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Wang YB, Tan B, Mu R, Chang Y, Wu M, Tu HQ, Zhang YC, Guo SS, Qin XH, Li T, Li WH, Li AL, Zhang XM, Li HY. Ubiquitin-associated domain-containing ubiquitin regulatory X (UBX) protein UBXN1 is a negative regulator of nuclear factor κB (NF-κB) signaling. J Biol Chem 2015; 290:10395-405. [PMID: 25681446 DOI: 10.1074/jbc.m114.631689] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Indexed: 01/17/2023] Open
Abstract
Excessive nuclear factor κB (NF-κB) activation should be precisely controlled as it contributes to multiple immune and inflammatory diseases. However, the negative regulatory mechanisms of NF-κB activation still need to be elucidated. Various types of polyubiquitin chains have proved to be involved in the process of NF-κB activation. Many negative regulators linked to ubiquitination, such as A20 and CYLD, inhibit IκB kinase activation in the NF-κB signaling pathway. To find new NF-κB signaling regulators linked to ubiquitination, we used a small scale siRNA library against 51 ubiquitin-associated domain-containing proteins and screened out UBXN1, which contained both ubiquitin-associated and ubiquitin regulatory X (UBX) domains as a negative regulator of TNFα-triggered NF-κB activation. Overexpression of UBXN1 inhibited TNFα-triggered NF-κB activation, although knockdown of UBXN1 had the opposite effect. UBX domain-containing proteins usually act as valosin-containing protein (VCP)/p97 cofactors. However, knockdown of VCP/p97 barely affected UBXN1-mediated NF-κB inhibition. At the same time, we found that UBXN1 interacted with cellular inhibitors of apoptosis proteins (cIAPs), E3 ubiquitin ligases of RIP1 in the TNFα receptor complex. UBXN1 competitively bound to cIAP1, blocked cIAP1 recruitment to TNFR1, and sequentially inhibited RIP1 polyubiquitination in response to TNFα. Therefore, our findings demonstrate that UBXN1 is an important negative regulator of the TNFα-triggered NF-κB signaling pathway by mediating cIAP recruitment independent of VCP/p97.
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Affiliation(s)
- Yu-Bo Wang
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Bo Tan
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Rui Mu
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Yan Chang
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Min Wu
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Hai-Qing Tu
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Yu-Cheng Zhang
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Sai-Sai Guo
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Xuan-He Qin
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Tao Li
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Wei-Hua Li
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Ai-Ling Li
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Xue-Min Zhang
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Hui-Yan Li
- From the Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
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Edwards DJ, Streich FC, Ronchi VP, Todaro DR, Haas AL. Convergent evolution in the assembly of polyubiquitin degradation signals by the Shigella flexneri IpaH9.8 ligase. J Biol Chem 2014; 289:34114-28. [PMID: 25342744 DOI: 10.1074/jbc.m114.609164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The human pathogen Shigella flexneri subverts host function and defenses by deploying a cohort of effector proteins via a type III secretion system. The IpaH family of 10 such effectors mimics ubiquitin ligases but bears no sequence or structural homology to their eukaryotic counterpoints. Using rates of (125)I-polyubiquitin chain formation as a functional read out, IpaH9.8 displays V-type positive cooperativity with respect to varying concentrations of its Ubc5B∼(125)I-ubiquitin thioester co-substrate in the nanomolar range ([S]½ = 140 ± 32 nm; n = 1.8 ± 0.1) and cooperative substrate inhibition at micromolar concentrations ([S]½ = 740 ± 240 nm; n = 1.7 ± 0.2), requiring ordered binding to two functionally distinct sites per subunit. The isosteric substrate analog Ubc5BC85S-ubiquitin oxyester acts as a competitive inhibitor of wild-type Ubc5B∼(125)I-ubiquitin thioester (Ki = 117 ± 29 nm), whereas a Ubc5BC85A product analog shows noncompetitive inhibition (Ki = 2.2 ± 0.5 μm), consistent with the two-site model. Re-evaluation of a related IpaH3 crystal structure (PDB entry 3CVR) identifies a symmetric dimer consistent with the observed cooperativity. Genetic disruption of the predicted IpaH9.8 dimer interface reduces the solution molecular weight and significantly ablates the kcat but not [S]½ for polyubiquitin chain formation. Other studies demonstrate that cooperativity requires the N-terminal leucine-rich repeat-targeting domain and is transduced through Phe(395). Additionally, these mechanistic features are conserved in a distantly related SspH2 Salmonella enterica ligase. Kinetic parallels between IpaH9.8 and the recently revised mechanism for E6AP/UBE3A (Ronchi, V. P., Klein, J. M., and Haas, A. L. (2013) E6AP/UBE3A ubiquitin ligase harbors two E2∼ubiquitin binding sites. J. Biol. Chem. 288, 10349-10360) suggest convergent evolution of the catalytic mechanisms for prokaryotic and eukaryotic ligases.
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Affiliation(s)
| | | | | | - Dustin R Todaro
- From the Department of Biochemistry and Molecular Biology and
| | - Arthur L Haas
- From the Department of Biochemistry and Molecular Biology and the Stanley S. Scott Cancer Center, Louisiana State University Health Science Center, New Orleans, Louisiana 70112
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Hooper C, Jackson SS, Coughlin EE, Coon JJ, Miyamoto S. Covalent modification of the NF-κB essential modulator (NEMO) by a chemical compound can regulate its ubiquitin binding properties in vitro. J Biol Chem 2014; 289:33161-74. [PMID: 25296760 DOI: 10.1074/jbc.m114.582478] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modification by ubiquitin plays important roles in multiple physiological and pathological processes. Ubiquitin-binding proteins play a critical role in recognizing and relaying polyubiquitin-based signaling. NEMO (NF-κB Essential Modulator) is a central player in canonical NF-κB signaling whose major function is to bind to Lys-63- and/or M1- (or linear) linked polyubiquitin chains generated in response to cell stimulation. Here we show that Withaferin A (WA), a steroidal lactone, causes a change in NEMO's interaction with specific types of polyubiquitin chains in vitro. WA induces full-length recombinant NEMO to bind to long Lys-48-linked polyubiquitin chains but not tetra-ubiquitin species. Significantly, the UBAN (ubiquitin binding in ABIN and NEMO) domain, essential for the ability of NEMO to bind M1/Lys-63-linked polyubiquitin, is dispensable for the WA-induced gain-of-function activity. Mass spectrometric analysis demonstrated that WA covalently modifies NEMO on a cysteine residue within the C-terminal zinc finger (ZF) domain. Point mutations to the ZF can reverse the WA-induced Lys-48-polyubiquitin binding phenotype. Our study demonstrates the feasibility of directly altering the ubiquitin interaction properties of an ubiquitin-binding protein by a chemical compound, thereby shedding light on a novel drug class to potentially alter polyubiquitin-based cellular processes.
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Affiliation(s)
- Christopher Hooper
- From the McArdle Laboratory for Cancer Research, Department of Oncology, Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53705 and
| | - Shawn S Jackson
- From the McArdle Laboratory for Cancer Research, Department of Oncology, Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53705 and Medical Scientist Training Program, and
| | - Emma E Coughlin
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706 Department of Chemistry, Department of Biomolecular Chemistry, and
| | - Shigeki Miyamoto
- From the McArdle Laboratory for Cancer Research, Department of Oncology, Cellular and Molecular Biology Program, University of Wisconsin-Madison, Madison, Wisconsin 53705 and Medical Scientist Training Program, and
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