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Wei M, Mo Y, Liu J, Zhai J, Li H, Xu Y, Peng Y, Tang Z, Wei T, Yang X, Huang L, Shao X, Li J, Zhou L, Zhong H, Wei C, Xie Q, Min M, Wu F. Ubiquitin ligase RNF125 targets PD-L1 for ubiquitination and degradation. Front Oncol 2022; 12:835603. [PMID: 35965501 PMCID: PMC9374197 DOI: 10.3389/fonc.2022.835603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
As a critical immune checkpoint molecule, PD-L1 is expressed at significantly higher levels in multiple neoplastic tissues compared to normal ones. PD-L1/PD-1 axis is a critical target for tumor immunotherapy, blocking the PD-L1/PD-1 axis is recognized and has achieved unprecedented success in clinical applications. However, the clinical efficacy of therapies targeting the PD-1/PD-L1 pathway remains limited, emphasizing the need for the mechanistic elucidation of PD-1/PD-L1 expression. In this study, we found that RNF125 interacted with PD-L1 and regulated PD-L1 protein expression. Mechanistically, RNF125 promoted K48-linked polyubiquitination of PD-L1 and mediated its degradation. Notably, MC-38 and H22 cell lines with RNF125 knockout, transplanted in C57BL/6 mice, exhibited a higher PD-L1 level and faster tumor growth than their parental cell lines. In contrast, overexpression of RNF125 in MC-38 and H22 cells had the opposite effect, resulting in lower PD-L1 levels and delayed tumor growth compared with parental cell lines. In addition, immunohistochemical analysis of MC-38 tumors with RNF125 overexpression showed significantly increased infiltration of CD4+, CD8+ T cells and macrophages. Consistent with these findings, analyses using The Cancer Genome Atlas (TCGA) public database revealed a positive correlation of RNF125 expression with CD4+, CD8+ T cell and macrophage tumor infiltration. Moreover, RNF125 expression was significantly downregulated in several human cancer tissues, and was negatively correlated with the clinical stage of these tumors, and patients with higher RNF125 expression had better clinical outcomes. Our findings identify a novel mechanism for regulating PD-L1 expression and may provide a new strategy to increase the efficacy of immunotherapy.
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Affiliation(s)
- Meng Wei
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Yunhai Mo
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Jialong Liu
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jingtong Zhai
- Department of Medical Oncology and State Key Laboratory of Molecular Oncology, National Cancer Center/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huilong Li
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Yixin Xu
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Yumeng Peng
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Zhihong Tang
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Tao Wei
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Xiaopan Yang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Linfei Huang
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiao Shao
- Department of Gastroenterology, First Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
| | - Jingfei Li
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Li Zhou
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Hui Zhong
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Congwen Wei
- Department of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Qiaosheng Xie
- Department of Radiation Oncology, China-Japan Friendship Hospital, Beijing, China
- *Correspondence: Qiaosheng Xie, ; Min Min, ; Feixiang Wu,
| | - Min Min
- Department of Gastroenterology, First Medical Center of Chinese People's Liberation Army General Hospital, Beijing, China
- *Correspondence: Qiaosheng Xie, ; Min Min, ; Feixiang Wu,
| | - Feixiang Wu
- Department of Hepatobiliary Surgery, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment (Guangxi Medical University), Ministry of Education, Nanning, China
- *Correspondence: Qiaosheng Xie, ; Min Min, ; Feixiang Wu,
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2
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WWP1 upregulation predicts poor prognosis and promotes tumor progression by regulating ubiquitination of NDFIP1 in intrahepatic cholangiocarcinoma. Cell Death Dis 2022; 8:107. [PMID: 35264565 PMCID: PMC8906119 DOI: 10.1038/s41420-022-00882-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/26/2022] [Accepted: 02/09/2022] [Indexed: 11/26/2022]
Abstract
WW domain-containing E3 ubiquitin protein ligase1 (WWP1) is reported to be upregulated in many types of human cancers; however, its expression and function in intrahepatic cholangiocarcinoma (ICC) remain unknown. Here, in this study we investigated the expression pattern, clinical prognosis, tumor biological functions, and molecular mechanisms of WWP1 in ICC. The expression of WWP1 in patient tissues was detected by western blotting, immunohistochemistry (IHC), and immunofluorescence. CCK-8, colony formation, EdU, transwell, and xenograft models were used to explore the role of WWP1 in the proliferation and metastasis of ICC. Co-immunoprecipitation, mass spectrometry, chromatin immunoprecipitation, and immunofluorescence were performed to detect the potential mechanisms. Our study revealed that WWP1 was highly expressed in ICC, and high levels of WWP1 were associated with poor prognosis. Functionally, WWP1 overexpression enhanced the proliferation and metastasis of ICC cells and vice versa. Mechanistically, MYC could be enriched in the promoter region of WWP1 to facilitate its expression. Then, WWP1 targets Nedd4 family interacting protein1 (NDFIP1) and reduces NDFIP1 protein levels via ubiquitination. Downregulation of NDFIP1 in ICC cells rescued the effects of silenced WWP1 expression. WWP1 expression was also negatively correlated with the protein level of NDFIP1 in patient tissues. In conclusion, WWP1 upregulated by MYC promotes the progression of ICC via ubiquitination of NDFIP1, which reveals that WWP1 might be a potential therapeutic target for ICC.
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3
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Zhang H, Rong X, Wang C, Liu Y, Lu L, Li Y, Zhao C, Zhou J. VBP1 modulates Wnt/β-catenin signaling by mediating the stability of the transcription factors TCF/LEFs. J Biol Chem 2020; 295:16826-16839. [PMID: 32989053 PMCID: PMC7864075 DOI: 10.1074/jbc.ra120.015282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/23/2020] [Indexed: 12/29/2022] Open
Abstract
The Wnt/β-catenin pathway is one of the major pathways that regulates embryonic development, adult homeostasis, and stem cell self-renewal. In this pathway, transcription factors T-cell factor and lymphoid enhancer factor (TCF/LEF) serve as a key switch to repress or activate Wnt target gene transcription by recruiting repressor molecules or interacting with the β-catenin effector, respectively. It has become evident that the protein stability of the TCF/LEF family members may play a critical role in controlling the activity of the Wnt/β-catenin signaling pathway. However, factors that regulate the stability of TCF/LEFs remain largely unknown. Here, we report that pVHL binding protein 1 (VBP1) regulates the Wnt/β-catenin signaling pathway by controlling the stability of TCF/LEFs. Surprisingly, we found that either overexpression or knockdown of VBP1 decreased Wnt/β-catenin signaling activity in both cultured cells and zebrafish embryos. Mechanistically, VBP1 directly binds to all four TCF/LEF family members and von Hippel-Lindau tumor-suppressor protein (pVHL). Either overexpression or knockdown of VBP1 increases the association between TCF/LEFs and pVHL and then decreases the protein levels of TCF/LEFs via proteasomal degradation. Together, our results provide mechanistic insights into the roles of VBP1 in controlling TCF/LEFs protein stability and regulating Wnt/β-catenin signaling pathway activity.
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Affiliation(s)
- Haifeng Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaozhi Rong
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Caixia Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yunzhang Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ling Lu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yun Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chengtian Zhao
- Institute of Evolution and Marine Biodiversity and College of Marine Biology, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jianfeng Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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4
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Jacoupy M, Hamon-Keromen E, Ordureau A, Erpapazoglou Z, Coge F, Corvol JC, Nosjean O, Mannoury la Cour C, Millan MJ, Boutin JA, Harper JW, Brice A, Guedin D, Gautier CA, Corti O. The PINK1 kinase-driven ubiquitin ligase Parkin promotes mitochondrial protein import through the presequence pathway in living cells. Sci Rep 2019; 9:11829. [PMID: 31413265 PMCID: PMC6694185 DOI: 10.1038/s41598-019-47352-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/28/2019] [Indexed: 01/05/2023] Open
Abstract
Most of over a thousand mitochondrial proteins are encoded by nuclear genes and must be imported from the cytosol. Little is known about the cytosolic events regulating mitochondrial protein import, partly due to the lack of appropriate tools for its assessment in living cells. We engineered an inducible biosensor for monitoring the main presequence-mediated import pathway with a quantitative, luminescence-based readout. This tool was used to explore the regulation of mitochondrial import by the PINK1 kinase-driven Parkin ubiquitin ligase, which is dysfunctional in autosomal recessive Parkinson's disease. We show that mitochondrial import was stimulated by Parkin, but not by disease-causing Parkin variants. This effect was dependent on Parkin activation by PINK1 and accompanied by an increase in the abundance of K11 ubiquitin chains on mitochondria and by ubiquitylation of subunits of the translocase of outer mitochondrial membrane. Mitochondrial import efficiency was abnormally low in cells from patients with PINK1- and PARK2-linked Parkinson's disease and was restored by phosphomimetic ubiquitin in cells with residual Parkin activity. Altogether, these findings uncover a role of ubiquitylation in mitochondrial import regulation and suggest that loss of this regulatory loop may underlie the pathophysiology of Parkinson's disease, providing novel opportunities for therapeutic intervention.
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Affiliation(s)
- M Jacoupy
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - E Hamon-Keromen
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - A Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Z Erpapazoglou
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - F Coge
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J-C Corvol
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Assistance-Publique Hôpitaux de Paris, Inserm, CIC-1422, Department of Neurology, Hôpital Pitié-Salpêtrière, F-75013, Paris, France
| | - O Nosjean
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | | | - M J Millan
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J A Boutin
- Institut de Recherches Servier, Croissy-sur-Seine, France
| | - J W Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - A Brice
- Inserm, U1127, F-75013, Paris, France.,CNRS, UMR 7225, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France.,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - D Guedin
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.,Laboratoire de Chémogénétique Servier, F-75013, Paris, France.,Institut de Recherches Servier, Croissy-sur-Seine, France
| | - C A Gautier
- Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France. .,Laboratoire de Chémogénétique Servier, F-75013, Paris, France. .,Institut de Recherches Servier, Croissy-sur-Seine, France.
| | - O Corti
- Inserm, U1127, F-75013, Paris, France. .,CNRS, UMR 7225, F-75013, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, F-75013, Paris, France. .,Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France.
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5
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Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP. Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science 2019; 363:363/6429/eaav4467. [PMID: 30792274 DOI: 10.1126/science.aav4467] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Abstract
Chloroplasts contain thousands of nucleus-encoded proteins that are imported from the cytosol by translocases in the chloroplast envelope membranes. Proteolytic regulation of the translocases is critically important, but little is known about the underlying mechanisms. We applied forward genetics and proteomics in Arabidopsis to identify factors required for chloroplast outer envelope membrane (OEM) protein degradation. We identified SP2, an Omp85-type β-barrel channel of the OEM, and CDC48, a cytosolic AAA+ (ATPase associated with diverse cellular activities) chaperone. Both proteins acted in the same pathway as the ubiquitin E3 ligase SP1, which regulates OEM translocase components. SP2 and CDC48 cooperated to bring about retrotranslocation of ubiquitinated substrates from the OEM (fulfilling conductance and motor functions, respectively), enabling degradation of the substrates by the 26S proteasome in the cytosol. Such chloroplast-associated protein degradation (CHLORAD) is vital for organellar functions and plant development.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - William Broad
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Raphael Trösch
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mats Töpel
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Amy Baldwin
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK. .,Department of Biology, University of Leicester, Leicester LE1 7RH, UK
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6
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Khattar V, Lee JH, Wang H, Bastola S, Ponnazhagan S. Structural determinants and genetic modifications enhance BMP2 stability and extracellular secretion. FASEB Bioadv 2019. [PMID: 31225515 DOI: 10.1096/fba.2018‐00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The short half-life and use of recombinant bone morphogenetic protein (BMP)-2 in large doses poses major limitations in the clinic. Events regulating post-translational processing and degradation of BMP2 in situ, linked to its secretion, have not been understood. Towards identifying mechanisms regulating intracellular BMP2 stability, we first discovered that inhibiting proteasomal degradation enhances both intracellular BMP2 level and its extracellular secretion. Next, we identified BMP2 degradation occurs through an ubiquitin-mediated mechanism. Since ubiquitination precedes proteasomal turnover and mainly occurs on lysine residues of nascent proteins, we systematically mutated individual lysine residues within BMP2 and tested them for enhanced stability. Results revealed that substitutions on four lysine residues within the pro-BMP2 region and three in the mature region increased both BMP2 turnover and extracellular secretion. Structural modeling revealed key lysine residues involved in proteasomal degradation occupy a lysine cluster near proprotein convertase cleavage site. Interestingly, mutations within these residues did not affect biological activity of BMP2. These data suggest preventing intracellular proteasomal loss of BMP2 through genetic modifications can overcome limitations related to its short half-life.
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Affiliation(s)
- Vinayak Khattar
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294
| | - Joo Hyoung Lee
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294
| | - Hong Wang
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294
| | - Soniya Bastola
- Department of Neurosurgery, The University of Alabama at Birmingham, Birmingham, AL 35294
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7
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Mayank AK, Pandey V, Vashisht AA, Barshop WD, Rayatpisheh S, Sharma T, Haque T, Powers DN, Wohlschlegel JA. An Oxygen-Dependent Interaction between FBXL5 and the CIA-Targeting Complex Regulates Iron Homeostasis. Mol Cell 2019; 75:382-393.e5. [PMID: 31229404 DOI: 10.1016/j.molcel.2019.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 04/03/2019] [Accepted: 05/10/2019] [Indexed: 01/06/2023]
Abstract
The iron-sensing protein FBXL5 is the substrate adaptor for a SKP1-CUL1-RBX1 E3 ubiquitin ligase complex that regulates the degradation of iron regulatory proteins (IRPs). Here, we describe a mechanism of FBXL5 regulation involving its interaction with the cytosolic Fe-S cluster assembly (CIA) targeting complex composed of MMS19, FAM96B, and CIAO1. We demonstrate that the CIA-targeting complex promotes the ability of FBXL5 to degrade IRPs. In addition, the FBXL5-CIA-targeting complex interaction is regulated by oxygen (O2) tension displaying a robust association in 21% O2 that is severely diminished in 1% O2 and contributes to O2-dependent regulation of IRP degradation. Together, these data identify a novel oxygen-dependent signaling axis that links IRP-dependent iron homeostasis with the Fe-S cluster assembly machinery.
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Affiliation(s)
- Adarsh K Mayank
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Shima Rayatpisheh
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Tanu Sharma
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Tisha Haque
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David N Powers
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
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8
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Samant RS, Frydman J. Methods for measuring misfolded protein clearance in the budding yeast Saccharomyces cerevisiae. Methods Enzymol 2019; 619:27-45. [PMID: 30910025 DOI: 10.1016/bs.mie.2018.12.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Protein misfolding in the cell is linked to an array of diseases, including cancers, cardiovascular disease, type II diabetes, and numerous neurodegenerative disorders. Therefore, investigating cellular pathways by which misfolded proteins are trafficked and cleared ("protein quality control") is of both mechanistic and therapeutic importance. The clearance of most misfolded proteins involves the covalent attachment of one or more ubiquitin molecules; however, the precise fate of the ubiquitinated protein varies greatly, depending on the linkages present in the ubiquitin chain. Here, we discuss approaches for quantifying linkage-specific ubiquitination and clearance of misfolded proteins in the budding yeast Saccharomyces cerevisiae-a model organism used extensively for interrogation of protein quality control pathways, but which presents its own unique challenges for cell and molecular biology experiments. We present a fluorescence microscopy-based assay for monitoring the clearance of misfolded protein puncta, a cycloheximide-chase assay for calculating misfolded protein half-life, and two antibody-based methods for quantifying specific ubiquitin linkages on tagged misfolded proteins, including a 96-well plate-based ELISA. We hope these methods will be of use to the protein quality control, protein degradation, and ubiquitin biology communities.
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Affiliation(s)
- Rahul S Samant
- Department of Biology, Stanford University, Stanford, CA, United States.
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, United States; Department of Genetics, Stanford University, Stanford, CA, United States.
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9
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Khattar V, Lee JH, Wang H, Bastola S, Ponnazhagan S. Structural determinants and genetic modifications enhance BMP2 stability and extracellular secretion. FASEB Bioadv 2019; 1:180-190. [PMID: 31225515 PMCID: PMC6586023 DOI: 10.1096/fba.2018-00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022] Open
Abstract
The short half-life and use of recombinant bone morphogenetic protein (BMP)-2 in large doses poses major limitations in the clinic. Events regulating post-translational processing and degradation of BMP2 in situ, linked to its secretion, have not been understood. Towards identifying mechanisms regulating intracellular BMP2 stability, we first discovered that inhibiting proteasomal degradation enhances both intracellular BMP2 level and its extracellular secretion. Next, we identified BMP2 degradation occurs through an ubiquitin-mediated mechanism. Since ubiquitination precedes proteasomal turnover and mainly occurs on lysine residues of nascent proteins, we systematically mutated individual lysine residues within BMP2 and tested them for enhanced stability. Results revealed that substitutions on four lysine residues within the pro-BMP2 region and three in the mature region increased both BMP2 turnover and extracellular secretion. Structural modeling revealed key lysine residues involved in proteasomal degradation occupy a lysine cluster near proprotein convertase cleavage site. Interestingly, mutations within these residues did not affect biological activity of BMP2. These data suggest preventing intracellular proteasomal loss of BMP2 through genetic modifications can overcome limitations related to its short half-life.
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Affiliation(s)
- Vinayak Khattar
- Department of PathologyThe University of Alabama at BirminghamBirminghamAL
| | - Joo Hyoung Lee
- Department of PathologyThe University of Alabama at BirminghamBirminghamAL
| | - Hong Wang
- Department of PathologyThe University of Alabama at BirminghamBirminghamAL
| | - Soniya Bastola
- Department of NeurosurgeryThe University of Alabama at BirminghamBirminghamAL
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10
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Dong D, Zhou H, Na SY, Niedra R, Peng Y, Wang H, Seed B, Zhou GL. GPR108, an NF-κB activator suppressed by TIRAP, negatively regulates TLR-triggered immune responses. PLoS One 2018; 13:e0205303. [PMID: 30332431 PMCID: PMC6192633 DOI: 10.1371/journal.pone.0205303] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/21/2018] [Indexed: 01/12/2023] Open
Abstract
Higher vertebrates have evolved innate and adaptive immune systems to defend against foreign substances and pathogens. Sophisticated regulatory circuits are needed to avoid inappropriate immune responses and inflammation. GPR108 is a seven-transmembrane family protein that activates NF-κB strongly when overexpressed. Surprisingly, its action in a physiological context is that of an antagonist of Toll-like receptor (TLR)-mediated signaling. Cells from Gpr108-null mice exhibit enhanced cytokine secretion and NF-κB and IRF3 signaling, whereas Gpr108-null macrophages reconstituted with GPR108 exhibit blunted signaling. Co-expression of TLRs and GPR108 reduces NF-κB and IFNβ promoter activation compared to expression of either TLRs or GPR108 alone. Upon TLR stimulation GPR108 abundance increases and the protein engages TLRs and their partners to reduce MyD88 expression and interfere with its binding to TLR4 through blocking MyD88 ubiquitination. In turn GPR108 is antagonized by TIRAP, an adaptor protein for TLR and MyD88. The interrelationships between GPR108 and innate immune signaling components are multifactorial and point to a membrane-associated signaling structure of significant complexity.
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Affiliation(s)
- Danfeng Dong
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haisheng Zhou
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Soon-Young Na
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rasma Niedra
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huajun Wang
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Brian Seed
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Guo Ling Zhou
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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11
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Capper CP, Liu J, McIntosh LR, Larios JM, Johnson MD, Hollenberg PF, Osawa Y, Auchus RJ, Rae JM. Functional characterization of the G162R and D216H genetic variants of human CYP17A1. J Steroid Biochem Mol Biol 2018; 178:159-166. [PMID: 29229304 PMCID: PMC5835412 DOI: 10.1016/j.jsbmb.2017.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/30/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
Cytochrome P450 17A1 (CYP17A1) is a dual-function enzyme catalyzing reactions necessary for cortisol and androgen biosynthesis. CYP17A1 is a validated drug target for prostate cancer as CYP17A1 inhibition significantly reduces circulating androgens and improves survival in castration-resistant prostate cancer. Germline CYP17A1 genetic variants with altered CYP17A1 activity manifesting as various endocrinopathies are extremely rare; however, characterizing these variants provides critical insights into CYP17A1 protein structure and function. By querying the dbSNP online database and publically available data from the 1000 genomes project (http://browser.1000genomes.org), we identified two CYP17A1 nonsynonymous genetic variants with unknown consequences for enzymatic activity and stability. We hypothesized that the resultant amino acid changes would alter CYP17A1 stability or activity. To test this hypothesis, we utilized a HEK-293T cell-based expression system to characterize the functional consequences of two CYP17A1 variants, D216H (rs200063521) and G162R (rs141821705). Cells transiently expressing the D216H variant demonstrate a selective impairment of 16α-hydroxyprogesterone synthesis by 2.1-fold compared to wild-type (WT) CYP17A1, while no effect on 17α-hydroxyprogesterone synthesis was observed. These data suggest that substrate orientations in the active site might be altered with this amino acid substitution. In contrast, the G162R substitution exhibits decreased CYP17A1 protein stability compared to WT with a near 70% reduction in protein levels as determined by immunoblot analysis. This variant is preferentially ubiquitinated and degraded prematurely, with an enzyme half-life calculated to be ∼2.5 h, and proteasome inhibitor treatment recovers G162R protein expression to WT levels. Together, these data provide new insights into CYP17A1 structure-function and stability mechanisms.
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Affiliation(s)
- C P Capper
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA; Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - J Liu
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - L R McIntosh
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - J M Larios
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - M D Johnson
- Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, D.C., USA
| | - P F Hollenberg
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Y Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - R J Auchus
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA; Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - J M Rae
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA; Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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12
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Kucharski TJ, Minshall PE, Moustafa-Kamal M, Turnell AS, Teodoro JG. Reciprocal Regulation between 53BP1 and the Anaphase-Promoting Complex/Cyclosome Is Required for Genomic Stability during Mitotic Stress. Cell Rep 2017; 18:1982-1995. [PMID: 28228263 DOI: 10.1016/j.celrep.2017.01.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/09/2017] [Accepted: 01/30/2017] [Indexed: 10/20/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that targets substrates for degradation to promote mitotic progression. Here, we show that the DNA damage response protein 53BP1 contains conserved KEN boxes that are required for APC/C-dependent degradation in early mitosis. Mutation of the 53BP1 KEN boxes stabilized the protein and extended mitotic duration, whereas 53BP1 knockdown resulted in a shorter and delayed mitosis. Loss of 53BP1 increased APC/C activity, and we show that 53BP1 is a direct APC/C inhibitor. Although 53BP1 function is not absolutely required for normal cell cycle progression, knockdown was highly toxic in combination with mitotic spindle poisons. Moreover, chemical inhibition of the APC/C was able to rescue the lethality of 53BP1 loss. Our findings reveal a reciprocal regulation between 53BP1 and APC/C that is required for response to mitotic stress and may contribute to the tumor-suppressor functions of 53BP1.
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Affiliation(s)
- Thomas J Kucharski
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Paul E Minshall
- School of Cancer and Genomic Sciences, College of Medical and Dental Sciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mohamed Moustafa-Kamal
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Andrew S Turnell
- School of Cancer and Genomic Sciences, College of Medical and Dental Sciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jose G Teodoro
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Microbiology and Immunology, Montreal, QC H3A 2B4, Canada.
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13
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Pae J, Cinalli RM, Marzio A, Pagano M, Lehmann R. GCL and CUL3 Control the Switch between Cell Lineages by Mediating Localized Degradation of an RTK. Dev Cell 2017; 42:130-142.e7. [PMID: 28743001 DOI: 10.1016/j.devcel.2017.06.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 05/15/2017] [Accepted: 06/27/2017] [Indexed: 11/29/2022]
Abstract
The separation of germline from somatic lineages is fundamental to reproduction and species preservation. Here, we show that Drosophila Germ cell-less (GCL) is a critical component in this process by acting as a switch that turns off a somatic lineage pathway. GCL, a conserved BTB (Broad-complex, Tramtrack, and Bric-a-brac) protein, is a substrate-specific adaptor for Cullin3-RING ubiquitin ligase complex (CRL3GCL). We show that CRL3GCL promotes PGC fate by mediating degradation of Torso, a receptor tyrosine kinase (RTK) and major determinant of somatic cell fate. This mode of RTK degradation does not depend upon receptor activation but is prompted by release of GCL from the nuclear envelope during mitosis. The cell-cycle-dependent change in GCL localization provides spatiotemporal specificity for RTK degradation and sequesters CRL3GCL to prevent it from participating in excessive activities. This precisely orchestrated mechanism of CRL3GCL function and regulation defines cell fate at the single-cell level.
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Affiliation(s)
- Juhee Pae
- HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Ryan M Cinalli
- HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Antonio Marzio
- HHMI, Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Michele Pagano
- HHMI, Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Ruth Lehmann
- HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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14
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Miao Y, Wu J, Abraham SN. Ubiquitination of Innate Immune Regulator TRAF3 Orchestrates Expulsion of Intracellular Bacteria by Exocyst Complex. Immunity 2017; 45:94-105. [PMID: 27438768 DOI: 10.1016/j.immuni.2016.06.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
Abstract
Although the intracellular trafficking system is integral to most physiologic activities, its role in mediating immune responses to infection has remained elusive. Here, we report that infected bladder epithelial cells (BECs) mobilized the exocyst complex, a powerful exporter of subcellular vesicles, to rapidly expel intracellular bacteria back for clearance. Toll-like receptor (TLR) 4 signals emanating from bacteria-containing vesicles (BCVs) were found to trigger K33-linked polyubiquitination of TRAF3 at Lys168, which was then detected by RalGDS, a guanine nucleotide exchange factor (GEF) that precipitated the assembly of the exocyst complex. Although this distinct modification of TRAF3 served to connect innate immune signaling to the cellular trafficking apparatus, it crucially ensured temporal and spatial accuracy in determining which among the many subcellular vesicles was recognized and selected for expulsion in response to innate immune signaling.
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Affiliation(s)
- Yuxuan Miao
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Jianxuan Wu
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | - Soman N Abraham
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA; Program in Emerging Infectious Diseases, Duke-National University of Singapore, Singapore 169857, Singapore
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15
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Bagheri-Yarmand R, Williams MD, Grubbs EG, Gagel RF. ATF4 Targets RET for Degradation and Is a Candidate Tumor Suppressor Gene in Medullary Thyroid Cancer. J Clin Endocrinol Metab 2017; 102:933-941. [PMID: 27935748 PMCID: PMC5460684 DOI: 10.1210/jc.2016-2878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/08/2016] [Indexed: 12/20/2022]
Abstract
CONTEXT Medullary thyroid cancer (MTC) is an aggressive tumor that harbors activating mutations of the RET proto-oncogene. We previously reported that RET inhibits transcriptional activity of ATF4, the master regulator of the stress response pathway, to prevent cell death. OBJECTIVE We hypothesized that loss of function of ATF4 plays a role in initiation of MTC. DESIGN Targeted deletion of Atf4 in mice was used to assess ATF4 function in the thyroid gland. ATF4 overexpression was achieved by adenoviral and lentiviral vectors. We used immunohistochemical analysis and western blotting of MTC tumors to determine protein levels of RET and ATF4 and the Kaplan-Meier method to determine their association with clinical outcome. RESULTS Targeted deletion of Atf4 in mice causes C-cell hyperplasia, a precancerous lesion for MTC. Forced ATF4 expression decreased survival of MTC cells and blocked the activation of RET downstream signaling pathways (phosphorylated ERK, phosphorylated AKT, and p70S6K). ATF4 knockdown decreased sensitivity to tyrosine kinase inhibitor-induced apoptosis. Moreover, ATF4 expression decreased RET protein levels by promoting RET ubiquitination. We found decreased or loss of ATF4 in 52% of MTC tumors (n = 39) compared with normal thyroid follicle cells. A negative correlation was observed between RET and ATF4 protein levels in MTC tumors, and low ATF4 expression was associated with poor overall survival in patients with MTC. CONCLUSIONS ATF4 was identified as a negative regulator of RET, a candidate tumor suppressor gene, and may be a molecular marker that distinguishes patients at high risk of MTC from those with a longer survival prognosis.
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Affiliation(s)
| | | | - Elizabeth G. Grubbs
- Surgical Oncology, The University of Texas, Maryland Anderson Cancer Center, Houston, Texas 77030
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16
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SUMO Modification Stabilizes Enterovirus 71 Polymerase 3D To Facilitate Viral Replication. J Virol 2016; 90:10472-10485. [PMID: 27630238 DOI: 10.1128/jvi.01756-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/15/2022] Open
Abstract
Accumulating evidence suggests that viruses hijack cellular proteins to circumvent the host immune system. Ubiquitination and SUMOylation are extensively studied posttranslational modifications (PTMs) that play critical roles in diverse biological processes. Cross talk between ubiquitination and SUMOylation of both host and viral proteins has been reported to result in distinct functional consequences. Enterovirus 71 (EV71), an RNA virus belonging to the family Picornaviridae, is a common cause of hand, foot, and mouth disease. Little is known concerning how host PTM systems interact with enteroviruses. Here, we demonstrate that the 3D protein, an RNA-dependent RNA polymerase (RdRp) of EV71, is modified by small ubiquitin-like modifier 1 (SUMO-1) both during infection and in vitro Residues K159 and L150/D151/L152 were responsible for 3D SUMOylation as determined by bioinformatics prediction combined with site-directed mutagenesis. Also, primer-dependent polymerase assays indicated that mutation of SUMOylation sites impaired 3D polymerase activity and virus replication. Moreover, 3D is ubiquitinated in a SUMO-dependent manner, and SUMOylation is crucial for 3D stability, which may be due to the interplay between the two PTMs. Importantly, increasing the level of SUMO-1 in EV71-infected cells augmented the SUMOylation and ubiquitination levels of 3D, leading to enhanced replication of EV71. These results together suggested that SUMO and ubiquitin cooperatively regulated EV71 infection, either by SUMO-ubiquitin hybrid chains or by ubiquitin conjugating to the exposed lysine residue through SUMOylation. Our study provides new insight into how a virus utilizes cellular pathways to facilitate its replication. IMPORTANCE Infection with enterovirus 71 (EV71) often causes neurological diseases in children, and EV71 is responsible for the majority of fatalities. Based on a better understanding of interplay between virus and host cell, antiviral drugs against enteroviruses may be developed. As a dynamic cellular process of posttranslational modification, SUMOylation regulates global cellular protein localization, interaction, stability, and enzymatic activity. However, little is known concerning how SUMOylation directly influences virus replication by targeting viral polymerase. Here, we found that EV71 polymerase 3D was SUMOylated during EV71 infection and in vitro Moreover, the SUMOylation sites were determined, and in vitro polymerase assays indicated that mutations at SUMOylation sites could impair polymerase synthesis. Importantly, 3D is ubiquitinated in a SUMOylation-dependent manner that enhances the stability of the viral polymerase. Our findings indicate that the two modifications likely cooperatively enhance virus replication. Our study may offer a new therapeutic strategy against virus replication.
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17
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Li T, Giagtzoglou N, Eberl DF, Jaiswal SN, Cai T, Godt D, Groves AK, Bellen HJ. The E3 ligase Ubr3 regulates Usher syndrome and MYH9 disorder proteins in the auditory organs of Drosophila and mammals. eLife 2016; 5. [PMID: 27331610 PMCID: PMC4978524 DOI: 10.7554/elife.15258] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023] Open
Abstract
Myosins play essential roles in the development and function of auditory organs and multiple myosin genes are associated with hereditary forms of deafness. Using a forward genetic screen in Drosophila, we identified an E3 ligase, Ubr3, as an essential gene for auditory organ development. Ubr3 negatively regulates the mono-ubiquitination of non-muscle Myosin II, a protein associated with hearing loss in humans. The mono-ubiquitination of Myosin II promotes its physical interaction with Myosin VIIa, a protein responsible for Usher syndrome type IB. We show that ubr3 mutants phenocopy pathogenic variants of Myosin II and that Ubr3 interacts genetically and physically with three Usher syndrome proteins. The interactions between Myosin VIIa and Myosin IIa are conserved in the mammalian cochlea and in human retinal pigment epithelium cells. Our work reveals a novel mechanism that regulates protein complexes affected in two forms of syndromic deafness and suggests a molecular function for Myosin IIa in auditory organs.
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Affiliation(s)
- Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States
| | - Nikolaos Giagtzoglou
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Daniel F Eberl
- Department of Biology, University of Iowa, Iowa City, United States
| | - Sonal Nagarkar Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Tiantian Cai
- Department of Neuroscience, Baylor College of Medicine, Houston, United States
| | - Dorothea Godt
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, United States
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18
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Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock. Proc Natl Acad Sci U S A 2015; 112:12420-5. [PMID: 26392558 DOI: 10.1073/pnas.1501204112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Regulated degradation of proteins by the proteasome is often critical to their function in dynamic cellular pathways. The molecular clock underlying mammalian circadian rhythms relies on the rhythmic expression and degradation of its core components. However, because the tools available for identifying the mechanisms underlying the degradation of a specific protein are limited, the mechanisms regulating clock protein degradation are only beginning to be elucidated. Here we describe a cell-based functional screening approach designed to quickly identify the ubiquitin E3 ligases that induce the degradation of potentially any protein of interest. We screened the nuclear hormone receptor RevErbα (Nr1d1), a key constituent of the mammalian circadian clock, for E3 ligases that regulate its stability and found Seven in absentia2 (Siah2) to be a key regulator of RevErbα stability. Previously implicated in hypoxia signaling, Siah2 overexpression destabilizes RevErbα/β, and siRNA depletion of Siah2 stabilizes endogenous RevErbα. Moreover, Siah2 depletion delays circadian degradation of RevErbα and lengthens period length. These results demonstrate the utility of functional screening approaches for identifying regulators of protein stability and reveal Siah2 as a previously unidentified circadian clockwork regulator that mediates circadian RevErbα turnover.
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19
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Keilhoff G, Titze M, Esser T, Langnaese K, Ebmeyer U. Constitutive and functional expression of YB-1 in microglial cells. Neuroscience 2015; 301:439-53. [DOI: 10.1016/j.neuroscience.2015.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 12/28/2022]
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20
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Thompson JW, Nagel J, Hoving S, Gerrits B, Bauer A, Thomas JR, Kirschner MW, Schirle M, Luchansky SJ. Quantitative Lys-ϵ-Gly-Gly (diGly) proteomics coupled with inducible RNAi reveals ubiquitin-mediated proteolysis of DNA damage-inducible transcript 4 (DDIT4) by the E3 ligase HUWE1. J Biol Chem 2014; 289:28942-55. [PMID: 25147182 DOI: 10.1074/jbc.m114.573352] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Targeted degradation of proteins through the ubiquitin-proteasome system (UPS) via the activities of E3 ubiquitin ligases regulates diverse cellular processes, and misregulation of these enzymes contributes to the pathogenesis of human diseases. One of the challenges facing the UPS field is to delineate the complete cohort of substrates for a particular E3 ligase. Advances in mass spectrometry and the development of antibodies recognizing the Lys-ϵ-Gly-Gly (diGly) remnant from ubiquitinated proteins following trypsinolysis have provided a tool to address this question. We implemented an inducible loss of function approach in combination with quantitative diGly proteomics to find novel substrates of HUWE1 (HECT, UBA, and WWE domain containing 1, E3 ubiquitin protein ligase), an E3 ligase implicated in cancer and intellectual disabilities. diGly proteomics results led to the identification of DNA damage-inducible transcript 4 (DDIT4) as a putative HUWE1 substrate. Cell-based assays demonstrated that HUWE1 interacts with and regulates ubiquitination and stability of DDIT4. Together these data suggest a model in which HUWE1 mediates DDIT4 proteasomal degradation. Our results demonstrate proof of concept that inducible knockdown of an E3 ligase in combination with diGly proteomics provides a potentially advantageous method for identifying novel E3 substrates that may help to identify candidates for therapeutic modulation in the UPS.
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Affiliation(s)
- Joel W Thompson
- From the Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Jane Nagel
- From the Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Sjouke Hoving
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, CH-4056 Basel, Switzerland, and
| | - Bertran Gerrits
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, CH-4056 Basel, Switzerland, and
| | - Andreas Bauer
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, CH-4056 Basel, Switzerland, and
| | - Jason R Thomas
- From the Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Markus Schirle
- From the Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139
| | - Sarah J Luchansky
- From the Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139,
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21
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Mustafa Rizvi SH, Parveen A, Verma AK, Ahmad I, Arshad M, Mahdi AA. Aluminium induced endoplasmic reticulum stress mediated cell death in SH-SY5Y neuroblastoma cell line is independent of p53. PLoS One 2014; 9:e98409. [PMID: 24878590 PMCID: PMC4039480 DOI: 10.1371/journal.pone.0098409] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/29/2014] [Indexed: 11/18/2022] Open
Abstract
Aluminium (Al) is the third most abundant element in the earth’s crust and its compounds are used in the form of house hold utensils, medicines and in antiperspirant etc. Increasing number of evidences suggest the involvement of Al+3 ions in a variety of neurodegenerative disorders including Alzheimer’s disease. Here, we have attempted to investigate the role of Al in endoplasmic reticulum stress and the regulation of p53 during neuronal apoptosis using neuroblastoma cell line. We observed that Al caused oxidative stress by increasing ROS production and intracellular calcium levels together with depletion of intracellular GSH levels. We also studied modulation of key pro- and anti-apoptotic proteins and found significant alterations in the levels of Nrf2, NQO1, pAKT, p21, Bax, Bcl2, Aβ1-40 and Cyt c together with increase in endoplasmic reticulum (ER) stress related proteins like CHOP and caspase 12. However, with respect to the role of p53, we observed downregulation of its transcript as well as protein levels while analysis of its ubiquitination status revealed no significant changes. Not only did Al increase the activities of caspase 9, caspase 12 and caspase 3, but, by the use of peptide inhibitors of specific and pan-caspases, we observed significant protection against neuronal cell death upon inhibition of caspase 12, demonstrating the prominent role of endoplasmic reticulum stress generated responses in Al toxicity. Overall our findings suggest that Al induces ER stress and ROS generation which compromises the antioxidant defenses of neuronal cells thereby promoting neuronal apoptosis in p53 independent pathway.
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Affiliation(s)
| | - Arshiya Parveen
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anoop K Verma
- Forensic Medicine & Toxicology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Iqbal Ahmad
- Fibre Toxicology Division, CSIR- Indian Institute of Toxicology Research, Lucknow, Uttar Pradesh, India
| | - Md Arshad
- Department of Zoology, Lucknow University, Lucknow, Uttar Pradesh, India
| | - Abbas Ali Mahdi
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India
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22
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Flannick J, Thorleifsson G, Beer NL, Jacobs SBR, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O, Groop L, Cox DR, Stefansson K, Altshuler D. Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nat Genet 2014; 46:357-63. [PMID: 24584071 DOI: 10.1038/ng.2915] [Citation(s) in RCA: 350] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/10/2014] [Indexed: 02/07/2023]
Abstract
Loss-of-function mutations protective against human disease provide in vivo validation of therapeutic targets, but none have yet been described for type 2 diabetes (T2D). Through sequencing or genotyping of ~150,000 individuals across 5 ancestry groups, we identified 12 rare protein-truncating variants in SLC30A8, which encodes an islet zinc transporter (ZnT8) and harbors a common variant (p.Trp325Arg) associated with T2D risk and glucose and proinsulin levels. Collectively, carriers of protein-truncating variants had 65% reduced T2D risk (P = 1.7 × 10(-6)), and non-diabetic Icelandic carriers of a frameshift variant (p.Lys34Serfs*50) demonstrated reduced glucose levels (-0.17 s.d., P = 4.6 × 10(-4)). The two most common protein-truncating variants (p.Arg138* and p.Lys34Serfs*50) individually associate with T2D protection and encode unstable ZnT8 proteins. Previous functional study of SLC30A8 suggested that reduced zinc transport increases T2D risk, and phenotypic heterogeneity was observed in mouse Slc30a8 knockouts. In contrast, loss-of-function mutations in humans provide strong evidence that SLC30A8 haploinsufficiency protects against T2D, suggesting ZnT8 inhibition as a therapeutic strategy in T2D prevention.
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Affiliation(s)
- Jason Flannick
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Nicola L Beer
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Suzanne B R Jacobs
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Noël P Burtt
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Fuchsberger
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Gil Atzmon
- 1] Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA. [2] Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Rafn Benediktsson
- Department of Endocrinology and Metabolism, Landspitali University Hospital, Reykjavik, Iceland
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Don W Bowden
- 1] Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA. [2] Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA. [3] Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA. [4] Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Ivan Brandslund
- 1] Department of Clinical Biochemistry, Vejle Hospital, Vejle, Denmark. [2] Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Julia Brosnan
- Cardiovascular & Metabolic Diseases Research Unit, Pfizer, Inc., Cambridge, Massachusetts, USA
| | - Frank Burslem
- Cardiovascular and Metabolic Diseases Practice, Prescient Life Sciences, London, UK
| | - John Chambers
- 1] Department of Epidemiology and Biostatistics, Imperial College London, London, UK. [2] Imperial College Healthcare National Health Service (NHS) Trust, London, UK. [3] Ealing Hospital NHS Trust, Middlesex, UK
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Korea
| | - Cramer Christensen
- Department of Internal Medicine and Endocrinology, Vejle Hospital, Vejle, Denmark
| | - Desirée A Douglas
- Unit of Diabetes and Celiac Diseases, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | - Zachary Dymek
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Yossi Farjoun
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Timothy Fennell
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Pierre Fontanillas
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Tom Forsén
- 1] Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland. [2] Diabetes Care Unit, Vaasa Health Care Centre, Vaasa, Finland
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Benjamin Glaser
- 1] Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel. [2] Israel Diabetes Research Group (IDRG), Holon, Israel
| | | | - Craig Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Torben Hansen
- 1] Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [2] Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Astradur B Hreidarsson
- Department of Endocrinology and Metabolism, Landspitali University Hospital, Reykjavik, Iceland
| | - Kristian Hveem
- Department of Public Health, Faculty of Medicine, Norwegian University of Science and Technology, Levanger, Norway
| | - Erik Ingelsson
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Bo Isomaa
- 1] Folkhalsan Research Centre, Helsinki, Finland. [2] Department of Social Services and Health Care, Jakobstad, Finland
| | - Stefan Johansson
- 1] KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway. [2] Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway. [3] Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Torben Jørgensen
- 1] Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark. [2] Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [3] Faculty of Medicine, University of Aalborg, Aalborg, Denmark
| | | | - Sekar Kathiresan
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Jaspal Kooner
- 1] Imperial College Healthcare National Health Service (NHS) Trust, London, UK. [2] Ealing Hospital NHS Trust, Middlesex, UK. [3] National Heart and Lung Institute (NHLI), Imperial College London, Hammersmith Hospital, London, UK
| | - Jasmina Kravic
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio Campus and Kuopio University Hospital, Kuopio, Finland
| | - Jong-Young Lee
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology, Chungcheongbuk-do, Korea
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Allan Linneberg
- 1] Research Centre for Prevention and Health, Glostrup University Hospital, Glostrup, Denmark. [2] Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. [3] Department of Clinical Experimental Research, Glostrup University Hospital, Glostrup, Denmark
| | | | - Thomas Meitinger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anders Molven
- 1] KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway. [2] Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway. [3] Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Andrew P Morris
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Shobha Potluri
- Applied Quantitative Genotherapeutics, Pfizer, Inc., South San Francisco, California, USA
| | - Rainer Rauramaa
- 1] Kuopio Research Institute of Exercise Medicine, Kuopio, Finland. [2] Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Rasmus Ribel-Madsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ann-Marie Richard
- Cardiovascular & Metabolic Diseases Research Unit, Pfizer, Inc., Cambridge, Massachusetts, USA
| | - Tim Rolph
- Cardiovascular & Metabolic Diseases Research Unit, Pfizer, Inc., Cambridge, Massachusetts, USA
| | - Veikko Salomaa
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Ayellet V Segrè
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hanna Skärstrand
- Unit of Diabetes and Celiac Diseases, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | - Heather M Stringham
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - E Shyong Tai
- 1] Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore. [2] Department of Medicine, National University of Singapore, National University Health System, Singapore. [3] Duke-National University of Singapore Graduate Medical School, Singapore
| | - Yik Ying Teo
- 1] Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore. [2] Centre for Molecular Epidemiology, National University of Singapore, Singapore. [3] Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore. [4] Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore. [5] Department of Statistics and Applied Probability, National University of Singapore, Singapore
| | - Tanya Teslovich
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Unnur Thorsteinsdottir
- 1] deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. [2] Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Jeff K Trimmer
- Cardiovascular & Metabolic Diseases Research Unit, Pfizer, Inc., Cambridge, Massachusetts, USA
| | - Tiinamaija Tuomi
- 1] Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland. [2] Folkhalsan Research Centre, Helsinki, Finland
| | - Jaakko Tuomilehto
- 1] Centre for Vascular Prevention, Danube-University Krems, Krems, Austria. [2] Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland. [3] Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fariba Vaziri-Sani
- Unit of Diabetes and Celiac Diseases, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Benjamin F Voight
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA. [3] Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Michael Boehnke
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark I McCarthy
- 1] Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK. [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [3] Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Pål R Njølstad
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway. [3] Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Leif Groop
- 1] Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, Sweden. [2] Finnish Institute for Molecular Medicine (FIMM), Helsinki University, Helsinki, Finland
| | - David R Cox
- Applied Quantitative Genotherapeutics, Pfizer, Inc., South San Francisco, California, USA
| | - Kari Stefansson
- 1] deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. [2] Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - David Altshuler
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [5] Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, USA. [6] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [7] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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23
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Kohrt D, Crary J, Zimmer M, Patrick AN, Ford HL, Hinds PW, Grossel MJ. CDK6 binds and promotes the degradation of the EYA2 protein. Cell Cycle 2013; 13:62-71. [PMID: 24196439 PMCID: PMC3925736 DOI: 10.4161/cc.26755] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cyclin-dependent kinase 6 (Cdk6) is a D-Cyclin-activated kinase that is directly involved in driving the cell cycle through inactivation of pRB in G1 phase. Increasingly, evidence suggests that CDK6, while directly driving the cell cycle, may only be essential for proliferation of specialized cell types, agreeing with the notion that CDK6 also plays an important role in differentiation. Here, evidence is presented that CDK6 binds to and promotes degradation of the EYA2 protein. The EYA proteins are a family of proteins that activate genes essential for the development of multiple organs, regulate cell proliferation, and are misregulated in several types of cancer. This interaction suggests that CDK6 regulates EYA2 activity, a mechanism that could be important in development and in cancer.
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Affiliation(s)
- Dawn Kohrt
- Department of Biology; Connecticut College; New London, CT USA
| | - Jennifer Crary
- Department of Biology; Connecticut College; New London, CT USA; Department of Developmental, Molecular, and Chemical Biology; Tufts University School of Medicine, and Molecular Oncology Research Institute; Tufts Medical Center; Boston, MA USA
| | - Marc Zimmer
- Department of Chemistry; Connecticut College; New London, CT USA
| | - Aaron N Patrick
- Department of Pharmacology; University of Colorado School of Medicine; Aurora, CO USA
| | - Heide L Ford
- Department of Pharmacology; University of Colorado School of Medicine; Aurora, CO USA
| | - Philip W Hinds
- Department of Developmental, Molecular, and Chemical Biology; Tufts University School of Medicine, and Molecular Oncology Research Institute; Tufts Medical Center; Boston, MA USA
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24
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Moustafa-Kamal M, Gamache I, Lu Y, Li S, Teodoro JG. BimEL is phosphorylated at mitosis by Aurora A and targeted for degradation by βTrCP1. Cell Death Differ 2013; 20:1393-403. [PMID: 23912711 DOI: 10.1038/cdd.2013.93] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 05/15/2013] [Accepted: 06/17/2013] [Indexed: 01/09/2023] Open
Abstract
Bcl-2-interacting mediator of cell death (Bim) is a pro-apoptotic B-cell lymphoma 2 family member implicated in numerous apoptotic stimuli. In particular, Bim is required for cell death mediated by antimitotic agents, however, mitotic regulation of Bim remains poorly understood. Here, we show that the major splice variant of Bim, BimEL, is regulated during mitosis by the Aurora A kinase and protein phosphatase 2A (PP2A). We observed that BimEL is phosphorylated by Aurora A early in mitosis and reversed by PP2A after mitotic exit. Aurora A phosphorylation stimulated binding of BimEL to the F-box protein beta-transducin repeat containing E3 ubiquitin protein ligase and promoted ubiquitination and degradation of BimEL. These findings describe a novel mechanism by which the oncogenic kinase Aurora A promotes cell survival during mitosis by downregulating proapoptotic signals. Notably, we observed that knockdown of Bim significantly increased resistance of cells to the Aurora A inhibitor MLN8054. Inhibitors of Aurora A are currently under investigation as cancer chemotherapeutics and our findings suggest that efficacy of this class of drugs may function in part by enhancing apoptotic activity of BimEL.
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Affiliation(s)
- M Moustafa-Kamal
- Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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25
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Scaglione KM, Basrur V, Ashraf NS, Konen JR, Elenitoba-Johnson KSJ, Todi SV, Paulson HL. The ubiquitin-conjugating enzyme (E2) Ube2w ubiquitinates the N terminus of substrates. J Biol Chem 2013; 288:18784-8. [PMID: 23696636 DOI: 10.1074/jbc.c113.477596] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Attachment of ubiquitin to substrate is typically thought to occur via formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin and a lysine residue in the substrate. In vitro, Ube2w is nonreactive with free lysine yet readily ubiquitinates substrate. Ube2w also contains novel residues within its active site that are important for its ability to ubiquitinate substrate. To identify the site of modification, we analyzed ubiquitinated substrates by mass spectrometry and found the N-terminal -NH2 group as the site of conjugation. To confirm N-terminal ubiquitination, we generated lysine-less and N-terminally blocked versions of one substrate, the polyglutamine disease protein ataxin-3, and showed that Ube2w can ubiquitinate a lysine-less, but not N-terminally blocked, ataxin-3. This was confirmed with a second substrate, the neurodegenerative disease protein Tau. Finally, we directly sequenced the N terminus of unmodified and ubiquitinated ataxin-3, demonstrating that Ube2w attaches ubiquitin to the N terminus of its substrates. Together these data demonstrate that Ube2w has novel enzymatic properties that direct ubiquitination of the N terminus of substrates.
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26
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Mahammad S, Murthy SNP, Didonna A, Grin B, Israeli E, Perrot R, Bomont P, Julien JP, Kuczmarski E, Opal P, Goldman RD. Giant axonal neuropathy-associated gigaxonin mutations impair intermediate filament protein degradation. J Clin Invest 2013; 123:1964-75. [PMID: 23585478 DOI: 10.1172/jci66387] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 02/14/2013] [Indexed: 11/17/2022] Open
Abstract
Giant axonal neuropathy (GAN) is an early-onset neurological disorder caused by mutations in the GAN gene (encoding for gigaxonin), which is predicted to be an E3 ligase adaptor. In GAN, aggregates of intermediate filaments (IFs) represent the main pathological feature detected in neurons and other cell types, including patients' dermal fibroblasts. The molecular mechanism by which these mutations cause IFs to aggregate is unknown. Using fibroblasts from patients and normal individuals, as well as Gan-/- mice, we demonstrated that gigaxonin was responsible for the degradation of vimentin IFs. Gigaxonin was similarly involved in the degradation of peripherin and neurofilament IF proteins in neurons. Furthermore, proteasome inhibition by MG-132 reversed the clearance of IF proteins in cells overexpressing gigaxonin, demonstrating the involvement of the proteasomal degradation pathway. Together, these findings identify gigaxonin as a major factor in the degradation of cytoskeletal IFs and provide an explanation for IF aggregate accumulation, the subcellular hallmark of this devastating human disease.
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Affiliation(s)
- Saleemulla Mahammad
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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27
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Abstract
The covalent attachment of ubiquitin to a protein is one of the most common post-translational modifications and regulates diverse eukaryotic cellular processes. Ubiquitination of MHC class I was first described in the context of viral proteins which target MHC class I for degradation in the endoplasmic reticulum and at the cell surface. Study of viral-induced MHC class I degradation has been extremely instructive in elucidating cellular pathways for degradation of membrane and secretory proteins. More recently, ubiquitination of endogenous MHC class I heavy chains which fail to achieve their native conformation and undergo endoplasmic-reticulum associated degradation has been demonstrated.In this chapter we describe methods for identification of endogenous ubiquitinated MHC class I heavy chains by MHC class I-immunoprecipitation and ubiquitin-specific immunoblot or by metabolic labeling and immunoprecipitation.
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Affiliation(s)
- Marian L Burr
- Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Jessica M Boname
- Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
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28
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Ling Q, Huang W, Baldwin A, Jarvis P. Chloroplast biogenesis is regulated by direct action of the ubiquitin-proteasome system. Science 2012; 338:655-9. [PMID: 23118188 DOI: 10.1126/science.1225053] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Development of chloroplasts and other plastids depends on the import of thousands of nucleus-encoded proteins from the cytosol. Import is initiated by TOC (translocon at the outer envelope of chloroplasts) complexes in the plastid outer membrane that incorporate multiple, client-specific receptors. Modulation of import is thought to control the plastid's proteome, developmental fate, and functions. Using forward genetics, we identified Arabidopsis SP1, which encodes a RING-type ubiquitin E3 ligase of the chloroplast outer membrane. The SP1 protein associated with TOC complexes and mediated ubiquitination of TOC components, promoting their degradation. Mutant sp1 plants performed developmental transitions that involve plastid proteome changes inefficiently, indicating a requirement for reorganization of the TOC machinery. Thus, the ubiquitin-proteasome system acts on plastids to control their development.
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Affiliation(s)
- Qihua Ling
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK
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29
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Differential ubiquitination and proteasome regulation of Ca(V)2.2 N-type channel splice isoforms. J Neurosci 2012; 32:10365-9. [PMID: 22836269 DOI: 10.1523/jneurosci.0851-11.2012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Ca(V)2.2 (N-type) calcium channels control the entry of calcium into neurons to regulate essential functions but most notably presynaptic transmitter release. Ca(V)2.2 channel expression levels are precisely controlled, but we know little of the cellular mechanisms involved. The ubiquitin proteasome system (UPS) is known to regulate expression of many synaptic proteins, including presynaptic elements, to optimize synaptic efficiency. However, we have limited information about ubiquitination of Ca(V)2 channels. Here we show that Ca(V)2.2 proteins are ubiquitinated, and that elements in the proximal C terminus of Ca(V)2.2 encoded by exon 37b of the mouse Cacna1b gene predispose cloned and native channels to downregulation by the UPS. Ca(V)2.2 channels containing e37b are expressed throughout the mammalian nervous system, but in some cells, notably nociceptors, sometimes e37a--not e37b--is selected during alternative splicing of Ca(V)2.2 pre-mRNA. By a combination of biochemical and functional analyses we show e37b promotes a form of ubiquitination that is coupled to reduced Ca(V)2.2 current density and increased sensitivity to the UPS. Cell-specific alternative splicing of e37a in nociceptors reduces Ca(V)2.2 channel ubiquitination and sensitivity to the UPS, suggesting a role in pain processing.
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30
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Sambuughin N, Swietnicki W, Techtmann S, Matrosova V, Wallace T, Goldfarb L, Maynard E. KBTBD13 interacts with Cullin 3 to form a functional ubiquitin ligase. Biochem Biophys Res Commun 2012; 421:743-9. [PMID: 22542517 DOI: 10.1016/j.bbrc.2012.04.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 04/13/2012] [Indexed: 12/18/2022]
Abstract
Autosomal dominant mutations in BTB and Kelch domain containing 13 protein (KBTBD13) are associated with a new type of Nemaline Myopathy (NEM). NEM is a genetically heterogeneous group of muscle disorders. Mutations causing phenotypically distinct NEM variants have previously been identified in components of muscle thin filament. KBTBD13 is a muscle specific protein composed of an N terminal BTB domain and a C terminal Kelch-repeat domain. The function of this newly identified protein in muscle remained unknown. In this study, we show that KBTBD13 interacts with Cullin 3 (Cul3) and the BTB domain mediates this interaction. Using ubiquitination assays, we determined that KBTBD13 participates in the formation of a Cul3 based RING ubiquitin ligase (Cul3-RL) capable of ubiquitin conjugation. Confocal microscopy of transiently expressed KBTBD13 revealed its co-localization with ubiquitin. Taken together, our results demonstrate that KBTBD13 is a putative substrate adaptor for Cul3-RL that functions as a muscle specific ubiquitin ligase, and thereby implicate the ubiquitin proteasome pathway in the pathogenesis of KBTBD13-associated NEM.
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Affiliation(s)
- Nyamkhishig Sambuughin
- Department of Anesthesiology, Uniformed Services University, 4301 Jones Bridge Rd., Bethesda, MD 20814, USA.
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31
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Tripartite motif containing protein 27 negatively regulates CD4 T cells by ubiquitinating and inhibiting the class II PI3K-C2β. Proc Natl Acad Sci U S A 2011; 108:20072-7. [PMID: 22128329 DOI: 10.1073/pnas.1111233109] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The K(+) channel KCa3.1 is required for Ca(2+) influx and the subsequent activation of CD4 T cells. The class II phosphatidylinositol 3 kinase C2β (PI3KC2β) is activated by the T-cell receptor (TCR) and is critical for KCa3.1 channel activation. Tripartite motif containing protein 27 (TRIM27) is a member of a large family of proteins that function as Really Interesting New Gene (RING) E3 ubiquitin ligases. We now show that TRIM27 functions as an E3 ligase and mediates lysine 48 polyubiquitination of PI3KC2β, leading to a decrease in PI3K enzyme activity. By inhibiting PI3KC2β, TRIM27 also functions to negatively regulate CD4 T cells by inhibiting KCa3.1 channel activity and TCR-stimulated Ca(2+) influx and cytokine production in Jurkat, primary human CD4 T cells, and Th0, Th1, and Th2 CD4 T cells generated from TRIM27(-/-) mice. These findings provide a unique mechanism for regulating class II PI3Ks, and identify TRIM27 as a previously undescribed negative regulator of CD4 T cells.
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Hu D, Liu W, Wu G, Wan Y. Nuclear translocation of Skp2 facilitates its destruction in response to TGFβ signaling. Cell Cycle 2011; 10:285-92. [PMID: 21212736 DOI: 10.4161/cc.10.2.14517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Skp2, a F-box protein that determines the substrate specificity for SCF ubiquitin ligase, has recently been demonstrated to be degraded by Cdh1/APC in response to TGFβ signaling. The TGFβ-induced Skp2 proteolysis results in the stabilization of p27 that is necessary to facilitate TGFβ cytostatic effect. Previous observation from immunocytochemistry indicates that Cdh1 principally localizes in the nucleus while Skp2 mainly localizes in the cytosol, which leaves us a puzzle on how Skp2 is recognized and then ubiquitylated by Cdh1/APC in response to TGFβ stimulation. Here, we report that Skp2 is rapidly translocated from the cytosol to the nucleus upon the cellular stimulation with TGFβ. Using a combinatorial approach of immunocytochemistry, biochemical-fraction-coupled immunoprecipitation, mutagenesis as well as protein degradation assay, we have demonstrated that the TGFβ-induced Skp2 nucleus translocation is critical for TGFβ cytostatic effect that allows physical interaction between Cdh1 and Skp2 and in turn facilitates the Skp2 ubquitylation by Cdh1/APC. Disruption of nuclear localization motifs on Skp2 stabilizes Skp2 in the presence of TGF-β signaling, which attenuates TGFβ-induced p27 accumulation and antagonizes TGFβ-induced growth inhibition. Our finding reveals a cellular mechanism that facilitates Skp2 ubiquitylation by Cdh1/APC in response to TGFβ.
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Affiliation(s)
- Dong Hu
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Gentilella A, Khalili K. BAG3 expression in glioblastoma cells promotes accumulation of ubiquitinated clients in an Hsp70-dependent manner. J Biol Chem 2011; 286:9205-15. [PMID: 21233200 DOI: 10.1074/jbc.m110.175836] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Disposal of damaged proteins and protein aggregates is a prerequisite for the maintenance of cellular homeostasis and impairment of this disposal can lead to a broad range of pathological conditions, most notably in brain-associated disorders including Parkinson and Alzheimer diseases, and cancer. In this respect, the Protein Quality Control (PQC) pathway plays a central role in the clearance of damaged proteins. The Hsc/Hsp70-co-chaperone BAG3 has been described as a new and critical component of the PQC in several cellular contexts. For example, the expression of BAG3 in the rodent brain correlates with the engagement of protein degradation machineries in response to proteotoxic stress. Nevertheless, little is known about the molecular events assisted by BAG3. Here we show that ectopic expression of BAG3 in glioblastoma cells leads to the activation of an HSF1-driven stress response, as attested by transcriptional activation of BAG3 and Hsp70. BAG3 overexpression determines an accumulation of ubiquitinated proteins and this event requires the N-terminal region, WW domain of BAG3 and the association of BAG3 with Hsp70. The ubiquitination mainly occurs on BAG3-client proteins and the inhibition of proteasomal activity results in a further accumulation of ubiquitinated clients. At the cellular level, overexpression of BAG3 in glioblastoma cell lines, but not in non-glial cells, results in a remarkable decrease in colony formation capacity and this effect is reverted when the binding of BAG3 to Hsp70 is impaired. These observations provide the first evidence for an involvement of BAG3 in the ubiquitination and turnover of its partners.
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Affiliation(s)
- Antonio Gentilella
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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Del Rincón SV, Rogers J, Widschwendter M, Sun D, Sieburg HB, Spruck C. Development and validation of a method for profiling post-translational modification activities using protein microarrays. PLoS One 2010; 5:e11332. [PMID: 20596523 PMCID: PMC2893156 DOI: 10.1371/journal.pone.0011332] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 06/03/2010] [Indexed: 12/20/2022] Open
Abstract
Background Post-translational modifications (PTMs) impact on the stability, cellular location, and function of a protein thereby achieving a greater functional diversity of the proteome. To fully appreciate how PTMs modulate signaling networks, proteome-wide studies are necessary. However, the evaluation of PTMs on a proteome-wide scale has proven to be technically difficult. To facilitate these analyses we have developed a protein microarray-based assay that is capable of profiling PTM activities in complex biological mixtures such as whole-cell extracts and pathological specimens. Methodology/Principal Findings In our assay, protein microarrays serve as a substrate platform for in vitro enzymatic reactions in which a recombinant ligase, or extracts prepared from whole cells or a pathological specimen is overlaid. The reactions include labeled modifiers (e.g., ubiquitin, SUMO1, or NEDD8), ATP regenerating system, and other required components (depending on the assay) that support the conjugation of the modifier. In this report, we apply this methodology to profile three molecularly complex PTMs (ubiquitylation, SUMOylation, and NEDDylation) using purified ligase enzymes and extracts prepared from cultured cell lines and pathological specimens. We further validate this approach by confirming the in vivo modification of several novel PTM substrates identified by our assay. Conclusions/Significance This methodology offers several advantages over currently used PTM detection methods including ease of use, rapidity, scale, and sample source diversity. Furthermore, by allowing for the intrinsic enzymatic activities of cell populations or pathological states to be directly compared, this methodology could have widespread applications for the study of PTMs in human diseases and has the potential to be directly applied to most, if not all, basic PTM research.
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Affiliation(s)
- Sonia V Del Rincón
- Signal Transduction Program, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
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Abstract
Transcription factors are usually unstable proteins. The degradation of the majority of transcription factors is through the ubiquitin proteasome pathway and is tightly regulated by E3 ubiquitin ligases. KLF5 is an important transcription factor regulating cell proliferation, cell cycle, survival, migration, differentiation, angiogenesis, and stem cell self-renewal. We have shown that the WWP1 E3 ligase targets KLF5 for ubiquitin-mediated degradation. Several methods to determine whether a protein is ubiquitinated have been described [Kaiser, Tagwerker (Methods Enzymol 399:243-248, 2005); Bloom, Pagano (Methods Enzymol 399:249-266, 2005)]. This chapter focuses on experimental approaches testing KLF5 transcription factor ubiquitination and degradation by its E3s.
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Affiliation(s)
- Ceshi Chen
- Center for Cell Biology and Cancer Research, Albany Medical College, Albany, NY, USA.
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Sgk1 activates MDM2-dependent p53 degradation and affects cell proliferation, survival, and differentiation. J Mol Med (Berl) 2009; 87:1221-39. [PMID: 19756449 DOI: 10.1007/s00109-009-0525-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 08/05/2009] [Accepted: 08/20/2009] [Indexed: 12/11/2022]
Abstract
Serum and glucocorticoid regulated kinase 1 (Sgk1) is a serine-threonine kinase that is activated by serum, steroids, insulin, vasopressin, and interleukin 2 at the transcriptional and post-translational levels. Sgk1 is also important in transduction of growth factors and steroid-dependent survival signals and may have a role in the development of resistance to cancer chemotherapy. In the present paper, we demonstrate that Sgk1 activates MDM2-dependent p53 ubiquitylation. The results were obtained in RKO cells and other cell lines by Sgk1-specific RNA silencing and were corroborated in an original mouse model as well as in transiently and in stably transfected HeLa cells expressing wild-type or dominant negative Sgk1 mutant. Sgk1 contributes to cell survival, cell-cycle progression, and epithelial de-differentiation. We also show that the effects of Sgk1 on the clonogenic potential of different cancer cells depend on the expression of wild-type p53. Since transcription of Sgk1 is activated by p53, we propose a finely tuned feedback model where Sgk1 down-regulates the expression of p53 by enhancing its mono- and polyubiquitylation.
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Abstract
The transcription factor p73, a member of the p53 family, mediates cell-cycle arrest and apoptosis in response to DNA damage-induced cellular stress, acting thus as a proapoptotic gene. Similar to p53, p73 activity is regulated by post-translational modification, including phosphorylation, acetylation and ubiquitylation. In C. elegans, the F-box protein FSN-1 controls germline apoptosis by regulating CEP-1, the single ancestral p53 family member. Here we report that FBXO45, the human ortholog of FSN-1, binds specifically to p73 triggering its proteasome-dependent degradation. Importantly, SCF(FBXO45) ubiquitylates p73 both in vivo and in vitro. Moreover, siRNA-mediated depletion of FBXO45 stabilizes p73 and concomitantly induces cell death in a p53-independent manner. All together, these results show that the orphan F-box protein FBXO45 regulates the stability of p73, highlighting a conserved pathway evolved from nematode to human by which the p53 members are regulated by an SCF-dependent mechanism.
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Mutations in the zinc finger domain of IKK gamma block the activation of NF-kappa B and the induction of IL-2 in stimulated T lymphocytes. Mol Immunol 2008; 45:1633-45. [PMID: 18207244 DOI: 10.1016/j.molimm.2007.09.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2007] [Accepted: 09/18/2007] [Indexed: 01/06/2023]
Abstract
Mutations in the zinc finger of I kappa B kinase gamma (IKK gamma) are associated with hypohidrotic ectodermal dysplasia-immune deficiency (HED-ID) in which the major immune deficit is the inability to switch Ab heavy chain class. However, the pathophysiologic role of the mutations has not been fully delineated. Since help from activated Th cells is essential in Ab class switching, we sought to examine how these mutations affect T cell activation. Using a human T cell line that was null for IKK gamma, we generated cells stably expressing two of the reported mutations, namely, D406V and C417R. Cells expressing either mutation failed to induce IL-2 following stimulation with PMA/ionomycin while the induction of IL-2 was restored in cells reconstituted with the wild type IKK gamma. The lack of IL-2 upregulation correlated with the lack of NF-kappaB activation as evidenced by the inability to induce I kappa B alpha degradation, NF-kappaB binding to DNA and the expression of a reporter gene. However, both mutations did not prevent the incorporation of IKK gamma into the IKK complex and, interestingly, the induced phosphorylation of I kappa B alpha at S32 and S36 and its subsequent ubiquitination were not affected. The suppression of IL-2 induction was solely due to the inhibition of NF-kappaB activation as the mutations did not impair the activation of AP-1 and NFAT. Our data indicated that the failure of T cells to undergo activation in response to TCR stimuli may play a role in the pathophysiology of HED-ID and also showed that IKK gamma has a role in the post-ubiquitination processing of I kappa B alpha.
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Staszczak M. An in vitro method for selective detection of free monomeric ubiquitin by using a C-terminally biotinylated form of ubiquitin. Int J Biochem Cell Biol 2007; 39:319-26. [PMID: 17030000 DOI: 10.1016/j.biocel.2006.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 08/23/2006] [Accepted: 08/24/2006] [Indexed: 10/24/2022]
Abstract
In an effort to design a selective assay allowing detection of free monomeric ubiquitin, an approach based on a C-terminally biotinylated form of ubiquitin is proposed. In the form of a polyubiquitin chain, ubiquitin marks proteins for degradation by the 26S proteasome. This covalently attached signal is assembled from multiple ubiquitins linked to each other via the C-terminus of one ubiquitin and the epsilon-amine of Lys48 of another ubiquitin. In the present study, a form of ubiquitin having the C-terminus modified with the addition of a biotinylation peptide tag was prepared. After expression, this modified ubiquitin was biotinylated in vitro using recombinant biotin ligase. Biotinylated ubiquitin was further purified using affinity chromatography on immobilized monovalent avidin. This tagged form of ubiquitin is blocked at the C-terminus and therefore can only act as an acceptor (Lys-48 donor) in polyubiquitin chain synthesis. In vitro enzymatic assembly of multiubiquitin chains from biotinylated monoubiquitin and natural monoubiquitin is demonstrated by Western blot analysis using horseradish peroxidase-conjugated streptavidin. Data obtained with this assay indicate potential uses of the C-terminally biotinylated form of ubiquitin for selective detection of monoubiquitin contamination in a cell extract experimentally depleted of ubiquitin, i.e. lysate Fraction II. Cell-free systems established for in vitro examination of ubiquitin involvement in proteolytic processes usually employ Fraction II, which should be essentially ubiquitin-free. It is suggested that the assay using biotinylated monoubiquitin can be useful to exclude the possibility that ubiquitin contamination of laboratory prepared lysate Fraction II accounts for protein degradation in this fraction.
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Affiliation(s)
- Magdalena Staszczak
- Department of Biochemistry, Maria Curie-Skłodowska University, pl. M. Curie-Skłodowskiej 3, 20-031 Lublin, Poland.
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