1
|
Dong B, Song X, Wang X, Dai T, Wang J, Zhiyong Y, Deng J, Evers BM, Wu Y. FBXO24 Suppresses Breast Cancer Tumorigenesis by Targeting LSD1 for Ubiquitination. Mol Cancer Res 2023; 21:1303-1316. [PMID: 37540490 PMCID: PMC10840093 DOI: 10.1158/1541-7786.mcr-23-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/27/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Lysine-specific demethylase 1 (LSD1), a critical chromatin modulator, functions as an oncogene by demethylation of H3K4me1/2. The stability of LSD1 is governed by a complex and intricate process involving ubiquitination and deubiquitination. Several deubiquitinases preserve LSD1 protein levels. However, the precise mechanism underlying the degradation of LSD1, which could mitigate its oncogenic function, remains unknown. To gain a better understanding of LSD1 degradation, we conducted an unbiased siRNA screening targeting all the human SCF family E3 ligases. Our screening identified FBXO24 as a genuine E3 ligase that ubiquitinates and degrades LSD1. As a result, FBXO24 inhibits LSD1-induced tumorigenesis and functions as a tumor suppressor in breast cancer cells. Moreover, FBXO24 exhibits an inverse correlation with LSD1 and is associated with a favorable prognosis in breast cancer patient samples. Taken together, our study uncovers the significant role of FBXO24 in impeding breast tumor progression by targeting LSD1 for degradation. IMPLICATIONS Our study provides comprehensive characterization of the significant role of FBXO24 in impeding breast tumor progression by targeting LSD1 for degradation.
Collapse
Affiliation(s)
- Bo Dong
- Department of Pharmacology & Nutritional Sciences, Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
| | - Xiang Song
- Department of Pharmacology & Nutritional Sciences, Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, People’s Republic of China
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, People’s Republic of China
| | - Xinzhao Wang
- Department of Pharmacology & Nutritional Sciences, Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
| | - Tao Dai
- Department of Pharmacology & Nutritional Sciences, Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
| | - Jianlin Wang
- Department of Pharmacology & Nutritional Sciences, Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
| | - Yu Zhiyong
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, People’s Republic of China
| | - Jiong Deng
- Medical Research Institute, Binzhou Medical University Hospital, Binzhou, China
| | - B. Mark Evers
- Department of Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, People’s Republic of China
| | - Yadi Wu
- Department of Pharmacology & Nutritional Sciences, Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
- Markey Cancer Center, the University of Kentucky, College of Medicine, Lexington, KY 40506, United States
| |
Collapse
|
2
|
Vulpetti A, Holzer P, Schmiedeberg N, Imbach-Weese P, Pissot-Soldermann C, Hollingworth GJ, Radimerski T, Thoma CR, Stachyra TM, Wojtynek M, Maschlej M, Chau S, Schuffenhauer A, Fernández C, Schröder M, Renatus M. Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field. ACS Med Chem Lett 2023; 14:949-954. [PMID: 37465299 PMCID: PMC10350940 DOI: 10.1021/acsmedchemlett.3c00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023] Open
Abstract
In this study, we describe the rapid identification of potent binders for the WD40 repeat domain (WDR) of DCAF1. This was achieved by two rounds of iterative focused screening of a small set of compounds selected on the basis of internal WDR domain knowledge followed by hit expansion. Subsequent structure-based design led to nanomolar potency binders with a clear exit vector enabling DCAF1-based bifunctional degrader exploration.
Collapse
Affiliation(s)
- Anna Vulpetti
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Philipp Holzer
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Niko Schmiedeberg
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Patricia Imbach-Weese
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Carole Pissot-Soldermann
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Gregory J. Hollingworth
- Global
Discovery Chemistry, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Thomas Radimerski
- Oncology
Drug Discovery, Novartis Institutes for
BioMedical Research, Basel 4002, Switzerland
| | - Claudio R. Thoma
- Oncology
Drug Discovery, Novartis Institutes for
BioMedical Research, Basel 4002, Switzerland
| | - Therese-Marie Stachyra
- Oncology
Drug Discovery, Novartis Institutes for
BioMedical Research, Basel 4002, Switzerland
| | - Matthias Wojtynek
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Magdalena Maschlej
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Suzanne Chau
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Ansgar Schuffenhauer
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - César Fernández
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Martin Schröder
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| | - Martin Renatus
- Chemical
Biology & Therapeutics, Novartis Institutes
for BioMedical Research, Basel 4002, Switzerland
| |
Collapse
|
3
|
Scinicariello S, Soderholm A, Schäfer M, Shulkina A, Schwartz I, Hacker K, Gogova R, Kalis R, Froussios K, Budroni V, Bestehorn A, Clausen T, Kovarik P, Zuber J, Versteeg GA. HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation. eLife 2023; 12:e83159. [PMID: 36961408 PMCID: PMC10038661 DOI: 10.7554/elife.83159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/26/2023] [Indexed: 03/25/2023] Open
Abstract
Tristetraprolin (TTP) is a critical negative immune regulator. It binds AU-rich elements in the untranslated-regions of many mRNAs encoding pro-inflammatory mediators, thereby accelerating their decay. A key but poorly understood mechanism of TTP regulation is its timely proteolytic removal: TTP is degraded by the proteasome through yet unidentified phosphorylation-controlled drivers. In this study, we set out to identify factors controlling TTP stability. Cellular assays showed that TTP is strongly lysine-ubiquitinated, which is required for its turnover. A genetic screen identified the ubiquitin E3 ligase HUWE1 as a strong regulator of TTP proteasomal degradation, which we found to control TTP stability indirectly by regulating its phosphorylation. Pharmacological assessment of multiple kinases revealed that HUWE1-regulated TTP phosphorylation and stability was independent of the previously characterized effects of MAPK-mediated S52/S178 phosphorylation. HUWE1 function was dependent on phosphatase and E3 ligase binding sites identified in the TTP C-terminus. Our findings indicate that while phosphorylation of S52/S178 is critical for TTP stabilization at earlier times after pro-inflammatory stimulation, phosphorylation of the TTP C-terminus controls its stability at later stages.
Collapse
Affiliation(s)
- Sara Scinicariello
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Adrian Soderholm
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Markus Schäfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Alexandra Shulkina
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Irene Schwartz
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Kathrin Hacker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Rebeca Gogova
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Robert Kalis
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Kimon Froussios
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Annika Bestehorn
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Pavel Kovarik
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| |
Collapse
|
4
|
Henning NJ, Manford AG, Spradlin JN, Brittain SM, Zhang E, McKenna JM, Tallarico JA, Schirle M, Rape M, Nomura DK. Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications. J Am Chem Soc 2022; 144:701-708. [PMID: 34994556 PMCID: PMC8928484 DOI: 10.1021/jacs.1c03980] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs), heterobifunctional compounds that consist of protein-targeting ligands linked to an E3 ligase recruiter, have arisen as a powerful therapeutic modality for targeted protein degradation (TPD). Despite the popularity of TPD approaches in drug discovery, only a small number of E3 ligase recruiters are available for the >600 E3 ligases that exist in human cells. Here, we have discovered a cysteine-reactive covalent ligand, EN106, that targets FEM1B, an E3 ligase recently discovered as the critical component of the cellular response to reductive stress. By targeting C186 in FEM1B, EN106 disrupts recognition of the key reductive stress substrate of FEM1B, FNIP1. We further establish that EN106 can be used as a covalent recruiter for FEM1B in TPD applications by demonstrating that a PROTAC linking EN106 to the BET bromodomain inhibitor JQ1 or the kinase inhibitor dasatinib leads to the degradation of BRD4 and BCR-ABL, respectively. Our study showcases a covalent ligand that targets a natural E3 ligase-substrate binding site and highlights the utility of covalent ligand screening in expanding the arsenal of E3 ligase recruiters suitable for TPD applications.
Collapse
Affiliation(s)
- Nathaniel J. Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Andrew G. Manford
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Jessica N. Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
| |
Collapse
|
5
|
Abstract
Post-translational protein modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins such as small ubiquitin-like modifier (SUMO) regulates processes including protein homeostasis, the DNA damage response, and the cell cycle. Proliferating cell nuclear antigen (PCNA) is modified by Ub or poly-Ub at lysine (Lys)164 after DNA damage to recruit repair factors. Yeast PCNA is modified by SUMO on Lys164 and Lys127 during S-phase to recruit the anti-recombinogenic helicase Srs2. Lys164 modification requires specialized E2/E3 enzyme pairs for SUMO or Ub conjugation. For SUMO, Lys164 modification is strictly dependent on the E3 ligase Siz1, suggesting the E3 alters E2 specificity to promote Lys164 modification. The structural basis for substrate interactions in activated E3/E2–Ub/Ubl complexes remains unclear. Here we report an engineered E2 protein and cross-linking strategies that trap an E3/E2–Ubl/substrate complex for structure determination, illustrating how an E3 can bypass E2 specificity to force-feed a substrate lysine into the E2 active site.
Collapse
|
6
|
Wang J, Qu B, Dou S, Li L, Yin D, Pang Z, Zhou Z, Tian M, Liu G, Xie Q, Tang D, Chen X, Zhu L. The E3 ligase OsPUB15 interacts with the receptor-like kinase PID2 and regulates plant cell death and innate immunity. BMC Plant Biol 2015; 15:49. [PMID: 25849162 PMCID: PMC4330927 DOI: 10.1186/s12870-015-0442-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice blast disease is one of the most destructive diseases of rice worldwide. We previously cloned the rice blast resistance gene Pid2, which encodes a transmembrane receptor-like kinase containing an extracellular B-lectin domain and an intracellular serine/threonine kinase domain. However, little is known about Pid2-mediated signaling. RESULTS Here we report the functional characterization of the U-box/ARM repeat protein OsPUB15 as one of the PID2-binding proteins. We found that OsPUB15 physically interacted with the kinase domain of PID2 (PID2K) in vitro and in vivo and the ARM repeat domain of OsPUB15 was essential for the interaction. In vitro biochemical assays indicated that PID2K possessed kinase activity and was able to phosphorylate OsPUB15. We also found that the phosphorylated form of OsPUB15 possessed E3 ligase activity. Expression pattern analyses revealed that OsPUB15 was constitutively expressed and its encoded protein OsPUB15 was localized in cytosol. Transgenic rice plants over-expressing OsPUB15 at early stage displayed cell death lesions spontaneously in association with a constitutive activation of plant basal defense responses, including excessive accumulation of hydrogen peroxide, up-regulated expression of pathogenesis-related genes and enhanced resistance to blast strains. We also observed that, along with plant growth, the cell death lesions kept spreading over the whole seedlings quickly resulting in a seedling lethal phenotype. CONCLUSIONS These results reveal that the E3 ligase OsPUB15 interacts directly with the receptor-like kinase PID2 and regulates plant cell death and blast disease resistance.
Collapse
Affiliation(s)
- Jing Wang
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- />Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130 China
| | - Baoyuan Qu
- />State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shijuan Dou
- />College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001 China
| | - Liyun Li
- />College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001 China
| | - Dedong Yin
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhiqian Pang
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- />CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Zhuangzhi Zhou
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Miaomiao Tian
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Guozhen Liu
- />College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001 China
| | - Qi Xie
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Dingzhong Tang
- />State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xuewei Chen
- />Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130 China
| | - Lihuang Zhu
- />State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| |
Collapse
|
7
|
Rubio MD, Wood K, Haroutunian V, Meador-Woodruff JH. Dysfunction of the ubiquitin proteasome and ubiquitin-like systems in schizophrenia. Neuropsychopharmacology 2013; 38:1910-20. [PMID: 23571678 DOI: 10.1038/npp.2013.84] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 02/06/2023]
Abstract
Protein expression abnormalities have been implicated in the pathophysiology of schizophrenia, but the underlying cause of these changes is not known. We sought to investigate ubiquitin and ubiquitin-like (UBL) systems (SUMOylation, NEDD8ylation, and Ufmylation) as putative mechanisms underlying protein expression abnormalities seen in schizophrenia. For this, we performed western blot analysis of total ubiquitination, free ubiquitin, K48- and K63-linked ubiquitination, and E1 activases, E2 conjugases, and E3 ligases involved in ubiquitination and UBL post-translational modifications in postmortem brain tissue samples from persons with schizophrenia (n=13) and comparison subjects (n=13). We studied the superior temporal gyrus (STG) of subjects from the Mount Sinai Medical Center brain collection that were matched for age, tissue pH, and sex. We found an overall reduction of protein ubiquitination, free ubiquitin, K48-linked ubiquitination, and increased K63 polyubiquitination in schizophrenia. Ubiquitin E1 activase UBA (ubiquitin activating enzyme)-6 and E3 ligase Nedd (neural precursor cell-expressed developmentally downregulated)-4 were decreased in this illness, as were E3 ligases involved in Ufmylation (UFL1) and SUMOylation (protein inhibitor of activated STAT 3, PIAS3). NEDD8ylation was also dysregulated in schizophrenia, with decreased levels of the E1 activase UBA3 and the E3 ligase Rnf7. This study of ubiquitin and UBL systems in schizophrenia found abnormalities of ubiquitination, Ufmylation, SUMOylation, and NEDD8ylation in the STG in this disorder. These results suggest a novel approach to the understanding of schizophrenia pathophysiology, where a disruption in homeostatic adaptation of the cell underlies discreet changes seen at the protein level in this illness.
Collapse
|
8
|
Jung HY, Wang X, Jun S, Park JI. Dyrk2-associated EDD-DDB1-VprBP E3 ligase inhibits telomerase by TERT degradation. J Biol Chem 2013; 288:7252-62. [PMID: 23362280 PMCID: PMC3591633 DOI: 10.1074/jbc.m112.416792] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 01/09/2013] [Indexed: 11/06/2022] Open
Abstract
Telomerase maintains the telomere, a specialized chromosomal end structure that is essential for genomic stability and cell immortalization. Telomerase is not active in most somatic cells, but its reactivation is one of the hallmarks of cancer. In this study, we found that dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 2 (Dyrk2) negatively regulates telomerase activity. Dyrk2 phosphorylates TERT protein, a catalytic subunit of telomerase. Phosphorylated TERT is then associated with the EDD-DDB1-VprBP E3 ligase complex for subsequent ubiquitin-mediated TERT protein degradation. During the cell cycle, Dyrk2 interacts with TERT at the G2/M phase and induces degradation. In contrast, depletion of endogenous Dyrk2 disrupts the cell cycle-dependent regulation of TERT and elicits the constitutive activation of telomerase. Similarly, a Dyrk2 nonsense mutation identified in breast cancer compromises ubiquitination-mediated TERT protein degradation. Our findings suggest the novel molecular mechanism of kinase-associated telomerase regulation.
Collapse
Affiliation(s)
- Hae-Yun Jung
- From the Department of Experimental Radiation Oncology and
| | - Xin Wang
- From the Department of Experimental Radiation Oncology and
| | - Sohee Jun
- From the Department of Experimental Radiation Oncology and
| | - Jae-Il Park
- From the Department of Experimental Radiation Oncology and
- Program in Cancer Biology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| |
Collapse
|
9
|
Stieglitz B, Morris-Davies AC, Koliopoulos MG, Christodoulou E, Rittinger K. LUBAC synthesizes linear ubiquitin chains via a thioester intermediate. EMBO Rep 2012; 13:840-6. [PMID: 22791023 PMCID: PMC3432797 DOI: 10.1038/embor.2012.105] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 06/21/2012] [Accepted: 06/22/2012] [Indexed: 01/31/2023] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) is a RING E3 ligase that regulates immune and inflammatory signalling pathways. Unlike classical RING E3 ligases, LUBAC determines the type of ubiquitin chain being formed, an activity normally associated with the E2 enzyme. We show that the RING-in-between-RING (RBR)-containing region of HOIP--the catalytic subunit of LUBAC--is sufficient to generate linear ubiquitin chains. However, this activity is inhibited by the N-terminal portion of the molecule, an inhibition that is released upon complex formation with HOIL-1L or SHARPIN. Furthermore, we demonstrate that HOIP transfers ubiquitin to the substrate through a thioester intermediate formed by a conserved cysteine in the RING2 domain, supporting the notion that RBR ligases act as RING/HECT hybrids.
Collapse
Affiliation(s)
- Benjamin Stieglitz
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Aylin C Morris-Davies
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Marios G Koliopoulos
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Evangelos Christodoulou
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Katrin Rittinger
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| |
Collapse
|
10
|
Abstract
Interferon cytokine family members shape the immune response to protect the host from both pathologic infections and tumorigenesis. To mediate their physiologic function, interferons evoke a robust and complex signal transduction pathway that leads to the induction of interferon-stimulated genes with both proinflammatory and antiviral functions. Numerous mechanisms exist to tightly regulate the extent and duration of these cellular responses. Among such mechanisms, the post-translational conjugation of ubiquitin polypeptides to protein mediators of interferon signaling has emerged as a crucially important mode of control. In this mini-review, we highlight recent advances in our understanding of these ubiquitin-mediated mechanisms, their exploitation by invading viruses, and their possible utilization for medical intervention.
Collapse
Affiliation(s)
- Serge Y Fuchs
- Department of Animal Biology and Mari Lowe Comparative Oncology Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA.
| |
Collapse
|
11
|
Abstract
The transforming growth factor β (TGFβ) superfamily of signal transduction molecules plays crucial roles in the regulation of cell behavior. TGFβ regulates gene transcription through Smad proteins and signals via non-Smad pathways. The TGFβ pathway is strictly regulated, and perturbations lead to tumorigenesis. Several pathway components are known to be targeted for proteasomal degradation via ubiquitination by E3 ligases. Smurfs are well known negative regulators of TGFβ, which function as E3 ligases recruited by adaptors such as I-Smads. TGFβ signaling can also be enhanced by E3 ligases, such as Arkadia, that target repressors for degradation. It is becoming clear that E3 ligases often target multiple pathways, thereby acting as mediators of signaling cross-talk. Regulation via ubiquitination involves a complex network of E3 ligases, adaptor proteins, and deubiquitinating enzymes (DUBs), the last-mentioned acting by removing ubiquitin from its targets. Interestingly, also non-degradative ubiquitin modifications are known to play important roles in TGFβ signaling. Ubiquitin modifications thus play a key role in TGFβ signal transduction, and in this review we provide an overview of known players, focusing on recent advances.
Collapse
Affiliation(s)
- Miriam De Boeck
- Department of Molecular Cell Biology and Centre for Biomedical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | | |
Collapse
|
12
|
Abstract
Ubiquitin-mediated protein degradation has been well demonstrated as a key regulatory mechanism in response to drought stress in Arabidopsis. However, the biological function of most E3 ligase genes in drought response is still unknown in rice. We recently showed that OsDIS1 (Oryza sativa drought-induced SINA protein 1), a SINA type E3 ligase, is involved in the drought-stress signal transduction in rice. OsDIS1 plays a negative role in drought stress tolerance through the transcriptional regulation of diverse stress-related genes and also possibly through the posttranslational regulation of its interacting protein OsNek6 in rice. Here we also show that OsDIS1 interacts with OsSKIPa, a drought and salt stress positive regulator in rice. Based on these results, we propose a working model for the function of OsDIS1 in regulating the stress signaling pathway in rice.
Collapse
Affiliation(s)
- Yuese Ning
- State Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; Beijing, China
- State Key Laboratory of Plant Genomics; National Center for Plant Gene Research; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing, China
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha Hunan, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics; National Center for Plant Gene Research; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing, China
- Correspondence to: Qi Xie, or Guo-Liang Wang,
| | - Guo-Liang Wang
- State Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; Beijing, China
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha Hunan, China
- Department of Plant Pathology; Ohio State University; Columbus, OH USA
- Correspondence to: Qi Xie, or Guo-Liang Wang,
| |
Collapse
|
13
|
Marcsisin SR, Narute PS, Emert-Sedlak LA, Kloczewiak M, Smithgall TE, Engen JR. On the solution conformation and dynamics of the HIV-1 viral infectivity factor. J Mol Biol 2011; 410:1008-22. [PMID: 21763503 PMCID: PMC3139145 DOI: 10.1016/j.jmb.2011.04.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/20/2011] [Accepted: 04/21/2011] [Indexed: 02/07/2023]
Abstract
Human immunodeficiency virus-1 (HIV-1) has evolved a cunning mechanism to circumvent the antiviral activity of the APOBEC3 family of host cell enzymes. HIV-1 Vif [viral (also called virion) infectivity factor], one of several HIV accessory proteins, targets APOBEC3 proteins for proteasomal degradation and downregulates their expression at the mRNA level. Despite the importance of Vif for HIV-1 infection, there is little conformational data on Vif alone or in complex with other cellular factors due to incompatibilities with many structural techniques and difficulties in producing suitable quantities of the protein for biophysical analysis. As an alternative, we have turned to hydrogen exchange mass spectrometry (HX MS), a conformational analysis method that is well suited for proteins that are difficult to study using X-ray crystallography and/or NMR. HX MS was used to probe the solution conformation of recombinant full-length HIV-1 Vif. Vif specifically interacted with the previously identified binding partner Hck and was able to cause kinase activation, suggesting that the Vif studied by HX MS retained a biochemically competent conformation relevant to Hck interaction. HX MS analysis of Vif alone revealed low deuteration levels in the N-terminal portion, indicating that this region contained structured or otherwise protected elements. In contrast, high deuteration levels in the C-terminal portion of Vif indicated that this region was likely unstructured in the absence of cellular interacting proteins. Several regions within Vif displayed conformational heterogeneity in solution, including the APOBEC3G/F binding site and the HCCH zinc finger. Taken together, these HX MS results provide new insights into the solution conformation of Vif.
Collapse
Affiliation(s)
- Sean R. Marcsisin
- Department of Chemistry & Chemical Biology and the Barnett Institute of Chemical & Biological Analysis, Northeastern University, Boston, MA 02115, USA
| | - Purushottam S. Narute
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John R. Engen
- Department of Chemistry & Chemical Biology and the Barnett Institute of Chemical & Biological Analysis, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
14
|
Affiliation(s)
- Kedra Cyrus
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| | - Marie Wehenkel
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| | - Eun-Young Choi
- Department of Molecular and Biomedical Pharmacology University of Kentucky 800 Rose Street, Lexington, KY 40536, USA
| | - Hollie Swanson
- Department of Molecular and Biomedical Pharmacology University of Kentucky 800 Rose Street, Lexington, KY 40536, USA
| | - Kyung-Bo Kim
- Department of Pharmaceutical Sciences University of Kentucky 789 South Limestone, Lexington, KY 40536-0596, USA
| |
Collapse
|
15
|
Mukoko Bopopi J, Vandeputte OM, Himanen K, Mol A, Vaessen Q, El Jaziri M, Baucher M. Ectopic expression of PtaRHE1, encoding a poplar RING-H2 protein with E3 ligase activity, alters plant development and induces defence-related responses. J Exp Bot 2010; 61:297-310. [PMID: 19892745 PMCID: PMC2791127 DOI: 10.1093/jxb/erp305] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/21/2009] [Accepted: 09/23/2009] [Indexed: 05/06/2023]
Abstract
RING (really interesting new gene)-H2 domain-containing proteins are widely represented in plants and play important roles in the regulation of many developmental processes as well as in plant-environment interactions. In the present report, experiments were performed to unravel the role of the poplar gene PtaRHE1, coding for a RING-H2 protein. In vitro ubiquitination assays indicate a functional E3 ligase activity for PtaRHE1 with the specific E2 ubiquitin-conjugating enzyme UbcH5a. The overexpression of PtaRHE1 in tobacco resulted in a pleiotropic phenotype characterized by a curling of the leaves, the formation of necrotic lesions on leaf blades, growth retardation, and a delay in floral transition. The plant gene expression response to PtaRHE1 overexpression provided evidence for the up-regulation of defence- and/or programmed cell death-related genes. Moreover, genes coding for WRKY transcription factors as well as for mitogen-activated protein kinases, such as wound-induced protein kinase (WIPK), were also found to be induced in the transgenic lines as compared with the wild type. In addition, histochemical beta-glucuronidase staining showed that the PtaRHE1 promoter is induced by plant pathogens and by elicitors such as salicylic acid and cellulase. Taken together, these results suggest that the E3 ligase PtaRHE1 plays a role in the ubiquitination-mediated regulation of defence response, possibly by acting upstream of WIPK and/or in the activation of WRKY factors.
Collapse
Affiliation(s)
- Johnny Mukoko Bopopi
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, 6041 Gosselies, Belgium
| | - Olivier M. Vandeputte
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, 6041 Gosselies, Belgium
| | - Kristiina Himanen
- Department of Plant Systems Biology, Flanders Institute for Biotechnology, Technologiepark 927, 9052 Gent, Belgium
| | - Adeline Mol
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, 6041 Gosselies, Belgium
| | - Quentin Vaessen
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, 6041 Gosselies, Belgium
| | - Mondher El Jaziri
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, 6041 Gosselies, Belgium
| | - Marie Baucher
- Laboratoire de Biotechnologie Végétale, Université Libre de Bruxelles, rue Adrienne Bolland 8, 6041 Gosselies, Belgium
| |
Collapse
|
16
|
Sun H, Leverson JD, Hunter T. Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins. EMBO J 2007; 26:4102-12. [PMID: 17762864 PMCID: PMC2230674 DOI: 10.1038/sj.emboj.7601839] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 08/02/2007] [Indexed: 12/31/2022] Open
Abstract
The function of small ubiquitin-like modifier (SUMO)-binding proteins is key to understanding how SUMOylation regulates cellular processes. We identified two related Schizosaccharomyces pombe proteins, Rfp1 and Rfp2, each having an N-terminal SUMO-interacting motif (SIM) and a C-terminal RING-finger domain. Genetic analysis shows that Rfp1 and Rfp2 have redundant functions; together, they are essential for cell growth and genome stability. Mammalian RNF4, an active ubiquitin E3 ligase, is an orthologue of Rfp1/Rfp2. Rfp1 and Rfp2 lack E3 activity but recruit Slx8, an active RING-finger ubiquitin ligase, through a RING-RING interaction, to form a functional E3. RNF4 complements the growth and genomic stability defects of rfp1rfp2, slx8, and rfp1rfp2slx8 mutant cells. Both the Rfp-Slx8 complex and RNF4 specifically ubiquitylate artificial SUMO-containing substrates in vitro in a SUMO binding-dependent manner. SUMOylated proteins accumulate in rfp1rfp2 double-null cells, suggesting that Rfp/Slx8 proteins may promote ubiquitin-dependent degradation of SUMOylated targets. Hence, we describe a family of SIM-containing RING-finger proteins that potentially regulates eukaryotic genome stability through linking SUMO-interaction with ubiquitin conjugation.
Collapse
Affiliation(s)
- Huaiyu Sun
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joel D Leverson
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| |
Collapse
|
17
|
Abstract
BACKGROUND The covalent attachment of ubiquitin to a substrate protein changes its fate. Notably, proteins typically tagged with a lysine48-linked polyubiquitin chain become substrates for degradation by the 26S proteasome. In recent years many experiments have been performed to characterize the proteins involved in the ubiquitylation process and to identify their substrates, in order to understand better the mechanisms that link specific protein degradation events to regulation of plant growth and development. SCOPE This review focuses on the role that ubiquitin plays in hormone synthesis, hormonal signalling cascades and plant defence mechanisms. Several examples are given of how targeted degradation of proteins affects downstream transcriptional regulation of hormone-responsive genes in the auxin, gibberellin, abscisic acid, ethylene and jasmonate signalling pathways. Additional experiments suggest that ubiquitin-mediated proteolysis may also act upstream of the hormonal signalling cascades by regulating hormone biosynthesis, transport and perception. Moreover, several experiments demonstrate that hormonal cross-talk can occur at the level of proteolysis. The more recently established role of the ubiquitin/proteasome system (UPS) in defence against biotic threats is also reviewed. CONCLUSIONS The UPS has been implicated in the regulation of almost every developmental process in plants, from embryogenesis to floral organ production probably through its central role in many hormone pathways. More recent evidence provides molecular mechanisms for hormonal cross-talk and links the UPS system to biotic defence responses.
Collapse
Affiliation(s)
- Kate Dreher
- Section of Molecular and Cellular Biology, Plant Biology Graduate Group Program, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
| | | |
Collapse
|
18
|
Silke J, Kratina T, Chu D, Ekert PG, Day CL, Pakusch M, Huang DCS, Vaux DL. Determination of cell survival by RING-mediated regulation of inhibitor of apoptosis (IAP) protein abundance. Proc Natl Acad Sci U S A 2005; 102:16182-7. [PMID: 16263936 PMCID: PMC1283416 DOI: 10.1073/pnas.0502828102] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Indexed: 11/18/2022] Open
Abstract
Inhibitor of apoptosis (IAP) proteins, which bind to caspases via their baculoviral IAP repeat domains, also bear RING domains that enable them to promote ubiquitylation of themselves and other interacting proteins. Here we show that the RING domain of cIAP1 allows it to bind directly to the RING of X-linked IAP, causing its ubiquitylation and degradation by the proteasome, thus revealing a mechanism by which IAPs can regulate their abundance. Expression of a construct containing the RING of cellular IAP1 was able to deplete melanoma cells of endogenous X-linked IAP, promoted apoptosis, and also markedly reduced their clonogenicity when treated with cisplatin. Cross control of protein levels by RING domains may therefore enable their levels to be manipulated therapeutically.
Collapse
Affiliation(s)
- John Silke
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3050, Australia.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
RAG1 and RAG2 initiate V(D)J recombination, which is the assembly of immunoglobulin and T cell receptor genes. The N-terminal region of RAG1 can be deleted, leaving an enzymatic "core" able to catalyze the complete reaction. Here we report that the N-terminal portion of RAG1 has a distinct enzymatic role separate from the rest of the protein. It acts as an E3 ligase in the ubiquitylation of a test substrate and formation of polyubiquitin chains in vitro. This finding suggests a new way in which V(D)J recombination can be regulated and coupled to other aspects of cell physiology.
Collapse
Affiliation(s)
- Vyacheslav Yurchenko
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | |
Collapse
|