1
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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2
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Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
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Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
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3
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Nyenhuis DA, Rajasekaran R, Watanabe S, Strub MP, Khan M, Powell M, Carter CA, Tjandra N. HECT domain interaction with ubiquitin binding sites on Tsg101-UEV controls HIV-1 egress, maturation, and infectivity. J Biol Chem 2023; 299:102901. [PMID: 36642186 PMCID: PMC9944984 DOI: 10.1016/j.jbc.2023.102901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The HECT domain of HECT E3 ligases consists of flexibly linked N- and C-terminal lobes, with a ubiquitin (Ub) donor site on the C-lobe that is directly involved in substrate modification. HECT ligases also possess a secondary Ub binding site in the N-lobe, which is thought to play a role in processivity, specificity, or regulation. Here, we report the use of paramagnetic solution NMR to characterize a complex formed between the isolated HECT domain of neural precursor cell-expressed developmentally downregulated 4-1 and the ubiquitin E2 variant (UEV) domain of tumor susceptibility gene 101 (Tsg101). Both proteins are involved in endosomal trafficking, a process driven by Ub signaling, and are hijacked by viral pathogens for particle assembly; however, a direct interaction between them has not been described, and the mechanism by which the HECT E3 ligase contributes to pathogen formation has not been elucidated. We provide evidence for their association, consisting of multiple sites on the neural precursor cell-expressed developmentally downregulated 4-1 HECT domain and elements of the Tsg101 UEV domain involved in noncovalent ubiquitin binding. Furthermore, we show using an established reporter assay that HECT residues perturbed by UEV proximity define determinants of viral maturation and infectivity. These results suggest the UEV interaction is a determinant of HECT activity in Ub signaling. As the endosomal trafficking pathway is hijacked by several human pathogens for egress, the HECT-UEV interaction could represent a potential novel target for therapeutic intervention.
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Affiliation(s)
- David A. Nyenhuis
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rohith Rajasekaran
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Susan Watanabe
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mahfuz Khan
- Department of Microbiology & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Michael Powell
- Department of Microbiology & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Carol A. Carter
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA,For correspondence: Nico Tjandra; Carol A. Carter
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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4
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Persaud A, Jiang C, Liu Z, Kefalas G, Demian WL, Rotin D. 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 DOI: 10.1073/pnas.2122495119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [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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5
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Hunkeler M, Jin CY, Ma MW, Monda JK, Overwijn D, Bennett EJ, Fischer ES. Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition. Mol Cell 2021; 81:3468-3480.e7. [PMID: 34314700 PMCID: PMC8476073 DOI: 10.1016/j.molcel.2021.06.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/19/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
HECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival factors, including Mcl1, p53, DDIT4, and Myc. Although mutations in HUWE1 and related HECT ligases are widely implicated in human disease, our molecular understanding remains limited. Here we present a comprehensive investigation of full-length HUWE1, deepening our understanding of this class of enzymes. The N-terminal ~3,900 amino acids of HUWE1 are indispensable for proper ligase function, and our cryo-EM structures of HUWE1 offer a complete molecular picture of this large HECT ubiquitin ligase. HUWE1 forms an alpha solenoid-shaped assembly with a central pore decorated with protein interaction modules. Structures of HUWE1 variants linked to neurodevelopmental disorders as well as of HUWE1 bound to a model substrate link the functions of this essential enzyme to its three-dimensional organization. Hunkeler et al. present the cryo-EM structure of HUWE1, a large HECT E3 ligase that forms a modular ring-shaped assembly with flexibly attached accessory domains. The influence of mutations associated with intellectual disabilities on HUWE1 activity and substrate recognition by HUWE1 is dissected biochemically and structurally.
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Affiliation(s)
- Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle W Ma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Julie K Monda
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daan Overwijn
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Eric J Bennett
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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6
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Henneberg LT, Schulman BA. Decoding the messaging of the ubiquitin system using chemical and protein probes. Cell Chem Biol 2021; 28:889-902. [PMID: 33831368 PMCID: PMC7611516 DOI: 10.1016/j.chembiol.2021.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modification of proteins by ubiquitin is required for nearly all aspects of eukaryotic cell function. The numerous targets of ubiquitylation, and variety of ubiquitin modifications, are often likened to a code, where the ultimate messages are diverse responses to target ubiquitylation. E1, E2, and E3 multiprotein enzymatic assemblies modify specific targets and thus function as messengers. Recent advances in chemical and protein tools have revolutionized our ability to explore the ubiquitin system, through enabling new high-throughput screening methods, matching ubiquitylation enzymes with their cellular targets, revealing intricate allosteric mechanisms regulating ubiquitylating enzymes, facilitating structural revelation of transient assemblies determined by multivalent interactions, and providing new paradigms for inhibiting and redirecting ubiquitylation in vivo as new therapeutics. Here we discuss the development of methods that control, disrupt, and extract the flow of information across the ubiquitin system and have enabled elucidation of the underlying molecular and cellular biology.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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7
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Lu C, Ning G, Si P, Zhang C, Liu W, Ge W, Cui K, Zhang R, Ge S. E3 ubiquitin ligase HECW1 promotes the metastasis of non-small cell lung cancer cells through mediating the ubiquitination of Smad4. Biochem Cell Biol 2021; 99:675-681. [PMID: 33529121 DOI: 10.1139/bcb-2020-0505] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death globally. Ubiquitin modification plays a crucial role in the regulation of gene expression, and is closely associated with cancer pathogenesis. The aim of our study was to clarify the role and mechanisms of action for HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 (HECW1) in non-small cell lung cancer (NSCLC). Herein, we demonstrate that the expression of HECW1 was significantly increased in NSCLC cell lines and tissues. Upregulation of HECW1 markedly enhanced the proliferation of NSCLC cells, whereas downregulation of HECW1 significantly inhibited proliferation. Moreover, the expression levels of HECW1 positively correlated with the migration and invasiveness of NSCLC cells. Upregulation or downregulation of HECW1 only affected the protein expression levels of SMAD family member 4 (Smad4), but had no effect on the mRNA expression levels. Furthermore, after treatment with MG-132, the relative protein level of Smad4 significantly increased in NSCLC cells. HECW1 promoted the proliferation, migration, and invasiveness of NSCLC cells by inducing the ubiquitination and degradation of Smad4, thus our data provide a novel target for NSCLC treatment.
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Affiliation(s)
- Chen Lu
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Guangyao Ning
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Panpan Si
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Chunsheng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Wenjian Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Wei Ge
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Kai Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Renquan Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
| | - Shenglin Ge
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, No.218 Jixi Road, Shushan District, Hefei 230022, Anhui, China
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8
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Sardana R, Emr SD. Membrane Protein Quality Control Mechanisms in the Endo-Lysosome System. Trends Cell Biol 2021; 31:269-283. [PMID: 33414051 DOI: 10.1016/j.tcb.2020.11.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023]
Abstract
Protein quality control (PQC) machineries play a critical role in selective identification and removal of mistargeted, misfolded, and aberrant proteins. This task is extremely complicated due to the enormous diversity of the proteome. It also requires nuanced and careful differentiation between 'normal' and 'folding intermediates' from 'abnormal' and 'misfolded' protein states. Multiple genetic and proteomic approaches have started to delineate the molecular underpinnings of how these machineries recognize their target and how their activity is regulated. In this review, we summarize our understanding of the various E3 ubiquitin ligases and associated machinery that mediate PQC in the endo-lysosome system in yeast and humans, how they are regulated, and mechanisms of target selection, with the intent of guiding future research in this area.
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Affiliation(s)
- Richa Sardana
- Weill Institute of Cell and Molecular Biology, Cornell University, Ithaca, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Scott D Emr
- Weill Institute of Cell and Molecular Biology, Cornell University, Ithaca, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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9
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Sala-Gaston J, Martinez-Martinez A, Pedrazza L, Lorenzo-Martín LF, Caloto R, Bustelo XR, Ventura F, Rosa JL. HERC Ubiquitin Ligases in Cancer. Cancers (Basel) 2020; 12:cancers12061653. [PMID: 32580485 PMCID: PMC7352365 DOI: 10.3390/cancers12061653] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/12/2020] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
HERC proteins are ubiquitin E3 ligases of the HECT family. The HERC subfamily is composed of six members classified by size into large (HERC1 and HERC2) and small (HERC3-HERC6). HERC family ubiquitin ligases regulate important cellular processes, such as neurodevelopment, DNA damage response, cell proliferation, cell migration, and immune responses. Accumulating evidence also shows that this family plays critical roles in cancer. In this review, we provide an integrated view of the role of these ligases in cancer, highlighting their bivalent functions as either oncogenes or tumor suppressors, depending on the tumor type. We include a discussion of both the molecular mechanisms involved and the potential therapeutic strategies.
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Affiliation(s)
- Joan Sala-Gaston
- Departament de Ciències Fisiològiques, Institut d’Investigació de Bellvitge (IDIBELL), Universitat de Barcelona, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (J.S.-G.); (A.M.-M.); (L.P.); (F.V.)
| | - Arturo Martinez-Martinez
- Departament de Ciències Fisiològiques, Institut d’Investigació de Bellvitge (IDIBELL), Universitat de Barcelona, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (J.S.-G.); (A.M.-M.); (L.P.); (F.V.)
| | - Leonardo Pedrazza
- Departament de Ciències Fisiològiques, Institut d’Investigació de Bellvitge (IDIBELL), Universitat de Barcelona, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (J.S.-G.); (A.M.-M.); (L.P.); (F.V.)
| | - L. Francisco Lorenzo-Martín
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and CIBERONC, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; (L.F.L.-M.); (R.C.); (X.R.B.)
| | - Rubén Caloto
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and CIBERONC, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; (L.F.L.-M.); (R.C.); (X.R.B.)
| | - Xosé R. Bustelo
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and CIBERONC, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, 37007 Salamanca, Spain; (L.F.L.-M.); (R.C.); (X.R.B.)
| | - Francesc Ventura
- Departament de Ciències Fisiològiques, Institut d’Investigació de Bellvitge (IDIBELL), Universitat de Barcelona, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (J.S.-G.); (A.M.-M.); (L.P.); (F.V.)
| | - Jose Luis Rosa
- Departament de Ciències Fisiològiques, Institut d’Investigació de Bellvitge (IDIBELL), Universitat de Barcelona, L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (J.S.-G.); (A.M.-M.); (L.P.); (F.V.)
- Correspondence:
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10
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Abstract
Huwe1 is a highly conserved member of the HECT E3 ubiquitin ligase family. Here, we explore the growing importance of Huwe1 in nervous system development, function and disease. We discuss extensive progress made in deciphering how Huwe1 regulates neural progenitor proliferation and differentiation, cell migration, and axon development. We highlight recent evidence indicating that Huwe1 regulates inhibitory neurotransmission. In covering these topics, we focus on findings made using both vertebrate and invertebrate in vivo model systems. Finally, we discuss extensive human genetic studies that strongly implicate HUWE1 in intellectual disability, and heighten the importance of continuing to unravel how Huwe1 affects the nervous system.
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Affiliation(s)
- Andrew C Giles
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Brock Grill
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA.
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11
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Wang Y, Argiles-Castillo D, Kane EI, Zhou A, Spratt DE. HECT E3 ubiquitin ligases - emerging insights into their biological roles and disease relevance. J Cell Sci 2020; 133:133/7/jcs228072. [PMID: 32265230 DOI: 10.1242/jcs.228072] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases play a critical role in various cellular pathways, including but not limited to protein trafficking, subcellular localization, innate immune response, viral infections, DNA damage responses and apoptosis. To date, 28 HECT E3 ubiquitin ligases have been identified in humans, and recent studies have begun to reveal how these enzymes control various cellular pathways by catalyzing the post-translational attachment of ubiquitin to their respective substrates. New studies have identified substrates and/or interactors with different members of the HECT E3 ubiquitin ligase family, particularly for E6AP and members of the neuronal precursor cell-expressed developmentally downregulated 4 (NEDD4) family. However, there still remains many unanswered questions about the specific roles that each of the HECT E3 ubiquitin ligases have in maintaining cellular homeostasis. The present Review discusses our current understanding on the biological roles of the HECT E3 ubiquitin ligases in the cell and how they contribute to disease development. Expanded investigations on the molecular basis for how and why the HECT E3 ubiquitin ligases recognize and regulate their intracellular substrates will help to clarify the biochemical mechanisms employed by these important enzymes in ubiquitin biology.
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Affiliation(s)
- Yaya Wang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, Shanxi, China 710054.,Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Diana Argiles-Castillo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Emma I Kane
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Anning Zhou
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, Shanxi, China 710054
| | - Donald E Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
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12
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Abstract
Protein ubiquitylation is essential for the maintenance of cellular homeostasis. E3 ubiquitin ligases are key components of the enzymatic machinery catalyzing the attachment of ubiquitin to substrate proteins. Consequently, enzymatic dysfunction has been associated with medical conditions including cancer, diabetes, and cardiovascular and neurodegenerative disorders. To safeguard substrate selection and ubiquitylation, the activity of E3 ligases is tightly regulated by post-translational modifications including phosphorylation, sumoylation, and ubiquitylation, as well as binding of alternative adaptor molecules and cofactors. Recent structural studies identified homotypic and heterotypic interactions between E3 ligases, adding another layer of control for rapid adaptation to changing environmental and physiological conditions. Here, we discuss the regulation of E3 ligase activity by combinatorial oligomerization and summarize examples of associated ubiquitylation pathways and mechanisms.
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Affiliation(s)
- Vishnu Balaji
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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13
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Grimsey NJ, Narala R, Rada CC, Mehta S, Stephens BS, Kufareva I, Lapek J, Gonzalez DJ, Handel TM, Zhang J, Trejo J. A Tyrosine Switch on NEDD4-2 E3 Ligase Transmits GPCR Inflammatory Signaling. Cell Rep 2018; 24:3312-3323.e5. [PMID: 30232011 DOI: 10.1016/j.celrep.2018.08.061] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [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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14
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Beasley SA, Bardhi R, Spratt DE. 1H, 13C, and 15N resonance assignments of the C-terminal lobe of the human HECT E3 ubiquitin ligase ITCH. Biomol NMR Assign 2019; 13:15-20. [PMID: 30229450 PMCID: PMC6439258 DOI: 10.1007/s12104-018-9843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
ITCH (aka Atrophin-1-interacting protein 4) is a prominent member of the NEDD4 HECT (Homologous to E6AP C-Terminus) E3 ubiquitin ligase family that regulates numerous cellular functions including inflammatory responses through T-cell activation, cell differentiation, and apoptosis. Known intracellular targets of ITCH-dependent ubiquitylation include receptor proteins, signaling molecules, and transcription factors. The HECT C-terminal lobe of ITCH contains the conserved catalytic cysteine required for the covalent attachment of ubiquitin onto a substrate and polyubiquitin chain assembly. We report here the complete experimentally determined 1H, 13C, and 15N backbone and sidechain resonance assignments for the HECT C-terminal lobe of ITCH (residues 784-903) using heteronuclear, multidimensional NMR spectroscopy. These resonance assignments will be used in future NMR-based studies to examine the role of dynamics and conformational flexibility in HECT-dependent ubiquitylation as well as deciphering the structural and biochemical basis for polyubiquitin chain synthesis and specificity by ITCH.
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Affiliation(s)
- Steven A Beasley
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA, 01610, USA
| | - Roela Bardhi
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA, 01610, USA
| | - Donald E Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA, 01610, USA.
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15
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Yanku Y, Bitman-Lotan E, Zohar Y, Kurant E, Zilke N, Eilers M, Orian A. Drosophila HUWE1 Ubiquitin Ligase Regulates Endoreplication and Antagonizes JNK Signaling During Salivary Gland Development. Cells 2018; 7:E151. [PMID: 30261639 PMCID: PMC6210797 DOI: 10.3390/cells7100151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 01/18/2023] Open
Abstract
The HECT-type ubiquitin ligase HECT, UBA and WWE Domain Containing 1, (HUWE1) regulates key cancer-related pathways, including the Myc oncogene. It affects cell proliferation, stress and immune signaling, mitochondria homeostasis, and cell death. HUWE1 is evolutionarily conserved from Caenorhabditis elegance to Drosophila melanogaster and Humans. Here, we report that the Drosophila ortholog, dHUWE1 (CG8184), is an essential gene whose loss results in embryonic lethality and whose tissue-specific disruption establishes its regulatory role in larval salivary gland development. dHUWE1 is essential for endoreplication of salivary gland cells and its knockdown results in the inability of these cells to replicate DNA. Remarkably, dHUWE1 is a survival factor that prevents premature activation of JNK signaling, thus preventing the disintegration of the salivary gland, which occurs physiologically during pupal stages. This function of dHUWE1 is general, as its inhibitory effect is observed also during eye development and at the organismal level. Epistatic studies revealed that the loss of dHUWE1 is compensated by dMyc proeitn expression or the loss of dmP53. dHUWE1 is therefore a conserved survival factor that regulates organ formation during Drosophila development.
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Affiliation(s)
- Yifat Yanku
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
| | - Eliya Bitman-Lotan
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
| | - Yaniv Zohar
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
- Institute of Pathology, RAMBAM Medical Center, Haifa 30196, Israel.
| | - Estee Kurant
- Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel.
| | - Norman Zilke
- Genome-Scale Biology Research Program Institute of Biomedicine University of Helsinki, 00290 Helsinki, Finland.
| | - Martin Eilers
- Theodor Boveri Institute, Biocenter, University of Würzburg, D-97074 Würzburg, Germany.
| | - Amir Orian
- Rappaport Research Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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16
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Pergolizzi B, Bozzaro S, Bracco E. G-Protein Dependent Signal Transduction and Ubiquitination in Dictyostelium. Int J Mol Sci 2017; 18:ijms18102180. [PMID: 29048338 PMCID: PMC5666861 DOI: 10.3390/ijms18102180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/20/2022] Open
Abstract
Signal transduction through G-protein-coupled receptors (GPCRs) is central for the regulation of virtually all cellular functions, and it has been widely implicated in human diseases. These receptors activate a common molecular switch that is represented by the heterotrimeric G-protein generating a number of second messengers (cAMP, cGMP, DAG, IP3, Ca2+ etc.), leading to a plethora of diverse cellular responses. Spatiotemporal regulation of signals generated by a given GPCR is crucial for proper signalling and is accomplished by a series of biochemical modifications. Over the past few years, it has become evident that many signalling proteins also undergo ubiquitination, a posttranslational modification that typically leads to protein degradation, but also mediates processes such as protein-protein interaction and protein subcellular localization. The social amoeba Dictyostelium discoideum has proven to be an excellent model to investigate signal transduction triggered by GPCR activation, as cAMP signalling via GPCR is a major regulator of chemotaxis, cell differentiation, and multicellular morphogenesis. Ubiquitin ligases have been recently involved in these processes. In the present review, we will summarize the most significant pathways activated upon GPCRs stimulation and discuss the role played by ubiquitination in Dictyostelium cells.
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Affiliation(s)
- Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Turin, AOUS. Luigi, 10043 Orbassano TO, Italy.
| | - Salvatore Bozzaro
- Department of Clinical and Biological Sciences, University of Turin, AOUS. Luigi, 10043 Orbassano TO, Italy.
| | - Enrico Bracco
- Department of Oncology, University of Turin, AOU S. Luigi, 10043 Orbassano TO, Italy.
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17
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French ME, Klosowiak JL, Aslanian A, Reed SI, Yates JR, Hunter T. Mechanism of ubiquitin chain synthesis employed by a HECT domain ubiquitin ligase. J Biol Chem 2017; 292:10398-10413. [PMID: 28461335 DOI: 10.1074/jbc.m117.789479] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 04/27/2017] [Indexed: 11/06/2022] Open
Abstract
Homologous to E6AP C-terminal (HECT) ubiquitin (Ub) ligases (E3s) are a large class of enzymes that bind to their substrates and catalyze ubiquitination through the formation of a Ub thioester intermediate. The mechanisms by which these E3s assemble polyubiquitin chains on their substrates remain poorly defined. We report here that the Nedd4 family HECT E3, WWP1, assembles substrate-linked Ub chains containing Lys-63, Lys-48, and Lys-11 linkages (Lys-63 > Lys-48 > Lys-11). Our results demonstrate that WWP1 catalyzes the formation of Ub chains through a sequential addition mechanism, in which Ub monomers are transferred in a successive fashion to the substrate, and that ubiquitination by WWP1 requires the presence of a low-affinity, noncovalent Ub-binding site within the HECT domain. Unexpectedly, we find that the formation of Ub chains by WWP1 occurs in two distinct phases. In the first phase, chains are synthesized in a unidirectional manner and are linked exclusively through Lys-63 of Ub. In the second phase, chains are elongated in a multidirectional fashion characterized by the formation of mixed Ub linkages and branched structures. Our results provide new insight into the mechanism of Ub chain formation employed by Nedd4 family HECT E3s and suggest a framework for understanding how this family of E3s generates Ub signals that function in proteasome-independent and proteasome-dependent pathways.
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Affiliation(s)
- Michael E French
- From the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037.,the Departments of Cell and Molecular Biology and
| | - Julian L Klosowiak
- the Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Aaron Aslanian
- From the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037.,Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, and
| | | | - John R Yates
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, and
| | - Tony Hunter
- From the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037,
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18
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Braganza A, Li J, Zeng X, Yates NA, Dey NB, Andrews J, Clark J, Zamani L, Wang XH, St Croix C, O'Sullivan R, Garcia-Exposito L, Brodsky JL, Sobol RW. UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase. J Biol Chem 2016; 292:2470-2484. [PMID: 28003368 DOI: 10.1074/jbc.m116.766824] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 11/06/2022] Open
Abstract
Recent genome-wide studies found that patients with hypotonia, developmental delay, intellectual disability, congenital anomalies, characteristic facial dysmorphic features, and low cholesterol levels suffer from Kaufman oculocerebrofacial syndrome (KOS, also reported as blepharophimosis-ptosis-intellectual disability syndrome). The primary cause of KOS is autosomal recessive mutations in the gene UBE3B However, to date, there are no studies that have determined the cellular or enzymatic function of UBE3B. Here, we report that UBE3B is a mitochondrion-associated protein with homologous to the E6-AP Cterminus (HECT) E3 ubiquitin ligase activity. Mutating the catalytic cysteine (C1036A) or deleting the entire HECT domain (amino acids 758-1068) results in loss of UBE3B's ubiquitylation activity. Knockdown of UBE3B in human cells induces changes in mitochondrial morphology and physiology, a decrease in mitochondrial volume, and a severe suppression of cellular proliferation. We also discovered that UBE3B interacts with calmodulin via its N-terminal isoleucine-glutamine (IQ) motif. Deletion of the IQ motif (amino acids 29-58) results in loss of calmodulin binding and a significant increase in the in vitro ubiquitylation activity of UBE3B. In addition, we found that changes in calcium levels in vitro disrupt the calmodulin-UBE3B interaction. These studies demonstrate that UBE3B is an E3 ubiquitin ligase and reveal that the enzyme is regulated by calmodulin. Furthermore, the modulation of UBE3B via calmodulin and calcium implicates a role for calcium signaling in mitochondrial protein ubiquitylation, protein turnover, and disease.
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Affiliation(s)
- Andrea Braganza
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Jianfeng Li
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, School of the Health Sciences, and
| | - Nathan A Yates
- the Hillman Cancer Center, University of Pittsburgh Cancer Institute.,Biomedical Mass Spectrometry Center, School of the Health Sciences, and.,the Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and
| | - Nupur B Dey
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Joel Andrews
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Jennifer Clark
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Leila Zamani
- the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
| | - Xiao-Hong Wang
- the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Claudette St Croix
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Roderick O'Sullivan
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Laura Garcia-Exposito
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.,the Hillman Cancer Center, University of Pittsburgh Cancer Institute
| | - Jeffrey L Brodsky
- the Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Robert W Sobol
- From the Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, .,the Hillman Cancer Center, University of Pittsburgh Cancer Institute.,the Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama 36604
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19
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Sánchez-Tena S, Cubillos-Rojas M, Schneider T, Rosa JL. Functional and pathological relevance of HERC family proteins: a decade later. Cell Mol Life Sci 2016; 73:1955-68. [PMID: 26801221 DOI: 10.1007/s00018-016-2139-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/22/2022]
Abstract
The HERC gene family encodes proteins with two characteristic domains in their sequence: the HECT domain and the RCC1-like domain (RLD). In humans, the HERC family comprises six members that can be divided into two groups based on their molecular mass and domain structure. Whereas large HERCs (HERC1 and HERC2) contain one HECT and more than one RLD, small HERCs (HERC3-6) possess single HECT and RLD domains. Accumulating evidence shows the HERC family proteins to be key components of a wide range of cellular functions, including neurodevelopment, DNA damage repair, cell growth and immune response. Considering the significant recent advances made regarding HERC functionality, an updated review summarizing the progress is greatly needed at 10 years since the last HERC review. We provide an integrated view of HERC function and go into detail about its implications for several human diseases such as cancer and neurological disorders.
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20
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Pan H, Xu X, Wu D, Qiu Q, Zhou S, He X, Zhou Y, Qu P, Hou J, He J, Zhou J. Novel somatic mutations identified by whole-exome sequencing in muscle-invasive transitional cell carcinoma of the bladder. Oncol Lett 2016; 11:1486-1492. [PMID: 26893765 DOI: 10.3892/ol.2016.4094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 11/11/2015] [Indexed: 11/06/2022] Open
Abstract
Transitional cell carcinoma (TCC) is the one of the most commonly observed types of cancer globally. The identification of novel disease-associated genes in TCC has had a significant effect on the diagnosis and treatment of bladder cancer; however, there may be a large number of novel genes that have not been identified. In the present study, the exomes of two individuals who were diagnosed with muscle-invasive TCC (MI-TCC) were sequenced to investigate potential variants. Subsequently, following algorithm and filter analysis, Sanger sequencing was used to validate the results of deep sequencing. Immunohistochemistry (IHC) was employed to observe the differences in HECT, C2 and WW domain-containing E3 ubiquitin protein ligase 1 (HECW1) protein expression between tumor tissues and para-carcinoma tissues. A total of 6 nonsynonymous mutation genes were identified in MI-TCC, identified as copine VII, RNA binding motif protein, X-linked-like 3, acyl-CoA synthetase medium-chain family member 2A, HECW1, zinc finger protein 273 and trichohyalin. Furthermore, 5 cases were identified to possess a HECW1 gene mutation in 61 MI-TCC specimens, and all of these were point mutations located at exon 11 on chromosome 7. The mutation categories of HECW1 had 4 missense mutations and 1 nonsense mutation. IHC revealed that HECW1 protein was expressed at significantly increased levels in MI-TCC compared with normal bladder urothelium (P<0.001). The present study provided a novel approach for investigating genetic changes in the MI-TCC exome, and identified the novel mutant gene HECW1, which may possess a significant role in the pathogenesis of TCC.
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Affiliation(s)
- Huixing Pan
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China; Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224006, P.R. China
| | - Xiaojian Xu
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Deyao Wu
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224006, P.R. China
| | - Qiaocheng Qiu
- Department of Human Leukocyte Antigen Laboratory, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Shoujun Zhou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Xuefeng He
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Yunfeng Zhou
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224006, P.R. China
| | - Ping Qu
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224006, P.R. China
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jun He
- Department of Human Leukocyte Antigen Laboratory, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Jian Zhou
- Department of Urology, The Fourth Affiliated Hospital of Nantong Medical College, Yancheng City No. 1 People's Hospital, Yancheng, Jiangsu 224006, P.R. China
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21
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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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22
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Henderson JM, Nisperos SV, Weeks J, Ghulam M, Marín I, Zayas RM. Identification of HECT E3 ubiquitin ligase family genes involved in stem cell regulation and regeneration in planarians. Dev Biol 2015; 404:21-34. [PMID: 25956527 DOI: 10.1016/j.ydbio.2015.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 12/28/2022]
Abstract
E3 ubiquitin ligases constitute a large family of enzymes that modify specific proteins by covalently attaching ubiquitin polypeptides. This post-translational modification can serve to regulate protein function or longevity. In spite of their importance in cell physiology, the biological roles of most ubiquitin ligases remain poorly understood. Here, we analyzed the function of the HECT domain family of E3 ubiquitin ligases in stem cell biology and tissue regeneration in planarians. Using bioinformatic searches, we identified 17 HECT E3 genes that are expressed in the Schmidtea mediterranea genome. Whole-mount in situ hybridization experiments showed that HECT genes were expressed in diverse tissues and most were expressed in the stem cell population (neoblasts) or in their progeny. To investigate the function of all HECT E3 ligases, we inhibited their expression using RNA interference (RNAi) and determined that orthologs of huwe1, wwp1, and trip12 had roles in tissue regeneration. We show that huwe1 RNAi knockdown led to a significant expansion of the neoblast population and death by lysis. Further, our experiments showed that wwp1 was necessary for both neoblast and intestinal tissue homeostasis as well as uncovered an unexpected role of trip12 in posterior tissue specification. Taken together, our data provide insights into the roles of HECT E3 ligases in tissue regeneration and demonstrate that planarians will be a useful model to evaluate the functions of E3 ubiquitin ligases in stem cell regulation.
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Affiliation(s)
- Jordana M Henderson
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Sean V Nisperos
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Joi Weeks
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Mahjoobah Ghulam
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
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23
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Caldeira MV, Salazar IL, Curcio M, Canzoniero LMT, Duarte CB. Role of the ubiquitin-proteasome system in brain ischemia: friend or foe? Prog Neurobiol 2013; 112:50-69. [PMID: 24157661 DOI: 10.1016/j.pneurobio.2013.10.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/08/2013] [Accepted: 10/15/2013] [Indexed: 11/26/2022]
Abstract
The ubiquitin-proteasome system (UPS) is a catalytic machinery that targets numerous cellular proteins for degradation, thus being essential to control a wide range of basic cellular processes and cell survival. Degradation of intracellular proteins via the UPS is a tightly regulated process initiated by tagging a target protein with a specific ubiquitin chain. Neurons are particularly vulnerable to any change in protein composition, and therefore the UPS is a key regulator of neuronal physiology. Alterations in UPS activity may induce pathological responses, ultimately leading to neuronal cell death. Brain ischemia triggers a complex series of biochemical and molecular mechanisms, such as an inflammatory response, an exacerbated production of misfolded and oxidized proteins, due to oxidative stress, and the breakdown of cellular integrity mainly mediated by excitotoxic glutamatergic signaling. Brain ischemia also damages protein degradation pathways which, together with the overproduction of damaged proteins and consequent upregulation of ubiquitin-conjugated proteins, contribute to the accumulation of ubiquitin-containing proteinaceous deposits. Despite recent advances, the factors leading to deposition of such aggregates after cerebral ischemic injury remain poorly understood. This review discusses the current knowledge on the role of the UPS in brain function and the molecular mechanisms contributing to UPS dysfunction in brain ischemia with consequent accumulation of ubiquitin-containing proteins. Chemical inhibitors of the proteasome and small molecule inhibitors of deubiquitinating enzymes, which promote the degradation of proteins by the proteasome, were both shown to provide neuroprotection in brain ischemia, and this apparent contradiction is also discussed in this review.
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Affiliation(s)
- Margarida V Caldeira
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal
| | - Ivan L Salazar
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal; Doctoral Programme in Experimental Biology and Biomedicine, Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra (IIIUC), Portugal
| | - Michele Curcio
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal; Department of Science and Technology, University of Sannio, Benevento, Italy
| | | | - Carlos B Duarte
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3004-517 Coimbra, Portugal.
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Abstract
The crystal structure of a HECT E3 enzyme has been captured as it transfers ubiquitin to a target protein, revealing the dramatic changes in shape that enable it to modify particular residues in its targets.
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Affiliation(s)
- Hermann-Josef Meyer
- is in the Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States
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25
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Kamadurai HB, Qiu Y, Deng A, Harrison JS, Macdonald C, Actis M, Rodrigues P, Miller DJ, Souphron J, Lewis SM, Kurinov I, Fujii N, Hammel M, Piper R, Kuhlman B, Schulman BA. Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. eLife 2013; 2:e00828. [PMID: 23936628 PMCID: PMC3738095 DOI: 10.7554/elife.00828] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/20/2013] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination by HECT E3 enzymes regulates myriad processes, including tumor suppression, transcription, protein trafficking, and degradation. HECT E3s use a two-step mechanism to ligate ubiquitin to target proteins. The first step is guided by interactions between the catalytic HECT domain and the E2∼ubiquitin intermediate, which promote formation of a transient, thioester-bonded HECT∼ubiquitin intermediate. Here we report that the second step of ligation is mediated by a distinct catalytic architecture established by both the HECT E3 and its covalently linked ubiquitin. The structure of a chemically trapped proxy for an E3∼ubiquitin-substrate intermediate reveals three-way interactions between ubiquitin and the bilobal HECT domain orienting the E3∼ubiquitin thioester bond for ligation, and restricting the location of the substrate-binding domain to prioritize target lysines for ubiquitination. The data allow visualization of an E2-to-E3-to-substrate ubiquitin transfer cascade, and show how HECT-specific ubiquitin interactions driving multiple reactions are repurposed by a major E3 conformational change to promote ligation. DOI:http://dx.doi.org/10.7554/eLife.00828.001 Ubiquitin is a small protein that can be covalently linked to other, ‘target’, proteins in a cell to influence their behavior. Ubiquitin can be linked to its targets either as single copies or as polyubiquitin chains in which several ubiquitin molecules are bound end-on-end to each other, with one end of the chain attached to the target protein. A multi-step cascade involving enzymes known as E1, E2, and E3 adds ubiquitin to its targets. These enzymes function in a manner like runners in a relay, with ubiquitin a baton that is passed from E1 to E2 to E3 to the target. The E3 enzyme is a ligase that catalyzes the formation of a new chemical bond between a ubiquitin and its target. There are approximately 600 different E3 enzymes in human cells that regulate a wide variety of target proteins. A major class of E3 enzymes, called HECT E3s, attaches ubiquitin to its targets in a unique two-step mechanism: the E2 enzymes covalently link a ubiquitin to a HECT E3 to form a complex that subsequently transfers the ubiquitin to its target protein. The ubiquitin is typically added to a particular amino acid, lysine, on the target protein, but the details of how HECT E3s execute this transfer are not well understood. To address this issue, Kamadurai et al. investigate how Rsp5, a HECT E3 ligase in yeast, attaches ubiquitin to a target protein called Sna3. All HECT E3s have a domain—the HECT domain—that catalyzes the transfer of ubiquitin to its target protein. This domain consists of two sub-structures: the C-lobe, which can receive ubiquitin from E2 and then itself become linked to ubiquitin, and the N-lobe. These lobes were previously thought to adopt various orientations relative to each other to deliver ubiquitin to sites on different target proteins (including to multiple lysines on a single target protein). Unexpectedly, Kamadurai et al. find that in order to transfer the ubiquitin to Sna3, Rsp5 adopts a discrete HECT domain architecture that creates an active site in which parts of the C-lobe and the N-lobe, which are normally separated, are brought together with a ubiquitin molecule. This architecture also provides a mechanism that dictates which substrate lysines can be ubiquitinated based on how accessible they are to this active site. The same regions of Rsp5 transfer ubiquitin to targets other than Sna3, suggesting that a uniform mechanism—which Kamadurai et al. show is conserved in two related human HECT E3 ligases—might transfer ubiquitin to all its targets. These studies therefore represent a significant step toward understanding how a major class of E3 enzymes modulates the functions of their targets. DOI:http://dx.doi.org/10.7554/eLife.00828.002
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Affiliation(s)
- Hari B Kamadurai
- Department of Structural Biology , St Jude Children's Research Hospital , Memphis , United States
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26
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Kim SJ, Kim WT. Suppression of Arabidopsis RING E3 ubiquitin ligase AtATL78 increases tolerance to cold stress and decreases tolerance to drought stress. FEBS Lett 2013; 587:2584-90. [PMID: 23831064 DOI: 10.1016/j.febslet.2013.06.038] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 06/25/2013] [Accepted: 06/25/2013] [Indexed: 12/24/2022]
Abstract
AtATL78 is an Arabidopsis RING E3 ubiquitin ligase. RT-PCR and promoter-GUS assays revealed that AtATL78 was up-regulated by cold stress and down-regulated by drought. AtATL78 was localized at the plasma-membrane. Suppression of AtATL78 increased tolerance to cold stress but decreased tolerance to drought. Our data suggests that AtATL78 is a negative regulator of cold stress response and a positive regulator of drought stress response in Arabidopsis. These results further suggest that AtATL78 plays opposing roles in cold and drought stress responses.
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Affiliation(s)
- Soo Jin Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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27
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McDowell GS, Philpott A. Non-canonical ubiquitylation: mechanisms and consequences. Int J Biochem Cell Biol 2013; 45:1833-42. [PMID: 23732108 DOI: 10.1016/j.biocel.2013.05.026] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/10/2013] [Accepted: 05/22/2013] [Indexed: 01/04/2023]
Abstract
Post-translational protein modifications initiate, regulate, propagate and terminate a wide variety of processes in cells, and in particular, ubiquitylation targets substrate proteins for degradation, subcellular translocation, cell signaling and multiple other cellular events. Modification of substrate proteins is widely observed to occur via covalent linkages of ubiquitin to the amine groups of lysine side-chains. However, in recent years several new modes of ubiquitin chain attachment have emerged. For instance, covalent modification of non-lysine sites in substrate proteins is theoretically possible according to basic chemical principles underlying the ubiquitylation process, and evidence is building that sites such as the N-terminal amine group of a protein, the hydroxyl group of serine and threonine residues and even the thiol groups of cysteine residues are all employed as sites of ubiquitylation. However, the potential importance of this "non-canonical ubiquitylation" of substrate proteins on sites other than lysine residues has been largely overlooked. This review aims to highlight the unusual features of the process of non-canonical ubiquitylation and the consequences of these events on the activity and fate of a protein.
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Affiliation(s)
- Gary S McDowell
- Department of Oncology, University of Cambridge, Hutchison/Medical Research Council (MRC) Research Centre, Cambridge, UK
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28
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Ryšlavá H, Doubnerová V, Kavan D, Vaněk O. Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 2013; 92:80-109. [PMID: 23603109 DOI: 10.1016/j.jprot.2013.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/22/2022]
Abstract
The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12840 Prague 2, Czech Republic.
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