1
|
DiRusso CJ, DeMaria AM, Wong J, Wang W, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A conserved core region of the scaffold NEMO is essential for signal-induced conformational change and liquid-liquid phase separation. J Biol Chem 2023; 299:105396. [PMID: 37890781 PMCID: PMC10694592 DOI: 10.1016/j.jbc.2023.105396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between the N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
Collapse
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.
| |
Collapse
|
2
|
DiRusso CJ, DeMaria AM, Wong J, Jordanides JJ, Whitty A, Allen KN, Gilmore TD. A Conserved Core Region of the Scaffold NEMO is Essential for Signal-induced Conformational Change and Liquid-liquid Phase Separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542299. [PMID: 37292615 PMCID: PMC10245932 DOI: 10.1101/2023.05.25.542299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Scaffold proteins help mediate interactions between protein partners, often to optimize intracellular signaling. Herein, we use comparative, biochemical, biophysical, molecular, and cellular approaches to investigate how the scaffold protein NEMO contributes to signaling in the NF-κB pathway. Comparison of NEMO and the related protein optineurin from a variety of evolutionarily distant organisms revealed that a central region of NEMO, called the Intervening Domain (IVD), is conserved between NEMO and optineurin. Previous studies have shown that this central core region of the IVD is required for cytokine-induced activation of IκB kinase (IKK). We show that the analogous region of optineurin can functionally replace the core region of the NEMO IVD. We also show that an intact IVD is required for the formation of disulfide-bonded dimers of NEMO. Moreover, inactivating mutations in this core region abrogate the ability of NEMO to form ubiquitin-induced liquid-liquid phase separation droplets in vitro and signal-induced puncta in vivo. Thermal and chemical denaturation studies of truncated NEMO variants indicate that the IVD, while not intrinsically destabilizing, can reduce the stability of surrounding regions of NEMO, due to the conflicting structural demands imparted on this region by flanking upstream and downstream domains. This conformational strain in the IVD mediates allosteric communication between N- and C-terminal regions of NEMO. Overall, these results support a model in which the IVD of NEMO participates in signal-induced activation of the IKK/NF-κB pathway by acting as a mediator of conformational changes in NEMO.
Collapse
Affiliation(s)
| | | | - Judy Wong
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | | |
Collapse
|
3
|
DiRusso CJ, Dashtiahangar M, Gilmore TD. Scaffold proteins as dynamic integrators of biological processes. J Biol Chem 2022; 298:102628. [PMID: 36273588 PMCID: PMC9672449 DOI: 10.1016/j.jbc.2022.102628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022] Open
Abstract
Scaffold proteins act as molecular hubs for the docking of multiple proteins to organize efficient functional units for signaling cascades. Over 300 human proteins have been characterized as scaffolds, acting in a variety of signaling pathways. While the term scaffold implies a static, supportive platform, it is now clear that scaffolds are not simply inert docking stations but can undergo conformational changes that affect their dependent signaling pathways. In this review, we catalog scaffold proteins that have been shown to undergo actionable conformational changes, with a focus on the role that conformational change plays in the activity of the classic yeast scaffold STE5, as well as three human scaffold proteins (KSR, NEMO, SHANK3) that are integral to well-known signaling pathways (RAS, NF-κB, postsynaptic density). We also discuss scaffold protein conformational changes vis-à-vis liquid-liquid phase separation. Changes in scaffold structure have also been implicated in human disease, and we discuss how aberrant conformational changes may be involved in disease-related dysregulation of scaffold and signaling functions. Finally, we discuss how understanding these conformational dynamics will provide insight into the flexibility of signaling cascades and may enhance our ability to treat scaffold-associated diseases.
Collapse
|
4
|
Ko MS, Cohen SN, Polley S, Mahata SK, Biswas T, Huxford T, Ghosh G. Regulatory subunit NEMO promotes polyubiquitin-dependent induction of NF-κB through a targetable second interaction with upstream activator IKK2. J Biol Chem 2022; 298:101864. [PMID: 35339487 PMCID: PMC9035715 DOI: 10.1016/j.jbc.2022.101864] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/16/2023] Open
Abstract
Canonical NF-κB signaling through the inhibitor of κB kinase (IKK) complex requires induction of IKK2/IKKβ subunit catalytic activity via specific phosphorylation within its activation loop. This process is known to be dependent upon the accessory ubiquitin (Ub)-binding subunit NF-κB essential modulator (NEMO)/IKKγ as well as poly-Ub chains. However, the mechanism through which poly-Ub binding serves to promote IKK catalytic activity is unclear. Here, we show that binding of NEMO/IKKγ to linear poly-Ub promotes a second interaction between NEMO/IKKγ and IKK2/IKKβ, distinct from the well-characterized interaction of the NEMO/IKKγ N terminus to the "NEMO-binding domain" at the C terminus of IKK2/IKKβ. We mapped the location of this second interaction to a stretch of roughly six amino acids immediately N-terminal to the zinc finger domain in human NEMO/IKKγ. We also showed that amino acid residues within this region of NEMO/IKKγ are necessary for binding to IKK2/IKKβ through this secondary interaction in vitro and for full activation of IKK2/IKKβ in cultured cells. Furthermore, we identified a docking site for this segment of NEMO/IKKγ on IKK2/IKKβ within its scaffold-dimerization domain proximal to the kinase domain-Ub-like domain. Finally, we showed that a peptide derived from this region of NEMO/IKKγ is capable of interfering specifically with canonical NF-κB signaling in transfected cells. These in vitro biochemical and cell culture-based experiments suggest that, as a consequence of its association with linear poly-Ub, NEMO/IKKγ plays a direct role in priming IKK2/IKKβ for phosphorylation and that this process can be inhibited to specifically disrupt canonical NF-κB signaling.
Collapse
Affiliation(s)
- Myung Soo Ko
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA; Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Samantha N Cohen
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Smarajit Polley
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Sushil K Mahata
- Department of Medicine, University of California, San Diego, La Jolla, California, USA; Medicine, VA San Diego Health Care System, San Diego, California, USA
| | - Tapan Biswas
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California, USA
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, USA.
| |
Collapse
|
5
|
Xing Y, Lin Y, Zhang Y, Hu J, Liu J, Tian Y, Zhao J, Chen W, Han B. Novel cytoplasmic lncRNA IKBKBAS promotes lung adenocarcinoma metastasis by upregulating IKKβ and consequential activation of NF-κB signaling pathway. Cell Death Dis 2021; 12:1004. [PMID: 34702815 PMCID: PMC8548314 DOI: 10.1038/s41419-021-04304-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
NF-κB signaling pathway is a critical link between inflammation and cancer. Emerging evidence suggested that long non-coding RNAs (lncRNAs) were involved in dysregulation of NF-κB. Herein, we reported a novel lncRNA IKBKBAS that activated NF-κB in lung adenocarcinoma (LUAD) by upregulating IKKβ, a key member of NF-κB signaling pathway, thereby promoting the metastasis of LUAD both in vitro and in vivo. The upregulated IKBKBAS functioned as a competing endogenous RNA (ceRNA) via competing with IKKβ mRNA for binding miR-4741, consequently leading to upregulation and activation of IKKβ, and ultimately activation of NF-κB. The abnormally elevated IKBKBAS in LUAD was mainly resulted from the extremely decrease of miR-512-5p that targeting IKBKBAS. Furthermore, we identified a positive feedback loop between NF-κB and IKBKBAS, in which NF-κB activation induced by overexpression of IKBKBAS could promote the transcription of IKBKBAS by binding the κB sites within IKBKBAS promoter. Our studies revealed that IKBKBAS was involved in the activation of NF-κB signaling by upregulating the expression of IKKβ, which made it serve as a potential novel target for therapies to LUAD.
Collapse
Affiliation(s)
- Yuanxin Xing
- grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| | - Yani Lin
- grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| | - Ying Zhang
- grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| | - Jing Hu
- grid.452402.50000 0004 1808 3430Department of Pathology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong China
| | - Junmei Liu
- grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| | - Yuanyuan Tian
- grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| | - Jian Zhao
- grid.452402.50000 0004 1808 3430Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, 250012 Shandong China
| | - Weiwen Chen
- grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| | - Bo Han
- grid.452402.50000 0004 1808 3430Department of Pathology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong China ,grid.27255.370000 0004 1761 1174The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong China
| |
Collapse
|
6
|
Ko MS, Biswas T, Mulero MC, Bobkov AA, Ghosh G, Huxford T. Structurally plastic NEMO and oligomerization prone IKK2 subunits define the behavior of human IKK2:NEMO complexes in solution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140526. [PMID: 32853772 DOI: 10.1016/j.bbapap.2020.140526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/30/2020] [Accepted: 08/08/2020] [Indexed: 10/23/2022]
Abstract
The human IκB Kinase (IKK) is a multisubunit protein complex of two kinases and one scaffolding subunit that controls induction of transcription factor NF-κB activity. IKK behaves as an entity of aberrantly high apparent molecular weight in solution. Recent X-ray crystallographic and cryo-electron microscopy structures of individual catalytic subunits (IKK1/IKKα and IKK2/IKKβ) reveal that they are both stably folded dimeric proteins that engage in extensive homo-oligomerization through unique surfaces that are required for activation of their respective catalytic activities. The NEMO/IKKγ subunit is a predominantly coiled coil protein that is required for activation of IKK through the canonical NF-κB signaling pathway. Here we report size-exclusion chromatography, multi-angle light scattering, analytical centrifugation, and thermal denaturation analyses of full-length human recombinant NEMO as well as deletion and disease-linked variants. We observe that NEMO is predominantly a dimer in solution, although by virtue of its modular coiled coil regions NEMO exhibits complicated solution dynamics involving portions that are mutually antagonistic toward homodimerization. This behavior causes NEMO to behave as a significantly larger sized particle in solution. Analyses of NEMO in complex with IKK2 indicate that NEMO preserves this structurally dynamic character within the multisubuit complex and provides the complex-bound IKK2 further propensity toward homo-oligomerization. These observations provide critical information on the structural plasticity of NEMO subunit dimers which helps clarify its role in diseases and in IKK regulation through oligomerization-dependent phosphorylation of catalytic IKK2 subunit dimers.
Collapse
Affiliation(s)
- Myung Soo Ko
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, United States; Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0357, United States
| | - Tapan Biswas
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0357, United States
| | | | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, United States
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0357, United States.
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, United States.
| |
Collapse
|
7
|
Babaei M, Liu Y, Wuerzberger-Davis SM, McCaslin EZ, DiRusso CJ, Yeo AT, Kagermazova L, Miyamoto S, Gilmore TD. CRISPR/Cas9-based editing of a sensitive transcriptional regulatory element to achieve cell type-specific knockdown of the NEMO scaffold protein. PLoS One 2019; 14:e0222588. [PMID: 31553754 PMCID: PMC6760803 DOI: 10.1371/journal.pone.0222588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 09/02/2019] [Indexed: 11/25/2022] Open
Abstract
The use of alternative promoters for the cell type-specific expression of a given mRNA/protein is a common cell strategy. NEMO is a scaffold protein required for canonical NF-κB signaling. Transcription of the NEMO gene is primarily controlled by two promoters: one (promoter B) drives NEMO transcription in most cell types and the second (promoter D) is largely responsible for NEMO transcription in liver cells. Herein, we have used a CRISPR/Cas9-based approach to disrupt a core sequence element of promoter B, and this genetic editing essentially eliminates expression of NEMO mRNA and protein in 293T human kidney cells. By cell subcloning, we have isolated targeted 293T cell lines that express no detectable NEMO protein, have defined genomic alterations at promoter B, and do not support activation of canonical NF-κB signaling in response to treatment with tumor necrosis factor. Nevertheless, non-canonical NF-κB signaling is intact in these NEMO-deficient cells. Expression of ectopic wild-type NEMO, but not certain human NEMO disease mutants, in the edited cells restores downstream NF-κB signaling in response to tumor necrosis factor. Targeting of the promoter B element does not substantially reduce NEMO expression (from promoter D) in the human SNU-423 liver cancer cell line. Thus, we have created a strategy for selectively eliminating cell type-specific expression from an alternative promoter and have generated 293T cell lines with a functional knockout of NEMO. The implications of these findings for further studies and for therapeutic approaches to target canonical NF-κB signaling are discussed.
Collapse
Affiliation(s)
- Milad Babaei
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Yuekun Liu
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Shelly M. Wuerzberger-Davis
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ethan Z. McCaslin
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Christopher J. DiRusso
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Alan T. Yeo
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Larisa Kagermazova
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Shigeki Miyamoto
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Thomas D. Gilmore
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|