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Li QJ, Fang XL, Li YQ, Lin JY, Huang CL, He SW, Huang SY, Li JY, Gong S, Liu N, Ma J, Zhao Y, Tang LL. DCAF7 Acts as A Scaffold to Recruit USP10 for G3BP1 Deubiquitylation and Facilitates Chemoresistance and Metastasis in Nasopharyngeal Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403262. [PMID: 38973296 DOI: 10.1002/advs.202403262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/13/2024] [Indexed: 07/09/2024]
Abstract
Despite docetaxel combined with cisplatin and 5-fluorouracil (TPF) being the established treatment for advanced nasopharyngeal carcinoma (NPC), there are patients who do not respond positively to this form of therapy. However, the mechanisms underlying this lack of benefit remain unclear. DCAF7 is identified as a chemoresistance gene attenuating the response to TPF therapy in NPC patients. DCAF7 promotes the cisplatin resistance and metastasis of NPC cells in vitro and in vivo. Mechanistically, DCAF7 serves as a scaffold protein that facilitates the interaction between USP10 and G3BP1, leading to the elimination of K48-linked ubiquitin moieties from Lys76 of G3BP1. This process helps prevent the degradation of G3BP1 via the ubiquitin‒proteasome pathway and promotes the formation of stress granule (SG)-like structures. Moreover, knockdown of G3BP1 successfully reversed the formation of SG-like structures and the oncogenic effects of DCAF7. Significantly, NPC patients with increased levels of DCAF7 showed a high risk of metastasis, and elevated DCAF7 levels are linked to an unfavorable prognosis. The study reveals DCAF7 as a crucial gene for cisplatin resistance and offers further understanding of how chemoresistance develops in NPC. The DCAF7-USP10-G3BP1 axis contains potential targets and biomarkers for NPC treatment.
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Affiliation(s)
- Qing-Jie Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Xue-Liang Fang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Ying-Qin Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Jia-Yi Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Cheng-Long Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Shi-Wei He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Sheng-Yan Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Jun-Yan Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Sha Gong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Na Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Jun Ma
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Yin Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
| | - Ling-Long Tang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 651 Dongfeng Road East, Guangzhou, Guangdong, 510060, China
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2
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DiRusso CJ, DeMaria AM, Wong J, Wang W, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A conserved core region of the scaffold NEMO is essential for signal-induced conformational change and liquid-liquid phase separation. J Biol Chem 2023; 299:105396. [PMID: 37890781 PMCID: PMC10694592 DOI: 10.1016/j.jbc.2023.105396] [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: 05/23/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between the N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | - Anthony M DeMaria
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Judy Wong
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Wei Wang
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jack J Jordanides
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, USA.
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3
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DiRusso CJ, DeMaria AM, Wong J, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A Conserved Core Region of the Scaffold NEMO is Essential for Signal-induced Conformational Change and Liquid-liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542299. [PMID: 37292615 PMCID: PMC10245932 DOI: 10.1101/2023.05.25.542299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO, due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
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Affiliation(s)
| | | | - Judy Wong
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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4
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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5
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Phelan T, Lawler C, Pichlmair A, Little MA, Bowie AG, Brady G. Molluscum Contagiosum Virus Protein MC008 Targets NF-κB Activation by Inhibiting Ubiquitination of NEMO. J Virol 2023; 97:e0010823. [PMID: 36916940 PMCID: PMC10062130 DOI: 10.1128/jvi.00108-23] [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: 01/20/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Molluscum contagiosum virus (MCV) is a human-adapted poxvirus that causes a common and persistent yet mild infection characterized by distinct, contagious, papular skin lesions. These lesions are notable for having little or no inflammation associated with them and can persist for long periods without an effective clearance response from the host. Like all poxviruses, MCV encodes potent immunosuppressive proteins that perturb innate immune pathways involved in virus sensing, the interferon response, and inflammation, which collectively orchestrate antiviral immunity and clearance, with several of these pathways converging at common signaling nodes. One such node is the regulator of canonical nuclear factor kappa B (NF-κB) activation, NF-κB essential modulator (NEMO). Here, we report that the MCV protein MC008 specifically inhibits NF-κB through its interaction with NEMO, disrupting its early ubiquitin-mediated activation and subsequent downstream signaling. MC008 is the third NEMO-targeting inhibitor to be described in MCV to date, with each inhibiting NEMO activation in distinct ways, highlighting strong selective pressure to evolve multiple ways of disabling this key signaling protein. IMPORTANCE Inflammation lies at the heart of most human diseases. Understanding the pathways that drive this response is the key to new anti-inflammatory therapies. Viruses evolve to target inflammation; thus, understanding how they do this reveals how inflammation is controlled and, potentially, how to disable it when it drives disease. Molluscum contagiosum virus (MCV) has specifically evolved to infect humans and displays an unprecedented ability to suppress inflammation in our tissue. We have identified a novel inhibitor of human innate signaling from MCV, MC008, which targets NEMO, a core regulator of proinflammatory signaling. Furthermore, MC008 appears to inhibit early ubiquitination, thus interrupting later events in NEMO activation, thereby validating current models of IκB kinase (IKK) complex regulation.
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Affiliation(s)
- Thomas Phelan
- Trinity Health Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, St. James’ Hospital Campus, Dublin, Ireland
| | - Clara Lawler
- Trinity Health Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, St. James’ Hospital Campus, Dublin, Ireland
| | | | - Mark A. Little
- Trinity Health Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, St. James’ Hospital Campus, Dublin, Ireland
| | - Andrew G. Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Gareth Brady
- Trinity Health Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, St. James’ Hospital Campus, Dublin, Ireland
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6
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DiRusso CJ, Dashtiahangar M, Gilmore TD. Scaffold proteins as dynamic integrators of biological processes. J Biol Chem 2022; 298:102628. [PMID: 36273588 PMCID: PMC9672449 DOI: 10.1016/j.jbc.2022.102628] [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] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022] Open
Abstract
Scaffold proteins act as molecular hubs for the docking of multiple proteins to organize efficient functional units for signaling cascades. Over 300 human proteins have been characterized as scaffolds, acting in a variety of signaling pathways. While the term scaffold implies a static, supportive platform, it is now clear that scaffolds are not simply inert docking stations but can undergo conformational changes that affect their dependent signaling pathways. In this review, we catalog scaffold proteins that have been shown to undergo actionable conformational changes, with a focus on the role that conformational change plays in the activity of the classic yeast scaffold STE5, as well as three human scaffold proteins (KSR, NEMO, SHANK3) that are integral to well-known signaling pathways (RAS, NF-κB, postsynaptic density). We also discuss scaffold protein conformational changes vis-à-vis liquid-liquid phase separation. Changes in scaffold structure have also been implicated in human disease, and we discuss how aberrant conformational changes may be involved in disease-related dysregulation of scaffold and signaling functions. Finally, we discuss how understanding these conformational dynamics will provide insight into the flexibility of signaling cascades and may enhance our ability to treat scaffold-associated diseases.
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7
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Bagnéris C, Senthil Kumar SL, Baratchian M, Britt HM, Assafa TE, Thalassinos K, Collins MK, Barrett TE. Mechanistic insights into the activation of the IKK kinase complex by the Kaposi's Sarcoma Herpes virus oncoprotein vFLIP. J Biol Chem 2022; 298:102012. [PMID: 35525271 PMCID: PMC9163697 DOI: 10.1016/j.jbc.2022.102012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/23/2022] Open
Abstract
Constitutive activation of the canonical NF-κB signaling pathway is a major factor in Kaposi’s sarcoma-associated herpes virus pathogenesis where it is essential for the survival of primary effusion lymphoma. Central to this process is persistent upregulation of the inhibitor of κB kinase (IKK) complex by the virally encoded oncoprotein vFLIP. Although the physical interaction between vFLIP and the IKK kinase regulatory component essential for persistent activation, IKKγ, has been well characterized, it remains unclear how the kinase subunits are rendered active mechanistically. Using a combination of cell-based assays, biophysical techniques, and structural biology, we demonstrate here that vFLIP alone is sufficient to activate the IKK kinase complex. Furthermore, we identify weakly stabilized, high molecular weight vFLIP–IKKγ assemblies that are key to the activation process. Taken together, our results are the first to reveal that vFLIP-induced NF-κB activation pivots on the formation of structurally specific vFLIP–IKKγ multimers which have an important role in rendering the kinase subunits active through a process of autophosphorylation. This mechanism of NF-κB activation is in contrast to those utilized by endogenous cytokines and cellular FLIP homologues.
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Affiliation(s)
- Claire Bagnéris
- Department of Biological Sciences, Institute of Structural Molecular Biology, Birkbeck College, London, UK
| | - Swathi L Senthil Kumar
- Department of Biological Sciences, Institute of Structural Molecular Biology, Birkbeck College, London, UK
| | - Mehdi Baratchian
- Genitourinary Malignancies Research Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hannah M Britt
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Tufa E Assafa
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Konstantinos Thalassinos
- Department of Biological Sciences, Institute of Structural Molecular Biology, Birkbeck College, London, UK; Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Mary K Collins
- Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa, Japan
| | - Tracey E Barrett
- Department of Biological Sciences, Institute of Structural Molecular Biology, Birkbeck College, London, UK.
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8
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Kwok A, Camacho IS, Winter S, Knight M, Meade RM, Van der Kamp MW, Turner A, O'Hara J, Mason JM, Jones AR, Arcus VL, Pudney CR. A Thermodynamic Model for Interpreting Tryptophan Excitation-Energy-Dependent Fluorescence Spectra Provides Insight Into Protein Conformational Sampling and Stability. Front Mol Biosci 2021; 8:778244. [PMID: 34926581 PMCID: PMC8681860 DOI: 10.3389/fmolb.2021.778244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
It is now over 30 years since Demchenko and Ladokhin first posited the potential of the tryptophan red edge excitation shift (REES) effect to capture information on protein molecular dynamics. While there have been many key efforts in the intervening years, a biophysical thermodynamic model to quantify the relationship between the REES effect and protein flexibility has been lacking. Without such a model the full potential of the REES effect cannot be realized. Here, we present a thermodynamic model of the tryptophan REES effect that captures information on protein conformational flexibility, even with proteins containing multiple tryptophan residues. Our study incorporates exemplars at every scale, from tryptophan in solution, single tryptophan peptides, to multitryptophan proteins, with examples including a structurally disordered peptide, de novo designed enzyme, human regulatory protein, therapeutic monoclonal antibodies in active commercial development, and a mesophilic and hyperthermophilic enzyme. Combined, our model and data suggest a route forward for the experimental measurement of the protein REES effect and point to the potential for integrating biomolecular simulation with experimental data to yield novel insights.
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Affiliation(s)
- A Kwok
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - I S Camacho
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, London, United Kingdom
| | - S Winter
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - R M Meade
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - M W Van der Kamp
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | | | - J M Mason
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - A R Jones
- Biometrology, Chemical and Biological Sciences Department, National Physical Laboratory, London, United Kingdom
| | - V L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | - C R Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,BLOC Laboratories Limited, Bath, United Kingdom
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9
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Song B, Chen Y, Liu X, Yuan F, Tan EYJ, Lei Y, Song N, Han Y, Pascal BD, Griffin PR, Luo C, Wu B, Luo D, Zheng J. Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains. Immunity 2021; 54:2218-2230.e5. [PMID: 34644557 DOI: 10.1016/j.immuni.2021.09.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/05/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
The RNA sensor MDA5 recruits the signaling adaptor MAVS to initiate type I interferon signaling and downstream antiviral responses, a process that requires K63-linked polyubiquitin chains. Here, we examined the mechanisms whereby K63-polyUb chain regulate MDA5 activation. Only long unanchored K63-polyUbn (n ≥ 8) could mediate tetramerization of the caspase activation and recruitment domains of MDA5 (MDA5CARDs). Cryoelectron microscopy structures of a polyUb13-bound MDA5CARDs tetramer and a polyUb11-bound MDA5CARDs-MAVSCARD assembly revealed a tower-like formation, wherein eight Ubs tethered along the outer rim of the helical shell, bridging MDA5CARDs and MAVSCARD tetramers into proximity. ATP binding and hydrolysis promoted the stabilization of RNA-bound MDA5 prior to MAVS activation via allosteric effects on CARDs-polyUb complex. Abundant ATP prevented basal activation of apo MDA5. Our findings reveal the ordered assembly of a MDA5 signaling complex competent to recruit and activate MAVS and highlight differences with RIG-I in terms of CARD orientation and Ub sensing that suggest different abilities to induce antiviral responses.
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Affiliation(s)
- Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yun Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xin Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fei Yuan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Eddie Yong Jun Tan
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Yixuan Lei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yinqi Han
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Patrick R Griffin
- The Scripps Research Institute, Department of Molecular Medicine, Jupiter, FL 33458, USA
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bin Wu
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Jie Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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10
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Song K, Cai X, Dong Y, Wu H, Wei Y, Shankavaram UT, Cui K, Lee Y, Zhu B, Bhattacharjee S, Wang B, Zhang K, Wen A, Wong S, Yu L, Xia L, Welm AL, Bielenberg DR, Camphausen KA, Kang Y, Chen H. Epsins 1 and 2 promote NEMO linear ubiquitination via LUBAC to drive breast cancer development. J Clin Invest 2021; 131:129374. [PMID: 32960814 DOI: 10.1172/jci129374] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
Estrogen receptor-negative (ER-negative) breast cancer is thought to be more malignant and devastating than ER-positive breast cancer. ER-negative breast cancer exhibits elevated NF-κB activity, but how this abnormally high NF-κB activity is maintained is poorly understood. The importance of linear ubiquitination, which is generated by the linear ubiquitin chain assembly complex (LUBAC), is increasingly appreciated in NF-κB signaling, which regulates cell activation and death. Here, we showed that epsin proteins, a family of ubiquitin-binding endocytic adaptors, interacted with LUBAC via its ubiquitin-interacting motif and bound LUBAC's bona fide substrate NEMO via its N-terminal homolog (ENTH) domain. Furthermore, epsins promoted NF-κB essential modulator (NEMO) linear ubiquitination and served as scaffolds for recruiting other components of the IκB kinase (IKK) complex, resulting in the heightened IKK activation and sustained NF-κB signaling essential for the development of ER-negative breast cancer. Heightened epsin levels in ER-negative human breast cancer are associated with poor relapse-free survival. We showed that transgenic and pharmacological approaches eliminating epsins potently impeded breast cancer development in both spontaneous and patient-derived xenograft breast cancer mouse models. Our findings established the pivotal role epsins played in promoting breast cancer. Thus, targeting epsins may represent a strategy to restrain NF-κB signaling and provide an important perspective into ER-negative breast cancer treatment.
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Affiliation(s)
- Kai Song
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaofeng Cai
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Yunzhou Dong
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hao Wu
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yong Wei
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.,Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Uma T Shankavaram
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Kui Cui
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yang Lee
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bo Zhu
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sudarshan Bhattacharjee
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Beibei Wang
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kun Zhang
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Aiyun Wen
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott Wong
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lili Yu
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lijun Xia
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Alana L Welm
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Diane R Bielenberg
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kevin A Camphausen
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.,Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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11
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Hou XN, Sekiyama N, Ohtani Y, Yang F, Miyanoiri Y, Akagi KI, Su XC, Tochio H. Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins. Chemphyschem 2021; 22:1505-1517. [PMID: 33928740 DOI: 10.1002/cphc.202100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Indexed: 11/06/2022]
Abstract
Linear polyubiquitin chains regulate diverse signaling proteins, in which the chains adopt various conformations to recognize different target proteins. Thus, the structural plasticity of the chains plays an important role in controlling the binding events. Herein, paramagnetic NMR spectroscopy is employed to explore the conformational space sampled by linear diubiquitin, a minimal unit of linear polyubiquitin, in its free state. Rigorous analysis of the data suggests that, regarding the relative positions of the ubiquitin units, particular regions of conformational space are preferentially sampled by the molecule. By combining these results with further data collected for charge-reversal derivatives of linear diubiquitin, structural insights into the factors underlying the binding events of linear diubiquitin are obtained.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yasuko Ohtani
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ken-Ichi Akagi
- NIBIOHN, Section of Laboratory Equipment, Osaka, 567-0085, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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12
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Blount JR, Johnson SL, Todi SV. Unanchored Ubiquitin Chains, Revisited. Front Cell Dev Biol 2020; 8:582361. [PMID: 33195227 PMCID: PMC7659471 DOI: 10.3389/fcell.2020.582361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
The small modifier protein, ubiquitin, holds a special place in eukaryotic biology because of its myriad post-translational effects that control normal cellular processes and are implicated in various diseases. By being covalently conjugated onto other proteins, ubiquitin changes their interaction landscape - fostering new interactions as well as inhibiting others - and ultimately deciding the fate of its substrates and controlling pathways that span most cell physiology. Ubiquitin can be attached onto other proteins as a monomer or as a poly-ubiquitin chain of diverse structural topologies. Among the types of poly-ubiquitin species generated are ones detached from another substrate - comprising solely ubiquitin as their constituent - referred to as unanchored, or free chains. Considered to be toxic byproducts, these species have recently emerged to have specific physiological functions in immune pathways and during cell stress. Free chains also do not appear to be detrimental to multi-cellular organisms; they can be active members of the ubiquitination process, rather than corollary species awaiting disassembly into mono-ubiquitin. Here, we summarize past and recent studies on unanchored ubiquitin chains, paying special attention to their emerging roles as second messengers in several signaling pathways. These investigations paint complex and flexible outcomes for free ubiquitin chains, and present a revised model of unanchored poly-ubiquitin biology that is in need of additional investigation.
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Affiliation(s)
- Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Neurology, Wayne State University School of Medicine, Detroit, MI, United States
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13
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Jussupow A, Messias AC, Stehle R, Geerlof A, Solbak SMØ, Paissoni C, Bach A, Sattler M, Camilloni C. The dynamics of linear polyubiquitin. SCIENCE ADVANCES 2020; 6:6/42/eabc3786. [PMID: 33055165 PMCID: PMC7556843 DOI: 10.1126/sciadv.abc3786] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/25/2020] [Indexed: 05/17/2023]
Abstract
Polyubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable them to regulate multiple biological pathways. Their dynamic is determined by the linkage between ubiquitins and by the number of ubiquitin units. Characterizing polyubiquitin behavior as a function of their length is hampered because of increasing system size and conformational variability. Here, we introduce a new approach to efficiently integrating small-angle x-ray scattering with simulations allowing us to accurately characterize the dynamics of linear di-, tri-, and tetraubiquitin in the free state as well as of diubiquitin in complex with NEMO, a central regulator in the NF-κB pathway. Our results show that the behavior of the diubiquitin subunits is independent of the presence of additional ubiquitin modules and that the dynamics of polyubiquitins with different lengths follow a simple model. Together with experimental data from multiple biophysical techniques, we then rationalize the 2:1 NEMO:polyubiquitin binding.
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Affiliation(s)
- Alexander Jussupow
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching 85747, Germany
| | - Ana C Messias
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milano, Italy
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Carlo Camilloni
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching 85747, Germany.
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milano, Italy
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14
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Blount JR, Libohova K, Silva GM, Todi SV. Isoleucine 44 Hydrophobic Patch Controls Toxicity of Unanchored, Linear Ubiquitin Chains through NF-κB Signaling. Cells 2020; 9:cells9061519. [PMID: 32580388 PMCID: PMC7348737 DOI: 10.3390/cells9061519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Ubiquitination is a post-translational modification that regulates cellular processes by altering the interactions of proteins to which ubiquitin, a small protein adduct, is conjugated. Ubiquitination yields various products, including mono- and poly-ubiquitinated substrates, as well as unanchored poly-ubiquitin chains whose accumulation is considered toxic. We previously showed that transgenic, unanchored poly-ubiquitin is not problematic in Drosophila melanogaster. In the fruit fly, free chains exist in various lengths and topologies and are degraded by the proteasome; they are also conjugated onto other proteins as one unit, eliminating them from the free ubiquitin chain pool. Here, to further explore the notion of unanchored chain toxicity, we examined when free poly-ubiquitin might become problematic. We found that unanchored chains can be highly toxic if they resemble linear poly-ubiquitin that cannot be modified into other topologies. These species upregulate NF-κB signaling, and modulation of the levels of NF-κB components reduces toxicity. In additional studies, we show that toxicity from untethered, linear chains is regulated by isoleucine 44, which anchors a key interaction site for ubiquitin. We conclude that free ubiquitin chains can be toxic, but only in uncommon circumstances, such as when the ability of cells to modify and regulate them is markedly restricted.
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Affiliation(s)
- Jessica R. Blount
- Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield St., Scott Hall Rm. 3108, Detroit, MI 48201, USA; (J.R.B.); (K.L.)
| | - Kozeta Libohova
- Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield St., Scott Hall Rm. 3108, Detroit, MI 48201, USA; (J.R.B.); (K.L.)
| | | | - Sokol V. Todi
- Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield St., Scott Hall Rm. 3108, Detroit, MI 48201, USA; (J.R.B.); (K.L.)
- Department of Neurology, Wayne State University School of Medicine, 540 East Canfield St., Scott Hall Rm. 3108, Detroit, MI 48201, USA
- Correspondence:
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15
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Shaffer R, DeMaria AM, Kagermazova L, Liu Y, Babaei M, Caban-Penix S, Cervantes A, Jehle S, Makowski L, Gilmore TD, Whitty A, Allen KN. A Central Region of NF-κB Essential Modulator Is Required for IKKβ-Induced Conformational Change and for Signal Propagation. Biochemistry 2019; 58:2906-2920. [PMID: 31145594 DOI: 10.1021/acs.biochem.8b01316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NF-κB essential modulator (NEMO) regulates NF-κB signaling by acting as a scaffold for the kinase IKKβ to direct its activity toward the NF-κB inhibitor, IκBα. Here, we show that a highly conserved central region of NEMO termed the intervening domain (IVD, amino acids 112-195) plays a key role in NEMO function. We determined a structural model of full-length NEMO by small-angle X-ray scattering and show that full-length, wild-type NEMO becomes more compact upon binding of a peptide comprising the NEMO binding domain of IKKβ (amino acids 701-745). Mutation of conserved IVD residues (9SG-NEMO) disrupts this conformational change in NEMO and abolishes the ability of NEMO to propagate NF-κB signaling in cells, although the affinity of 9SG-NEMO for IKKβ compared to that of the wild type is unchanged. On the basis of these results, we propose a model in which the IVD is required for a conformational change in NEMO that is necessary for its ability to direct phosphorylation of IκBα by IKKβ. Our findings suggest a molecular explanation for certain disease-associated mutations within the IVD and provide insight into the role of conformational change in signaling scaffold proteins.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lee Makowski
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States
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16
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Hauenstein AV, Xu G, Kabaleeswaran V, Wu H. Evidence for M1-Linked Polyubiquitin-Mediated Conformational Change in NEMO. J Mol Biol 2017; 429:3793-3800. [PMID: 29111346 PMCID: PMC5705538 DOI: 10.1016/j.jmb.2017.10.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/24/2022]
Abstract
The NF-κB essential modulator (NEMO) is the scaffolding subunit of the inhibitor of κB kinase (IKK) holocomplex and is required for the activation of the catalytic IKK subunits, IKKα and IKKβ, during the canonical inflammatory response. Although structures of shorter constructs of NEMO have been solved, efforts to elucidate the full-length structure of NEMO have proved difficult due to its apparent high conformational plasticity. To better characterize the gross dimensions of full-length NEMO, we employed in-line size exclusion chromatography-small-angle X-ray scattering. We show that NEMO adopts a more compact conformation (Dmax=320Å) than predicted for a fully extended coiled-coil structure (>500Å). In addition, we map a region of NEMO (residues 112-150) in its coiled-coil 1 domain that impedes the binding of linear (M1-linked) di-ubiquitin to its coiled-coil 2-leucine zipper ubiquitin binding domain. This ubiquitin binding inhibition can be overcome by a longer chain of linear, but not K63-linked polyubiquitin. Collectively, these observations suggest that NEMO may be auto-inhibited in the resting state by intramolecular interactions and that during signaling, NEMO may be allosterically activated by binding to long M1-linked polyubiquitin chains.
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Affiliation(s)
- Arthur V Hauenstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, United States
| | - Guozhou Xu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, United States
| | - Venkataraman Kabaleeswaran
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, United States
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, United States.
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17
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Maubach G, Schmädicke AC, Naumann M. NEMO Links Nuclear Factor-κB to Human Diseases. Trends Mol Med 2017; 23:1138-1155. [PMID: 29128367 DOI: 10.1016/j.molmed.2017.10.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/16/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
The nuclear factor (NF)-κB essential modulator (NEMO) is a key regulator in NF-κB-mediated signaling. By transmitting extracellular or intracellular signals, NEMO can control NF-κB-regulated genes. NEMO dysfunction is associated with inherited diseases such as incontinentia pigmenti (IP), ectodermal dysplasia, anhidrotic, with immunodeficiency (EDA-ID), and some cancers. We focus on molecular studies, human case reports, and mouse models emphasizing the significance of NEMO molecular interactions and modifications in health and diseases. This knowledge opens new opportunities to engineer suitable drugs that may putatively target precise NEMO functions attributable to various diseases, while leaving other functions intact, and eliminating cytotoxicity. Indeed, with the advent of novel gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)9, treating some inherited diseases may in the long run, become a reality.
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Affiliation(s)
- Gunter Maubach
- Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Ann-Christin Schmädicke
- Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany.
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18
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Styles MQ, Nesbitt EA, Marr S, Hutchby M, Leak DJ. Characterization of the first naturally thermostable terpene synthases and development of strategies to improve thermostability in this family of enzymes. FEBS J 2017; 284:1700-1711. [PMID: 28371548 PMCID: PMC6849719 DOI: 10.1111/febs.14072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/20/2017] [Accepted: 03/27/2017] [Indexed: 12/24/2022]
Abstract
The terpenoid family of natural products is being targeted for heterologous microbial production as a cheaper and more reliable alternative to extraction from plants. The key enzyme responsible for diversification of terpene structure is the class-I terpene synthase (TS), and these often require engineering to improve properties such as thermostability, robustness and catalytic activity before they are suitable for industrial use. Improving thermostability typically relies on screening a large number of mutants, as there are no naturally thermostable TSs described upon which to base rational design decisions. We have characterized the first examples of natural TSs exhibiting thermostability, which catalyse the formation of the sesquiterpene τ-muurolol at temperatures up to 78 °C. We also report an enzyme with a kcat value of 0.95 s-1 at 65 °C, the highest kcat recorded for a bacterial sesquiterpene synthase. In turn, these thermostable enzymes were used as a model to inform the rational engineering of another TS, with the same specificity but low sequence identity to the model. The newly engineered variant displayed increased thermostability and turnover. Given the high structural homology of the class-I TS domain, this approach could be generally applicable to improving the properties of other enzymes in this class. DATABASE Model data are available in the PMDB database under the accession number PM0080780.
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Affiliation(s)
| | | | - Scott Marr
- Department of Biology and Biochemistry, University of Bath, UK
| | | | - David J Leak
- Department of Biology and Biochemistry, University of Bath, UK
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19
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Catici DAM, Amos HE, Yang Y, van den Elsen JMH, Pudney CR. The red edge excitation shift phenomenon can be used to unmask protein structural ensembles: implications for NEMO-ubiquitin interactions. FEBS J 2016; 283:2272-84. [PMID: 27028374 DOI: 10.1111/febs.13724] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/29/2016] [Indexed: 02/02/2023]
Abstract
To understand complex molecular interactions, it is necessary to account for molecular flexibility and the available equilibrium of conformational states. Only a small number of experimental approaches can access such information. Potentially steady-state red edge excitation shift (REES) spectroscopy can act as a qualitative metric of changes to the protein free energy landscape (FEL) and the equilibrium of conformational states. First, we validate this hypothesis using a single Trp-containing protein, NF-κB essential modulator (NEMO). We provide detailed evidence from chemical denaturation studies, macromolecular crowding studies, and the first report of the pressure dependence of the REES effect. Combination of these data demonstrate that the REES effect can report on the 'ruggedness' of the FEL and we present a phenomenological model, based on realistic physical interpretations, for fitting steady-state REES data to allow quantification of this aspect of the REES effect. We test the conceptual framework we have developed by correlating findings from NEMO ligand-binding studies with the REES data in a range of NEMO-ligand binary complexes. Our findings shed light on the nature of the interaction between NEMO and poly-ubiquitin, suggesting that NEMO is differentially regulated by poly-ubiquitin chain length and that this regulation occurs via a modulation of the available equilibrium of conformational states, rather than gross structural change. This study therefore demonstrates the potential of REES as a powerful tool for tackling contemporary issues in structural biology and biophysics and elucidates novel information on the structure-function relationship of NEMO and key interaction partners.
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Affiliation(s)
- Dragana A M Catici
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Hope E Amos
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | - Yi Yang
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
| | | | - Christopher R Pudney
- Department of Biology and Biochemistry, Faculty of Science, University of Bath, UK
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20
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Schwob A, Mahieux R, Journo C. Les chaînes libres d’ubiquitine. Med Sci (Paris) 2016; 32:329-32. [DOI: 10.1051/medsci/20163204006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Thach TT, Shin D, Han S, Lee S. New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:524-35. [PMID: 27050132 DOI: 10.1107/s2059798316001510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022]
Abstract
The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.
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Affiliation(s)
- Trung Thanh Thach
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi 16419, Republic of Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi 16419, Republic of Korea
| | - Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi 16419, Republic of Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi 16419, Republic of Korea
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22
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Park ES, Elangovan M, Kim YJ, Yoo YJ. UbcD4, an ortholog of E2-25K/Ube2K, is essential for activation of the immune deficiency pathway in Drosophila. Biochem Biophys Res Commun 2015; 469:891-6. [PMID: 26707646 DOI: 10.1016/j.bbrc.2015.12.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/15/2015] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a key regulatory mechanism in the immune deficiency (IMD) pathway in Drosophila. In this study, we first developed a simple immunoblot method to identify components involved in this pathway. Considering the emerging roles of ubiquitin-conjugating enzymes (E2s) in determining ubiquitin chain types and ubiquitination speed, we screened for E2s required for IMD activation. We found that UbcD4, in addition to the previously reported E2s Effete and Bendless, was required for activation of the IMD pathway. RNAi-mediated knockdown of the UbcD4 ortholog, E2-25K/Ube2K, inhibited TNFα- and LPS-mediated activation of the NF-κB pathway, implying that UbcD4 and E2-25K/Ube2K play a conserved role as positive regulators in both pathways.
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Affiliation(s)
- Eun Sil Park
- School of Life Sciences, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, South Korea
| | - Muthukumar Elangovan
- School of Life Sciences, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, South Korea
| | - Young-Joon Kim
- School of Life Sciences, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, South Korea
| | - Yung Joon Yoo
- School of Life Sciences, Gwangju Institute of Science & Technology (GIST), Gwangju 500-712, South Korea.
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