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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [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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2
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Yang C, Shu J, Miao Y, Liu X, Zheng T, Hou R, Xiao J, Feng H. TRIM25 negatively regulates IKKε-mediated interferon signaling in black carp. Fish Shellfish Immunol 2023; 142:109095. [PMID: 37730077 DOI: 10.1016/j.fsi.2023.109095] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
IKKε plays an important role in the activation of IRF3/IRF7 and the production of interferon (IFN), however, its regulation remains obscure in human. E3 ligase TRIM25 has been reported to manipulate the K63-linked ubiquitination of RIG-I, leading to the activation of RIG-I/IFN signaling. To elucidate the role of TRIM25 in teleost, a TRIM25 homolog (bcTRIM25) was cloned and characterized from black carp (Mylopharyngodon piceus). bcTRIM25 contains 653 amino acids, possessing conservative RING, B-box and SPRY domain, which is highly expressed in muscle, spleen and skin. bcTRIM25 knock-down enhanced the antiviral ability of host cells. bcTRIM25 over-expression alone in EPC cells attenuated bcIFNa promoter transcription in the reporter assays and impeded PKR and MX1 expression in qRT-PCR. Interestingly, co-IP assays indicated that bcTRIM25 interacted with bcIKKε and the induced bcIFNa promoter transcription by bcIKKε was notably hindered by bcTRIM25. Furthermore, bcIKKε-induced expression of interferon stimulated genes (ISGs) and antiviral activity were dampened by bcTRIM25. Further exploration showed that bcTRIM25 visibly enhanced the ubiquitination of bcIKKε but significantly attenuated the phosphorylation of bcIKKε. Thus, our data demonstrate for the first time in vertebrate that TRIM25 negatively regulates IKKε through enhancing its ubiquitination, which sheds a light on the regulation of IKKε/IFN signaling.
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Affiliation(s)
- Can Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Juanjuan Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yujia Miao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaoyu Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Tianle Zheng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ruixin Hou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Abbasi M, Mahboubi-Rabbani M, Kashfi K, Sadeghi-Aliabadi H. Prediction of dual NF-κB/IκB inhibitors using an integrative in-silico approaches. J Biomol Struct Dyn 2023; 41:14164-14178. [PMID: 36789516 DOI: 10.1080/07391102.2023.2178507] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
Abstract
Multiple lines of evidence indicate that the NF-κB signaling pathway plays a pivotal role in carcinogenesis; activation of NF-κB in cancer increases cell proliferation and suppresses apoptosis, both of which define tumor mass development. Inhibiting NF-κB leads to tumor suppression by blocking the IKK-α/β enzymes, thus inhibiting its translocation. Furthermore, protecting p65 from acetylation and phosphorylation inhibits NF-κB through its active site. Some small molecules are assumed to inhibit NF-κB and IκB function separately. This study took one of the previously reported NF-κB inhibitors (compound D4) as a promising lead and predicted some dual NF-κB and IκB inhibitors. We performed a virtual screening (VS) workflow on a library with 186,146 compounds with 75% similarity to compound D4 on both NF-κB and IκB proteins. A total of 186 compounds were extracted from three steps of VS 36 were common in both proteins. These compounds were subjected to the quantum polarized ligand docking to elect potent compounds with the highest binding affinity for NF-κB and IκB proteins. The MM-GBSA method calculates the lowest binding free energy for eight selected compounds. These analyses found three top-ranked compounds for each protein with suitable pharmacokinetics properties and higher in-silico inhibitory ability. In the last screening, compound CID_4969 was introduced to a molecular dynamics (MDs) simulation study as a common inhibitor for both proteins. The MDs confirmed the main interactions between the final elected compound and NF-κB/IκB proteins. Consequently, the presented computational approaches could be used for designing promising anti-cancer agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maryam Abbasi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Mahboubi-Rabbani
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Khosrow Kashfi
- Department of Molecular, Cellular, and Biomedical Sciences, Sophie Davis School of Biomedical Education, City University of New York School of Medicine, New York, NY, USA
| | - Hojjat Sadeghi-Aliabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
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de Jesus MSM, Macabeo APG, Ramos JDA, de Leon VNO, Asamitsu K, Okamoto T. Voacanga globosa Spirobisindole Alkaloids Exert Antiviral Activity in HIV Latently Infected Cell Lines by Targeting the NF-kB Cascade: In Vitro and In Silico Investigations. Molecules 2022; 27:1078. [PMID: 35164343 PMCID: PMC8840767 DOI: 10.3390/molecules27031078] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Since the efficiency in the transcription of the HIV genome contributes to the success of viral replication and infectivity, we investigated the downregulating effects of the spirobisindole alkaloids globospiramine (1), deoxyvobtusine (2), and vobtusine lactone (3) from the endemic Philippine medicinal plant, Voacanga globosa, during HIV gene transcription. Alkaloids 1-3 were explored for their inhibitory activity on TNF-α-induced viral replication in two latently HIV-infected cell lines, OM10.1 and J-Lat. The induction of HIV replication from OM10.1 and J-Lat cells elicited by TNF-α was blocked by globospiramine (1) within noncytotoxic concentrations. Furthermore, globospiramine (1) was found to target the NF-ĸB activation cascade in a dose-dependent manner when the transcriptional step at which inhibitory activity is exerted was examined in TNF-α-induced 293 human cells using transient reporter (luciferase) gene expression systems (HIV LTR-luc, ĸB-luc, and mutant ĸB-luc). Interrogation through molecular docking against the NF-ĸB p50/p65 heterodimer and target sites of the subunits comprising the IKK complex revealed high binding affinities of globospiramine (1) against the S281 pocket of the p65 subunit (BE = -9.2 kcal/mol) and the IKKα activation loop (BE = -9.1 kcal/mol). These findings suggest globospiramine (1) as a molecular inspiration to discover new alkaloid-based anti-HIV derivatives.
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Affiliation(s)
- Ma. Sheila M. de Jesus
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - Allan Patrick G. Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - John Donnie A. Ramos
- The Graduate School, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Molecular Diagnostics and Therapeutics Laboratory, Research Center for Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines
| | - Von Novi O. de Leon
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - Kaori Asamitsu
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya 4678601, Japan; (K.A.); (T.O.)
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Graduate School of Medical Sciences, Nagoya City University, Nagoya 4678601, Japan; (K.A.); (T.O.)
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Lopreiato M, Di Cristofano S, Cocchiola R, Mariano A, Guerrizio L, Scandurra R, Mosca L, Raimondo D, d’Abusco AS. Biochemical and Computational Studies of the Interaction between a Glucosamine Derivative, NAPA, and the IKK α Kinase. Int J Mol Sci 2021; 22:ijms22041643. [PMID: 33562013 PMCID: PMC7915277 DOI: 10.3390/ijms22041643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/23/2022] Open
Abstract
The glucosamine derivative 2-(N-Acetyl)-L-phenylalanylamido-2-deoxy-β-D-glucose (NAPA), was shown to inhibit the kinase activity of IKKα, one of the two catalytic subunits of IKK complex, decreasing the inflammatory status in osteoarthritis chondrocytes. In the present work we have investigated the inhibition mechanism of IKKα by NAPA by combining computational simulations, in vitro assays and Mass Spectrometry (MS) technique. The kinase in vitro assay was conducted using a recombinant IKKα and IKKtide, a 20 amino acid peptide substrate derived from IkBα kinase protein and containing the serine residues Ser32 and Ser36. Phosphorylated peptide production was measured by Ultra Performance Liquid Chromatography coupled with Mass Spectrometry (UPLC-MS), and the atomic interaction between IKKα and NAPA has been studied by molecular docking and Molecular Dynamics (MD) approaches. Here we report that NAPA was able to inhibit the IKKα kinase activity with an IC50 of 0.5 mM, to decrease the Km value from 0.337 mM to 0.402 mM and the Vmax from 0.0257 mM·min−1 to 0.0076 mM·min−1. The computational analyses indicate the region between the KD, ULD and SDD domains of IKKα as the optimal binding site explored by NAPA. Biochemical data indicate that there is a non-significant difference between Km and Ki whereas there is a statistically significant difference between the two Vmax values. This evidence, combined with computational results, consistently indicates that the inhibition is non-competitive, and that the NAPA binding site is different than that of ATP or IKKtide.
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Affiliation(s)
- Mariangela Lopreiato
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
- Department of Medicina Sperimentale, Università Magna Graecia, Campus S. Venuta, 88100 Catanzaro, Italy
| | - Samuele Di Cristofano
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy;
| | - Rossana Cocchiola
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
- Clinical Trial Unit, Bambino Gesù Children’s Hospital, IRCSS, P. Sant’Onofrio 4, 00165 Rome, Italy
| | - Alessia Mariano
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
| | - Libera Guerrizio
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
| | - Roberto Scandurra
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
| | - Luciana Mosca
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
| | - Domenico Raimondo
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome, Italy;
- Correspondence: (D.R.); (A.S.d.)
| | - Anna Scotto d’Abusco
- Department of Biochemical Sciences, Sapienza University of Roma, P.le Aldo Moro 5, 00185 Rome, Italy; (M.L.); (R.C.); (A.M.); (L.G.); (R.S.); (L.M.)
- Correspondence: (D.R.); (A.S.d.)
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6
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Li H, Wu X, Chen T, Jiang X, Ren C. Molecular characterization, inducible expression and functional analysis of an IKKβ from the tropical sea cucumber Holothuria leucospilota. Fish Shellfish Immunol 2020; 104:622-632. [PMID: 32585358 DOI: 10.1016/j.fsi.2020.06.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/28/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
The inhibitory kappa B kinase (IKK) is a critical regulator for the nuclear factor-κB (NF-κB) pathway. In this study, an IKKβ named as HLIKKβ was identified from the sea cucumber Holothuria leucospilota. The full-length cDNA of HLIKKβ is 4246 bp in size, containing a 132 bp 5'-untranslated region (UTR), a 1783 bp 3'-UTR and a 2331 bp open reading frame (ORF) encoding a protein of 776 amino acids with a deduced molecular weight of 89.66 kDa. HLIKKβ contains a kinase domain (KD) at its N-terminal, a leucine zipper (LZ) and a helix-loop-helix (HLH) motif at its C-terminal. In the KD, a conserved active loop (SXXXS) were identified. The results of luciferase reporter assay and ELISA assay showed that over-expressed HLIKKβ in HEK293T cells could activate the nuclear factor-κB (NF-κB) and induce the secretion of proinflammatory cytokines TNF-α and IL-1β. When HLIKKβ was silenced by siRNA, the apoptosis rate of sea cucumber coelomocytes was increased significantly, indicating the anti-apoptotic function of HLIKKβ. Moreover, the up-regulation of HLIKKβ mRNA was observed in the sea cucumber coelomocytes after polyriboinosinic polyribocytidylic acid [Poly (I:C)] or lipopolysaccharides (LPS) challenge, suggesting that the HLIKKβ might play important roles in the innate immune defense of sea cucumber against the viral and bacterial infections.
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Affiliation(s)
- Haipeng Li
- Guangzhou University, School of Environmental Science and Engineering, Guangzhou, 510006, PR China.
| | - Xiaofen Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China.
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China.
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China.
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, ISEE, CAS, PR China.
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Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Nature 2020; 583:852-857. [PMID: 32699416 PMCID: PMC7517595 DOI: 10.1038/s41586-020-2533-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/05/2020] [Indexed: 01/07/2023]
Abstract
Complex organisms can rapidly induce select genes in response to diverse environmental cues. This regulation occurs in the context of large genomes condensed by histone proteins into chromatin. The sensing of pathogens by macrophages engages conserved signalling pathways and transcription factors to coordinate the induction of inflammatory genes1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a general feature of dynamically regulated chromatin and transcription4-7. However, how chromatin is regulated at induced genes, and what features of H3.3 might enable rapid and high-level transcription, are unknown. The amino terminus of H3.3 contains a unique serine residue (Ser31) that is absent in 'canonical' H3.1 and H3.2. Here we show that this residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along rapidly induced genes in mouse macrophages. This selective mark of stimulation-responsive genes directly engages the histone methyltransferase SETD2, a component of the active transcription machinery, and 'ejects' the elongation corepressor ZMYND118,9. We propose that features of H3.3 at stimulation-induced genes, including H3.3S31ph, provide preferential access to the transcription apparatus. Our results indicate dedicated mechanisms that enable rapid transcription involving the histone variant H3.3, its phosphorylation, and both the recruitment and the ejection of chromatin regulators.
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Affiliation(s)
- Anja Armache
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Shuang Yang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Alexia Martínez de Paz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lexi E Robbins
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ceyda Durmaz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jin Q Cheong
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arjun Ravishankar
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W Daman
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dughan J Ahimovic
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thaís Klevorn
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Yue
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Tanja Arslan
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Shu Lin
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Tanya Panchenko
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Joel Hrit
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Samuel Thudium
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Erica Korb
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Sandra B Hake
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
- Institute for Genetics, Justus-Liebig-University, Giessen, Germany
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Steven Z Josefowicz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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8
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He L, Zhao Y, Tang L, Yu X, Ye Z, Lin H, Zhang Y, Li S, Lu D. Molecular characterization and functional analysis of IKKα in orange-spotted grouper (Epinephelus coioides). Fish Shellfish Immunol 2020; 101:159-167. [PMID: 32194248 DOI: 10.1016/j.fsi.2020.03.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 06/10/2023]
Abstract
Inhibitor of nuclear factor kappa-B kinase subunit alpha (IKKα) plays crucial roles in regulating activation of nuclear factor kappa-B (NF-κB) in response to pathogens infections. Here, we cloned and identified IKKα gene of orange-spotted grouper (Epinephelus coioides), named as EcIKKα. The gene transcript contained a 2262 bp open reading frame, which encoded 753 amino acids. The typically conserved IKKα structure, including serine kinase domain (KD), leucine chain (LZ) structure, helix-loop-helix (HLH) motif and IKKβ-NEMO-binding domain, was identified in EcIKKα. Phylogenetic analysis suggested that EcIKKα had the closest relationship with large yellow croaker (Larimichthy crocea) IKKα. Ecikkα was ubiquitously expressed in all tissues tested and the highest expression level was in ovary. After lipopolysaccharide (LPS), flagellin, polyinosinic-polycytidylic acid (poly I:C), polyadenylic-polyuridylic acid (poly A:U), and Vibrio parahaemolyticus stimulation, the expression of Ecikkα increased in grouper spleen (GS) cells. In the luciferase assay, NF-κB-luc activity was significantly up-regulated when human embryonic kidney 293T (HEK 293T) cells were transfected with EcIKKα plasmid. Moreover, overexpression of EcIKKα significantly increased LPS- and flagellin-induced proinflammatory cytokines (interleukin-6 (il-6) and tumor necrosis factor-α (tnf-α)) expression, but did not significantly affect poly I:C- and poly A:U-induced cytokines (il-6 and tnf-α) expression. Overall, these results suggested that EcIKKα functions like that of mammals to activate NF-κB, and it could be involved in host defense against invading pathogens.
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Affiliation(s)
- Liangge He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yulin Zhao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Lin Tang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Xue Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhifeng Ye
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266373, PR China; College of Ocean, Hainan University, Haikou, 570228, PR China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266373, PR China
| | - Shuisheng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
| | - Danqi Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
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9
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Han R, Wang JL, Chen HP, Luo XC, Li AX, Dan XM, Li YW. IκB kinase α-1 and -2 regulate cytokine expression in the orange-spotted grouper (Epinephelus coioides). Fish Shellfish Immunol 2020; 101:291-301. [PMID: 32276035 DOI: 10.1016/j.fsi.2020.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/07/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
IκB kinase (IKK) is the core regulator of the nuclear factor-κB (NF-κB) pathway, which is involved in cellular development and proliferation, as well as the inflammatory response. IKKα is an important subunit of the IKK complex. In this study, two IKKαs (EcIKKα-1 and -2) were characterized in E. coioides. Similar to IKKα of other species, EcIKKα-1 and -2 contained a kinase domain, a leucine zipper, a helix-loop-helix domain and a beta NF-κB essential modulator-binding domain. Sequence alignment indicated that EcIKKα-1 and -2 shared high degrees of sequence identity with IKKs from other species (about 63%-96%). EcIKKα-1 and -2 are widely expressed in all tissues, but have different expression profiles in normal groupers. Additionally, EcIKKα-1 and -2 responded rapidly to Cryptocaryon irritans infection at the local infection site (i.e., gill tissue), but there was no significant change in EcIKKα-2 expression. In GS cells, EcIKKα-1 was uniformly distributed in the cytoplasm, while EcIKKα-2 was observed uniformly both in the cytoplasm and nucleus. Both EcIKKα-1 and -2 were found to activate NF-κB, but the luciferase activity of EcIKKα-2 was twice that of EcIKKα-1. In addition, EcIKKα-1 and -2 can regulate the expression of immune-related cytokines (IL-1β, IL-6, IL-8, IL-12 [p35 subunit], and TNF-α). These findings should prove helpful to further elucidate the innate immunity function of IKKα in fish.
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Affiliation(s)
- Rui Han
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China
| | - Jiu-Le Wang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China
| | - Hong-Ping Chen
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China
| | - Xiao-Chun Luo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - An-Xing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial Key Lab for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong Province, China
| | - Xue-Ming Dan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China.
| | - Yan-Wei Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China.
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10
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Martínez-Sánchez SM, Pérez-Sánchez H, Antonio Gabaldón J, Abellán-Alemán J, Montoro-García S. Multifunctional Peptides from Spanish Dry-Cured Pork Ham: Endothelial Responses and Molecular Modeling Studies. Int J Mol Sci 2019; 20:ijms20174204. [PMID: 31466215 PMCID: PMC6747274 DOI: 10.3390/ijms20174204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/24/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022] Open
Abstract
Food peptides contain a very wide range of diversified structures, which explains their diverse range of functional activities. Proatherogenic endothelium is related to vasoconstriction, inflammation, and oxidative stress. In this line, four synthetic bioactive peptides from dry-cured pork ham, previously identified according to their Angiotensin I Converting Enzyme (ACE) inhibitory capacity and high bioavailability, were tested. Among them, KPVAAP displayed an estimated IC50 of 59.22 µM for human ACE inhibition, and docking simulations demonstrated the consistency of the noncompetitive binding with the protein. The addition of synthetic peptides to human endothelial cells significantly prevents the expression of genes related to endothelial dysfunction and inflammation (eNOS, ICAM-1, VCAM-1, IL-6) and lowers NF-κB activation (all p < 0.05). In silico dockings showed that the four bioactive peptides interact with the regulatory subunit NEMO of the NF-κB transcription factor at the same site as other characterized inhibitors (CC2-LZ region). This is the first study linking experimental and computational approaches that shows NF-κB to be the target of biopeptides of food origin. These multifunctional peptides from dry-cured pork ham make them good candidates for further research into their therapeutic or preventive use to attenuate the inflammatory atherosclerotic process.
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Affiliation(s)
- Sara María Martínez-Sánchez
- Laboratorio de Cultivo Celular, Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
- Departamento Tecnología de la Alimentación y Nutrición, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Guadalupe 30107, Murcia, Spain
| | - José Antonio Gabaldón
- Departamento Tecnología de la Alimentación y Nutrición, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
| | - José Abellán-Alemán
- Cátedra de Riesgo Cardiovascular, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain
| | - Silvia Montoro-García
- Laboratorio de Cultivo Celular, Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain.
- Cátedra de Riesgo Cardiovascular, UCAM Universidad Católica San Antonio de Murcia, Campus de los Jerónimos s/n, Guadalupe 30107, Murcia, Spain.
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11
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Anaya-Eugenio GD, Addo EM, Ezzone N, Henkin JM, Ninh TN, Ren Y, Soejarto DD, Kinghorn AD, Carcache de Blanco EJ. Caspase-Dependent Apoptosis in Prostate Cancer Cells and Zebrafish by Corchorusoside C from Streptocaulon juventas. J Nat Prod 2019; 82:1645-1655. [PMID: 31120251 PMCID: PMC6615048 DOI: 10.1021/acs.jnatprod.9b00140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Corchorusoside C (1), isolated from Streptocaulon juventas collected in Vietnam, was found to be nontoxic in a zebrafish ( Danio rerio) model and to induce cytotoxicity in several cancer cell lines with notable selective activity against prostate DU-145 cancer cells (IC50 0.08 μM). Moreover, corchorusoside C induced DU-145 cell shrinkage and cell detachment. In CCD-112CoN colon normal cells, 1 showed significantly reduced cytotoxic activity (IC50 2.3 μM). A preliminary mechanistic study indicated that 1 inhibits activity and protein expression of NF-κB (p50 and p65), IKK (α and β), and ICAM-1 in DU-145 cells. ROS concentrations increased at 5 h post-treatment, and MTP decreased in a dose-dependent manner. Moreover, decreased protein expression of Bcl-2 and increased expression of PARP-1 was observed. Furthermore, corchorusoside C increased both the activity and protein levels of caspases 3 and 7. Additionally, 1 induced sub-G1 population increase of DU-145 cells and modulated caspases in zebrafish with nondifferential morphological effects. Therefore, corchorusoside C (1) induces apoptosis in DU-145 cells and targets the same pathways both in vitro and in vivo in zebrafish. Thus, the use of zebrafish assays seems worthy of wider application than is currently employed for the evaluation of potential anticancer agents of natural origin.
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Affiliation(s)
- Gerardo D. Anaya-Eugenio
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ermias Mekuria Addo
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nathan Ezzone
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Joshua M. Henkin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Tran Ngoc Ninh
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Yulin Ren
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Djaja D. Soejarto
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - A. Douglas Kinghorn
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Esperanza J. Carcache de Blanco
- Division of Pharmacy Practice and Science, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Corresponding Author Tel (E. J. Carcache de Blanco): +1 (614)-247-7815, Fax: +1 (614)-292-1335.
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12
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Peng M, Qiang L, Xu Y, Li C, Li T, Wang J. Modification of Cysteine 179 in IKKβ by Ursolic Acid Inhibits Titanium-Wear-Particle-Induced Inflammation, Osteoclastogenesis, and Hydroxylapatite Resorption. Mol Pharm 2018; 15:5244-5251. [PMID: 30265541 DOI: 10.1021/acs.molpharmaceut.8b00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Indexed: 11/28/2022]
Abstract
Aseptic loosening of artificial joints mainly accounts for the failure of arthroplasty. We previously reported that ursolic acid (UA) inhibited osteolysis caused by titanium (Ti) wear particles via suppression of NF-kB signaling. In the present study, that the suppressive effect of UA on Ti-particle-induced inflammation and osteoclastogenesis targets on IKKβ cys-179 was demonstrated. A retrovirus packaged IKKβC179A plasmid with a Cys-179 mutation replaced by Ala was constructed. qRT-PCR, immunoblot, and immunofluorescence were used to evaluate the gene expressions. Secreted inflammatory cytokines were detected by ELISA. Formation and function of osteoclastogenesis were evaluated by TRAP stain and hydroxylapatite resorption assays. As a result, a mutation of IKKβC179A rescued the therapeutic effect of UA on Ti-particle-induced inflammation, including morphological transforms, upregulation of iNOS and COX-2, increased secretions of TNF-α, IL-1β, and IL-6, and decreased secretion of IL-10. Meanwhile, inhibition of osteoclastogenesis and hydroxylapatite resorptions were restored by transfection of IKKβC179A. Phosphorylations of p65 and the IKKα/β complex and translocation of p65 into the nucleus were suppressed by UA but rescued by a mutation of IKKβC179A. Conclusively, UA inhibits Ti-wear-particle-induced inflammation, osteoclastogenesis, and hydroxylapatite resorption via modifying cysteine 179 of IKKβ.
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Affiliation(s)
- Mingzheng Peng
- Shanghai Key Laboratory of Orthopaedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital , Shanghai Jiao Tong University School of Medicine , 639 Zhizaoju Road , Shanghai 200011 , China
| | - Lei Qiang
- Southwest Jiaotong University College Of Medicine , No.111, North Section, Second Ring Road , Chengdu , Sichuan 610031 , P.R. China
| | - Yan Xu
- Southwest Jiaotong University College Of Medicine , No.111, North Section, Second Ring Road , Chengdu , Sichuan 610031 , P.R. China
| | - Cuidi Li
- Med-X Research Institute, School of Biomedical Engineering , Shanghai Jiao Tong University , 1804 Huashan Road , Shanghai 200030 , China
| | - Tao Li
- Shanghai Key Laboratory of Orthopaedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital , Shanghai Jiao Tong University School of Medicine , 639 Zhizaoju Road , Shanghai 200011 , China
| | - Jinwu Wang
- Shanghai Key Laboratory of Orthopaedic Implant, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital , Shanghai Jiao Tong University School of Medicine , 639 Zhizaoju Road , Shanghai 200011 , China
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13
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Meyer AN, Gallo LH, Ko J, Cardenas G, Nelson KN, Siari A, Campos AR, Whisenant TC, Donoghue DJ. Oncogenic mutations in IKKβ function through global changes induced by K63-linked ubiquitination and result in autocrine stimulation. PLoS One 2018; 13:e0206014. [PMID: 30335863 PMCID: PMC6193727 DOI: 10.1371/journal.pone.0206014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/04/2018] [Indexed: 02/05/2023] Open
Abstract
Mutations at position K171 in the kinase activation loop of Inhibitor of κB kinase beta (IKKβ) occur in multiple myeloma, spleen marginal zone lymphoma and mantle cell lymphoma. Previously, we demonstrated that these result in constitutive kinase activation and stimulate Signal Transducer and Activator of Transcription 3 (STAT3). This work also identified K147 as a site of K63-linked regulatory ubiquitination required for activation of signaling pathways. We now present a more detailed analysis of ubiquitination sites together with a comprehensive examination of the signaling pathways activated by IKKβ K171E mutants. Downstream activation of STAT3 is dependent upon the activity of: UBE2N, the E2 ubiquitin ligase involved in K63-linked ubiquitination; TAK1 (MAP3K7), or TGFβ Activated Kinase, which forms a complex required for NFκB activation; JAK kinases, involved proximally in the phosphorylation of STAT transcription factors in response to inflammatory cytokines; and gp130, or IL-6 Receptor Subunit Beta which, upon binding IL-6 or other specific cytokines, undergoes homodimerization leading to activation of associated JAKs, resulting in STAT activation. We further demonstrate, using an IL-6-responsive cell line, that IKKβ K171E mutants stimulate the release of IL-6 activity into conditioned media. These results show that IKKβ K171E mutants trigger an autocrine loop in which IL-6 is secreted and binds to the IL-6 receptor complex gp130, resulting in JAK activation. Lastly, by examining the differential abundance of proteins associated with K63-only-ubiquitinated IKKβ K171E, proteomic analysis demonstrates the global activation of proliferative responses. As cancers harboring K171-mutated IKKβ are likely to also exhibit activated STAT3 and p44/42 MAPK (Erk1/2), this suggests the possibility of using MAPK (Erk1/2) and JAK inhibitors, or specific ubiquitination inhibitors. K63-linked ubiquitination occurs in other kinases at sites homologous to K147 in IKKβ, including K578 in BRAF V600E, which serves as an oncogenic driver in melanoma and other cancers.
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Affiliation(s)
- April N. Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Leandro H. Gallo
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Juyeon Ko
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Guillermo Cardenas
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Katelyn N. Nelson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Asma Siari
- Université Joseph Fourier Grenoble, Grenoble, France
| | - Alexandre R. Campos
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Thomas C. Whisenant
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, California, United States of America
| | - Daniel J. Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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14
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Zhao J, Zhang L, Mu X, Doebelin C, Nguyen W, Wallace C, Reay DP, McGowan SJ, Corbo L, Clemens PR, Wilson GM, Watkins SC, Solt LA, Cameron MD, Huard J, Niedernhofer LJ, Kamenecka TM, Robbins PD. Development of novel NEMO-binding domain mimetics for inhibiting IKK/NF-κB activation. PLoS Biol 2018; 16:e2004663. [PMID: 29889904 PMCID: PMC6013238 DOI: 10.1371/journal.pbio.2004663] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 06/21/2018] [Accepted: 05/21/2018] [Indexed: 01/24/2023] Open
Abstract
Nuclear factor κB (NF-κB) is a transcription factor important for regulating innate and adaptive immunity, cellular proliferation, apoptosis, and senescence. Dysregulation of NF-κB and its upstream regulator IκB kinase (IKK) contributes to the pathogenesis of multiple inflammatory and degenerative diseases as well as cancer. An 11-amino acid peptide containing the NF-κB essential modulator (NEMO)-binding domain (NBD) derived from the C-terminus of β subunit of IKK, functions as a highly selective inhibitor of the IKK complex by disrupting the association of IKKβ and the IKKγ subunit NEMO. A structure-based pharmacophore model was developed to identify NBD mimetics by in silico screening. Two optimized lead NBD mimetics, SR12343 and SR12460, inhibited tumor necrosis factor α (TNF-α)- and lipopolysaccharide (LPS)-induced NF-κB activation by blocking the interaction between IKKβ and NEMO and suppressed LPS-induced acute pulmonary inflammation in mice. Chronic treatment of a mouse model of Duchenne muscular dystrophy (DMD) with SR12343 and SR12460 attenuated inflammatory infiltration, necrosis and muscle degeneration, demonstrating that these small-molecule NBD mimetics are potential therapeutics for inflammatory and degenerative diseases.
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Affiliation(s)
- Jing Zhao
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Lei Zhang
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Xiaodong Mu
- Department of Orthopaedic Surgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Christelle Doebelin
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - William Nguyen
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Callen Wallace
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daniel P. Reay
- Department of Neurology, University of Pittsburgh, Pennsylvania, United States of America
| | - Sara J. McGowan
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Lana Corbo
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Paula R. Clemens
- Department of Neurology, University of Pittsburgh, Pennsylvania, United States of America
| | - Gabriela Mustata Wilson
- Department of Health Informatics and Information Management, College of Nursing and Health Professions, University of Southern Indiana, Evansville, Indiana, United States of America
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Laura A. Solt
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Michael D. Cameron
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Johnny Huard
- Department of Orthopaedic Surgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Laura J. Niedernhofer
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Theodore M. Kamenecka
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Paul D. Robbins
- Department of Molecular Medicine and the TSRI Center on Aging, The Scripps Research Institute, Jupiter, Florida, United States of America
- * E-mail:
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15
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Li J, Tian Y, Liu J, Wang C, Feng C, Wu H, Feng H. Lysine 39 of IKKε of black carp is crucial for its regulation on IRF7-mediated antiviral signaling. Fish Shellfish Immunol 2018; 77:410-418. [PMID: 29635067 DOI: 10.1016/j.fsi.2018.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/28/2018] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Interferon regulatory factor 7 (IRF7) plays a crucial role in the interferon (IFN) signaling in mammals, in which it is activated by the TBK1/IKKε complex during host antiviral innate immune response. There are few reports about the relation between IRF7 and IKKε in teleost fishes. In this study, the IRF7 homologue (bcIRF7) of black carp (Mylopharyngodon Piceus) has been cloned and characterized. The transcription of bcIRF7 gene increased in host cells in response to the stimulation of LPS, poly (I:C) and viral infection. bcIRF7 migrated around 56 KDa in immunoblot assay and was identified as a predominantly cytosolic protein by immunofluorescent staining. bcIRF7 showed IFN-inducing ability in reporter assay and EPC cells expressing bcIRF7 showed enhanced antiviral ability against both grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV). IKKε of black carp (bcIKKε) was found to be recruited into host innate immune response initiated by SVCV and GCRV in the previous work; in this paper, the kinase dead mutant of bcIKKε, bcIKKε-K39A was constructed and showed no IFN-inducing activity. The data of reporter assay and plaque assay demonstrated that bcIKKε but not bcIKKε-K39A obviously enhanced bcIRF7-mediated IFN production and antiviral activity. Our data support the conclusion that bcIKKε upregulates bcIRF7-mediated antiviral signaling, which most likely depends on its kinase activity.
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Affiliation(s)
- Jun Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yu Tian
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Ji Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Chanyuan Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Chaoliang Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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He J, Li J, Liu H, Yang Z, Zhou F, Wei T, Dong Y, Xue H, Tang L, Liu M. Scandoside Exerts Anti-Inflammatory Effect Via Suppressing NF-κB and MAPK Signaling Pathways in LPS-Induced RAW 264.7 Macrophages. Int J Mol Sci 2018; 19:E457. [PMID: 29401674 PMCID: PMC5855679 DOI: 10.3390/ijms19020457] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 01/07/2018] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 02/07/2023] Open
Abstract
The iridoids of Hedyotis diffusa Willd play an important role in the anti-inflammatory process, but the specific iridoid with anti-inflammatory effect and its mechanism has not be thoroughly studied. An iridoid compound named scandoside (SCA) was isolated from H. diffusa and its anti-inflammatory effect was investigated in lipopolysaccharide (LPS)-induced RAW 264.7 macrophages. Its anti-inflammatory mechanism was confirmed by in intro experiments and molecular docking analyses. As results, SCA significantly decreased the productions of nitric oxide (NO), prostaglandin E₂ (PGE₂), tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) and inhibited the levels of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), TNF-α and IL-6 messenger RNA (mRNA) expression in LPS-induced RAW 264.7 macrophages. SCA treatment suppressed the phosphorylation of inhibitor of nuclear transcription factor kappa-B alpaha (IκB-α), p38, extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK). The docking data suggested that SCA had great binding abilities to COX-2, iNOS and IκB. Taken together, the results indicated that the anti-inflammatory effect of SCA is due to inhibition of pro-inflammatory cytokines and mediators via suppressing the nuclear transcription factor kappa-B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways, which provided useful information for its application and development.
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Affiliation(s)
- Jingyu He
- Bioengineering Research Centre, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou 511458, China.
| | - Jiafeng Li
- Bioengineering Research Centre, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou 511458, China.
| | - Han Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Zichao Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Fenghua Zhou
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Ting Wei
- Bioengineering Research Centre, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou 511458, China.
| | - Yaqian Dong
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Hongjiao Xue
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Lan Tang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Menghua Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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17
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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] [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: 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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18
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Veerappan K, Natarajan S, Ethiraj P, Vetrivel U, Samuel S. Inhibition of IKKβ by celastrol and its analogues - an in silico and in vitro approach. Pharm Biol 2017; 55:368-373. [PMID: 27931154 PMCID: PMC6130723 DOI: 10.1080/13880209.2016.1241809] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/01/2016] [Accepted: 09/23/2016] [Indexed: 05/25/2023]
Abstract
CONTEXT Alzheimer's disease (AD) is the most common form of dementia affecting the aged population and neuroinflammation is one of the most observed AD pathologies. NF-κB is the central regulator of inflammation and inhibitor κB kinase (IKK) is the converging point in NF-κB activation. Celastrol is a natural triterpene used as a treatment for inflammatory conditions. OBJECTIVE This study determines the neuroprotective and inhibitory effect of celastrol on amyloid beta1-42 (Aβ1-42) induced cytotoxicity and IKKβ activity, respectively. MATERIALS AND METHODS Retinoic acid differentiated IMR-32 cells were treated with celastrol (1 μM) before treatment with Aβ1-42 (IC30 10 μM) for 24 h. The cytotoxicity and IKK phosphorylation were measured by MTT and western blotting analysis, respectively. We screened 36 celastrol analogues for the IKKβ inhibition by molecular docking and evaluated their drug like properties to delineate the neuroprotective effects. RESULTS Celastrol (1 μM) inhibited Aβ1-42 (10 μM) induced IκBα phosphorylation and protected IMR-32 cells from cell death. Celastrol and 25 analogues showed strong binding affinity with IKKβ as evidenced by strong hydrogen-bonding interactions with critical active site residues. All the 25 analogues displayed strong anti-inflammatory properties but only 11 analogues showed drug-likeness. Collectively, molecule 15 has highest binding affinity, CNS activity and more drug likeness than parent compound celastrol. DISCUSSION AND CONCLUSION The decreased expression of pIκBα in celastrol pretreated cells affirms the functional representation of inhibited IKKβ activity in these cells. The neuroprotective potentials of celastrol and its analogues may be related to IKK inhibition.
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Affiliation(s)
- Karpagam Veerappan
- Department of Biochemistry, VRR Institute of Biomedical Science (Affiliated to University of Madras), Chennai, Tamilnadu, India
| | | | - Purushoth Ethiraj
- Department of Medical Research, SRM Medical College Hospital and Research Centre, SRM University, Kattankulathur, Tamilnadu, India
| | - Umashankar Vetrivel
- Center for Bioinformatics, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamilnadu, India
| | - Shila Samuel
- Department of Biochemistry, VRR Institute of Biomedical Science (Affiliated to University of Madras), Chennai, Tamilnadu, India
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19
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Anthony NG, Baiget J, Berretta G, Boyd M, Breen D, Edwards J, Gamble C, Gray AI, Harvey AL, Hatziieremia S, Ho KH, Huggan JK, Lang S, Llona-Minguez S, Luo JL, McIntosh K, Paul A, Plevin RJ, Robertson MN, Scott R, Suckling CJ, Sutcliffe OB, Young LC, Mackay SP. Inhibitory Kappa B Kinase α (IKKα) Inhibitors That Recapitulate Their Selectivity in Cells against Isoform-Related Biomarkers. J Med Chem 2017; 60:7043-7066. [PMID: 28737909 PMCID: PMC5578373 DOI: 10.1021/acs.jmedchem.7b00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Indexed: 01/01/2023]
Abstract
IKKβ plays a central role in the canonical NF-kB pathway, which has been extensively characterized. The role of IKKα in the noncanonical NF-kB pathway, and indeed in the canonical pathway as a complex with IKKβ, is less well understood. One major reason for this is the absence of chemical tools designed as selective inhibitors for IKKα over IKKβ. Herein, we report for the first time a series of novel, potent, and selective inhibitors of IKKα. We demonstrate effective target engagement and selectivity with IKKα in U2OS cells through inhibition of IKKα-driven p100 phosphorylation in the noncanonical NF-kB pathway without affecting IKKβ-dependent IKappa-Bα loss in the canonical pathway. These compounds represent the first chemical tools that can be used to further characterize the role of IKKα in cellular signaling, to dissect this from IKKβ and to validate it in its own right as a target in inflammatory diseases.
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Affiliation(s)
- Nahoum G. Anthony
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Jessica Baiget
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Giacomo Berretta
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Marie Boyd
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - David Breen
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Joanne Edwards
- Wolfson Wohl Cancer Research Centre, Institute
of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland, United Kingdom
| | - Carly Gamble
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Alexander I. Gray
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Alan L. Harvey
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Sophia Hatziieremia
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Ka Ho Ho
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Judith K. Huggan
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Stuart Lang
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Sabin Llona-Minguez
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Jia Lin Luo
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Kathryn McIntosh
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Andrew Paul
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Robin J. Plevin
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Murray N. Robertson
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Rebecca Scott
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Colin J. Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, Scotland, United Kingdom
| | - Oliver B. Sutcliffe
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Louise C. Young
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
| | - Simon P. Mackay
- Strathclyde Institute
of Pharmacy and Biomedical Sciences, University
of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, Scotland, United
Kingdom
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20
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Huang L, Xiong T, Yu H, Zhang Q, Zhang K, Li C, Hu L, Zhang Y, Zhang L, Liu Q, Wang S, He X, Bu Z, Cai X, Cui S, Li J, Weng C. Encephalomyocarditis virus 3C protease attenuates type I interferon production through disrupting the TANK-TBK1-IKKε-IRF3 complex. Biochem J 2017; 474:2051-2065. [PMID: 28487378 PMCID: PMC5465970 DOI: 10.1042/bcj20161037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 11/28/2016] [Revised: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
TRAF family member-associated NF-κB activator (TANK) is a scaffold protein that assembles into the interferon (IFN) regulator factor 3 (IRF3)-phosphorylating TANK-binding kinase 1 (TBK1)-(IκB) kinase ε (IKKε) complex, where it is involved in regulating phosphorylation of the IRF3 and IFN production. However, the functions of TANK in encephalomyocarditis virus (EMCV) infection-induced type I IFN production are not fully understood. Here, we demonstrated that, instead of stimulating type I IFN production, the EMCV-HB10 strain infection potently inhibited Sendai virus- and polyI:C-induced IRF3 phosphorylation and type I IFN production in HEK293T cells. Mechanistically, EMCV 3C protease (EMCV 3C) cleaved TANK and disrupted the TANK-TBK1-IKKε-IRF3 complex, which resulted in the reduction in IRF3 phosphorylation and type I IFN production. Taken together, our findings demonstrate that EMCV adopts a novel strategy to evade host innate immune responses through cleavage of TANK.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Tao Xiong
- College of Life Sciences, Yangtze University, Jingzhou 434100, China
| | - Huibin Yu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Quan Zhang
- College of Life Sciences, Yangtze University, Jingzhou 434100, China
| | - Kunli Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Changyao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Liang Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Yuanfeng Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Lijie Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Qinfang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Shengnan Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Xijun He
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Shangjin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiangnan Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Changjiang Weng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
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21
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Godwin RC, Melvin RL, Gmeiner WH, Salsbury FR. Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator). Biochemistry 2017; 56:623-633. [PMID: 28035815 PMCID: PMC5718349 DOI: 10.1021/acs.biochem.6b00755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.
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Affiliation(s)
- Ryan C. Godwin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, United States
| | - Ryan L. Melvin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, United States
| | - William H. Gmeiner
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27107, United States
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, United States
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22
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Melvin RL, Godwin RC, Xiao J, Thompson WG, Berenhaut KS, Salsbury FR. Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge. J Chem Theory Comput 2016; 12:6130-6146. [PMID: 27802394 PMCID: PMC5719493 DOI: 10.1021/acs.jctc.6b00757] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning trajectories into conformational bins. Of the methods available, the vast majority require users to either have some a priori knowledge about the system to be clustered or to tune clustering parameters through trial and error. Here we present non-parametric uses of two modern clustering techniques suitable for first-pass investigation of an MD trajectory. Being non-parametric, these methods require neither prior knowledge nor parameter tuning. The first method, HDBSCAN, is fast-relative to other popular clustering methods-and is able to group unstructured or intrinsically disordered systems (such as intrinsically disordered proteins, or IDPs) into bins that represent global conformational shifts. HDBSCAN is also useful for determining the overall stability of a system-as it tends to group stable systems into one or two bins-and identifying transition events between metastable states. The second method, iMWK-Means, with explicit rescaling followed by K-Means, while slower than HDBSCAN, performs well with stable, structured systems such as folded proteins and is able to identify higher resolution details such as changes in relative position of secondary structural elements. Used in conjunction, these clustering methods allow a user to discern quickly and without prior knowledge the stability of a simulated system and identify both local and global conformational changes.
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Affiliation(s)
- Ryan L. Melvin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Ryan C. Godwin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - William G. Thompson
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Kenneth S. Berenhaut
- Department of Mathematics & Statistics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
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23
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Ma X, Liu X, Zhou D, Bai Y, Gao B, Zhang Z, Qin Z. The NF-κB pathway participates in the response to sulfide stress in Urechis unicinctus. Fish Shellfish Immunol 2016; 58:229-238. [PMID: 27633672 DOI: 10.1016/j.fsi.2016.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/31/2016] [Accepted: 09/11/2016] [Indexed: 05/26/2023]
Abstract
The NF-κB pathway is known to be involved in regulating apoptosis, inflammation and immunity in organisms. In this study, we first identified full-length cDNA sequences of two key molecules in the NF-κB pathway, namely, NEMO and p65, and characterized their responses in the hindgut of Urechis unicinctus (Echiura, Urechidae) exposed to sulfide. The full-length of cDNA was 2491 bp for U. unicinctus NEMO (UuNEMO) and 1971 bp for U. unicinctus p65 (Uup65), and both polyclonal antibodies were prepared using UuNEMO or Uup65 expressed prokaryotically with the sequence of their whole open reading frame. Immunoprecipitation and Western blotting showed that the NF-κB pathway was activated in U. unicinctus exposed to sulfide, in which the content of UuNEMO ubiquitination and nuclear Uup65 increased significantly (p < 0.05) in hindgut tissue of U. unicinctus exposed to sulfide. Furthermore, the mRNA level of UuBcl-xL, a downstream anti-apoptosis gene of the NF-κB pathway, increased significantly (p < 0.05) from 48 h to 72 h and the mRNA level of UuBax, a Bcl-xL antagonist gene, decreased significantly (p < 0.05) at 48 h in the hindgut of U. unicinctus exposed to 50 μM sulfide. During the 150 μM sulfide exposure, the level of UuBcl-xL showed no obvious change, whereas the UuBax mRNA level increased significantly (p < 0.05) at 72 h post-exposure to 150 μM sulfide. We suggested that the activated NF-κB pathway up-regulates UuBcl-xL expression, and evokes an anti-apoptotic response to resist sulfide damage at 50 μM in U. unicinctus. Meanwhile, a Bax-mediated pro-apoptotic response occurs when U. unicinctus is exposed to 150 μM sulfide.
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Affiliation(s)
- Xiaoyu Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaolong Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Di Zhou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yajiao Bai
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Beibei Gao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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24
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Qu Y, Zhou M, Peng L, Li J, Yan J, Yang P, Feng H. Molecular cloning and characterization of IKKε gene from black carp Mylopharyngodon piceus. Fish Shellfish Immunol 2015; 47:122-129. [PMID: 26332502 DOI: 10.1016/j.fsi.2015.08.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/22/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
IKKε is an IκB kinase functioning in NF-κB signal pathway in the innate immune system of higher vertebrates. To exploit the function of IKKε of black carp (bcIKKε) in its antiviral innate immunity, the IKKε gene has been cloned from the RNA isolated from the spleen of black carp. The full-length cDNA of bcIKKε is 2537 bp, which encodes the peptide of 723 amino acids. bcIKKε contains a S-Tkc domain, a PKc domain and a UBL-TBK1-like domain and bcIKKε shares the highest amino acid sequence similarity with that of grass carp. bcIKKε was constitutively transcribed in the selected tissues of black carp including gill, kidney, heart, intestine, liver, muscle, skin and spleen; and the mRNA level of bcIKKε in these tissues varied right after SVCV or GCRV infection. bcIKKε had been well expressed in HEK293T cells and western blot assay determined that this fish kinase was around 80 KDa. The immunofluorescence assay of both NH3T3 cells and EPC cells demonstrated that bcIKKε was located in the cytosolic part of the cell. Report assay result showed that overexpression of bcIKKε in EPC cells activated the expression of both zebrafish IFN and EPC IFN. All our data suggest that bcIKKε is a novel fish kinase functioning in the innate antiviral immune response of black carp.
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Affiliation(s)
- Yixiao Qu
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Man Zhou
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Linzhi Peng
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Li
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Yan
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Peilin Yang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hao Feng
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Li J, Zhou M, Peng L, Sun W, Yang P, Yan J, Feng H. Identification and characterization of IKKε gene from grass carp Ctenopharyngodon idella. Fish Shellfish Immunol 2015; 47:255-263. [PMID: 26370541 DOI: 10.1016/j.fsi.2015.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/01/2015] [Accepted: 09/07/2015] [Indexed: 06/05/2023]
Abstract
IKKε is an IKK-related kinase implicated in antiviral immune response in higher vertebrates. To elucidate the function of IKKε in teleost fish, grass carp IKKε (gcIKKε) has been cloned and characterized in this paper. The full-length cDNA of gcIKKε is composed of 2529 nucleotides and encodes a polypeptide of 723 amino acids. The mRNA transcription of gcIKKε was constitutively detected in all the selected tissues and the gcIKKε mRNA level increased at 36 h after GCRV infection. Western blot data of both HEK293T cells and EPC cells demonstrated that gcIKKε was around 80 KDa; and immunofluorescence staining data of both NIH3T3 cells and EPC cells determined gcIKKε was a cytosolic protein. The mRNA level of gcIKKε in CIK cells was increased more than 150 times right after poly(I:C) treatment and PMA treatment triggered gcIKKε mRNA transcription in CIK cells more than 100 times. Over-expression of gcIKKε in EPC cells activated the promoter activity of both zebrafish IFN and fathead minnow IFN. gcIKKε mRNA transcription level in CIK cells was increased from 48 h post GCRV infection with different MOIs. All the data support the idea that gcIKKε is a novel teleost IκB kinase recruited in the IFN-mediated antiviral immunity of grass carp.
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Affiliation(s)
- Jun Li
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Man Zhou
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Lingzhi Peng
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Wenzheng Sun
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Peilin Yang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Jun Yan
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Hao Feng
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education of China, College of Life Science, Hunan Normal University, Changsha 410081, China.
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Bagnéris C, Rogala KB, Baratchian M, Zamfir V, Kunze MBA, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CWM. Probing the Solution Structure of IκB Kinase (IKK) Subunit γ and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit β by EPR Spectroscopy. J Biol Chem 2015; 290:16539-49. [PMID: 25979343 PMCID: PMC4505408 DOI: 10.1074/jbc.m114.622928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/13/2015] [Indexed: 01/04/2023] Open
Abstract
Viral flice-interacting protein (vFLIP), encoded by the oncogenic Kaposi sarcoma-associated herpes virus (KSHV), constitutively activates the canonical nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) pathway. This is achieved through subversion of the IκB kinase (IKK) complex (or signalosome), which involves a physical interaction between vFLIP and the modulatory subunit IKKγ. Although this interaction has been examined both in vivo and in vitro, the mechanism by which vFLIP activates the kinase remains to be determined. Because IKKγ functions as a scaffold, recruiting both vFLIP and the IKKα/β subunits, it has been proposed that binding of vFLIP could trigger a structural rearrangement in IKKγ conducive to activation. To investigate this hypothesis we engineered a series of mutants along the length of the IKKγ molecule that could be individually modified with nitroxide spin labels. Subsequent distance measurements using electron paramagnetic resonance spectroscopy combined with molecular modeling and molecular dynamics simulations revealed that IKKγ is a parallel coiled-coil whose response to binding of vFLIP or IKKβ is localized twisting/stiffening and not large-scale rearrangements. The coiled-coil comprises N- and C-terminal regions with distinct registers accommodated by a twist: this structural motif is exploited by vFLIP, allowing it to bind and subsequently activate the NF-κB pathway. In vivo assays confirm that NF-κB activation by vFLIP only requires the N-terminal region up to the transition between the registers, which is located directly C-terminal of the vFLIP binding site.
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Affiliation(s)
- Claire Bagnéris
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Kacper B Rogala
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom, Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Mehdi Baratchian
- MRC Centre for Medical Molecular Virology, UCL Cancer Institute and National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom
| | - Vlad Zamfir
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom, Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Micha B A Kunze
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Selina Dagless
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Katharina F Pirker
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Mary K Collins
- MRC Centre for Medical Molecular Virology, UCL Cancer Institute and National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom
| | - Benjamin A Hall
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, United Kingdom, and
| | - Tracey E Barrett
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom,
| | - Christopher W M Kay
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom, London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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Patil KR, Mohapatra P, Patel HM, Goyal SN, Ojha S, Kundu CN, Patil CR. Pentacyclic Triterpenoids Inhibit IKKβ Mediated Activation of NF-κB Pathway: In Silico and In Vitro Evidences. PLoS One 2015; 10:e0125709. [PMID: 25938234 PMCID: PMC4418667 DOI: 10.1371/journal.pone.0125709] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 03/17/2015] [Indexed: 01/02/2023] Open
Abstract
Pentacyclic Triterpenoids (PTs) and their analogues as well as derivatives are emerging as important drug leads for various diseases. They act through a variety of mechanisms and a majority of them inhibit the nuclear factor kappa-beta (NF-κB) signaling pathway. In this study, we examined the effects of the naturally occurring PTs on IκB kinase-β (IKKβ), which has great scientific relevance in the NF-κB signaling pathway. On virtual screening, 109 PTs were screened through the PASS (prediction of activity spectra of substances) software for prediction of NF-κB inhibitory activity followed by docking on the NEMO/IKKβ association complex (PDB: 3BRV) and testing for compliance with the softened Lipinski’s Rule of Five using Schrodinger (LLC, New York, USA). Out of the projected 45 druggable PTs, Corosolic Acid (CA), Asiatic Acid (AA) and Ursolic Acid (UA) were assayed for IKKβ kinase activity in the cell free medium. The UA exhibited a potent IKKβ inhibitory effect on the hotspot kinase assay with IC50 of 69 μM. Whereas, CA at 50 μM concentration markedly reduced the NF-κB luciferase activity and phospho-IKKβ protein expressions. The PTs tested, attenuated the expression of the NF-κB cascade proteins in the LPS-stimulated RAW 264.7 cells, prevented the phosphorylation of the IKKα/β and blocked the activation of the Interferon-gamma (IFN-γ). The results suggest that the IKKβ inhibition is the major mechanism of the PTs-induced NF-κB inhibition. PASS predictions along with in-silico docking against the NEMO/IKKβ can be successfully applied in the selection of the prospective NF-κB inhibitory downregulators of IKKβ phosphorylation.
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Affiliation(s)
- Kalpesh R. Patil
- Department of Pharmacology, H. R. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist- Dhule, Maharashtra, India
| | - Purusottam Mohapatra
- Cancer Biology Laboratory, KIIT School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - Harun M. Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist- Dhule, Maharashtra, India
| | - Sameer N. Goyal
- Department of Pharmacology, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist- Dhule, Maharashtra, India
| | - Shreesh Ojha
- Department of Pharmacology and Therapeutics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates, UAE
| | - Chanakya N. Kundu
- Cancer Biology Laboratory, KIIT School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
- * E-mail: (CRP); (CNK); (KRP)
| | - Chandragouda R. Patil
- Department of Pharmacology, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Dist- Dhule, Maharashtra, India
- * E-mail: (CRP); (CNK); (KRP)
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Kadioglu O, Nass J, Saeed MEM, Schuler B, Efferth T. Kaempferol Is an Anti-Inflammatory Compound with Activity towards NF-κB Pathway Proteins. Anticancer Res 2015; 35:2645-2650. [PMID: 25964540] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND The nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway is critical in inflammation, proliferation and carcinogenesis. There exist three main players in this pathway. The inhibitor of NF-κB (IκB), IκB kinase (IκK)- NF-κB essential modulator (NEMO) complex and NF-κB. The IkK-NEMO complex activates NF-κB via phosphorylation of Iκβ and, eventually, leads to its proteasomal degradation. This leads to nuclear translocation of NF-κB and activation of target genes, such as cyclooxygenases and interleukins. The identification of anti-inflammatory compounds might be an effective strategy to target inflammatory disorders and cancer. MATERIALS AND METHODS In the present investigation, kaempferol was investigated in terms of its effect on NF-κB activity with a SEAP-driven reporter cell line, NF-κB DNA binding with electromobility shift assay (EMSA) and translocation of NF-κB-p65 from cytosol to the nucleus with western blot in Jurkat cells. RESULTS Kaempferol revealed anti-inflammatory activity, as shown in vitro and in silico. Molecular docking studies of kaempferol revealed comparable binding energies and similar docking poses on target proteins such as MG-132, a known NF-κB inhibitor. CONCLUSION We conclude that kaempferol possesses anti-inflammatory activity.
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Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Janine Nass
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Mohamed E M Saeed
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Barbara Schuler
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
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Dubosclard V, Fontan E, Agou F. Use of fluorescence spectroscopy for quantitative investigations of ubiquitin interactions with the ubiquitin-binding domains of NEMO. Methods Mol Biol 2015; 1280:321-37. [PMID: 25736758 DOI: 10.1007/978-1-4939-2422-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Ubiquitin serves as a signal for a variety of cellular processes and its specific interaction with ubiquitin-binding domain (UBD) regulates key cellular events including protein degradation, cell-cycle control, DNA repair, and kinase activation. Several binding mechanisms for isolated UBDs have been reported in recent years. However, little is known about the mechanism through which proteins containing multiple-UBDs achieve specificity for a particular oligomer of polyUb. The NF-κB essential modulator (NEMO, also known IKKγ), which plays a key role in the NF-κB signaling pathway, belongs to the latter family of proteins since it contains two distal NOA (also known UBAN/CC2-LZ/NUB) and ZF UBDs, separated by an unstructured proline-rich linker of about 40 residues in length. Here, we show a new procedure for fast purification of this bipartite domain. We also describe the use of intrinsic fluorescence spectroscopy for quantitative investigations of ubiquitin interactions between two distal ubiquitin-binding domains of NEMO (NOA and ZF). This spectroscopic method has many advantages over other techniques like GST pulldown and Biacore's SPR for monitoring avid interactions between two UBDs, especially when UBDs are located at significant distance from each other within the protein.
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Affiliation(s)
- Virginie Dubosclard
- Unité de Signalisation Moléculaire et Activation Cellulaire, Département de Biologie Cellulaire et Infection, Institut Pasteur, 25 rue du Dr. Roux, 75015, Paris, France
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Cullen S, Ponnappan S, Ponnappan U. Redox-regulated pathway of tyrosine phosphorylation underlies NF-κB induction by an atypical pathway independent of the 26S proteasome. Biomolecules 2015; 5:95-112. [PMID: 25671697 PMCID: PMC4384113 DOI: 10.3390/biom5010095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/25/2014] [Accepted: 01/28/2015] [Indexed: 12/21/2022] Open
Abstract
Alternative redox stimuli such as pervanadate or hypoxia/reoxygenation, induce transcription factor NF-κB by phospho-tyrosine-dependent and proteasome-independent mechanisms. While considerable attention has been paid to the absence of proteasomal regulation of tyrosine phosphorylated IκBα, there is a paucity of information regarding proteasomal regulation of signaling events distinct from tyrosine phosphorylation of IκBα. To delineate roles for the ubiquitin-proteasome pathway in the phospho-tyrosine dependent mechanism of NF-κB induction, we employed the proteasome inhibitor, Aclacinomycin, and the phosphotyrosine phosphatase inhibitor, pervanadate (PV). Results from these studies demonstrate that phospho-IκBα (Tyr-42) is not subject to proteasomal degradation in a murine stromal epithelial cell line, confirming results previously reported. Correspondingly, proteasome inhibition had no discernable effect on the key signaling intermediaries, Src and ERK1/2, involved in the phospho-tyrosine mechanisms regulating PV-mediated activation of NF-κB. Consistent with previous reports, a significant redox imbalance leading to the activation of tyrosine kinases, as occurs with pervanadate, is required for the induction of NF-κB. Strikingly, our studies demonstrate that proteasome inhibition can potentiate oxidative stress associated with PV-stimulation without impacting kinase activation, however, other cellular implications for this increase in intracellular oxidation remain to be fully delineated.
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Affiliation(s)
- Sarah Cullen
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Subramaniam Ponnappan
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Usha Ponnappan
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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Fatima A, Abdul ABH, Abdullah R, Karjiban RA, Lee VS. Binding mode analysis of zerumbone to key signal proteins in the tumor necrosis factor pathway. Int J Mol Sci 2015; 16:2747-66. [PMID: 25629232 PMCID: PMC4346863 DOI: 10.3390/ijms16022747] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/07/2015] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the second most common cancer among women worldwide. Several signaling pathways have been implicated as causative and progression agents. The tumor necrosis factor (TNF) α protein plays a dual role in promoting and inhibiting cancer depending largely on the pathway initiated by the binding of the protein to its receptor. Zerumbone, an active constituent of Zingiber zerumbet, Smith, is known to act on the tumor necrosis factor pathway upregulating tumour necrosis factor related apoptosis inducing ligand (TRAIL) death receptors and inducing apoptosis in cancer cells. Zerumbone is a sesquiterpene that is able to penetrate into the hydrophobic pockets of proteins to exert its inhibiting activity with several proteins. We found a good binding with the tumor necrosis factor, kinase κB (IKKβ) and the Nuclear factor κB (NF-κB) component proteins along the TNF pathway. Our results suggest that zerumbone can exert its apoptotic activities by inhibiting the cytoplasmic proteins. It inhibits the IKKβ kinase that activates the NF-κB and also binds to the NF-κB complex in the TNF pathway. Blocking both proteins can lead to inhibition of cell proliferating proteins to be downregulated and possibly ultimate induction of apoptosis.
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Affiliation(s)
- Ayesha Fatima
- UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Ahmad Bustamam Hj Abdul
- UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Rasedee Abdullah
- UPM-MAKNA Cancer Research Laboratory, Institute of Biosciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Roghayeh Abedi Karjiban
- Department of Chemistry, Faculty of Science, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University Malaya, Petaling Jaya, 50603 Selangor, Malaysia.
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Polley S, Huang DB, Hauenstein AV, Fusco AJ, Zhong X, Vu D, Schröfelbauer B, Kim Y, Hoffmann A, Verma IM, Ghosh G, Huxford T. A structural basis for IκB kinase 2 activation via oligomerization-dependent trans auto-phosphorylation. PLoS Biol 2013; 11:e1001581. [PMID: 23776406 PMCID: PMC3678999 DOI: 10.1371/journal.pbio.1001581] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/01/2013] [Indexed: 01/03/2023] Open
Abstract
Activation of the IκB kinase (IKK) is central to NF-κB signaling. However, the precise activation mechanism by which catalytic IKK subunits gain the ability to induce NF-κB transcriptional activity is not well understood. Here we report a 4 Å x-ray crystal structure of human IKK2 (hIKK2) in its catalytically active conformation. The hIKK2 domain architecture closely resembles that of Xenopus IKK2 (xIKK2). However, whereas inactivated xIKK2 displays a closed dimeric structure, hIKK2 dimers adopt open conformations that permit higher order oligomerization within the crystal. Reversible oligomerization of hIKK2 dimers is observed in solution. Mutagenesis confirms that two of the surfaces that mediate oligomerization within the crystal are also critical for the process of hIKK2 activation in cells. We propose that IKK2 dimers transiently associate with one another through these interaction surfaces to promote trans auto-phosphorylation as part of their mechanism of activation. This structure-based model supports recently published structural data that implicate strand exchange as part of a mechanism for IKK2 activation via trans auto-phosphorylation. Moreover, oligomerization through the interfaces identified in this study and subsequent trans auto-phosphorylation account for the rapid amplification of IKK2 phosphorylation observed even in the absence of any upstream kinase.
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Affiliation(s)
- Smarajit Polley
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
| | - De-Bin Huang
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
| | - Arthur V. Hauenstein
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, United States of America
| | - Amanda J. Fusco
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
| | - Xiangyang Zhong
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
| | - Don Vu
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
| | - Bärbel Schröfelbauer
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
- Signaling Systems Laboratory, University of California–San Diego, La Jolla, California, United States of America
| | - Youngchang Kim
- Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Alexander Hoffmann
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
- Signaling Systems Laboratory, University of California–San Diego, La Jolla, California, United States of America
| | - Inder M. Verma
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California–San Diego, La Jolla, California, United States of America
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, United States of America
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Kasthuri SR, Whang I, Navaneethaiyer U, Lim BS, Choi CY, Lee J. Molecular characterization and expression analysis of IκB from Haliotis discus discus. Fish Shellfish Immunol 2013; 34:1596-1604. [PMID: 23499215 DOI: 10.1016/j.fsi.2013.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/29/2012] [Accepted: 02/15/2013] [Indexed: 06/01/2023]
Abstract
Innate immune system relies on the recognition of pathogen associated molecular patterns present in the microbes by the pattern recognition receptors leading to the activation of signaling cascade and subsequent synthesis of cytokines. NF-κB is a major stimulus activated transcription factor, which regulates the expression of a diverse array of genes. IκB is an inhibitor of NF-κB, retaining NF-κB in an inactive state in the cytoplasm. In this study, we have reported the characterization of first abalone IκB (HdIκB). The cDNA possessed an ORF of 1200 bp coding for a protein of 400 amino acids with molecular mass of 45 kDa and isoelectric point of 4.7. HdIκB protein possessed a conserved phosphorylation site (58)DSGIFS(63) in the N-terminal region, six ankyrin repeats, and a PEST sequence in the C-terminal region. A casein kinase II phosphorylation site could also be observed in the PEST sequence. Constitutive expression of HdIκB revealed its physiological significance since NF-κB is known to be activated by various stimuli. Elevated expression of HdIκB transcripts could be observed in abalones challenged with various mitogens and live microbes. This novel characterization of abalone IκB would further be a positive approach in the affirmation of evolutionary conservation and significance of this protein as a repressor/inhibitor of a pleiotropic transcription factor like NF-κB.
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Affiliation(s)
- Saranya Revathy Kasthuri
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province, Republic of Korea
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Golden MS, Cote SM, Sayeg M, Zerbe BS, Villar EA, Beglov D, Sazinsky SL, Georgiadis RM, Vajda S, Kozakov D, Whitty A. Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface. J Am Chem Soc 2013; 135:6242-56. [PMID: 23506214 PMCID: PMC3680600 DOI: 10.1021/ja400914z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report a comprehensive analysis of binding energy hot spots at the protein-protein interaction (PPI) interface between nuclear factor kappa B (NF-κB) essential modulator (NEMO) and IκB kinase subunit β (IKKβ), an interaction that is critical for NF-κB pathway signaling, using experimental alanine scanning mutagenesis and also the FTMap method for computational fragment screening. The experimental results confirm that the previously identified NEMO binding domain (NBD) region of IKKβ contains the highest concentration of hot-spot residues, the strongest of which are W739, W741, and L742 (ΔΔG = 4.3, 3.5, and 3.2 kcal/mol, respectively). The region occupied by these residues defines a potentially druggable binding site on NEMO that extends for ~16 Å to additionally include the regions that bind IKKβ L737 and F734. NBD residues D738 and S740 are also important for binding but do not make direct contact with NEMO, instead likely acting to stabilize the active conformation of surrounding residues. We additionally found two previously unknown hot-spot regions centered on IKKβ residues L708/V709 and L719/I723. The computational approach successfully identified all three hot-spot regions on IKKβ. Moreover, the method was able to accurately quantify the energetic importance of all hot-spot residues involving direct contact with NEMO. Our results provide new information to guide the discovery of small-molecule inhibitors that target the NEMO/IKKβ interaction. They additionally clarify the structural and energetic complementarity between "pocket-forming" and "pocket-occupying" hot-spot residues, and further validate computational fragment mapping as a method for identifying hot spots at PPI interfaces.
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Affiliation(s)
- Mary S. Golden
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Shaun M. Cote
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Marianna Sayeg
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Brandon S. Zerbe
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Elizabeth A. Villar
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Stephen L. Sazinsky
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Rosina M. Georgiadis
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Sandor Vajda
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Adrian Whitty
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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Shi J, Chen J, Serradji N, Xu X, Zhou H, Ma Y, Sun Z, Jiang P, Du Y, Yang J, Dong C, Wang Q. PMS1077 sensitizes TNF-α induced apoptosis in human prostate cancer cells by blocking NF-κB signaling pathway. PLoS One 2013; 8:e61132. [PMID: 23593410 PMCID: PMC3621893 DOI: 10.1371/journal.pone.0061132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 03/05/2013] [Indexed: 01/05/2023] Open
Abstract
Our previous studies have demonstrated that PMS1077, a platelet-activating factor (PAF) antagonist, could induce apoptosis of Raji cells. However, the mechanism of action has not yet been determined. The nuclear transcription factor-kappa B (NF-κB) signaling pathway plays a critical role in tumor cell survival, proliferation, invasion, metastasis, and angiogenesis, so we determined the effects of PMS1077 and its structural analogs on tumor necrosis factor-α (TNF-α) induced activation of NF-κB signaling. In this study, we found that PMS1077 inhibited TNF-α induced expression of the NF-κB regulated reporter gene in a dose dependent manner. Western blot assay indicated that PMS1077 suppressed the TNF-α induced inhibitor of κB-α (IκB-α) phosphorylation, IκB-α degradation, and p65 phosphorylation. PMS1077 consistently blocked TNF-α induced p65 nuclear translocation as demonstrated in the immunofluorescence assay used. Docking studies by molecular modeling predicted that PMS1077 might interact directly with the IκB kinase-β (IKK-β) subunit. These results suggested that PMS1077 might suppress the activation of NF-κB by targeting IKK-β involved in the NF-κB signaling pathway. Finally, we showed that PMS1077 sensitized cells to TNF-α induced apoptosis by suppressing the expression of NF-κB regulated anti-apoptotic genes. Our results reveal a novel function of PMS1077 on the NF-κB signaling pathway and imply that PMS1077 can be considered as an anti-tumor lead compound.
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Affiliation(s)
- Jie Shi
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jing Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Serradji
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, CNRS UMR 7086, Paris, France
| | - Ximing Xu
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative, CNRS EAC4413, Paris, France
| | - Heng Zhou
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yinxing Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhihong Sun
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Peng Jiang
- Université Paris Diderot, Sorbonne Paris Cité, UMR S-698, Paris, France
| | - Yuping Du
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jinbo Yang
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Changzhi Dong
- Université Paris Diderot, Sorbonne Paris Cité, ITODYS, CNRS UMR 7086, Paris, France
- * E-mail: (CD); (QW)
| | - Qin Wang
- School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (CD); (QW)
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36
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Xue JY, Zhou B, Zhang DY, Wu XM. [Research progress of the biological characteristics of IkappaB kinase and its inhibitors]. Yao Xue Xue Bao 2011; 46:253-260. [PMID: 21626777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The NF-kappaB pathway regulates the expression of over 150 target genes, e.g., cytokines, chemokines, leukocyte adhesion molecules and inducible effector enzymes. Consequently, it plays a crucial role in innate and adaptive immune responses, inflammatory response, stress responses, apoptosis and so on. IkappaB kinase (IKK) is the key of this pathway, and it owns a special structure which consists of catalytic subunit and regulatory subunit. Naturally, the activation of IKK needs the interaction of the two subunits and phosphorylation by its upstream kinases. Actually, there are two methods of activation of the NF-kappaB pathway, and both of the methods need the IKK complex. Given to the crucial role of IKK, researchers have isolated and synthesized amounts of IKK inhibitors, and these provide a great convenience to develop novel anti-inflammatory and anti-tumor drugs.
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Affiliation(s)
- Jian-Yue Xue
- Department of Chemistry and Materials, Chaohu College, Chaohu 238000, China
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37
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Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Pinent M, Zoete V, Grosdidier A, Garcia-Vallvé S, Michielin O, Pujadas G. Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays. PLoS One 2011; 6:e16903. [PMID: 21390216 PMCID: PMC3044726 DOI: 10.1371/journal.pone.0016903] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 01/14/2011] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Their large scaffold diversity and properties, such as structural complexity and drug similarity, form the basis of claims that natural products are ideal starting points for drug design and development. Consequently, there has been great interest in determining whether such molecules show biological activity toward protein targets of pharmacological relevance. One target of particular interest is hIKK-2, a serine-threonine protein kinase belonging to the IKK complex that is the primary component responsible for activating NF-κB in response to various inflammatory stimuli. Indeed, this has led to the development of synthetic ATP-competitive inhibitors for hIKK-2. Therefore, the main goals of this study were (a) to use virtual screening to identify potential hIKK-2 inhibitors of natural origin that compete with ATP and (b) to evaluate the reliability of our virtual-screening protocol by experimentally testing the in vitro activity of selected natural-product hits. METHODOLOGY/PRINCIPAL FINDINGS We thus predicted that 1,061 out of the 89,425 natural products present in the studied database would inhibit hIKK-2 with good ADMET properties. Notably, when these 1,061 molecules were merged with the 98 synthetic hIKK-2 inhibitors used in this study and the resulting set was classified into ten clusters according to chemical similarity, there were three clusters that contained only natural products. Five molecules from these three clusters (for which no anti-inflammatory activity has been previously described) were then selected for in vitro activity testing, in which three out of the five molecules were shown to inhibit hIKK-2. CONCLUSIONS/SIGNIFICANCE We demonstrated that our virtual-screening protocol was successful in identifying lead compounds for developing new inhibitors for hIKK-2, a target of great interest in medicinal chemistry. Additionally, all the tools developed during the current study (i.e., the homology model for the hIKK-2 kinase domain and the pharmacophore) will be made available to interested readers upon request.
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Affiliation(s)
- Esther Sala
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Laura Guasch
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Miquel Mulero
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Maria-Josepa Salvadó
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Montserrat Pinent
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Aurélien Grosdidier
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Santiago Garcia-Vallvé
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
- Centre Tecnològic de Nutrició i Salut, Reus, Catalonia, Spain
| | - Olivier Michielin
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, Lausanne, Switzerland
| | - Gerard Pujadas
- Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, Tarragona, Catalonia, Spain
- Centre Tecnològic de Nutrició i Salut, Reus, Catalonia, Spain
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38
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Avila CM, Lopes AB, Gonçalves AS, da Silva LL, Romeiro NC, Miranda ALP, Sant'Anna CMR, Barreiro EJ, Fraga CAM. Structure-based design and biological profile of (E)-N-(4-Nitrobenzylidene)-2-naphthohydrazide, a novel small molecule inhibitor of IκB kinase-β. Eur J Med Chem 2011; 46:1245-53. [PMID: 21334796 DOI: 10.1016/j.ejmech.2011.01.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/14/2011] [Accepted: 01/25/2011] [Indexed: 01/04/2023]
Abstract
In this study, we describe the rational design, molecular modeling and pharmacological profile of a novel IKK-β inhibitor (E)-N-(4-nitrobenzylidene)-2-naphthohydrazide (LASSBio-1524). The design based on the IKK-β active site, and a privileged structure template yielded a novel IKK-β inhibitor scaffold with significant selectivity over IKK-α and CHK2, as assessed by an in vitro kinase assay. For a better understanding of the structural requirements of IKK-β inhibition, molecular dynamics simulations of LASSBio-1524 (3) were performed. The NAH derivative LASSBio-1524 (3), was able to suppress arachidonic acid-induced edema formation in a dose-dependent manner, demonstrating an in vivo anti-inflammatory effect. The molecular architecture of this novel, low-molecular weight IKK-β inhibitor is encouraging for further lead optimization toward the development of innovative anti-inflammatory drug candidates.
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Affiliation(s)
- Carolina M Avila
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, PO Box 68023, 21941-902 Rio de Janeiro, Brazil
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39
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You DJ, Kim YL, Park CR, Kim DK, Yeom J, Lee C, Ahn C, Seong JY, Hwang JI. Regulation of IκB kinase by GβL through recruitment of the protein phosphatases. Mol Cells 2010; 30:527-32. [PMID: 21110129 DOI: 10.1007/s10059-010-0155-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 09/13/2010] [Accepted: 09/17/2010] [Indexed: 12/13/2022] Open
Abstract
G protein β-like (GβL) is a member of WD repeat-containing family which are involved in various intracellular signaling events. In our previous report, we demonstrated that GβL regulates TNFα-stimulated NF-κB signaling by interacting with and inhibiting phosphorylation of IκB kinase. However, GβL itself does not seem to regulate IKK directly, because it contains no functional domains except WD domains. Here, using immunoprecipitation and proteomic analyses, we identified protein phosphatase 4 as a new binding partner of GβL. We also found that GβL interacts with PP2A and PP6, other members of the same phosphatase family. By interacting with protein phosphatases, which do not directly bind to IKKβ, GβL mediates the association of phosphatases with IKKβ. Overexpression of protein phosphatases inhibited TNFκ-induced activation of NF-κB signaling, which is an effect similar to that of GβL overexpression. Down-regulation of GβL by small interfering RNA diminished the inhibitory effect of phosphatases, resulting in restoration of NF-κB signaling. Thus, we propose that GβL functions as a negative regulator of NF-κB signaling by recruiting protein phosphatases to the IKK complex.
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Affiliation(s)
- Dong-Joo You
- Graduate School of Medicine, Laboratory of G Protein Coupled Receptors, Korea University, Seoul 136-705, Korea
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40
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Sughra K, Birbach A, de Martin R, Schmid JA. Interaction of the TNFR-receptor associated factor TRAF1 with I-kappa B kinase-2 and TRAF2 indicates a regulatory function for NF-kappa B signaling. PLoS One 2010; 5:e12683. [PMID: 20856938 PMCID: PMC2938345 DOI: 10.1371/journal.pone.0012683] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/12/2010] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND I-kappa B kinase 2 (IKK2 or IKK-beta) is one of the most crucial signaling kinases for activation of NF-kappa B, a transcription factor that is important for inflammation, cell survival and differentiation. Since many NF-kappa B activating pathways converge at the level of IKK2, molecular interactions of this kinase are pivotal for regulation of NF-kappa B signaling. METHODOLOGY/PRINCIPAL FINDINGS We searched for proteins interacting with IKK2 using the C-terminal part (amino acids 466-756) as bait in a yeast two-hybrid system and identified the N-terminal part (amino acids 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner. The interaction was confirmed in human cells by mammalian two-hybrid and coimmunoprecipitation experiments. The IKK2/TRAF1 interaction seemed weaker than the interaction between TRAF1 and TRAF2, an important activating adapter molecule of NF-kappa B signaling. Reporter gene and kinase assays using ectopic expression of TRAF1 indicated that it can both activate and inhibit IKK2 and NF-kappa B. Co-expression of fluorescently tagged TRAF1 and TRAF2 at different ratios implied that TRAF1 can affect clustering and presumably the activating function of TRAF2 in a dose dependent manner. CONCLUSIONS/SIGNIFICANCE The observation that TRAF1 can either activate or inhibit the NF-kappa B pathway and the fact that it influences the oligomerization of TRAF2 indicates that relative levels of IKK2, TRAF1 and TRAF2 may be important for regulation of NF-kappa B activity. Since TRAF1 is an NF-kappa B induced gene, it might act as a feedback effector molecule.
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Affiliation(s)
- Kalsoom Sughra
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
| | - Andreas Birbach
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
| | - Rainer de Martin
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
| | - Johannes A. Schmid
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria
- * E-mail:
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41
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Abstract
Upon activation, NF-kappaB translocates into the nucleus and initiates many biological events. This NF-kappaB signaling is mainly induced by the protein kinase IKK beta. Early in this signaling pathway, IKK beta is phosphorylated for activation by several factors, such as pro-inflammatory cytokines and the Tax oncoprotein of human T-cell leukemia virus type 1 (HTLV-1). In cells expressing Tax protein, IKK beta is persistently phosphorylated, which chronically activates NF-kappaB signaling. But the active IKK beta is conjugated with a monoubiquitin by the E3 ubiquitin ligase Ro52, and the IKK beta-induced NF-kappaB signaling is downregulated. However, the mechanism of the downregulation has been unknown. Here, we show that Ro52-mediated monoubiquitination is involved in the subcellular translocation of active IKK beta to autophagosomes. Furthermore, using reporter assays, we show that Ro52 suppresses IKK beta-induced NF-kappaB signaling and that this suppression is blocked by an autophagy inhibitor. These results suggest that Ro52-mediated monoubiquitination plays a critical role in the downregulation of active IKK beta through autophagy.
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Affiliation(s)
- Motoko Niida
- Department of Cardiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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Liu P, Lu M, Tian B, Li K, Garofalo RP, Prusak D, Wood TG, Brasier AR. Expression of an IKKgamma splice variant determines IRF3 and canonical NF-kappaB pathway utilization in ssRNA virus infection. PLoS One 2009; 4:e8079. [PMID: 19956647 PMCID: PMC2778955 DOI: 10.1371/journal.pone.0008079] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 11/05/2009] [Indexed: 11/19/2022] Open
Abstract
UNLABELLED Single stranded RNA (ssRNA) virus infection activates the retinoic acid inducible gene I (RIG-I)- mitochondrial antiviral signaling (MAVS) complex, a complex that coordinates the host innate immune response via the NF-kappaB and IRF3 pathways. Recent work has shown that the IkappaB kinase (IKK)gamma scaffolding protein is the final common adapter protein required by RIG-I.MAVS to activate divergent rate-limiting kinases downstream controlling the NF-kappaB and IRF3 pathways. Previously we discovered a ubiquitous IKKgamma splice-variant, IKKgammaDelta, that exhibits distinct signaling properties. METHODOLOGY/PRINCIPAL FINDINGS We examined the regulation and function of IKKgamma splice forms in response to ssRNA virus infection, a condition that preferentially induces full length IKKgamma-WT mRNA expression. In IKKgammaDelta-expressing cells, we found increased viral translation and cytopathic effect compared to those expressing full length IKKgamma-WT. IKKgammaDelta fails to support viral-induced IRF3 activation in response to ssRNA infections; consequently type I IFN production and the induction of anti-viral interferon stimulated genes (ISGs) are significantly attenuated. By contrast, ectopic RIG-I.MAVS or TNFalpha-induced canonical NF-kappaB activation is preserved in IKKgammaDelta expressing cells. Increasing relative levels of IKKgamma-WT to IKKgammaDelta (while keeping total IKKgamma constant) results in increased type I IFN expression. Conversely, overexpressing IKKgammaDelta (in a background of constant IKKgamma-WT expression) shows IKKgammaDelta functions as a dominant-negative IRF3 signaling inhibitor. IKKgammaDelta binds both IKK-alpha and beta, but not TANK and IKKepsilon, indicating that exon 5 encodes an essential TANK binding domain. Finally, IKKgammaDelta displaces IKKgammaWT from MAVS explaining its domainant negative effect. CONCLUSIONS/SIGNIFICANCE Relative endogenous IKKgammaDelta expression affects cellular selection of inflammatory/anti-viral pathway responses to ssRNA viral infection.
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Affiliation(s)
- Ping Liu
- Department of Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Muping Lu
- Department of Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Bing Tian
- Department of Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Kui Li
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Roberto P. Garofalo
- Department of Pediatrics, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Deborah Prusak
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Thomas G. Wood
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Allan R. Brasier
- Department of Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- * E-mail:
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43
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Abstract
Here, we first report that a specific protein-DNA (RNA) interaction between p53 protein and divergent I kappa B kinase interacting protein (IKIP)-Apaf1 DNA promoter region, and between poliovirus 3CD protein and the 5' terminal region of the RNA sequence can be successfully elucidated with a sequence Fourier analysis, alike various specific protein-protein interactions described previously. Based on these, the intermolecular frequency symmetry would be evolutionarily conserved in a specific interaction of the bioactive structure of various long-chain sequences. In addition, the symmetry is fairly sensitive to a substitution (or a point mutation) on the sequence.
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Affiliation(s)
- Naganori Numao
- BioFrontier Institute Inc., 5-4-21 Nishi-Hashimoto, Sagamihara, Kanagawa 229-1131, Japan.
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44
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Ivins F, Montgomery M, Smith S, Morris-Davies A, Taylor I, Rittinger K. NEMO oligomerization and its ubiquitin-binding properties. Biochem J 2009; 421:243-51. [PMID: 19422324 PMCID: PMC2708934 DOI: 10.1042/bj20090427] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/01/2009] [Accepted: 05/07/2009] [Indexed: 11/17/2022]
Abstract
The IKK [IkappaB (inhibitory kappaB) kinase] complex is a key regulatory component of NF-kappaB (nuclear factor kappaB) activation and is responsible for mediating the degradation of IkappaB, thereby allowing nuclear translocation of NF-kappaB and transcription of target genes. NEMO (NF-kappaB essential modulator), the regulatory subunit of the IKK complex, plays a pivotal role in this process by integrating upstream signals, in particular the recognition of polyubiquitin chains, and relaying these to the activation of IKKalpha and IKKbeta, the catalytic subunits of the IKK complex. The oligomeric state of NEMO is controversial and the mechanism by which it regulates activation of the IKK complex is poorly understood. Using a combination of hydrodynamic techniques we now show that apo-NEMO is a highly elongated, dimeric protein that is in weak equilibrium with a tetrameric assembly. Interaction with peptides derived from IKKbeta disrupts formation of the tetrameric NEMO complex, indicating that interaction with IKKalpha and IKKbeta and tetramerization are mutually exclusive. Furthermore, we show that NEMO binds to linear di-ubiquitin with a stoichiometry of one molecule of di-ubiquitin per NEMO dimer. This stoichiometry is preserved in a construct comprising the second coiled-coil region and the leucine zipper and in one that essentially spans the full-length protein. However, our data show that at high di-ubiquitin concentrations a second weaker binding site becomes apparent, implying that two different NEMO-di-ubiquitin complexes are formed during the IKK activation process. We propose that the role of these two complexes is to provide a threshold for activation, thereby ensuring sufficient specificity during NF-kappaB signalling.
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Key Words
- analytical ultracentrifugation (auc)
- ikk (inhibitory κb kinase) complex
- isothermal titration calorimetry (itc)
- multi-angle light scattering (mals)
- protein–protein interaction
- ubiquitin
- auc, analytical ultracentrifugation
- cozi, c-terminal portion of nemo encompassing the second coiled-coil region and the leucine zipper domain
- iκb, inhibitory κb
- ikk, iκb kinase
- ikknbd, ikkβ nemo-binding domain
- itc, isothermal titration calorimetry
- lz, leucine zipper
- mals, multi-angle laser light scattering
- nf-κb, nuclear factor κb
- nemo, nf-κb essential modulator
- nemo355, nemo residues 1–355, with mutations c54s and k285n
- sec, size-exclusion chromatography
- tcep, tris-(2-carboxyethyl)phosphine
- ri, refractive index
- rip1, receptor interaction protein kinase
- vflip, viral flice [fadd (fas-associated death domain)-like interleukin 1β-converting enzyme]-inhibitory protein
- zf, zinc finger
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Affiliation(s)
- Frank J. Ivins
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, U.K
| | - Mark G. Montgomery
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, U.K
| | - Susan J. M. Smith
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, U.K
| | - Aylin C. Morris-Davies
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, U.K
| | - Ian A. Taylor
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, U.K
| | - Katrin Rittinger
- Division of Molecular Structure, MRC-National Institute for Medical Research, The Ridgeway, London NW7 1AA, U.K
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45
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Zhang D, Jiang S, Qiu L, Su T, Wu K, Li Y, Zhu C, Xu X. Molecular characterization and expression analysis of the IkappaB gene from pearl oyster Pinctada fucata. Fish Shellfish Immunol 2009; 26:84-90. [PMID: 19010421 DOI: 10.1016/j.fsi.2008.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/07/2008] [Accepted: 10/08/2008] [Indexed: 05/27/2023]
Abstract
Inhibitor of NF-kappaB (IkappaB) is one important member of NF-kappaB signal pathway and plays a pivotal role in regulating the innate immune response of invertebrate. Herein, we described the isolation and characterization of pearl oyster Pinctada fucata IkappaB gene (designated as poIkappaB). The poIkappaB cDNA was 1975 bp long and consisted of a 5' untranslated region (UTR) of 73 bp, a 3' UTR of 807 bp with three RNA instability motifs (ATTTA) and a polyadenylation signal (AATAAA) at 13 nucleotides upstream of the poly (A) tail, and an open reading frame (ORF) of 1095 bp encoding a polypeptide of 364 amino acids with an estimated molecular mass of 40.11 kDa and theoretical isoelectric point of 4.61. A conserved degradation motif (DS(35)GFSS(39)) and six ankyrin repeats were identified in the poIkappaB by SMART analysis. Homology analysis of the deduced amino acid sequence of the poIkappaB with other known IkappaB sequences by MatGAT software revealed that the poIkappaB shared 23.5-63.3% similarities with other known IkappaB isoforms. The poIkappaB mRNA was constitutively expressed in all studied tissues with the most abundant mRNA in the haemocyte. The poIkappaB mRNA was up-regulated and increased 4.13- and 5.28-fold after LPS and Vibrio alginolyticus stimulation, respectively. These results suggested that the poIkappaB was a constitutive and inducible acute-phase protein that perhaps involved in the immune defense of pearl oyster.
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Affiliation(s)
- Dianchang Zhang
- School of Life Science, Shanghai Ocean University, Shanghai 200090, China
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46
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Wyler E, Kaminska M, Coïc YM, Baleux F, Véron M, Agou F. Inhibition of NF-kappaB activation with designed ankyrin-repeat proteins targeting the ubiquitin-binding/oligomerization domain of NEMO. Protein Sci 2007; 16:2013-22. [PMID: 17766391 PMCID: PMC2206981 DOI: 10.1110/ps.072924907] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The link between the NF-kappaB signal transduction pathway and cancer is now well established. Inhibiting this pathway is therefore a promising approach in the treatment of certain cancers through a pro-apoptotic effect in malignant cells. Owing to its central role in the pathway, the IkappaB kinase (IKK) complex is a privileged target for designing inhibitors. Previously, we showed that oligomerization of NEMO is necessary for IKK activation and defined a minimal oligomerization domain (CC2-LZ) for NEMO, and we developed NEMO peptides inhibiting NF-kappaB activation at the level of the IKK complex. To improve the low-affinity inhibitors, we used ribosome display to select small and stable proteins with high affinity against the individual CC2-LZ because the entire NEMO protein is poorly soluble. Several binders with affinities in the low nanomolar range were obtained. When expressed in human cells, some of the selected molecules, despite their partial degradation, inhibited TNF-alpha-mediated NF-kappaB activation while having no effect on the basal activity. Controls with a naive library member or null plasmid had no effect. Furthermore, we could show that this NF-kappaB inhibition occurs through a specific interaction between the binders and the endogenous NEMO, resulting in decreased IKK activation. These results indicate that in vitro selections with the NEMO subdomain alone as a target may be sufficient to lead to interesting compounds that are able to inhibit NF-kappaB activation.
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Affiliation(s)
- Emanuel Wyler
- Unité Régulation Enzymatique des Activités Cellulaires, Institut Pasteur, CNRS URA 2185, 75724 Paris Cedex 15, France
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47
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Kim BH, Lee JY, Seo JH, Lee HY, Ryu SY, Ahn BW, Lee CK, Hwang BY, Han SB, Kim Y. Artemisolide is a typical inhibitor of IκB kinase β targeting cysteine-179 residue and down-regulates NF-κB-dependent TNF-α expression in LPS-activated macrophages. Biochem Biophys Res Commun 2007; 361:593-8. [PMID: 17669364 DOI: 10.1016/j.bbrc.2007.07.069] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 07/10/2007] [Indexed: 11/18/2022]
Abstract
Nuclear factor (NF)-kappaB regulates a central common signaling for immunity and cell survival. Artemisolide (ATM) was previously isolated as a NF-kappaB inhibitor from a plant of Artemisia asiatica. However, molecular basis of ATM on NF-kappaB activation remains to be defined. Here, we demonstrate that ATM is a typical inhibitor of IkappaB kinase beta (IKKbeta), resulting in inhibition of lipopolysaccharide (LPS)-induced NF-kappaB activation in RAW 264.7 macrophages. ATM inhibited the kinase activity of highly purified IKKbeta and also LPS-induced IKK activity in the cells. Moreover, the effect of ATM on IKKbeta activity was completely abolished by substitution of Cys-179 residue of IKKbeta to Ala residue, indicating direct targeting site of ATM. ATM could inhibit IkappaBalpha phosphorylation in LPS-activated RAW 264.7 cells and subsequently prevent NF-kappaB activation. Further, we demonstrate that ATM down-regulates NF-kappaB-dependent TNF-alpha expression. Taken together, this study provides a pharmacological potential of ATM in NF-kappaB-dependent inflammatory disorders.
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Affiliation(s)
- Byung Hak Kim
- College of Pharmacy, Chungbuk National University, Cheongju 361-763, Republic of Korea
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Sebban-Benin H, Pescatore A, Fusco F, Pascuale V, Gautheron J, Yamaoka S, Moncla A, Ursini MV, Courtois G. Identification of TRAF6-dependent NEMO polyubiquitination sites through analysis of a new NEMO mutation causing incontinentia pigmenti. Hum Mol Genet 2007; 16:2805-15. [PMID: 17728323 DOI: 10.1093/hmg/ddm237] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The regulatory subunit NEMO is involved in the mechanism of activation of IkappaB kinase (IKK), the kinase complex that controls the NF-kappaB signaling pathway. During this process, NEMO is modified post-translationally through K63-linked polyubiquitination. We report the molecular characterization of a new missense mutation of NEMO (A323P) which causes a severe form of incontinentia pigmenti (OMIM#308300), an inherited disease characterized predominantly by skin inflammation. The A323P mutation was found to impair TNF-, IL-1-, LPS- and PMA/ionomycin-induced NF-kappaB activation, as well as to disrupt TRAF6-dependent NEMO polyubiquitination, due to a defective NEMO/TRAF6 interaction. Mutagenesis identified the affected ubiquitination sites as three lysine residues located in the vicinity of A323. Unexpectedly, these lysines were ubiquitinated together with two previously identified lysines not connected to TRAF6. Mutation of all these ubiquitination sites severely impaired NF-kappaB activation induced by stimulation with IL-1, LPS, Nod2/RICK or serum/LPA. In contrast, mutation at all of these sites had only a limited effect on stimulation by TNF. These findings indicate that post-translational modification of NEMO through K63-linked polyubiquitination is a key event in IKK activation and that perturbation of this step may cause human pathophysiology.
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Hutti JE, Turk BE, Asara JM, Ma A, Cantley LC, Abbott DW. IkappaB kinase beta phosphorylates the K63 deubiquitinase A20 to cause feedback inhibition of the NF-kappaB pathway. Mol Cell Biol 2007; 27:7451-61. [PMID: 17709380 PMCID: PMC2169042 DOI: 10.1128/mcb.01101-07] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Misregulation of NF-kappaB signaling leads to infectious, inflammatory, or autoimmune disorders. IkappaB kinase beta (IKKbeta) is an essential activator of NF-kappaB and is known to phosphorylate the NF-kappaB inhibitor, IkappaBalpha, allowing it to undergo ubiquitin-mediated proteasomal degradation. However, beyond IkappaBalpha, few additional IKKbeta substrates have been identified. Here we utilize a peptide library and bioinformatic approach to predict likely substrates of IKKbeta. This approach predicted Ser381 of the K63 deubiquitinase A20 as a likely site of IKKbeta phosphorylation. While A20 is a known negative regulator of innate immune signaling pathways, the mechanisms regulating the activity of A20 are poorly understood. We show that IKKbeta phosphorylates A20 in vitro and in vivo at serine 381, and we further show that this phosphorylation event increases the ability of A20 to inhibit the NF-kappaB signaling pathway. Phosphorylation of A20 by IKKbeta thus represents part of a novel feedback loop that regulates the duration of NF-kappaB signaling following activation of innate immune signaling pathways.
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Affiliation(s)
- Jessica E Hutti
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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50
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Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem 2007; 77:4626-39. [PMID: 16013882 DOI: 10.1021/ac050102d] [Citation(s) in RCA: 424] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reliable identification of posttranslational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational modifications using tandem mass spectrometry data. InsPecT constructs database filters that proved to be very successful in genomics searches. Given an MS/MS spectrum S and a database D, a database filter selects a small fraction of database D that is guaranteed (with high probability) to contain a peptide that produced S. InsPecT uses peptide sequence tags as efficient filters that reduce the size of the database by a few orders of magnitude while retaining the correct peptide with very high probability. In addition to filtering, InsPecT also uses novel algorithms for scoring and validating in the presence of modifications, without explicit enumeration of all variants. InsPecT identifies modified peptides with better or equivalent accuracy than other database search tools while being 2 orders of magnitude faster than SEQUEST, and substantially faster than X!TANDEM on complex mixtures. The tool was used to identify a number of novel modifications in different data sets, including many phosphopeptides in data provided by Alliance for Cellular Signaling that were missed by other tools.
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Affiliation(s)
- Stephen Tanner
- Department of Bioengineering and Computer Science Department, APM 3832, University of California-San Diego, 9500 Gilman Drive, La Jolla, California 92093-0114, USA.
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