cell interactome of CD81 and provides new insight into the distinct cell invasion mechanisms of HCV and malaria parasites.
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22
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Mammalian TRIM67 Functions in Brain Development and Behavior. eNeuro 2018; 5:eN-NWR-0186-18. [PMID: 29911180 PMCID: PMC6002264 DOI: 10.1523/eneuro.0186-18.2018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023] Open
Abstract
Class I members of the tripartite motif (TRIM) family of E3 ubiquitin ligases evolutionarily appeared just prior to the advent of neuronal like cells and have been implicated in neuronal development from invertebrates to mammals. The single Class I TRIM in Drosophila melanogaster and Caenorhabditis elegans and the mammalian Class I TRIM9 regulate axon branching and guidance in response to the guidance cue netrin, whereas mammalian TRIM46 establishes the axon initial segment. In humans, mutations in TRIM1 and TRIM18 are implicated in Opitz Syndrome, characterized by midline defects and often intellectual disability. We find that although TRIM67 is the least studied vertebrate Class I TRIM, it is the most evolutionarily conserved. Here we show that mammalian TRIM67 interacts with both its closest paralog TRIM9 and the netrin receptor DCC and is differentially enriched in specific brain regions during development and adulthood. We describe the anatomical and behavioral consequences of deletion of murine Trim67. While viable, mice lacking Trim67 exhibit abnormal anatomy of specific brain regions, including hypotrophy of the hippocampus, striatum, amygdala, and thalamus, and thinning of forebrain commissures. Additionally, Trim67-/- mice display impairments in spatial memory, cognitive flexibility, social novelty preference, muscle function, and sensorimotor gating, whereas several other behaviors remain intact. This study demonstrates the necessity for TRIM67 in appropriate brain development and behavior.
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23
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Abdi K, Lai CH, Paez-Gonzalez P, Lay M, Pyun J, Kuo CT. Uncovering inherent cellular plasticity of multiciliated ependyma leading to ventricular wall transformation and hydrocephalus. Nat Commun 2018; 9:1655. [PMID: 29695808 PMCID: PMC5916891 DOI: 10.1038/s41467-018-03812-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 03/14/2018] [Indexed: 12/26/2022] Open
Abstract
Specialized, differentiated cells often perform unique tasks that require them to maintain a stable phenotype. Multiciliated ependymal cells (ECs) are unique glial cells lining the brain ventricles, important for cerebral spinal fluid circulation. While functional ECs are needed to prevent hydrocephalus, they have also been reported to generate new neurons: whether ECs represent a stable cellular population remains unclear. Via a chemical screen we found that mature ECs are inherently plastic, with their multiciliated state needing constant maintenance by the Foxj1 transcription factor, which paradoxically is rapidly turned over by the ubiquitin-proteasome system leading to cellular de-differentiation. Mechanistic analyses revealed a novel NF-κB-independent IKK2 activity stabilizing Foxj1 in mature ECs, and we found that known IKK2 inhibitors including viruses and growth factors robustly induced Foxj1 degradation, EC de-differentiation, and hydrocephalus. Although mature ECs upon de-differentiation can divide and regenerate multiciliated ECs, we did not detect evidence supporting EC’s neurogenic potential. Multiciliated ependymal cells (ECs) in the mammalian brain are glial cells facilitating cerebral spinal fluid movement. This study describes an inherent cellular plasticity of ECs as maintained by Foxj1 and IKK2 signaling, and shows resulting hydrocephalus when EC de-differentiation is triggered.
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Affiliation(s)
- Khadar Abdi
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Chun-Hsiang Lai
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | | | - Mark Lay
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Joon Pyun
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Chay T Kuo
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA. .,Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA. .,Preston Robert Tisch Brain Tumor Center, Duke University School of Medicine, Durham, NC, 27710, USA. .,Brumley Neonatal/Perinatal Research Institute, Duke University School of Medicine, Durham, NC, 27710, USA. .,Institute for Brain Sciences, Duke University School of Medicine, Durham, NC, 27710, USA.
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24
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Hülsmann J, Kravic B, Weith M, Gstaiger M, Aebersold R, Collins BC, Meyer H. AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. Mol Cell Proteomics 2018; 17:1295-1307. [PMID: 29599191 DOI: 10.1074/mcp.ra117.000471] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/07/2018] [Indexed: 12/27/2022] Open
Abstract
The ubiquitin-directed AAA-ATPase VCP/p97 facilitates degradation of damaged or misfolded proteins in diverse cellular stress response pathways. Resolving the complexity of its interactions with partner and substrate proteins and understanding its links to stress signaling is therefore a major challenge. Here, we used affinity-purification SWATH mass spectrometry (AP-SWATH) to identify proteins that specifically interact with the substrate-trapping mutant, p97-E578Q. AP-SWATH identified differential interactions over a large detection range from abundant p97 cofactors to pathway-specific partners and individual ligases such as RNF185 and MUL1 that were trapped in p97-E578Q complexes. In addition, we identified various substrate proteins and candidates including the PP1 regulator CReP/PPP1R15B that dephosphorylates eIF2α and thus counteracts attenuation of translation by stress-kinases. We provide evidence that p97 with its Ufd1-Npl4 adapter ensures rapid constitutive turnover and balanced levels of CReP in unperturbed cells. Moreover, we show that p97-mediated degradation, together with a reduction in CReP synthesis, is essential for timely stress-induced reduction of CReP levels and, consequently, for robust eIF2α phosphorylation to enforce the stress response. Thus, our results demonstrate that p97 not only facilitates bulk degradation of misfolded proteins upon stress, but also directly modulates the integrated stress response at the level of signaling.
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Affiliation(s)
- Julia Hülsmann
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Bojana Kravic
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Matthias Weith
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Matthias Gstaiger
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.,¶Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Ben C Collins
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland;
| | - Hemmo Meyer
- From the ‡Molecular Biology I, Centre for Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany;
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25
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Gray KM, Kaifer KA, Baillat D, Wen Y, Bonacci TR, Ebert AD, Raimer AC, Spring AM, Have ST, Glascock JJ, Gupta K, Van Duyne GD, Emanuele MJ, Lamond AI, Wagner EJ, Lorson CL, Matera AG. Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCF Slmb degron. Mol Biol Cell 2018; 29:96-110. [PMID: 29167380 PMCID: PMC5909936 DOI: 10.1091/mbc.e17-11-0627] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/14/2017] [Indexed: 12/16/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by homozygous mutations in human SMN1 Expression of a duplicate gene (SMN2) primarily results in skipping of exon 7 and production of an unstable protein isoform, SMNΔ7. Although SMN2 exon skipping is the principal contributor to SMA severity, mechanisms governing stability of survival motor neuron (SMN) isoforms are poorly understood. We used a Drosophila model system and label-free proteomics to identify the SCFSlmb ubiquitin E3 ligase complex as a novel SMN binding partner. SCFSlmb interacts with a phosphor degron embedded within the human and fruitfly SMN YG-box oligomerization domains. Substitution of a conserved serine (S270A) interferes with SCFSlmb binding and stabilizes SMNΔ7. SMA-causing missense mutations that block multimerization of full-length SMN are also stabilized in the degron mutant background. Overexpression of SMNΔ7S270A, but not wild-type (WT) SMNΔ7, provides a protective effect in SMA model mice and human motor neuron cell culture systems. Our findings support a model wherein the degron is exposed when SMN is monomeric and sequestered when SMN forms higher-order multimers.
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Affiliation(s)
- Kelsey M Gray
- Curriculum in Genetics and Molecular Biology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Integrative Program in Biological and Genome Sciences, Department of Biology and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| | - Kevin A Kaifer
- Molecular Pathogenesis and Therapeutics Program, Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211
| | - David Baillat
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550
| | - Ying Wen
- Integrative Program in Biological and Genome Sciences, Department of Biology and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| | - Thomas R Bonacci
- Curriculum in Genetics and Molecular Biology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599
| | - Allison D Ebert
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Amanda C Raimer
- Curriculum in Genetics and Molecular Biology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Integrative Program in Biological and Genome Sciences, Department of Biology and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| | - Ashlyn M Spring
- Integrative Program in Biological and Genome Sciences, Department of Biology and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| | - Sara Ten Have
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD15EH, UK
| | - Jacqueline J Glascock
- Molecular Pathogenesis and Therapeutics Program, Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Gregory D Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Michael J Emanuele
- Curriculum in Genetics and Molecular Biology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD15EH, UK
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550
| | - Christian L Lorson
- Molecular Pathogenesis and Therapeutics Program, Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Integrative Program in Biological and Genome Sciences, Department of Biology and Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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26
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Abstract
Our knowledge of cell cycle regulatory mechanisms in apicomplexan parasites is very limited. In this study, we describe a novel Toxoplasma gondii factor that has a vital role in chromosome replication and the regulation of cytoplasmic and nuclear mitotic structures, and we named this factor ECR1 for essential for chromosome replication 1. ECR1 was discovered by complementation of a temperature-sensitive (ts) mutant that suffers lethal, uncontrolled chromosome replication at 40°C similar to a ts mutant carrying a defect in topoisomerase. ECR1 is a 52-kDa protein containing divergent RING and TRAF-Sina-like zinc binding domains that are dynamically expressed in the tachyzoite cell cycle. ECR1 first appears in the unique spindle compartment of the Apicomplexa (centrocone) of the nuclear envelope in early S phase and then in the nucleus in late S phase where it reaches maximum expression. Following nuclear division, but before daughter parasites separate from the mother parasite, ECR1 is downregulated and is absent in new daughter parasites. The proteomics of ECR1 identified interactions with the ubiquitin-mediated protein degradation machinery and the minichromosome maintenance complex, and the loss of ECR1 led to increased stability of a key member of this complex, MCM2. ECR1 also forms a stable complex with the cyclin-dependent kinase (CDK)-related kinase, Tgondii Crk5 (TgCrk5), which displays a similar cell cycle expression and localization during tachyzoite replication. Importantly, the localization of ECR1/TgCrk5 in the centrocone indicates that this Apicomplexa-specific spindle compartment houses important regulatory factors that control the parasite cell cycle.IMPORTANCE Parasites of the apicomplexan family are important causes of human disease, including malaria, toxoplasmosis, and cryptosporidiosis. Parasite growth is the underlying cause of pathogenesis, yet despite this importance, the molecular basis for parasite replication is poorly understood. Filling this knowledge gap cannot be accomplished by mining recent whole-genome sequencing data because apicomplexan cell cycles differ substantially and lack many of the key regulatory factors of well-studied yeast and mammalian cell division models. We have utilized forward genetics to discover essential factors that regulate cell division in these parasites using the Toxoplasma gondii model. An example of this approach is described here with the discovery of a putative E3 ligase/protein kinase mechanism involved in regulating chromosome replication and mitotic processes of asexual stage parasites.
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Trim9 Deletion Alters the Morphogenesis of Developing and Adult-Born Hippocampal Neurons and Impairs Spatial Learning and Memory. J Neurosci 2017; 36:4940-58. [PMID: 27147649 DOI: 10.1523/jneurosci.3876-15.2016] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/07/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED During hippocampal development, newly born neurons migrate to appropriate destinations, extend axons, and ramify dendritic arbors to establish functional circuitry. These developmental stages are recapitulated in the dentate gyrus of the adult hippocampus, where neurons are continuously generated and subsequently incorporate into existing, local circuitry. Here we demonstrate that the E3 ubiquitin ligase TRIM9 regulates these developmental stages in embryonic and adult-born mouse hippocampal neurons in vitro and in vivo Embryonic hippocampal and adult-born dentate granule neurons lacking Trim9 exhibit several morphological defects, including excessive dendritic arborization. Although gross anatomy of the hippocampus was not detectably altered by Trim9 deletion, a significant number of Trim9(-/-) adult-born dentate neurons localized inappropriately. These morphological and localization defects of hippocampal neurons in Trim9(-/-) mice were associated with extreme deficits in spatial learning and memory, suggesting that TRIM9-directed neuronal morphogenesis may be involved in hippocampal-dependent behaviors. SIGNIFICANCE STATEMENT Appropriate generation and incorporation of adult-born neurons in the dentate gyrus are critical for spatial learning and memory and other hippocampal functions. Here we identify the brain-enriched E3 ubiquitin ligase TRIM9 as a novel regulator of embryonic and adult hippocampal neuron shape acquisition and hippocampal-dependent behaviors. Genetic deletion of Trim9 elevated dendritic arborization of hippocampal neurons in vitro and in vivo Adult-born dentate granule cells lacking Trim9 similarly exhibited excessive dendritic arborization and mislocalization of cell bodies in vivo These cellular defects were associated with severe deficits in spatial learning and memory.
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28
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Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. Sci Rep 2017; 7:6829. [PMID: 28754924 PMCID: PMC5533708 DOI: 10.1038/s41598-017-05748-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 06/02/2017] [Indexed: 12/21/2022] Open
Abstract
The emergence of genes implicated across multiple comorbid neurologic disorders allows to identify shared underlying molecular pathways. Recently, investigation of patients with diverse neurologic disorders found TANC1 and TANC2 as possible candidate disease genes. While the TANC proteins have been reported as postsynaptic scaffolds influencing synaptic spines and excitatory synapse strength, their molecular functions remain unknown. Here, we conducted a comprehensive in silico analysis of the TANC protein family to characterize their molecular role and understand possible neurobiological consequences of their disruption. The known Ankyrin and tetratricopeptide repeat (TPR) domains have been modeled. The newly predicted N-terminal ATPase domain may function as a regulated molecular switch for downstream signaling. Several putative conserved protein binding motifs allowed to extend the TANC interaction network. Interestingly, we highlighted connections with different signaling pathways converging to modulate neuronal activity. Beyond a known role for TANC family members in the glutamate receptor pathway, they seem linked to planar cell polarity signaling, Hippo pathway, and cilium assembly. This suggests an important role in neuron projection, extension and differentiation.
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29
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VprBP/DCAF1 Regulates the Degradation and Nonproteolytic Activation of the Cell Cycle Transcription Factor FoxM1. Mol Cell Biol 2017; 37:MCB.00609-16. [PMID: 28416635 DOI: 10.1128/mcb.00609-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/10/2017] [Indexed: 02/07/2023] Open
Abstract
The oncogenic transcription factor FoxM1 plays a vital role in cell cycle progression, is activated in numerous human malignancies, and is linked to chromosome instability. We characterize here a cullin 4-based E3 ubiquitin ligase and its substrate receptor, VprBP/DCAF1 (CRL4VprBP), which we show regulate FoxM1 ubiquitylation and degradation. Paradoxically, we also found that the substrate receptor VprBP is a potent FoxM1 activator. VprBP depletion reduces expression of FoxM1 target genes and impairs mitotic entry, whereas ectopic VprBP expression strongly activates a FoxM1 transcriptional reporter. VprBP binding to CRL4 is reduced during mitosis, and our data suggest that VprBP activation of FoxM1 is ligase independent. This implies a nonproteolytic activation mechanism that is reminiscent of, yet distinct from, the ubiquitin-dependent transactivation of the oncoprotein Myc by other E3s. Significantly, VprBP protein levels were upregulated in high-grade serous ovarian patient tumors, where the FoxM1 signature is amplified. These data suggest that FoxM1 abundance and activity are controlled by VprBP and highlight the functional repurposing of E3 ligase substrate receptors independent of the ubiquitin system.
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30
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Systematic approaches to identify E3 ligase substrates. Biochem J 2017; 473:4083-4101. [PMID: 27834739 PMCID: PMC5103871 DOI: 10.1042/bcj20160719] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022]
Abstract
Protein ubiquitylation is a widespread post-translational modification, regulating cellular signalling with many outcomes, such as protein degradation, endocytosis, cell cycle progression, DNA repair and transcription. E3 ligases are a critical component of the ubiquitin proteasome system (UPS), determining the substrate specificity of the cascade by the covalent attachment of ubiquitin to substrate proteins. Currently, there are over 600 putative E3 ligases, but many are poorly characterized, particularly with respect to individual protein substrates. Here, we highlight systematic approaches to identify and validate UPS targets and discuss how they are underpinning rapid advances in our understanding of the biochemistry and biology of the UPS. The integration of novel tools, model systems and methods for target identification is driving significant interest in drug development, targeting various aspects of UPS function and advancing the understanding of a diverse range of disease processes.
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31
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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32
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ZNF395 Is an Activator of a Subset of IFN-Stimulated Genes. Mediators Inflamm 2017; 2017:1248201. [PMID: 28316371 PMCID: PMC5339479 DOI: 10.1155/2017/1248201] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 11/17/2022] Open
Abstract
Activation of the interferon (IFN) pathway in response to infection with pathogens results in the induction of IFN-stimulated genes (ISGs) including proinflammatory cytokines, which mount the proper antiviral immune response. However, aberrant expression of these genes is pathogenic to the host. In addition to IFN-induced transcription factors non-IFN-regulated factors contribute to the transcriptional control of ISGs. Here, we show by genome wide expression analysis, siRNA-mediated suppression and Doxycycline-induced overexpression that the cellular transcription factor ZNF395 activates a subset of ISGs including the chemokines CXCL10 and CXCL11 in keratinocytes. We found that ZNF395 acts independently of IFN but enhances the IFN-induced expression of CXCL10 and CXCL11. Luciferase reporter assays revealed a requirement of intact NFκB-binding sites for ZNF395 to stimulate the CXCL10 promoter. The transcriptional activation of CXCL10 and CXCL11 by ZNF395 was abolished after inhibition of IKK by BMS-345541, which increased the stability of ZNF395. ZNF395 encodes at least two motifs that mediate the enhanced degradation of ZNF395 in response to IKK activation. Thus, IKK is required for ZNF395-mediated activation of transcription and enhances its turn-over to keep the activity of ZNF395 low. Our results support a previously unrecognized role of ZNF395 in the innate immune response and inflammation.
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33
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The nonreceptor tyrosine kinase c-Src attenuates SCF(β-TrCP) E3-ligase activity abrogating Taz proteasomal degradation. Proc Natl Acad Sci U S A 2017; 114:1678-1683. [PMID: 28154141 DOI: 10.1073/pnas.1610223114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The polyomavirus middle T antigen (PyMT) oncogene activates the cellular nonreceptor tyrosine kinase c-Src and recruits the Hippo pathway effectors, Yap (yes-associated protein) and Taz (transcriptional coactivator with PDZ-binding motif), as key steps in oncogenesis. Yap and Taz are transcription coactivators shuttling from the cytoplasm to the nucleus. The Hippo pathway kinase Lats1/2 (large tumor suppressor homolog) reduces Yap/Taz nuclear localization and minimizes their cytoplasmic levels by facilitating their ubiquitination by the E3 ligase SCF(β-TrCP). In contrast, PyMT increases the cytoplasmic Taz level. Here we show that this unique PyMT behavior is mediated by Src. We demonstrate that PyMT-induced Src activation inhibits degradation of both wild-type and tyrosine-less Taz, ruling out Taz modification as a mechanism of escaping degradation. Instead, we found that Src attenuates the SCF(β-TrCP) E3-ligase activity in blunting Taz proteasomal degradation. The role of Src in rescuing Taz from TrCP-mediated degradation gives rise to higher cell proliferation under dense cell culture. Finally, IkB (NF-kappa-B inhibitor), a known substrate of β-TrCP, was rescued by Src, suggesting a wider effect of Src on β-TrCP substrates. These findings introduce the Src tyrosine kinase as a regulator of SCF(β-TrCP).
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34
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Shimizu K, Fukushima H, Ogura K, Lien EC, Nihira NT, Zhang J, North BJ, Guo A, Nagashima K, Nakagawa T, Hoshikawa S, Watahiki A, Okabe K, Yamada A, Toker A, Asara JM, Fukumoto S, Nakayama KI, Nakayama K, Inuzuka H, Wei W. The SCFβ-TRCP E3 ubiquitin ligase complex targets Lipin1 for ubiquitination and degradation to promote hepatic lipogenesis. Sci Signal 2017; 10:10/460/eaah4117. [PMID: 28049764 DOI: 10.1126/scisignal.aah4117] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The SCFβ-TRCP E3 ubiquitin ligase complex plays pivotal roles in normal cellular physiology and in pathophysiological conditions. Identification of β-transducin repeat-containing protein (β-TRCP) substrates is therefore critical to understand SCFβ-TRCP biology and function. We used a β-TRCP-phosphodegron motif-specific antibody in a β-TRCP substrate screen coupled with tandem mass spectrometry and identified multiple β-TRCP substrates. One of these substrates was Lipin1, an enzyme and suppressor of the family of sterol regulatory element-binding protein (SREBP) transcription factors, which activate genes encoding lipogenic factors. We showed that SCFβ-TRCP specifically interacted with and promoted the polyubiquitination of Lipin1 in a manner that required phosphorylation of Lipin1 by mechanistic target of rapamycin 1 (mTORC1) and casein kinase I (CKI). β-TRCP depletion in HepG2 hepatocellular carcinoma cells resulted in increased Lipin1 protein abundance, suppression of SREBP-dependent gene expression, and attenuation of triglyceride synthesis. Moreover, β-TRCP1 knockout mice showed increased Lipin1 protein abundance and were protected from hepatic steatosis induced by a high-fat diet. Together, these data reveal a critical physiological function of β-TRCP in regulating hepatic lipid metabolic homeostasis in part through modulating Lipin1 stability.
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Affiliation(s)
- Kouhei Shimizu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Hidefumi Fukushima
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Kohei Ogura
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,Department of Infectious Diseases, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Evan C Lien
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Naoe Taira Nihira
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ailan Guo
- Cell Signaling Technology Inc., Danvers, MA 01923, USA
| | - Katsuyuki Nagashima
- Department of Physiological Science and Molecular Biology, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | - Tadashi Nakagawa
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Seira Hoshikawa
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan.,Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Asami Watahiki
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Koji Okabe
- Department of Physiological Science and Molecular Biology, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | - Aya Yamada
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Satoshi Fukumoto
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan.,Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Keiichi I Nakayama
- Division of Cell Regulation Systems, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. .,Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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35
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36
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Mulvaney KM, Matson JP, Siesser PF, Tamir TY, Goldfarb D, Jacobs TM, Cloer EW, Harrison JS, Vaziri C, Cook JG, Major MB. Identification and Characterization of MCM3 as a Kelch-like ECH-associated Protein 1 (KEAP1) Substrate. J Biol Chem 2016; 291:23719-23733. [PMID: 27621311 DOI: 10.1074/jbc.m116.729418] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Indexed: 12/30/2022] Open
Abstract
KEAP1 is a substrate adaptor protein for a CUL3-based E3 ubiquitin ligase. Ubiquitylation and degradation of the antioxidant transcription factor NRF2 is considered the primary function of KEAP1; however, few other KEAP1 substrates have been identified. Because KEAP1 is altered in a number of human pathologies and has been proposed as a potential therapeutic target therein, we sought to better understand KEAP1 through systematic identification of its substrates. Toward this goal, we combined parallel affinity capture proteomics and candidate-based approaches. Substrate-trapping proteomics yielded NRF2 and the related transcription factor NRF1 as KEAP1 substrates. Our targeted investigation of KEAP1-interacting proteins revealed MCM3, an essential subunit of the replicative DNA helicase, as a new substrate. We show that MCM3 is ubiquitylated by the KEAP1-CUL3-RBX1 complex in cells and in vitro Using ubiquitin remnant profiling, we identify the sites of KEAP1-dependent ubiquitylation in MCM3, and these sites are on predicted exposed surfaces of the MCM2-7 complex. Unexpectedly, we determined that KEAP1 does not regulate total MCM3 protein stability or subcellular localization. Our analysis of a KEAP1 targeting motif in MCM3 suggests that MCM3 is a point of direct contact between KEAP1 and the MCM hexamer. Moreover, KEAP1 associates with chromatin in a cell cycle-dependent fashion with kinetics similar to the MCM2-7 complex. KEAP1 is thus poised to affect MCM2-7 dynamics or function rather than MCM3 abundance. Together, these data establish new functions for KEAP1 within the nucleus and identify MCM3 as a novel substrate of the KEAP1-CUL3-RBX1 E3 ligase.
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Affiliation(s)
- Kathleen M Mulvaney
- From the Departments of Cell Biology and Physiology.,Lineberger Comprehensive Cancer Center, and
| | | | | | - Tigist Y Tamir
- Lineberger Comprehensive Cancer Center, and.,Pharmacology
| | - Dennis Goldfarb
- Lineberger Comprehensive Cancer Center, and.,Computer Science, and
| | - Timothy M Jacobs
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Erica W Cloer
- From the Departments of Cell Biology and Physiology.,Lineberger Comprehensive Cancer Center, and
| | - Joseph S Harrison
- Lineberger Comprehensive Cancer Center, and.,Biochemistry and Biophysics
| | - Cyrus Vaziri
- Lineberger Comprehensive Cancer Center, and.,Pathology
| | - Jeanette G Cook
- Lineberger Comprehensive Cancer Center, and .,Biochemistry and Biophysics
| | - Michael B Major
- From the Departments of Cell Biology and Physiology, .,Lineberger Comprehensive Cancer Center, and.,Pharmacology.,Computer Science, and
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37
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The E3 Ubiquitin Ligase TRIM9 Is a Filopodia Off Switch Required for Netrin-Dependent Axon Guidance. Dev Cell 2016; 35:698-712. [PMID: 26702829 DOI: 10.1016/j.devcel.2015.11.022] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/09/2015] [Accepted: 10/19/2015] [Indexed: 02/01/2023]
Abstract
Neuronal growth cone filopodia contain guidance receptors and contribute to axon guidance; however, the mechanism by which the guidance cue netrin increases filopodia density is unknown. Here, we demonstrate that TRIM9, an E3 ubiquitin ligase that localizes to filopodia tips and binds the netrin receptor DCC, interacts with and ubiquitinates the barbed-end polymerase VASP to modulate filopodial stability during netrin-dependent axon guidance. Studies with murine Trim9(+/+) and Trim9(-/-) cortical neurons, along with a non-ubiquitinatable VASP mutant, demonstrate that TRIM9-mediated ubiquitination of VASP reduces VASP filopodial tip localization, VASP dynamics at tips, and filopodial stability. Upon netrin treatment, VASP is deubiquitinated, which promotes VASP tip localization and filopodial stability. Trim9 deletion induces axon guidance defects in vitro and in vivo, whereas a gradient of deubiquitinase inhibition promotes axon turning in vitro. We conclude that a gradient of TRIM9-mediated ubiquitination of VASP creates a filopodial stability gradient during axon turning.
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38
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Esquerdo M, Grau-Bové X, Garanto A, Toulis V, Garcia-Monclús S, Millo E, López-Iniesta MJ, Abad-Morales V, Ruiz-Trillo I, Marfany G. Expression Atlas of the Deubiquitinating Enzymes in the Adult Mouse Retina, Their Evolutionary Diversification and Phenotypic Roles. PLoS One 2016; 11:e0150364. [PMID: 26934049 PMCID: PMC4774998 DOI: 10.1371/journal.pone.0150364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Ubiquitination is a relevant cell regulatory mechanism to determine protein fate and function. Most data has focused on the role of ubiquitin as a tag molecule to target substrates to proteasome degradation, and on its impact in the control of cell cycle, protein homeostasis and cancer. Only recently, systematic assays have pointed to the relevance of the ubiquitin pathway in the development and differentiation of tissues and organs, and its implication in hereditary diseases. Moreover, although the activity and composition of ubiquitin ligases has been largely addressed, the role of the deubiquitinating enzymes (DUBs) in specific tissues, such as the retina, remains mainly unknown. In this work, we undertook a systematic analysis of the transcriptional levels of DUB genes in the adult mouse retina by RT-qPCR and analyzed the expression pattern by in situ hybridization and fluorescent immunohistochemistry, thus providing a unique spatial reference map of retinal DUB expression. We also performed a systematic phylogenetic analysis to understand the origin and the presence/absence of DUB genes in the genomes of diverse animal taxa that represent most of the known animal diversity. The expression landscape obtained supports the potential subfunctionalization of paralogs in those families that expanded in vertebrates. Overall, our results constitute a reference framework for further characterization of the DUB roles in the retina and suggest new candidates for inherited retinal disorders.
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Affiliation(s)
- Mariona Esquerdo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Xavier Grau-Bové
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biologia Evolutiva (CSIC- Universitat Pompeu Fabra), Barcelona, Spain
| | - Alejandro Garanto
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Vasileios Toulis
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Garcia-Monclús
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Erica Millo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Ma José López-Iniesta
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Víctor Abad-Morales
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biologia Evolutiva (CSIC- Universitat Pompeu Fabra), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- * E-mail:
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Guharoy M, Bhowmick P, Tompa P. Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System. J Biol Chem 2016; 291:6723-31. [PMID: 26851277 DOI: 10.1074/jbc.r115.692665] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons, and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core.
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Affiliation(s)
- Mainak Guharoy
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Pallab Bhowmick
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and
| | - Peter Tompa
- From the VIB Structural Biology Research Center (SBRC), Vlaams Instituut voor Biotechnologie, 1050 Brussel, Belgium, the Structural Biology Brussels (SBB), Vrije Universiteit Brussel, 1050 Brussels, Belgium, and the Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, 1117 Budapest, Hungary
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40
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Mudhasani R, Tran JP, Retterer C, Kota KP, Whitehouse CA, Bavari S. Protein Kinase R Degradation Is Essential for Rift Valley Fever Virus Infection and Is Regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 Ligase. PLoS Pathog 2016; 12:e1005437. [PMID: 26837067 PMCID: PMC4737497 DOI: 10.1371/journal.ppat.1005437] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/13/2016] [Indexed: 12/11/2022] Open
Abstract
Activated protein kinase R (PKR) plays a vital role in antiviral defense primarily by inhibiting protein synthesis and augmenting interferon responses. Many viral proteins have adopted unique strategies to counteract the deleterious effects of PKR. The NSs (Non-structural s) protein which is encoded by Rift Valley fever virus (RVFV) promotes early PKR proteasomal degradation through a previously undefined mechanism. In this study, we demonstrate that NSs carries out this activity by assembling the SCF (SKP1-CUL1-F-box)FBXW11 E3 ligase. NSs binds to the F-box protein, FBXW11, via the six amino acid sequence DDGFVE called the degron sequence and recruits PKR through an alternate binding site to the SCFFBXW11 E3 ligase. We further show that disrupting the assembly of the SCFFBXW11-NSs E3 ligase with MLN4924 (a small molecule inhibitor of SCF E3 ligase activity) or NSs degron viral mutants or siRNA knockdown of FBXW11 can block PKR degradation. Surprisingly, under these conditions when PKR degradation was blocked, NSs was essential and sufficient to activate PKR causing potent inhibition of RVFV infection by suppressing viral protein synthesis. These antiviral effects were antagonized by the loss of PKR expression or with a NSs deleted mutant virus. Therefore, early PKR activation by disassembly of SCFFBXW11-NSs E3 ligase is sufficient to inhibit RVFV infection. Furthermore, FBXW11 and BTRC are the two homologues of the βTrCP (Beta-transducin repeat containing protein) gene that were previously described to be functionally redundant. However, in RVFV infection, among the two homologues of βTrCP, FBXW11 plays a dominant role in PKR degradation and is the limiting factor in the assembly of the SCFFBXW11 complex. Thus, FBXW11 serves as a master regulator of RVFV infection by promoting PKR degradation. Overall these findings provide new insights into NSs regulation of PKR activity and offer potential opportunities for therapeutic intervention of RVFV infection. Rift Valley fever (RVF) is a severe disease caused by infection with the Rift Valley fever virus (RVFV) that affects humans and livestock and occurs in large epidemics. Currently there are no FDA-approved drugs or vaccines to treat RVF. Many viruses have evolved unique strategies to overcome host immune responses in order to establish infection. One protein of RVFV called NSs is responsible for over-powering cellular antiviral defenses. NSs is known to degrade double-stranded (ds) RNA-dependent protein kinase (PKR), but neither the mechanism nor the functional significance of this activity has been fully understood. In this study we show that NSs promotes PKR degradation by recruiting PKR to the E3 ligase complex called SCF (SKP1-CUL1-F-box)FBXW11. A short stretch of six amino acids called the degron sequence in NSs regulates the NSs- FBXW11 interaction and is required for the assembly of the SCFFBXW11 complex. We further show that disruption of the SCFFBXW11-NSs complex, with either a small molecule or with NSs degron viral mutants, can block PKR degradation. Surprisingly, when NSs mediated PKR degradation was blocked, NSs was essential and sufficient to activate PKR, causing potent inhibition of RVFV infection by suppressing viral protein synthesis. Therefore early PKR activation induced by inactivation of the SCFFBXW11 is sufficient to induce potent inhibition of RVFV infection. These findings may provide new molecular targets for therapeutic intervention of this important disease.
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Affiliation(s)
- Rajini Mudhasani
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Julie P. Tran
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Cary Retterer
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Krishna P. Kota
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
- Perkin Elmer, Waltham, Massachusetts, United States of America
| | - Chris A. Whitehouse
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Sina Bavari
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
- * E-mail:
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41
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Isolation of ubiquitinated substrates by tandem affinity purification of E3 ligase-polyubiquitin-binding domain fusions (ligase traps). Nat Protoc 2016; 11:291-301. [PMID: 26766115 DOI: 10.1038/nprot.2016.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ubiquitination is an essential protein modification that influences eukaryotic processes ranging from substrate degradation to nonproteolytic pathway alterations, including DNA repair and endocytosis. Previous attempts to analyze substrates via physical association with their respective ubiquitin ligases have had some success. However, because of the transient nature of enzyme-substrate interactions and rapid protein degradation, detection of substrates remains a challenge. Ligase trapping is an affinity purification approach in which ubiquitin ligases are fused to a polyubiquitin-binding domain, which allows the isolation of ubiquitinated substrates. Immunoprecipitation is first used to enrich for proteins that are bound to the ligase trap. Subsequently, affinity purification is used under denaturing conditions to capture proteins conjugated with hexahistidine-tagged ubiquitin. By using this protocol, ubiquitinated substrates that are specific for a given ligase can be isolated for mass spectrometry or western blot analysis. After cells have been collected, the described protocol can be completed in 2-3 d.
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42
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Loveless TB, Topacio BR, Vashisht AA, Galaang S, Ulrich KM, Young BD, Wohlschlegel JA, Toczyski DP. DNA Damage Regulates Translation through β-TRCP Targeting of CReP. PLoS Genet 2015; 11:e1005292. [PMID: 26091241 PMCID: PMC4474599 DOI: 10.1371/journal.pgen.1005292] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/20/2015] [Indexed: 02/07/2023] Open
Abstract
The Skp1-Cul1-F box complex (SCF) associates with any one of a number of F box proteins, which serve as substrate binding adaptors. The human F box protein βTRCP directs the conjugation of ubiquitin to a variety of substrate proteins, leading to the destruction of the substrate by the proteasome. To identify βTRCP substrates, we employed a recently-developed technique, called Ligase Trapping, wherein a ubiquitin ligase is fused to a ubiquitin-binding domain to “trap” ubiquitinated substrates. 88% of the candidate substrates that we examined were bona fide substrates, comprising twelve previously validated substrates, eleven new substrates and three false positives. One βTRCP substrate, CReP, is a Protein Phosphatase 1 (PP1) specificity subunit that targets the translation initiation factor eIF2α to promote the removal of a stress-induced inhibitory phosphorylation and increase cap-dependent translation. We found that CReP is targeted by βTRCP for degradation upon DNA damage. Using a stable CReP allele, we show that depletion of CReP is required for the full induction of eIF2α phosphorylation upon DNA damage, and contributes to keeping the levels of translation low as cells recover from DNA damage. Approximately 600 human genes encode enzymes that act as ubiquitin ligases, which facilitate the transfer of the small protein ubiquitin to thousands of substrate proteins; “tagging” with ubiquitin often promotes the degradation of the substrate by the proteasome. In this paper, we adapt a technique called Ligase Trapping for use in mammalian cells. Ligase Trapping is a highly accurate method for determining which substrates are targeted by a ubiquitin ligase. Here we use it to identify new substrates of the human cell cycle regulator βTRCP. Our screen was indeed highly accurate, as we were able to validate 88% of the candidate substrates we identified by mass spectrometry. Some of these new substrates were unstable proteins that were stabilized by inhibition of βTRCP, or of the entire class of ubiquitin ligases of which βTRCP is a part. However, others appear to be stable or redundantly-targeted substrates, which have been more difficult to identify with current techniques. This suggests that Ligase Trapping will be able to reliably identify new substrates of human ubiquitin ligases. Further, one of the new βTRCP substrates, CReP, is specifically depleted upon DNA damage, and depletion of CReP contributes to inactivation of the translational machinery upon DNA damage.
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Affiliation(s)
- Theresa B. Loveless
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Benjamin R. Topacio
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Ajay A. Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Shastyn Galaang
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Katie M. Ulrich
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Brian D. Young
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James A. Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California, United States of America
| | - David P. Toczyski
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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43
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Coyaud E, Mis M, Laurent EMN, Dunham WH, Couzens AL, Robitaille M, Gingras AC, Angers S, Raught B. BioID-based Identification of Skp Cullin F-box (SCF)β-TrCP1/2 E3 Ligase Substrates. Mol Cell Proteomics 2015; 14:1781-95. [PMID: 25900982 DOI: 10.1074/mcp.m114.045658] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 11/06/2022] Open
Abstract
The identification of ubiquitin E3 ligase substrates has been challenging, due in part to low-affinity, transient interactions, the rapid degradation of targets and the inability to identify proteins from poorly soluble cellular compartments. SCF(β-TrCP1) and SCF(β-TrCP2) are well-studied ubiquitin E3 ligases that target substrates for proteasomal degradation, and play important roles in Wnt, Hippo, and NFκB signaling. Combining 26S proteasome inhibitor (MG132) treatment with proximity-dependent biotin labeling (BioID) and semiquantitative mass spectrometry, here we identify SCF(β-TrCP1/2) interacting partners. Based on their enrichment in the presence of MG132, our data identify over 50 new putative SCF(β-TrCP1/2) substrates. We validate 12 of these new substrates and reveal previously unsuspected roles for β-TrCP in the maintenance of nuclear membrane integrity, processing (P)-body turnover and translational control. Together, our data suggest that β-TrCP is an important hub in the cellular stress response. The technique presented here represents a complementary approach to more standard IP-MS methods and should be broadly applicable for the identification of substrates for many ubiquitin E3 ligases.
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Affiliation(s)
- Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network
| | - Monika Mis
- §Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto
| | | | - Wade H Dunham
- ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital
| | - Amber L Couzens
- ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital
| | - Melanie Robitaille
- §Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto
| | - Anne-Claude Gingras
- ¶Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital; ‖Department of Molecular Genetics, University of Toronto
| | - Stephane Angers
- §Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto; **Department of Biochemistry, University of Toronto
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network; ‡‡Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
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