1
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Morgenstern TJ, Darko-Boateng A, Afriyie E, Shanmugam SK, Zhou X, Choudhury P, Desai M, Kass RS, Clarke OB, Colecraft HM. Ion channel inhibition by targeted recruitment of NEDD4-2 with divalent nanobodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596281. [PMID: 38854018 PMCID: PMC11160594 DOI: 10.1101/2024.05.28.596281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Targeted recruitment of E3 ubiquitin ligases to degrade traditionally undruggable proteins is a disruptive paradigm for developing new therapeutics. Two salient limitations are that <2% of the ~600 E3 ligases in the human genome have been exploited to produce proteolysis targeting chimeras (PROTACs), and the efficacy of the approach has not been demonstrated for a vital class of complex multi-subunit membrane proteins- ion channels. NEDD4-1 and NEDD4-2 are physiological regulators of myriad ion channels, and belong to the 28-member HECT (homologous to E6AP C-terminus) family of E3 ligases with widespread roles in cell/developmental biology and diverse diseases including various cancers, immunological and neurological disorders, and chronic pain. The potential efficacy of HECT E3 ligases for targeted protein degradation is unexplored, constrained by a lack of appropriate binders, and uncertain due to their complex regulation by layered intra-molecular and posttranslational mechanisms. Here, we identified a nanobody that binds with high affinity and specificity to a unique site on the N-lobe of the NEDD4-2 HECT domain at a location physically separate from sites critical for catalysis- the E2 binding site, the catalytic cysteine, and the ubiquitin exosite- as revealed by a 3.1 Å cryo-electron microscopy reconstruction. Recruiting endogenous NEDD4-2 to diverse ion channel proteins (KCNQ1, ENaC, and CaV2.2) using a divalent (DiVa) nanobody format strongly reduced their functional expression with minimal off-target effects as assessed by global proteomics, compared to simple NEDD4-2 overexpression. The results establish utility of a HECT E3 ligase for targeted protein downregulation, validate a class of complex multi-subunit membrane proteins as susceptible to this modality, and introduce endogenous E3 ligase recruitment with DiVa nanobodies as a general method to generate novel genetically-encoded ion channel inhibitors.
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Affiliation(s)
- Travis J. Morgenstern
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY
| | - Arden Darko-Boateng
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
| | - Emmanuel Afriyie
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
| | - Sri Karthika Shanmugam
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
| | - Xinle Zhou
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY
| | - Papiya Choudhury
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
| | | | - Robert S. Kass
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY
| | - Oliver B. Clarke
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY
| | - Henry M. Colecraft
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY
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2
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Wright KM, Nathan S, Jiang H, Xia W, Kim H, Chakouri N, Nwafor JN, Fossier L, Srinivasan L, Chen Z, Boronina T, Post J, Paul S, Cole RN, Ben-Johny M, Cole PA, Gabelli SB. NEDD4L intramolecular interactions regulate its auto and substrate Na V1.5 ubiquitination. J Biol Chem 2024; 300:105715. [PMID: 38309503 PMCID: PMC10933555 DOI: 10.1016/j.jbc.2024.105715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/05/2024] Open
Abstract
NEDD4L is a HECT-type E3 ligase that catalyzes the addition of ubiquitin to intracellular substrates such as the cardiac voltage-gated sodium channel, NaV1.5. The intramolecular interactions of NEDD4L regulate its enzymatic activity which is essential for proteostasis. For NaV1.5, this process is critical as alterations in Na+ current is involved in cardiac diseases including arrhythmias and heart failure. In this study, we perform extensive biochemical and functional analyses that implicate the C2 domain and the first WW-linker (1,2-linker) in the autoregulatory mechanism of NEDD4L. Through in vitro and electrophysiological experiments, the NEDD4L 1,2-linker was determined to be important in substrate ubiquitination of NaV1.5. We establish the preferred sites of ubiquitination of NEDD4L to be in the second WW-linker (2,3-linker). Interestingly, NEDD4L ubiquitinates the cytoplasmic linker between the first and second transmembrane domains of the channel (DI-DII) of NaV1.5. Moreover, we design a genetically encoded modulator of Nav1.5 that achieves Na+ current reduction using the NEDD4L HECT domain as cargo of a NaV1.5-binding nanobody. These investigations elucidate the mechanisms regulating the NEDD4 family and furnish a new molecular framework for understanding NaV1.5 ubiquitination.
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Affiliation(s)
- Katharine M Wright
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Sara Nathan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Wendy Xia
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - HyoJeon Kim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Nourdine Chakouri
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York, USA
| | - Justin N Nwafor
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Lucile Fossier
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York, USA
| | - Lakshmi Srinivasan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Zan Chen
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Tatiana Boronina
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeremy Post
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Suman Paul
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert N Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Manu Ben-Johny
- Department of Physiology and Cellular Biophysics, Columbia University, New York, New York, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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3
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Rotin D, Prag G. Physiological Functions of the Ubiquitin Ligases Nedd4-1 and Nedd4-2. Physiology (Bethesda) 2024; 39:18-29. [PMID: 37962894 DOI: 10.1152/physiol.00023.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/15/2023] Open
Abstract
The Nedd4 family of E3 ubiquitin ligases, consisting of a C2-WW(n)-HECT domain architecture, includes the closely related Nedd4/Nedd4-1 and Nedd4L/Nedd4-2, which play critical roles in human physiology and pathophysiology.This review focuses on the regulation of enzymatic activity of these Nedd4 proteins, as well as on their roles in regulating stability and function of membrane and other signaling proteins, such as ion channels, ion transporters, and growth factor receptors. The diseases caused by impairment of such regulation are discussed, as well as opportunities and challenges for targeting these enzymes for therapy.
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Affiliation(s)
- Daniela Rotin
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Biochemistry Department, University of Toronto, Ontario, Canada
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
- Sagol School of Neuroscience, Tel Aviv University, Israel
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4
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Kefalas G, Rotin D. Primate-specific isoform of Nedd4-1 regulates substrate binding via Ser/Thr phosphorylation and 14-3-3 binding. Sci Rep 2023; 13:17903. [PMID: 37863970 PMCID: PMC10589272 DOI: 10.1038/s41598-023-44761-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023] Open
Abstract
Nedd4 (Nedd4-1) is an E3 ubiquitin ligase involved in crucial biological processes such as growth factor receptor signaling. While canonical Nedd4-1 comprises a C2-WW(4)-HECT domain architecture, alternative splicing produces non-canonical isoforms that are poorly characterized. Here we characterized Nedd4-1(NE), a primate-specific isoform of Nedd4-1 that contains a large N-terminal Extension (NE) that replaces most of the C2 domain. We show that Nedd4-1(NE) mRNA is ubiquitously expressed in human tissues and cell lines. Moreover, we found that Nedd4-1(NE) is more active than the canonical Nedd4-1 isoform, likely due to the absence of a C2 domain-mediated autoinhibitory mechanism. Additionally, we identified two Thr/Ser phosphoresidues in the NE region that act as binding sites for 14-3-3 proteins, and show that phosphorylation on these sites reduces substrate binding. Finally, we show that the NE region can act as a binding site for the RPB2 subunit of RNA polymerase II, a unique substrate of Nedd4-1(NE) but not the canonical Nedd4-1. Taken together, our results demonstrate that alternative splicing of the ubiquitin ligase Nedd4-1 can produce isoforms that differ in their catalytic activity, binding partners and substrates, and mechanisms of regulation.
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Affiliation(s)
- George Kefalas
- Cell Biology Program, the Hospital for Sick Children, PGCRL 19-9715, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Biochemistry Department, University of Toronto, Toronto, ON, M5G 0A4, Canada
| | - Daniela Rotin
- Cell Biology Program, the Hospital for Sick Children, PGCRL 19-9715, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
- Biochemistry Department, University of Toronto, Toronto, ON, M5G 0A4, Canada.
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5
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Cheng F, Dou J, Yang Y, Sun S, Chen R, Zhang Z, Wei H, Li J, Wu Z. Drug-induced lactate confers ferroptosis resistance via p38-SGK1-NEDD4L-dependent upregulation of GPX4 in NSCLC cells. Cell Death Discov 2023; 9:165. [PMID: 37188685 DOI: 10.1038/s41420-023-01463-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
Ferroptosis is a newly defined non-apoptotic programmed cell death resulting from the accumulation of lipid peroxides. Whether ferroptosis plays any role in chemotherapy remains to be established. Here, we reported that ferroptosis represents a part of the chemotherapeutic drug etoposide-induced cell death response in Small Cell Lung Cancer (SCLC) cells and adaptive signaling molecule lactate protects Non-Small Cell Lung Cancer (NSCLC) from etoposide-induced ferroptosis. Lactate derived from metabolic reprogramming increases the expression of glutathione peroxidase 4 (GPX4) to promote ferroptosis resistance in NSCLC. Furthermore, we identified E3-ubiquitin ligase NEDD4L as a major regulator of GPX4 stability. Mechanistically, Lactate increases mitochondrial ROS generation and drives activation of the p38-SGK1 pathway, which attenuates the interaction of NEDD4L with GPX4 and subsequent ubiquitination and degradation of GPX4. Our data implicated the role of ferroptosis in chemotherapeutic resistance and identified a novel post-translational regulatory mechanism for the key Ferroptosis mediator GPX4.
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Affiliation(s)
- Feng Cheng
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
| | - Jintao Dou
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- School of Anesthesiology, Wannan Medical College, 241001, Wuhu, China
| | - Yi Yang
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- School of Pharmacy, Wannan Medical College, 241001, Wuhu, China
| | - Shaojie Sun
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- School of Medical Imageology, Wannan Medical College, 241001, Wuhu, China
| | - Ruiqi Chen
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- School of Stomatology, Wannan Medical College, 241001, Wuhu, China
| | - Zhijian Zhang
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, 241001, Wuhu, China
| | - Huijun Wei
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- Anhui Province Key laboratory of Active Biological Macro-molecules Research, Wannan Medical College, 241001, Wuhu, China
- Provincial Engineering Laboratory for Screening and Re-evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Wannan Medical College, 241001, Wuhu, China
| | - Jianhui Li
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China
- School of Stomatology, Wannan Medical College, 241001, Wuhu, China
| | - Zhihao Wu
- Research laboratory of Tumor Microenvironment, Wannan Medical College, 241001, Wuhu, China.
- Provincial Engineering Laboratory for Screening and Re-evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Wannan Medical College, 241001, Wuhu, China.
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, 241001, Wuhu, China.
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6
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Liu J, Hu J, Duan Y, Qin R, Guo C, Zhou H, Liu H, Liu C. Genetic analysis of periventricular nodular heterotopia 7 caused by a novel NEDD4L missense mutation: Case and literature summary. Mol Genet Genomic Med 2023:e2169. [PMID: 36934385 DOI: 10.1002/mgg3.2169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/01/2023] [Accepted: 03/01/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders associated with periventricular nodular heterotopia (PVNH) are characterized by phenotypic and genetic heterogeneity. NEDD4L mutation can lead to PVNH7. However, at present, only eight NEDD4L pathogenic variants have been identified across 15 cases of PVNH7 worldwide. Given this dearth of evidence, the precise correlations between genetic pathogenesis and phenotypes remain to be determined. METHODS This report discusses the case of a 19-month-old male child with cleft palate, seizures, psychomotor retardation, and hypotonia, for whom we verified the genetic etiology using Trio-whole-exome and Sanger sequencing to analyze the potential pathogenicity of the mutant protein structure. Mutant plasmids were constructed for in vitro analyses. After transfection into human 293 T cells, the mutant transcription process was analyzed using real-time PCR (RT-PCR), and levels of mutant protein expression were examined using western blotting (WB) and immunofluorescence (IF) experiments. RESULTS Genetic analyses revealed a novel missense mutation Gln900Arg, located in the homologous to E6-APC terminal (HECT) domain of NEDD4L and that the parents were wild-type, suggestive of a de novo mutation. The variant was predicted to be pathogenic by bioinformatics software, which also suggested alterations in the structural stability of the mutant protein. RT-PCR results indicated that the mutation did not affect mRNA expression, whereas WB and IF results indicated that the level of mutant protein was significantly reduced by 41.07%. CONCLUSION Functional experiments demonstrated that Gln900Arg probably did not lead to transcriptional abnormalities in this patient, instead leading to increased ubiquitination activity owing to the constitutive activation of the HECT domain, thereby promoting protein degradation. Extensive clinical reports should be generated for patients presenting with PVNH and/or polymicrogyria, developmental delay, syndactyly, and hypotonia to increase the pool of evidence related to NEDD4L.
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Affiliation(s)
- Juan Liu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Jihong Hu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Yaqing Duan
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Rong Qin
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Chunguang Guo
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Hongtao Zhou
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Hua Liu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
| | - Chunlei Liu
- Department of Rehabilitation, Hunan Children's Hospital, Changsha, China
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7
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Elevated intracellular Na + and osmolarity stimulate catalytic activity of the ubiquitin ligase Nedd4-2. Proc Natl Acad Sci U S A 2022; 119:e2122495119. [PMID: 35858421 PMCID: PMC9335340 DOI: 10.1073/pnas.2122495119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Regulation of catalytic activity of E3 ubiquitin ligases is critical for their cellular functions. We identified an unexpected mode of regulation of E3 catalytic activity by ions and osmolarity; enzymatic activity of the HECT family E3 Nedd4-2/Nedd4L is enhanced by increased intracellular Na+ ([Na+]i) and by hyperosmolarity. This stimulated activity is mediated by activation of p38-MAPK and is inhibited by WNKs. Moreover, protease (Furin)-mediated activation of the epithelial Na+ channel ENaC (a bona fide Nedd4-2 substrate), which leads to increased [Na+]i and osmolarity, results in enhanced Nedd4-2 catalytic activity. This enhancement is inhibited by a Furin inhibitor, by a protease-resistant ENaC mutant, or by treatment with the ENaC inhibitor amiloride. Moreover, WNK inhibition, which stimulates catalytic activity of Nedd4-2, leads to reduced levels of cell-surface ENaC and reduced channel activity. ENaC activity does not affect Nedd4-2:ENaC binding. Therefore, these results demonstrate activation of a ubiquitin ligase by Na+ and osmotic changes. Importantly, they reveal a negative feedback loop in which active ENaC leads to stimulation of catalytic activity of its own suppressor, Nedd4-2, to protect cells from excessive Na+ loading and hyperosmotic stress and to protect the animal from hypertension.
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8
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The Role of NEDD4 E3 Ubiquitin–Protein Ligases in Parkinson’s Disease. Genes (Basel) 2022; 13:genes13030513. [PMID: 35328067 PMCID: PMC8950476 DOI: 10.3390/genes13030513] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/03/2022] [Indexed: 01/25/2023] Open
Abstract
Parkinson’s disease (PD) is a debilitating neurodegenerative disease that causes a great clinical burden. However, its exact molecular pathologies are not fully understood. Whilst there are a number of avenues for research into slowing, halting, or reversing PD, one central idea is to enhance the clearance of the proposed aetiological protein, oligomeric α-synuclein. Oligomeric α-synuclein is the main constituent protein in Lewy bodies and neurites and is considered neurotoxic. Multiple E3 ubiquitin-protein ligases, including the NEDD4 (neural precursor cell expressed developmentally downregulated protein 4) family, parkin, SIAH (mammalian homologues of Drosophila seven in absentia), CHIP (carboxy-terminus of Hsc70 interacting protein), and SCFFXBL5 SCF ubiquitin ligase assembled by the S-phase kinase-associated protein (SKP1), cullin-1 (Cul1), a zinc-binding RING finger protein, and the F-box domain/Leucine-rich repeat protein 5-containing protein FBXL5), have been shown to be able to ubiquitinate α-synuclein, influencing its subsequent degradation via the proteasome or lysosome. Here, we explore the link between NEDD4 ligases and PD, which is not only via α-synuclein but further strengthened by several additional substrates and interaction partners. Some members of the NEDD4 family of ligases are thought to crosstalk even with PD-related genes and proteins found to be mutated in familial forms of PD. Mutations in NEDD4 family genes have not been observed in PD patients, most likely because of their essential survival function during development. Following further in vivo studies, it has been thought that NEDD4 ligases may be viable therapeutic targets in PD. NEDD4 family members could clear toxic proteins, enhancing cell survival and slowing disease progression, or might diminish beneficial proteins, reducing cell survival and accelerating disease progression. Here, we review studies to date on the expression and function of NEDD4 ubiquitin ligases in the brain and their possible impact on PD pathology.
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9
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Liu R, Liu L, Bian Y, Zhang S, Wang Y, Chen H, Jiang X, Li G, Chen Q, Xue C, Li M, Liu L, Liu X, Ma S. The Dual Regulation Effects of ESR1/NEDD4L on SLC7A11 in Breast Cancer Under Ionizing Radiation. Front Cell Dev Biol 2022; 9:772380. [PMID: 35252218 PMCID: PMC8888677 DOI: 10.3389/fcell.2021.772380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Radiotherapy is one of the most important treatments for breast cancer. Ferroptosis is a recently recognized form of regulated cell death that is characterized by lipid peroxidation. However, whether ionizing radiation (IR) could induce ferroptosis in breast cancer and how it works remain unknown. Bioinformatics analysis were performed to screen ferroptosis-related genes differentially expressed in breast tumor tissue and normal tissue. Then, breast cancer cell lines with different estrogen receptor (ER) phenotypes were used for studies in vitro, including ER-positive (MCF-7 and ZR-75-1) and ER-negative (MDA-MB-231) cells. The dynamic changes of mRNA and protein levels were examined after x-ray of 8 Gy by qRT-PCR and Western blotting, respectively. Immunoprecipitation (IP) was used to explore the interaction between proteins. Luciferase assay was used to analyze the transcriptional regulation effect of ESR1 on SLC7A11. BODIPY C11 and trypan blue dyes were used to determine lipid peroxidation and cell death, respectively. The result showed that the ferroptosis-related gene SLC7A11 was higher in breast cancer tissues compared with normal tissues and associated with poor survival. A positive correlation exists between ESR1 and SLC7A11 expression. ESR1 promoted SLC7A11 expression at the early stage after IR. ESR1/SLC7A11 knockdown significantly enhanced IR-induced ferroptosis in ER-positive cells. At 12 h after IR, the IP data showed the interaction between E3 ubiquitin ligase NEDD4L and SLC7A11 increased, followed by the ubiquitylation and degradation of SLC7A11. Thus, SLC7A11 expression was regulated by both ESR1 and NEDD4L, in opposite ways. For the first time, we elucidated that ESR1 and NEDD4L functioned together after radiation treatment and finally induced ferroptosis in breast cancer cells, which provides novel insight into the guidance of clinical treatment of breast cancer.
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Affiliation(s)
- Rui Liu
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China
| | - Lin Liu
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Yan Bian
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Shinan Zhang
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Yue Wang
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Huajian Chen
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Xinyue Jiang
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Guanghui Li
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Qing Chen
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Chang Xue
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Mengke Li
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Lianchang Liu
- NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China.,The Second Affiliated Hospital of Jilin University, Changchun, China
| | - Xiaodong Liu
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
| | - Shumei Ma
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Radiobiology, School of Public Health of Jilin University, Changchun, China.,Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, China
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10
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Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. PLoS One 2021; 16:e0258315. [PMID: 34637467 PMCID: PMC8509885 DOI: 10.1371/journal.pone.0258315] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/23/2021] [Indexed: 01/07/2023] Open
Abstract
The Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand protein interactor recognition mechanisms across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we find that, on average, half of Nedd4 family interactions are likely PY-motif mediated. Further, we find that PPxY motifs are more prevalent than LPxY motifs and are more likely to occur in proline-rich regions and that PPxY regions are more disordered on average relative to LPxY-containing regions. Informed by consensus sequences for PY motifs across the Nedd4 interactome, we rationally designed a focused peptide library and employed a computational screen, revealing sequence- and biomolecular interaction-dependent determinants of WW-domain/PY-motif interactions. Cumulatively, our efforts provide a new bioinformatic tool and expand our understanding of sequence and structural factors that contribute to PY-motif mediated interactor recognition across the Nedd4 family.
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11
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Tril dampens Nodal signaling through Pellino2- and Traf6-mediated activation of Nedd4l. Proc Natl Acad Sci U S A 2021; 118:2104661118. [PMID: 34475212 DOI: 10.1073/pnas.2104661118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Toll-like receptor 4 (Tlr) interactor with leucine-rich repeats (Tril) functions as a Tlr coreceptor to mediate innate immunity in adults. In Xenopus embryos, Tril triggers degradation of the transforming growth factor β (Tgf-ß) family inhibitor, Smad7. This enhances bone morphogenetic protein (Bmp) signaling to enable ventral mesoderm to commit to a blood fate. Here, we show that Tril simultaneously dampens Nodal signaling by catalytically activating the ubiquitin ligase NEDD4 Like (Nedd4l). Nedd4l then targets Nodal receptors for degradation. How Tril signals are transduced in a nonimmune context is unknown. We identify the ubiquitin ligase Pellino2 as a protein that binds to the cytoplasmic tail of Tril and subsequently forms a complex with Nedd4l and another E3 ligase, TNF-receptor associated factor 6 (Traf6). Pellino2 and Traf6 are essential for catalytic activation of Nedd4l, both in Xenopus and in mammalian cells. Traf6 ubiquitinates Nedd4l, which is then recruited to membrane compartments where activation occurs. Collectively, our findings reveal that Tril initiates a noncanonical Tlr-like signaling cascade to activate Nedd4l, thereby coordinately regulating the Bmp and Nodal arms of the Tgf-ß superfamily during vertebrate development.
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12
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14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains. Commun Biol 2021; 4:899. [PMID: 34294877 PMCID: PMC8298602 DOI: 10.1038/s42003-021-02419-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
Neural precursor cell expressed developmentally down-regulated 4 ligase (Nedd4-2) is an E3 ubiquitin ligase that targets proteins for ubiquitination and endocytosis, thereby regulating numerous ion channels, membrane receptors and tumor suppressors. Nedd4-2 activity is regulated by autoinhibition, calcium binding, oxidative stress, substrate binding, phosphorylation and 14-3-3 protein binding. However, the structural basis of 14-3-3-mediated Nedd4-2 regulation remains poorly understood. Here, we combined several techniques of integrative structural biology to characterize Nedd4-2 and its complex with 14-3-3. We demonstrate that phosphorylated Ser342 and Ser448 are the key residues that facilitate 14-3-3 protein binding to Nedd4-2 and that 14-3-3 protein binding induces a structural rearrangement of Nedd4-2 by inhibiting interactions between its structured domains. Overall, our findings provide the structural glimpse into the 14-3-3-mediated Nedd4-2 regulation and highlight the potential of the Nedd4-2:14-3-3 complex as a pharmacological target for Nedd4-2-associated diseases such as hypertension, epilepsy, kidney disease and cancer. Pohl et al. investigated the structural basis of Nedd4-2 regulation by 14-3-3 and found that phosphorylated Ser342 and Ser448 are the main residues that facilitate 14-3-3 binding to Nedd4-2. The authors propose that the Nedd4-2:14-3-3 complex then stimulates a structural rearrangement of Nedd4-2 through inhibiting interaction of its structured domains.
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13
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Rheinemann L, Thompson T, Mercenne G, Paine EL, Peterson FC, Volkman BF, Alam SL, Alian A, Sundquist WI. Interactions between AMOT PPxY motifs and NEDD4L WW domains function in HIV-1 release. J Biol Chem 2021; 297:100975. [PMID: 34284061 PMCID: PMC8368996 DOI: 10.1016/j.jbc.2021.100975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/23/2021] [Accepted: 07/15/2021] [Indexed: 12/03/2022] Open
Abstract
Like most enveloped viruses, HIV must acquire a lipid membrane as it assembles and buds through the plasma membrane of infected cells to spread infection. Several sets of host cell machinery facilitate this process, including proteins of the endosomal sorting complexes required for transport pathway, which mediates the membrane fission reaction required to complete viral budding, as well as angiomotin (AMOT) and NEDD4L, which bind one another and promote virion membrane envelopment. AMOT and NEDD4L interact through the four NEDD4L WW domains and three different AMOT Pro-Pro-x (any amino acid)-Tyr (PPxY) motifs, but these interactions are not yet well defined. Here, we report that individual AMOT PPxY and NEDD4L WW domains interact with the following general affinity hierarchies: AMOT PPxY1>PPxY2>PPxY3 and NEDD4L WW3>WW2>WW1∼WW4. The unusually high-affinity of the AMOT PPxY1–NEDD4L WW3 interaction accounts for most of the AMOT–NEDD4L binding and is critical for stimulating HIV-1 release. Comparative structural, binding, and virological analyses reveal that complementary ionic and hydrophobic contacts on both sides of the WW–PPxY core interaction account for the unusually high affinity of the AMOT PPxY1–NEDD4L WW3 interaction. Taken together, our studies reveal how the first AMOT PPxY1 motif binds the third NEDD4L WW domain to stimulate HIV-1 viral envelopment and promote infectivity.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Tuscan Thompson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Gaelle Mercenne
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Elliott L Paine
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Steven L Alam
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Akram Alian
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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14
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Wei Y, Li W. Calcium, an Emerging Intracellular Messenger for the Hippo Pathway Regulation. Front Cell Dev Biol 2021; 9:694828. [PMID: 34268313 PMCID: PMC8275986 DOI: 10.3389/fcell.2021.694828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/09/2021] [Indexed: 12/22/2022] Open
Abstract
The Hippo pathway is a conserved signaling network regulating organ development and tissue homeostasis. Dysfunction of this pathway may lead to various diseases, such as regeneration defect and cancer. Studies over the past decade have found various extracellular and intracellular signals that can regulate this pathway. Among them, calcium (Ca2+) is emerging as a potential messenger that can transduce certain signals, such as the mechanical cue, to the main signaling machinery. In this process, rearrangement of the actin cytoskeleton, such as calcium-activated actin reset (CaAR), may construct actin filaments at the cell cortex or other subcellular domains that provide a scaffold to launch Hippo pathway activators. This article will review studies demonstrating Ca2+-mediated Hippo pathway modulation and discuss its implication in understanding the role of actin cytoskeleton in regulating the Hippo pathway.
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Affiliation(s)
- Yiju Wei
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, United States
| | - Wei Li
- Division of Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, United States.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, United States
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15
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The Role of HECT-Type E3 Ligase in the Development of Cardiac Disease. Int J Mol Sci 2021; 22:ijms22116065. [PMID: 34199773 PMCID: PMC8199989 DOI: 10.3390/ijms22116065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Despite advances in medicine, cardiac disease remains an increasing health problem associated with a high mortality rate. Maladaptive cardiac remodeling, such as cardiac hypertrophy and fibrosis, is a risk factor for heart failure; therefore, it is critical to identify new therapeutic targets. Failing heart is reported to be associated with hyper-ubiquitylation and impairment of the ubiquitin–proteasome system, indicating an importance of ubiquitylation in the development of cardiac disease. Ubiquitylation is a post-translational modification that plays a pivotal role in protein function and degradation. In 1995, homologous to E6AP C-terminus (HECT) type E3 ligases were discovered. E3 ligases are key enzymes in ubiquitylation and are classified into three families: really interesting new genes (RING), HECT, and RING-between-RINGs (RBRs). Moreover, 28 HECT-type E3 ligases have been identified in human beings. It is well conserved in evolution and is characterized by the direct attachment of ubiquitin to substrates. HECT-type E3 ligase is reported to be involved in a wide range of human diseases and health. The role of HECT-type E3 ligases in the development of cardiac diseases has been uncovered in the last decade. There are only a few review articles summarizing recent advancements regarding HECT-type E3 ligase in the field of cardiac disease. This study focused on cardiac remodeling and described the role of HECT-type E3 ligases in the development of cardiac disease. Moreover, this study revealed that the current knowledge could be exploited for the development of new clinical therapies.
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16
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Gao P, Ma X, Yuan M, Yi Y, Liu G, Wen M, Jiang W, Ji R, Zhu L, Tang Z, Yu Q, Xu J, Yang R, Xia S, Yang M, Pan J, Yuan H, An H. E3 ligase Nedd4l promotes antiviral innate immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3. Nat Commun 2021; 12:1194. [PMID: 33608556 PMCID: PMC7895832 DOI: 10.1038/s41467-021-21456-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
Ubiquitination is one of the most prevalent protein posttranslational modifications. Here, we show that E3 ligase Nedd4l positively regulates antiviral immunity by catalyzing K29-linked cysteine ubiquitination of TRAF3. Deficiency of Nedd4l significantly impairs type I interferon and proinflammatory cytokine production induced by virus infection both in vitro and in vivo. Nedd4l deficiency inhibits virus-induced ubiquitination of TRAF3, the binding between TRAF3 and TBK1, and subsequent phosphorylation of TBK1 and IRF3. Nedd4l directly interacts with TRAF3 and catalyzes K29-linked ubiquitination of Cys56 and Cys124, two cysteines that constitute zinc fingers, resulting in enhanced association between TRAF3 and E3 ligases, cIAP1/2 and HECTD3, and also increased K48/K63-linked ubiquitination of TRAF3. Mutation of Cys56 and Cys124 diminishes Nedd4l-catalyzed K29-linked ubiquitination, but enhances association between TRAF3 and the E3 ligases, supporting Nedd4l promotes type I interferon production in response to virus by catalyzing ubiquitination of the cysteines in TRAF3.
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Affiliation(s)
- Peng Gao
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Xianwei Ma
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Ming Yuan
- Immunology Department & National Key Laboratory of Medical Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Yulan Yi
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Guoke Liu
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Mingyue Wen
- Immunology Department & National Key Laboratory of Medical Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Wei Jiang
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Ruihua Ji
- Department of Anesthesiology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Lingxi Zhu
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Zhen Tang
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Qingzhuo Yu
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Jing Xu
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China
| | - Rui Yang
- Department of Anesthesiology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Sheng Xia
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Mingjin Yang
- Immunology Department & National Key Laboratory of Medical Immunology, Second Military Medical University, Shanghai, 200433, China
| | - Jianping Pan
- Department of Clinical Medicine, Zhejiang University City College School of Medicine, Hangzhou, 310015, China
| | - Hongbin Yuan
- Department of Anesthesiology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China.
| | - Huazhang An
- Clinical Cancer Institute, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China.
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17
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Adaptors as the regulators of HECT ubiquitin ligases. Cell Death Differ 2021; 28:455-472. [PMID: 33402750 DOI: 10.1038/s41418-020-00707-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022] Open
Abstract
The HECT (homologous to E6AP C-terminus) ubiquitin ligases (E3s) are a small family of highly conserved enzymes involved in diverse cellular functions and pathological conditions. Characterised by a C-terminal HECT domain that accepts ubiquitin from E2 ubiquitin conjugating enzymes, these E3s regulate key signalling pathways. The activity and functional regulation of HECT E3s are controlled by several factors including post-translational modifications, inter- and intramolecular interactions and binding of co-activators and adaptor proteins. In this review, we focus on the regulation of HECT E3s by accessory proteins or adaptors and discuss various ways by which adaptors mediate their regulatory roles to affect physiological outcomes. We discuss common features that are conserved from yeast to mammals, regardless of the type of E3s as well as shed light on recent discoveries explaining some existing enigmas in the field.
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18
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Hughes JR, Parsons JL. The E3 Ubiquitin Ligase NEDD4L Targets OGG1 for Ubiquitylation and Modulates the Cellular DNA Damage Response. Front Cell Dev Biol 2020; 8:607060. [PMID: 33282879 PMCID: PMC7688902 DOI: 10.3389/fcell.2020.607060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/23/2020] [Indexed: 11/23/2022] Open
Abstract
8-Oxoguanine DNA glycosylase (OGG1) is the major cellular enzyme required for the excision of 8-oxoguanine DNA base lesions in DNA through the base excision repair (BER) pathway, and therefore plays a major role in suppressing mutagenesis and in controlling genome stability. However, the mechanism of regulation of cellular OGG1 protein, particularly in response to oxidative stress, is unclear. We have purified the major E3 ubiquitin ligase responsible for OGG1 ubiquitylation from human cell extracts, and identify this as E3 ubiquitin-protein ligase NEDD4-like (NEDD4L). We demonstrate that recombinant NEDD4L stimulates ubiquitylation of OGG1 in vitro, particularly on lysine 341, and that NEDD4L and OGG1 interact in U2OS cells. Depletion of NEDD4L in U2OS cells has no impact on the stability and steady-state protein levels of OGG1, however, OGG1 stability is enhanced in response to oxidative stress induced by ionizing radiation. Furthermore, ubiquitylation of OGG1 by NEDD4L in vitro inhibits its DNA glycosylase/lyase activity. As a consequence of prolonged OGG1 stability and increased excision activity in the absence of NEDD4L, cells display increased DNA repair capacity but conversely that this decreases cell survival post-irradiation. This effect can be reproduced following OGG1 overexpression, suggesting that dysregulation of OGG1 increases the formation of lethal intermediate DNA lesions. Our study therefore highlights the importance of balancing OGG1 protein levels and BER capacity in maintaining genome stability.
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Affiliation(s)
- Jonathan R Hughes
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jason L Parsons
- Cancer Research Centre, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.,Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, United Kingdom
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19
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Yang H, Zhu J, Wang G, Liu H, Zhou Y, Qian J. STK35 Is Ubiquitinated by NEDD4L and Promotes Glycolysis and Inhibits Apoptosis Through Regulating the AKT Signaling Pathway, Influencing Chemoresistance of Colorectal Cancer. Front Cell Dev Biol 2020; 8:582695. [PMID: 33117809 PMCID: PMC7578231 DOI: 10.3389/fcell.2020.582695] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The development of colorectal cancer (CRC) is often sporadic, but its etiology is multifactorial. Chemoresistance of CRC leads to tumor recurrence and poor prognosis in patients. The phosphorylation of protein kinase B (AKT) can activate metabolic reprogramming toward cellular glycolysis. Serine/threonine kinase 35 (STK35) regulates the cell cycle and is frequently associated with cancer progression, whereas little is known about its specific roles in CRC. In the current study, bioinformatics analyses were performed to investigate the relationship between STK35 and CRC prognosis. STK35 knockdown and overexpressing CRC cells were established to examine its functions in CRC. Fluorouracil (5-FU) was utilized to evaluate the effect of STK35 on CRC chemoresistance. Moreover, co-immunoprecipitation was performed to explore the ubiquitination of STK35. STK35 was highly expressed in CRC, and its protein expression was negatively correlated with the survival of CRC patients. Furthermore, STK35 overexpression could promote glycolysis, suppress apoptosis, upregulate p-AKT, and counteract the antitumor functions of 5-FU and neural precursor cell expressed developmentally downregulated gene 4-like (NEDD4L) in CRC cells. NEDD4L was associated with and could ubiquitinate STK35. STK35 could be a prognostic biomarker for CRC prognosis and has promotive effects on CRC cellular activities, partially through the AKT pathway. Moreover, STK35 also interferes with the chemosensitivity of CRC.
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Affiliation(s)
- Haojun Yang
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jie Zhu
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Guangyao Wang
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Hanyang Liu
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yan Zhou
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jun Qian
- Department of Gastrointestinal Center, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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20
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LeBlanc N, Mallette E, Zhang W. Targeted modulation of E3 ligases using engineered ubiquitin variants. FEBS J 2020; 288:2143-2165. [PMID: 32867007 DOI: 10.1111/febs.15536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitination plays an essential role in signal transduction to regulate most if not all cellular processes. Among the enzymes that are involved in the ubiquitin (Ub) signaling cascade, tremendous efforts have been focused on elucidating the roles of E3 Ub ligases as they determine the complexity and specificity of ubiquitination. Not surprisingly, the malfunction of E3 ligases is directly implicated in many human diseases, including cancer. Therefore, there is an urgent need to develop potent and specific molecules to modulate E3 ligase activity as intracellular probes for target validation and as pharmacological agents in preclinical research. Unfortunately, the progress has been hampered by the dynamic regulation mechanisms for different types of E3 ligases. Here, we summarize the progress of using protein engineering to develop Ub variant (UbV) inhibitors for all major families of E3 ligases and UbV activators for homologous with E6-associated protein C terminus E3s and homodimeric RING E3s. We believe that this provides a general strategy and a valuable toolkit for the research community to inhibit or activate E3 ligases and these synthetic molecules have important implications in exploring protein degradation for drug discovery.
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Affiliation(s)
- Nicole LeBlanc
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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21
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Hatstat AK, McCafferty DG. Robust and facile purification of full-length, untagged human Nedd4 as a recombinant protein from Escherichia coli. Protein Expr Purif 2020; 173:105649. [PMID: 32334140 DOI: 10.1016/j.pep.2020.105649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/07/2020] [Accepted: 04/19/2020] [Indexed: 12/20/2022]
Abstract
Nedd4 is an E3 ubiquitin ligase that has received increased attention due to its role in the maintenance of proteostasis and in cellular stress responses. Investigation of Nedd4 enzymology has revealed a complex enzymatic mechanism that involves intermolecular interactions with upstream E2 conjugating enzymes and with substrates and intramolecular interactions that serve to regulate Nedd4 function. Thus, it is imperative that investigations of Nedd4 enzymology that employ recombinant enzyme be conducted with Nedd4 in its native, untagged form. We report herein an optimized, facile method for purification of recombinant human Nedd4 in its full-length form as a stable and active recombinant enzyme. Specifically, Nedd4 can be purified through a two-step purification which employs glutathione-S-transferase and hexahistidine sequences as orthogonal affinity tags. Proteolytic cleavage of Nedd4 was optimized to enable removal of the affinity tags with TEV protease, providing access to the untagged enzyme in yields of 2-3 mg/L. Additionally, investigation of Nedd4 storage conditions reveal that the enzyme is not stable through freeze-thaw cycles, and storage conditions should be carefully considered for preservation of enzyme stability. Finally, Nedd4 activity was validated through three activity assays which measure ubiquitin chain formation, Nedd4 autoubiquitination, and monoubiquitin consumption, respectively. Comparison of the method described herein with previously reported purification methods reveal that our optimized purification strategy enables access to Nedd4 in fewer chromatographic steps and eliminates reagents and materials that are potentially cost-prohibitive. This method, therefore, is more efficient and provides a more accessible route for purifying recombinant full-length Nedd4.
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Affiliation(s)
| | - Dewey G McCafferty
- Department of Chemistry, Duke University, Durham, NC, 27708, United States; Department of Biochemistry, Duke University, Durham, NC, 27708, United States.
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22
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A Tyrosine Switch on NEDD4-2 E3 Ligase Transmits GPCR Inflammatory Signaling. Cell Rep 2019; 24:3312-3323.e5. [PMID: 30232011 PMCID: PMC6226018 DOI: 10.1016/j.celrep.2018.08.061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/05/2018] [Accepted: 08/21/2018] [Indexed: 02/03/2023] Open
Abstract
Ubiquitination is essential for protein degradation and signaling and pivotal to many physiological processes. Ubiquitination of a subset of G-protein-coupled receptors (GPCRs) by the E3 ligase NEDD4–2 is required for p38 activation, but how GPCRs activate NEDD4–2 to promote ubiquitinmediated signaling is not known. Here, we report that the GPCR protease-activated receptor-1 (PAR1) stimulates c-Src-mediated tyrosine phosphorylation and activation of NEDD4–2 to promote p38 signaling and endothelial barrier disruption. Using mass spectrometry, we identified a unique phosphorylated tyrosine (Y)-485 within the 2,3-linker peptide between WW domain 2 and 3 of NEDD4–2 in agonist-stimulated cells. Mutation of NEDD4–2 Y485 impaired E3 ligase activity and failed to rescue PAR1-stimulated p38 activation and endothelial barrier permeability. The purinergic P2Y1 receptor also required c-Src and NEDD4–2 tyrosine phosphorylation for p38 activation. These studies reveal a novel role for c-Src in GPCR-induced NEDD4–2 activation, which is critical for driving ubiquitin-mediated p38 inflammatory signaling. Grimsey et al. report that GPCRs stimulate activation of NEDD4–2 E3 ubiquitin ligase via c-Src to induce endothelial p38 inflammatory signaling. c-Src phosphorylates NEDD4–2 at tyrosine-485, releasing the autoinhibitory linker peptide that is critical for enhancing E3 ligase activity, and provides mechanistic insight of how GPCRs activate E3 ubiquitin ligases.
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23
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The many substrates and functions of NEDD4-1. Cell Death Dis 2019; 10:904. [PMID: 31787758 PMCID: PMC6885513 DOI: 10.1038/s41419-019-2142-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/24/2019] [Accepted: 11/12/2019] [Indexed: 01/08/2023]
Abstract
Tumorigenesis, tumor growth, and prognosis are highly related to gene alterations and post-translational modifications (PTMs). Ubiquitination is a critical PTM that governs practically all aspects of cellular function. An increasing number of studies show that E3 ubiquitin ligases (E3s) are important enzymes in the process of ubiquitination that primarily determine substrate specificity and thus need to be tightly controlled. Among E3s, neural precursor cell expressed developmentally downregulated 4-1 (NEDD4-1) has been shown to play a critical role in modulating the proliferation, migration, and invasion of cancer cells and the sensitivity of cancer cells to anticancer therapies via regulating multiple substrates. This review discusses some significant discoveries on NEDD4-1 substrates and the signaling pathways in which NEDD4-1 participates. In addition, we introduce the latest potential therapeutic strategies that inhibit or activate NEDD4-1 activity using small molecules. NEDD4-1 likely acts as a novel drug target or diagnostic marker in the battle against cancer.
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24
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Wang Z, Liu Z, Chen X, Li J, Yao W, Huang S, Gu A, Lei QY, Mao Y, Wen W. A multi-lock inhibitory mechanism for fine-tuning enzyme activities of the HECT family E3 ligases. Nat Commun 2019; 10:3162. [PMID: 31320636 PMCID: PMC6639328 DOI: 10.1038/s41467-019-11224-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
HECT E3 ligases control the degradation and functioning of numerous oncogenic/tumor-suppressive factors and signaling proteins, and their activities must be tightly regulated to prevent cancers and other diseases. Here we show that the Nedd4 family HECT E3 WWP1 adopts an autoinhibited state, in which its multiple WW domains sequester HECT using a multi-lock mechanism. Removing WW2 or WW34 led to a partial activation of WWP1. The structure of fully inhibited WWP1 reveals that many WWP1 mutations identified in cancer patients result in a partially active state with increased E3 ligase activity, and the WWP1 mutants likely promote cell migration by enhancement of ∆Np63α degradation. We further demonstrate that WWP2 and Itch utilize a highly similar multi-lock autoinhibition mechanism as that utilized by WWP1, whereas Nedd4/4 L and Smurf2 utilize a slightly variant version. Overall, these results reveal versatile autoinhibitory mechanisms that fine-tune the ligase activities of the HECT family enzymes. HECT type E3 ligases are key regulators of cell growth and proliferation. Here the authors present the crystal structures of the Nedd4 family E3 ligase WWP1 in a closed and semi-open state and in combination with mutagenesis experiments identify a multi-lock regulatory mechanism that allows the fine-tuning of activities of Nedd4 family E3 ligases.
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Affiliation(s)
- Zhen Wang
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ziheng Liu
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xing Chen
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jingyu Li
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Weiyi Yao
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shijing Huang
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Aihong Gu
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qun-Ying Lei
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Fudan University Shanghai Cancer Center and Cancer Metabolism Laboratory, Fudan University, Shanghai, 200032, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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25
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Burton JC, Grimsey NJ. Ubiquitination as a Key Regulator of Endosomal Signaling by GPCRs. Front Cell Dev Biol 2019; 7:43. [PMID: 30984758 PMCID: PMC6449645 DOI: 10.3389/fcell.2019.00043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of therapeutic targets for FDA approved drugs. Therefore, understanding the molecular regulation of their signaling pathways is of paramount importance. Similarly, the mitogen activated protein kinase (MAPK) p38 is a critical mediator of proinflammatory disease. Yet despite decades of intense investigation, therapeutically viable inhibitors have struggled to make it into the clinic. New studies describing the regulation and activation of a GPCR dependent atypical p38 signaling pathway represents a novel therapeutic avenue to the treatment of many proinflammatory disorders. These recent studies have defined how thrombin and ADP can induce Src dependent activation of the E3 ubiquitin ligase NEDD4-2. Src dependent phosphorylation of a 2,3-linker peptide releases NEDD4-2 auto-inhibition and triggers the induction of proinflammatory atypical p38 signaling from the endosome. Activation of the atypical p38 pathway requires the direct interaction between an adaptor protein TAB1 and p38, that bypasses the requirement for the classical MKK3/6 dependent activation of p38. Therefore, providing a mechanism to specifically block proinflammatory GPCR atypical p38 activation while leaving basic p38 activity intact. Critically, new studies demonstrated that disruption of the TAB1-p38 interface is a druggable target, that would enable the selective inhibition of proinflammatory p38 signaling and ischemic injury. Atypical p38 signaling is linked to multiple clinically relevant pathologies including inflammation, cardiotoxicity, myocardial ischemia and ischemia reperfusion injury. Therefore, GPCR induced endosomal p38 signaling represents a novel understudied branch of proinflammatory p38 signaling and an ideal potential therapeutic target that warrants further investigation.
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Affiliation(s)
- Jeremy C Burton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, United States
| | - Neil J Grimsey
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, United States
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26
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Sizek H, Hamel A, Deritei D, Campbell S, Ravasz Regan E. Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K. PLoS Comput Biol 2019; 15:e1006402. [PMID: 30875364 PMCID: PMC6436762 DOI: 10.1371/journal.pcbi.1006402] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 03/27/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The PI3K/AKT signaling pathway plays a role in most cellular functions linked to cancer progression, including cell growth, proliferation, cell survival, tissue invasion and angiogenesis. It is generally recognized that hyperactive PI3K/AKT1 are oncogenic due to their boost to cell survival, cell cycle entry and growth-promoting metabolism. That said, the dynamics of PI3K and AKT1 during cell cycle progression are highly nonlinear. In addition to negative feedback that curtails their activity, protein expression of PI3K subunits has been shown to oscillate in dividing cells. The low-PI3K/low-AKT1 phase of these oscillations is required for cytokinesis, indicating that oncogenic PI3K may directly contribute to genome duplication. To explore this, we construct a Boolean model of growth factor signaling that can reproduce PI3K oscillations and link them to cell cycle progression and apoptosis. The resulting modular model reproduces hyperactive PI3K-driven cytokinesis failure and genome duplication and predicts the molecular drivers responsible for these failures by linking hyperactive PI3K to mis-regulation of Polo-like kinase 1 (Plk1) expression late in G2. To do this, our model captures the role of Plk1 in cell cycle progression and accurately reproduces multiple effects of its loss: G2 arrest, mitotic catastrophe, chromosome mis-segregation / aneuploidy due to premature anaphase, and cytokinesis failure leading to genome duplication, depending on the timing of Plk1 inhibition along the cell cycle. Finally, we offer testable predictions on the molecular drivers of PI3K oscillations, the timing of these oscillations with respect to division, and the role of altered Plk1 and FoxO activity in genome-level defects caused by hyperactive PI3K. Our model is an important starting point for the predictive modeling of cell fate decisions that include AKT1-driven senescence, as well as the non-intuitive effects of drugs that interfere with mitosis.
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Affiliation(s)
- Herbert Sizek
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Andrew Hamel
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Dávid Deritei
- Department of Physics, Pennsylvania State University, State College, PA, United States of America
- Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Sarah Campbell
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Erzsébet Ravasz Regan
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
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27
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Elbracht M, Kraft F, Begemann M, Holschbach P, Mull M, Kabat IM, Müller B, Häusler M, Kurth I, Hehr U. Familial NEDD4L variant in periventricular nodular heterotopia and in a fetus with hypokinesia and flexion contractures. Mol Genet Genomic Med 2018; 6:1255-1260. [PMID: 30393983 PMCID: PMC6305664 DOI: 10.1002/mgg3.490] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/19/2018] [Accepted: 10/02/2018] [Indexed: 12/23/2022] Open
Abstract
Background Mutations in the HECT domain of NEDD4L have recently been identified in a cohort of eight patients with a syndromic form of bilateral periventricular nodular heterotopia (PVNH) in association with neurodevelopmental delay, cleft palate, and toe syndactyly (PVNH7). Methods Case report based on NGS sequencing. Results Here, we describe a girl with a novel heterozygous NEDD4L missense variant, p.Tyr679His, and characteristic clinical findings, including bilateral periventricular nodular heterotopia, cleft palate and mild toe syndactyly. Molecular testing from peripheral blood identified the healthy father to carry the NEDD4L variant in mosaic state. Notably, a previous pregnancy of the couple had been terminated due to a complex fetal developmental disorder, including hypokinesia and flexion contractures. Upon review, this affected fetus was also shown to carry the familial NEDD4L variant. Conclusion Our findings may suggest a broader spectrum of NEDD4L‐associated phenotypes, including severe prenatal neurodevelopmental manifestations, which might represent yet another genetic form of fetal hypokinesia with flexion contractures.
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Affiliation(s)
- Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Petra Holschbach
- Division of Neuropediatrics and Social Pediatrics, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Michael Mull
- Department of Diagnostic and Interventional Neuroradiology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ildiko M Kabat
- Department of Radiology, Radiologie Universität Bonn Ildiko M. Kabat, University Hospital Bonn, Bonn, Germany
| | - Britta Müller
- Division of Neuropediatrics and Social Pediatrics, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Martin Häusler
- Division of Neuropediatrics and Social Pediatrics, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ute Hehr
- Department of Human Genetics, Medical Center, University of Regensburg, Regensburg, Germany
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28
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Chen D, Gehringer M, Lorenz S. Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases for Therapeutic Applications: Challenges and Opportunities. Chembiochem 2018; 19:2123-2135. [PMID: 30088849 PMCID: PMC6471174 DOI: 10.1002/cbic.201800321] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 12/11/2022]
Abstract
The ubiquitin system regulates countless physiological and disease-associated processes and has emerged as an attractive entryway for therapeutic efforts. With over 600 members in the human proteome, ubiquitin ligases are the most diverse class of ubiquitylation enzymes and pivotal in encoding specificity in ubiquitin signaling. Although considerable progress has been made in the identification of small molecules targeting RING ligases, relatively little is known about the "druggability" of HECT (homologous to E6AP C terminus) ligases, many of which are critically implicated in human pathologies. A major obstacle to optimizing the few available ligands is our incomplete understanding of their inhibitory mechanisms and the structural basis of catalysis in HECT ligases. Here, we survey recent approaches to manipulate the activities of HECT ligases with small molecules to showcase the particular challenges and opportunities these enzymes hold as therapeutic targets.
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Affiliation(s)
- Dan Chen
- Rudolf Virchow Center for Experimental BiomedicineUniversity of WürzburgJosef-Schneider-Strasse 2, Haus D1597080WürzburgGermany
| | - Matthias Gehringer
- Institute of Pharmaceutical SciencesDepartment of Pharmaceutical/Medicinal ChemistryUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental BiomedicineUniversity of WürzburgJosef-Schneider-Strasse 2, Haus D1597080WürzburgGermany
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29
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Yao W, Shan Z, Gu A, Fu M, Shi Z, Wen W. WW domain-mediated regulation and activation of E3 ubiquitin ligase Suppressor of Deltex. J Biol Chem 2018; 293:16697-16708. [PMID: 30213861 DOI: 10.1074/jbc.ra118.003781] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/27/2018] [Indexed: 12/22/2022] Open
Abstract
The Nedd4 family E3 ligases Itch and WWP1/2 play crucial roles in the regulation of cell cycle progression and apoptosis and are closely correlated with cancer development and metastasis. It has been recently shown that the ligase activities of Itch and WWP1/2 are tightly regulated, with the HECT domain sequestered intramolecularly by a linker region connecting WW2 and WW3. Here, we show that a similar autoinhibitory mechanism is utilized by the Drosophila ortholog of Itch and WWP1/2, Suppressor of Deltex (Su(dx)). We show that Su(dx) adopts an inactive steady state with the WW domain region interacting with the HECT domain. We demonstrate that both the linker and preceding WW2 are required for the efficient binding and regulation of Su(dx) HECT. Recruiting the multiple-PY motif-containing adaptor dNdfip via WW domains relieves the inhibitory state of Su(dx) and leads to substrate (e.g. Notch) ubiquitination. Our study demonstrates an evolutionarily conservative mechanism governing the regulation and activation of some Nedd4 family E3 ligases. Our results also suggest a dual regulatory mechanism for specific Notch down-regulation via dNdfip-Su(dx)-mediated Notch ubiquitination.
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Affiliation(s)
- Weiyi Yao
- From the Department of Neurosurgery, Huashan Hospital, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China and
| | - Zelin Shan
- From the Department of Neurosurgery, Huashan Hospital, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China and
| | - Aihong Gu
- From the Department of Neurosurgery, Huashan Hospital, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China and
| | - Minjie Fu
- From the Department of Neurosurgery, Huashan Hospital, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China and
| | - Zhifeng Shi
- From the Department of Neurosurgery, Huashan Hospital, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China and
| | - Wenyu Wen
- From the Department of Neurosurgery, Huashan Hospital, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200040, China and .,the Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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30
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Sluimer J, Distel B. Regulating the human HECT E3 ligases. Cell Mol Life Sci 2018; 75:3121-3141. [PMID: 29858610 PMCID: PMC6063350 DOI: 10.1007/s00018-018-2848-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 01/09/2023]
Abstract
Ubiquitination, the covalent attachment of ubiquitin to proteins, by E3 ligases of the HECT (homologous to E6AP C terminus) family is critical in controlling diverse physiological pathways. Stringent control of HECT E3 ligase activity and substrate specificity is essential for cellular health, whereas deregulation of HECT E3s plays a prominent role in disease. The cell employs a wide variety of regulatory mechanisms to control HECT E3 activity and substrate specificity. Here, we summarize the current understanding of these regulatory mechanisms that control HECT E3 function. Substrate specificity is generally determined by interactions of adaptor proteins with domains in the N-terminal extensions of HECT E3 ligases. These N-terminal domains have also been found to interact with the HECT domain, resulting in the formation of inhibitory conformations. In addition, catalytic activity of the HECT domain is commonly regulated at the level of E2 recruitment and through HECT E3 oligomerization. The previously mentioned regulatory mechanisms can be controlled through protein-protein interactions, post-translational modifications, the binding of calcium ions, and more. Functional activity is determined not only by substrate recruitment and catalytic activity, but also by the type of ubiquitin polymers catalyzed to the substrate. While this is often determined by the specific HECT member, recent studies demonstrate that HECT E3s can be modulated to alter the type of ubiquitin polymers they catalyze. Insight into these diverse regulatory mechanisms that control HECT E3 activity may open up new avenues for therapeutic strategies aimed at inhibition or enhancement of HECT E3 function in disease-related pathways.
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Affiliation(s)
- Jasper Sluimer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Distel
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Neuroscience, Erasmus Medical Center, Wijtemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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31
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Lorenz S. Structural mechanisms of HECT-type ubiquitin ligases. Biol Chem 2018; 399:127-145. [PMID: 29016349 DOI: 10.1515/hsz-2017-0184] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/25/2017] [Indexed: 12/31/2022]
Abstract
Ubiquitin ligases (E3 enzymes) transfer ubiquitin from ubiquitin-conjugating (E2) enzymes to target proteins. By determining the selection of target proteins, modification sites on those target proteins, and the types of ubiquitin modifications that are formed, E3 enzymes are key specificity factors in ubiquitin signaling. Here, I summarize our knowledge of the structural mechanisms in the HECT E3 subfamily, many members of which play important roles in human disease. I discuss interactions of the conserved HECT domain with E2 enzymes, ubiquitin and target proteins, as well as macromolecular interactions with regulatory functions. While we understand individual steps in the catalytic cycle of HECT E3 enzymes on a structural level, this review also highlights key aspects that have yet to be elucidated. For instance, it remains unclear how diverse target proteins are presented to the catalytic center and how certain HECT E3 enzymes achieve specificity in ubiquitin linkage formation. The structural and functional properties of the N-terminal regions of HECT E3 enzymes that likely act as signaling hubs are also largely unknown. Structural insights into these aspects may open up routes for a therapeutic intervention with specific HECT E3 functions in distinct pathophysiological settings.
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Affiliation(s)
- Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
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32
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Mund T, Pelham HR. Substrate clustering potently regulates the activity of WW-HECT domain-containing ubiquitin ligases. J Biol Chem 2018; 293:5200-5209. [PMID: 29463679 PMCID: PMC5892558 DOI: 10.1074/jbc.ra117.000934] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/06/2018] [Indexed: 11/28/2022] Open
Abstract
The Nedd4 family of HECT domain–containing E3 ligases ubiquitinate many transcription factors and signaling proteins, and their activity is tightly regulated. Normally, intramolecular interactions curb the catalytic activity of the HECT domain, but these can be broken by the binding of PY motifs, found on substrate molecules and adaptors, to the WW domains characteristic of this E3 ligase family. This raises the prospect of substrates automatically activating the ligases, frustrating the purpose of ligase regulation. Here we show that soluble protein substrates and adaptors such as α arrestins, even with multiple PY elements, cannot activate ligase activity efficiently. However, we found that polymerization or membrane tethering of these substrates dramatically increases the ligase activity both in vivo and in vitro. Aggregation of luciferase-containing substrates upon heat shock had a similar effect and could also expose cryptic PY elements in the substrates. We inferred that ligase activation critically requires a substantial array of clustered PY motifs and that the formation of such arrays on membranes or in polymeric aggregates may be an essential step in this mode of ligase regulation. We conclude that recruitment of α arrestins to membrane receptors and aggregation of unstable proteins after heat shock may be physiologically relevant mechanisms for triggering ubiquitination by Nedd4 family HECT domain–containing E3 ligases.
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Affiliation(s)
- Thomas Mund
- From the Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Hugh R Pelham
- From the Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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33
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Todaro DR, Augustus-Wallace AC, Klein JM, Haas AL. The mechanism of neural precursor cell expressed developmentally down-regulated 4-2 (Nedd4-2)/NEDD4L-catalyzed polyubiquitin chain assembly. J Biol Chem 2017; 292:19521-19536. [PMID: 28972136 DOI: 10.1074/jbc.m117.817882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Indexed: 11/06/2022] Open
Abstract
The mechanism of Nedd4-2 has been quantitatively explored for the first time using biochemically defined kinetic assays examining rates of 125I-polyubiquitin chain assembly as a functional readout. We demonstrate that Nedd4-2 exhibits broad specificity for E2 paralogs of the Ubc4/5 clade to assemble Lys63-linked polyubiquitin chains. Full-length Nedd4-2 catalyzes free 125I-polyubiquitin chain assembly by hyperbolic Michaelis-Menten kinetics with respect to Ubc5B∼ubiquitin thioester concentration (Km = 44 ± 6 nm; kcat = 0.020 ± 0.007 s-1) and substrate inhibition above 0.5 μm (Ki = 2.5 ± 1.3 μm) that tends to zero velocity, requiring ordered binding at two functionally distinct E2∼ubiquitin-binding sites. The Ubc5BC85A product analog non-competitively inhibits Nedd4-2 (Ki = 2.0 ± 0.5 μm), consistent with the presence of the second E2-binding site. In contrast, the isosteric Ubc5BC85S-ubiquitin oxyester substrate analog exhibits competitive inhibition at the high-affinity Site 1 (Ki = 720 ± 340 nm) and non-essential activation at the lower-affinity Site 2 (Kact = 750 ± 260 nm). Additional studies utilizing Ubc5BF62A, defective in binding the canonical E2 site, demonstrate that the cryptic Site 1 is associated with thioester formation, whereas binding at the canonical site (Site 2) is associated with polyubiquitin chain elongation. Finally, previously described Ca2+-dependent C2 domain-mediated autoinhibition of Nedd4-2 is not observed under our reported experimental conditions. These studies collectively demonstrate that Nedd4-2 catalyzes polyubiquitin chain assembly by an ordered two-step mechanism requiring two dynamically linked E2∼ubiquitin-binding sites analogous to that recently reported for E6AP, the founding member of the Hect ligase family.
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Affiliation(s)
- Dustin R Todaro
- From the Department of Biochemistry and Molecular Biology and
| | | | | | - Arthur L Haas
- From the Department of Biochemistry and Molecular Biology and .,the Stanley S. Scott Cancer Center, Louisiana State University School of Medicine, New Orleans, Louisiana 70112
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34
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Chen Z, Jiang H, Xu W, Li X, Dempsey DR, Zhang X, Devreotes P, Wolberger C, Amzel LM, Gabelli SB, Cole PA. A Tunable Brake for HECT Ubiquitin Ligases. Mol Cell 2017; 66:345-357.e6. [PMID: 28475870 DOI: 10.1016/j.molcel.2017.03.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/15/2017] [Accepted: 03/31/2017] [Indexed: 12/24/2022]
Abstract
The HECT E3 ligases ubiquitinate numerous transcription factors and signaling molecules, and their activity must be tightly controlled to prevent cancer, immune disorders, and other diseases. In this study, we have found unexpectedly that peptide linkers tethering WW domains in several HECT family members are key regulatory elements of their catalytic activities. Biochemical, structural, and cellular analyses have revealed that the linkers can lock the HECT domain in an inactive conformation and block the proposed allosteric ubiquitin binding site. Such linker-mediated autoinhibition of the HECT domain can be relieved by linker post-translational modifications, but complete removal of the brake can induce hyperactive autoubiquitination and E3 self destruction. These results clarify the mechanisms of several HECT protein cancer associated mutations and provide a new framework for understanding how HECT ubiquitin ligases must be finely tuned to ensure normal cellular behavior.
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Affiliation(s)
- Zan Chen
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Hanjie Jiang
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Wei Xu
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Xiaoguang Li
- Department of Cell Biology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Dempsey
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Xiangbin Zhang
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Peter Devreotes
- Department of Cell Biology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - L Mario Amzel
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, John Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, John Hopkins School of Medicine, Baltimore, MD 21205, USA.
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35
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Fajner V, Maspero E, Polo S. Targeting HECT-type E3 ligases - insights from catalysis, regulation and inhibitors. FEBS Lett 2017; 591:2636-2647. [PMID: 28771691 DOI: 10.1002/1873-3468.12775] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 12/27/2022]
Abstract
Ubiquitination plays a pivotal role in most cellular processes and is critical for protein degradation and signalling. E3 ligases are the matchmakers in the ubiquitination cascade, responsible for substrate recognition and modification with specific polyubiquitin chains. Until recently, it was not clear how the catalytic activity of E3s is modulated, but major recent studies on HECT E3 ligases is filling this void. These enzymes appear to be held in a closed, inactive conformation, which is relieved by biochemical manoeuvres unique to each member, thus ensuring exquisite regulation and specificity of the enzymes. The new advances and their significance to the function of HECT E3s are described here, with a particular focus on the Nedd4 family members.
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Affiliation(s)
- Valentina Fajner
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Elena Maspero
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.,DiPO, Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Italy
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Ehrlichia chaffeensis TRP120 Moonlights as a HECT E3 Ligase Involved in Self- and Host Ubiquitination To Influence Protein Interactions and Stability for Intracellular Survival. Infect Immun 2017. [PMID: 28630068 DOI: 10.1128/iai.00290-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ehrlichia chaffeensis secretes tandem repeat protein (TRP) effectors that are involved in a diverse array of host cell interactions, some of which directly activate cell signaling pathways and reprogram host gene transcription to promote survival in the mononuclear phagocyte. However, the molecular details of these effector-host interactions and roles in pathobiology are incompletely understood. In this study, we determined that the E. chaffeensis effector TRP120 is posttranslationally modified by ubiquitin (Ub) and that ubiquitination occurs through intrinsic and host-mediated HECT ligase activity. A functional HECT E3 ligase domain with a conserved catalytic site was identified in the C-terminal region of TRP120, and TRP120 autoubiquitination occurred in vitro in the presence of host UbcH5b/c E2 enzymes. TRP120 ubiquitination sites were mapped using a high-density microfluidic peptide array and confirmed by ectopic expression of TRP120 lysine mutants in cells. Moreover, we determined that the HECT E3 ubiquitin ligase, Nedd4L, interacts with TRP120 during infection and also mediates TRP120 ubiquitination. Nedd4L knockdown resulted in the reduction of TRP120-Ub, decreased ehrlichial infection, and reduced recruitment of a known TRP120-interacting host protein, PCGF5, to ehrlichial inclusions. TRP120-mediated PCGF5 polyubiquitination was associated with a reduction in PCGF5 levels. Inhibition of ubiquitination with small molecules also significantly decreased ehrlichial infection, indicating that the Ub pathway is critical for ehrlichial intracellular replication and survival. The current study identified a novel E. chaffeensis ubiquitin ligase and revealed an important role for the ubiquitin pathway in effector-host interactions and pathogen-mediated host protein stability in order to promote intracellular survival.
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Zhu K, Shan Z, Chen X, Cai Y, Cui L, Yao W, Wang Z, Shi P, Tian C, Lou J, Xie Y, Wen W. Allosteric auto-inhibition and activation of the Nedd4 family E3 ligase Itch. EMBO Rep 2017; 18:1618-1630. [PMID: 28747490 DOI: 10.15252/embr.201744454] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
The Nedd4 family E3 ligases are key regulators of cell growth and proliferation and are often misregulated in human cancers and other diseases. The ligase activities of Nedd4 E3s are tightly controlled via auto-inhibition. However, the molecular mechanism underlying Nedd4 E3 auto-inhibition and activation is poorly understood. Here, we show that the WW domains proceeding the catalytic HECT domain play an inhibitory role by binding directly to HECT in the Nedd4 E3 family member Itch. Our structural and biochemical analyses of Itch reveal that the WW2 domain and a following linker allosterically lock HECT in an inactive state inhibiting E2-E3 transthiolation. Binding of the Ndfip1 adaptor or JNK1-mediated phosphorylation relieves the auto-inhibition of Itch in a WW2-dependent manner. Aberrant activation of Itch leads to migration defects of cortical neurons during development. Our study provides a new mechanism governing the regulation of Itch.
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Affiliation(s)
- Kang Zhu
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zelin Shan
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xing Chen
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yuqun Cai
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Lei Cui
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Weiyi Yao
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhen Wang
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Pan Shi
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Changlin Tian
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunli Xie
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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Sang Y, Zhang R, Creagh AL, Haynes CA, Straus SK. Interactions of U24 from Roseolovirus with WW domains: canonical vs noncanonical. Biochem Cell Biol 2017; 95:350-358. [PMID: 28314105 DOI: 10.1139/bcb-2016-0250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
U24 is a C-terminal membrane-anchored protein found in both human herpes virus type 6 and 7 (HHV-6 and HHV-7), with an N-terminal segment that is rich in prolines (PPxY motif in both HHV-6A and 7; PxxP motif in HHV-6A). Previous work has shown that U24 interacts strongly with Nedd4 WW domains, in particular, hNedd4L-WW3*. It was also shown that this interaction depends strongly on the nature of the amino acids that are upstream from the PY motif in U24. In this contribution, data was obtained from pull-downs, isothermal titration calorimetry, and NMR to further determine what modulates U24:WW domain interactions. Specifically, 3 non-canonical WW domains from human Smad ubiquitination regulatory factor (Smurf), namely hSmurf2-WW2, hSmurf2-WW3, and a tandem construct hSmurf2-WW2 + 3, were studied. Overall, the interactions between U24 and these Smurf WW domains were found to be weaker than those in U24:Nedd4 WW domain pairs, suggesting that U24 function is tightly linked to specific E3 ubiqitin ligases.
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Affiliation(s)
- Yurou Sang
- a Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Rui Zhang
- a Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - A Louise Creagh
- b Michael Smith Laboratories and Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Charles A Haynes
- b Michael Smith Laboratories and Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Suzana K Straus
- a Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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Sander B, Xu W, Eilers M, Popov N, Lorenz S. A conformational switch regulates the ubiquitin ligase HUWE1. eLife 2017; 6:e21036. [PMID: 28193319 PMCID: PMC5308896 DOI: 10.7554/elife.21036] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/27/2017] [Indexed: 12/27/2022] Open
Abstract
The human ubiquitin ligase HUWE1 has key roles in tumorigenesis, yet it is unkown how its activity is regulated. We present the crystal structure of a C-terminal part of HUWE1, including the catalytic domain, and reveal an asymmetric auto-inhibited dimer. We show that HUWE1 dimerizes in solution and self-associates in cells, and that both occurs through the crystallographic dimer interface. We demonstrate that HUWE1 is inhibited in cells and that it can be activated by disruption of the dimer interface. We identify a conserved segment in HUWE1 that counteracts dimer formation by associating with the dimerization region intramolecularly. Our studies reveal, intriguingly, that the tumor suppressor p14ARF binds to this segment and may thus shift the conformational equilibrium of HUWE1 toward the inactive state. We propose a model, in which the activity of HUWE1 underlies conformational control in response to physiological cues-a mechanism that may be exploited for cancer therapy.
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Affiliation(s)
- Bodo Sander
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Wenshan Xu
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Würzburg, Germany
| | - Martin Eilers
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Theodor-Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nikita Popov
- Comprehensive Cancer Center Mainfranken, Würzburg, Germany
- Department of Radiation Oncology, University Hospital Würzburg, Würzburg, Germany
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
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40
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Sang Y, Zhang R, Scott WRP, Creagh AL, Haynes CA, Straus SK. U24 from Roseolovirus interacts strongly with Nedd4 WW Domains. Sci Rep 2017; 7:39776. [PMID: 28051106 PMCID: PMC5209733 DOI: 10.1038/srep39776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/28/2016] [Indexed: 01/20/2023] Open
Abstract
U24 is a protein found in both roseoloviruses Human Herpes Virus type 6 and 7 (HHV-6 and HHV-7), with an N-terminus that is rich in prolines (PY motif in both HHV-6A and 7; PxxP motif in HHV-6A). Previous work has shown that the interaction between U24 and WW domains is important for endocytic recycling of T-cell receptors, but a cognate ligand was never identified. In this contribution, data was obtained from pull-downs, ITC, NMR and molecular dynamics simulations to show that a specific interaction exists between U24 and Nedd4 WW domains. ITC experiments were also carried out for U24 from HHV-6A phosphorylated at Thr6 (pU24-6A) and a peptide containing the PY motif from Nogo-A, a protein implicated in both the initial inflammatory and the neurodegenerative phases of multiple sclerosis (MS). The results suggest that phosphorylation of U24 from HHV-6A may be crucial for its potential role in MS.
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Affiliation(s)
- Yurou Sang
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rui Zhang
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Walter R P Scott
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories and Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles A Haynes
- Michael Smith Laboratories and Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzana K Straus
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada
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41
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Regulation of primary cilia formation by the ubiquitin–proteasome system. Biochem Soc Trans 2016; 44:1265-1271. [DOI: 10.1042/bst20160174] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/17/2022]
Abstract
Primary cilia form at the surface of most vertebrate cell types, where they are essential signalling antennae for signal transduction pathways important for development and cancer, including Hedgehog. The importance of primary cilia in development is clearly demonstrated by numerous disorders (known as ciliopathies) associated with disrupted cilia formation (ciliogenesis). Recent advances describing functional regulators of the primary cilium highlight an emerging role for the ubiquitin–proteasome system (UPS) as a key regulator of ciliogenesis. Although there are well-documented examples of E3 ubiquitin ligases and deubiquitases in the regulation of cilia proteins, many putative components remain unvalidated. This review explores current understanding of how the UPS influences primary cilia formation, and also how recent screen data have identified more putative regulators of the UPS. Emerging research has identified many promising leads in the search for regulators of this important organelle and may identify potential novel therapeutic targets for intervention in cancer and other disease contexts.
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Mutations in the HECT domain of NEDD4L lead to AKT-mTOR pathway deregulation and cause periventricular nodular heterotopia. Nat Genet 2016; 48:1349-1358. [PMID: 27694961 PMCID: PMC5086093 DOI: 10.1038/ng.3676] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/24/2016] [Indexed: 12/16/2022]
Abstract
Neurodevelopmental disorders with periventricular nodular heterotopia (PNH) are etiologically heterogeneous, and their genetic causes remain in many cases unknown. Here we show that missense mutations in NEDD4L mapping to the HECT domain of the encoded E3 ubiquitin ligase lead to PNH associated with toe syndactyly, cleft palate and neurodevelopmental delay. Cellular and expression data showed sensitivity of PNH-associated mutants to proteasome degradation. Moreover, an in utero electroporation approach showed that PNH-related mutants and excess wild-type NEDD4L affect neurogenesis, neuronal positioning and terminal translocation. Further investigations, including rapamycin-based experiments, found differential deregulation of pathways involved. Excess wild-type NEDD4L leads to disruption of Dab1 and mTORC1 pathways, while PNH-related mutations are associated with deregulation of mTORC1 and AKT activities. Altogether, these data provide insights into the critical role of NEDD4L in the regulation of mTOR pathways and their contributions in cortical development.
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43
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Kaminska J, Rzepnikowska W, Polak A, Flis K, Soczewka P, Bala K, Sienko M, Grynberg M, Kaliszewski P, Urbanek A, Ayscough K, Zoladek T. Phosphatidylinositol-3-phosphate regulates response of cells to proteotoxic stress. Int J Biochem Cell Biol 2016; 79:494-504. [PMID: 27498190 DOI: 10.1016/j.biocel.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022]
Abstract
Human Nedd4 ubiquitin ligase, or its variants, inhibit yeast cell growth by disturbing the actin cytoskeleton organization and dynamics, and lead to an increase in levels of ubiquitinated proteins. In a screen for multicopy suppressors which rescue growth of yeast cells producing Nedd4 ligase with an inactive WW4 domain (Nedd4w4), we identified a fragment of ATG2 gene encoding part of the Atg2 core autophagy protein. Expression of the Atg2-C1 fragment (aa 1074-1447) improved growth, actin cytoskeleton organization, but did not significantly change the levels of ubiquitinated proteins in these cells. The GFP-Atg2-C1 protein in Nedd4w4-producing cells primarily localized to a single defined structure adjacent to the vacuole, surrounded by an actin filament ring, containing Hsp42 and Hsp104 chaperones. This localization was not affected in several atg deletion mutants, suggesting that it might be distinct from the phagophore assembly site (PAS). However, deletion of ATG18 encoding a phosphatidylinositol-3-phosphate (PI3P)-binding protein affected the morphology of the GFP-Atg2-C1 structure while deletion of ATG14 encoding a subunit of PI3 kinase suppressed toxicity of Nedd4w4 independently of GFP-Atg2-C1. Further analysis of the Atg2-C1 revealed that it contains an APT1 domain of previously uncharacterized function. Most importantly, we showed that this domain is able to bind phosphatidylinositol phosphates, especially PI3P, which is abundant in the PAS and endosomes. Together our results suggest that human Nedd4 ubiquitinates proteins in yeast and causes proteotoxic stress and, with some Atg proteins, leads to formation of a perivacuolar structure, which may be involved in sequestration, aggregation or degradation of proteins.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Polak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Bala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marzena Sienko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Kaliszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Agnieszka Urbanek
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Kathryn Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
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Wang Z, Dang T, Liu T, Chen S, Li L, Huang S, Fang M. NEDD4L Protein Catalyzes Ubiquitination of PIK3CA Protein and Regulates PI3K-AKT Signaling. J Biol Chem 2016; 291:17467-77. [PMID: 27339899 DOI: 10.1074/jbc.m116.726083] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 11/06/2022] Open
Abstract
Oncogenic PIK3CA (p110α), the catalytic subunit of class IA PI3K, plays a major role in PI3K-related cancer progression. The mechanisms underlying the dynamic regulation of PIK3CA protein levels remain unknown. Here we demonstrated that PIK3CA is regulated by polyubiquitination. We identified NEDD4L as the E3 ligase that catalyzes PIK3CA polyubiquitination, leading to its proteasome-dependent degradation. NEDD4L ubiquitinates both the free and regulatory subunit-bound PIK3CA but does not ubiquitinate the regulatory subunit of PI3K. Overexpression of NEDD4L accelerates the turnover rate of PIK3CA, whereas suppression of NEDD4L results in not only the accumulation of PIK3CA but also a paradoxical decrease of AKT activation. Thus, we propose that NEDD4L negatively regulates PIK3CA protein levels via ubiquitination and is required for the maintenance of PI3K-AKT signaling pathway.
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Affiliation(s)
- Zixi Wang
- From the Division of Cell Biology, College of Life Sciences, and Joint Center for Life Sciences, Peking University, Yiheyuan Road No. 5, Haidian District, Beijing 100871, China and
| | - Tingting Dang
- From the Division of Cell Biology, College of Life Sciences, and Joint Center for Life Sciences, Peking University, Yiheyuan Road No. 5, Haidian District, Beijing 100871, China and
| | - Tingting Liu
- From the Division of Cell Biology, College of Life Sciences, and Joint Center for Life Sciences, Peking University, Yiheyuan Road No. 5, Haidian District, Beijing 100871, China and
| | - She Chen
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Song Huang
- National Institute of Biological Sciences, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Min Fang
- From the Division of Cell Biology, College of Life Sciences, and Joint Center for Life Sciences, Peking University, Yiheyuan Road No. 5, Haidian District, Beijing 100871, China and
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Zhang W, Wu KP, Sartori MA, Kamadurai HB, Ordureau A, Jiang C, Mercredi PY, Murchie R, Hu J, Persaud A, Mukherjee M, Li N, Doye A, Walker JR, Sheng Y, Hao Z, Li Y, Brown KR, Lemichez E, Chen J, Tong Y, Harper JW, Moffat J, Rotin D, Schulman BA, Sidhu SS. System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Mol Cell 2016; 62:121-36. [PMID: 26949039 DOI: 10.1016/j.molcel.2016.02.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/23/2016] [Accepted: 02/03/2016] [Indexed: 11/20/2022]
Abstract
HECT-family E3 ligases ubiquitinate protein substrates to control virtually every eukaryotic process and are misregulated in numerous diseases. Nonetheless, understanding of HECT E3s is limited by a paucity of selective and potent modulators. To overcome this challenge, we systematically developed ubiquitin variants (UbVs) that inhibit or activate HECT E3s. Structural analysis of 6 HECT-UbV complexes revealed UbV inhibitors hijacking the E2-binding site and activators occupying a ubiquitin-binding exosite. Furthermore, UbVs unearthed distinct regulation mechanisms among NEDD4 subfamily HECTs and proved useful for modulating therapeutically relevant targets of HECT E3s in cells and intestinal organoids, and in a genetic screen that identified a role for NEDD4L in regulating cell migration. Our work demonstrates versatility of UbVs for modulating activity across an E3 family, defines mechanisms and provides a toolkit for probing functions of HECT E3s, and establishes a general strategy for systematic development of modulators targeting families of signaling proteins.
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Affiliation(s)
- Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Kuen-Phon Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maria A Sartori
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Hari B Kamadurai
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chong Jiang
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Peter Y Mercredi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan Murchie
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Jicheng Hu
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Avinash Persaud
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Manjeet Mukherjee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Anne Doye
- Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Equipe Labellisée La Ligue Contre Le Cancer, Université de Nice-Sophia Antipolis, 151 Route St Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex, France
| | - John R Walker
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Yi Sheng
- Department of Biology, York University, Toronto, Ontario M3J1P3, Canada
| | - Zhenyue Hao
- Campbell Family Cancer Research Institute, University Health Network, Toronto, ON M5G2C1, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada
| | - Kevin R Brown
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Emmanuel Lemichez
- Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Equipe Labellisée La Ligue Contre Le Cancer, Université de Nice-Sophia Antipolis, 151 Route St Antoine de Ginestière, BP 2 3194, 06204 Nice Cedex, France
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Yufeng Tong
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5G1L7, Canada
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Cir, Toronto, ON M5S1A8, Canada
| | - Daniela Rotin
- Program in Cell Biology, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Cir, Toronto, ON M5S1A8, Canada.
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Panwalkar V, Neudecker P, Schmitz M, Lecher J, Schulte M, Medini K, Stoldt M, Brimble MA, Willbold D, Dingley AJ. The Nedd4–1 WW Domain Recognizes the PY Motif Peptide through Coupled Folding and Binding Equilibria. Biochemistry 2016; 55:659-74. [DOI: 10.1021/acs.biochem.5b01028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vineet Panwalkar
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Philipp Neudecker
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | | | - Justin Lecher
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Marianne Schulte
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | | | - Matthias Stoldt
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | | | - Dieter Willbold
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Andrew J. Dingley
- ICS-6
(Strukturbiochemie), Forschungszentrum Jülich, 52425 Jülich, Germany
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Riling C, Kamadurai H, Kumar S, O'Leary CE, Wu KP, Manion EE, Ying M, Schulman BA, Oliver PM. Itch WW Domains Inhibit Its E3 Ubiquitin Ligase Activity by Blocking E2-E3 Ligase Trans-thiolation. J Biol Chem 2015; 290:23875-87. [PMID: 26245901 DOI: 10.1074/jbc.m115.649269] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 12/22/2022] Open
Abstract
Nedd4-family E3 ubiquitin ligases regulate an array of biologic processes. Autoinhibition maintains these catalytic ligases in an inactive state through several mechanisms. However, although some Nedd4 family members are activated by binding to Nedd4 family-interacting proteins (Ndfips), how binding activates E3 function remains unclear. Our data reveal how these two regulatory processes are linked functionally. In the absence of Ndfip1, the Nedd4 family member Itch can bind an E2 but cannot accept ubiquitin onto its catalytic cysteine. This is because Itch is autoinhibited by an intramolecular interaction between its HECT (homologous to the E6-AP carboxy terminus domain) and two central WW domains. Ndfip1 binds these WW domains to release the HECT, allowing trans-thiolation and Itch catalytic activity. This molecular switch also regulates the closely related family member WWP2. Importantly, multiple PY motifs are required for Ndfip1 to activate Itch, functionally distinguishing Ndfips from single PY-containing substrates. These data establish a novel mechanism for control of the function of a subfamily of Nedd4 E3 ligases at the level of E2-E3 trans-thiolation.
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Affiliation(s)
- Christopher Riling
- From the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Hari Kamadurai
- the St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | | | - Claire E O'Leary
- From the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kuen-Phon Wu
- the St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | | | - Mingjie Ying
- the Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Brenda A Schulman
- the St. Jude Children's Research Hospital, Memphis, Tennessee 38105, the Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, and
| | - Paula M Oliver
- From the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, the Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, the Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Vittal V, Stewart MD, Brzovic PS, Klevit RE. Regulating the Regulators: Recent Revelations in the Control of E3 Ubiquitin Ligases. J Biol Chem 2015; 290:21244-51. [PMID: 26187467 DOI: 10.1074/jbc.r115.675165] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since its discovery as a post-translational signal for protein degradation, our understanding of ubiquitin (Ub) has vastly evolved. Today, we recognize that the role of Ub signaling is expansive and encompasses diverse processes including cell division, the DNA damage response, cellular immune signaling, and even organismal development. With such a wide range of functions comes a wide range of regulatory mechanisms that control the activity of the ubiquitylation machinery. Ub attachment to substrates occurs through the sequential action of three classes of enzymes, E1s, E2s, and E3s. In humans, there are 2 E1s, ∼ 35 E2s, and hundreds of E3s that work to attach Ub to thousands of cellular substrates. Regulation of ubiquitylation can occur at each stage of the stepwise Ub transfer process, and substrates can also impact their own modification. Recent studies have revealed elegant mechanisms that have evolved to control the activity of the enzymes involved. In this minireview, we highlight recent discoveries that define some of the various mechanisms by which the activities of E3-Ub ligases are regulated.
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Affiliation(s)
- Vinayak Vittal
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Mikaela D Stewart
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Peter S Brzovic
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Rachel E Klevit
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
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