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1.  A Structural Guide to Proteins of the NF-κB Signaling Module 
The prosurvival transcription factor NF-κB specifically binds promoter DNA to activate target gene expression. NF-κB is regulated through interactions with IκB inhibitor proteins. Active proteolysis of these IκB proteins is, in turn, under the control of the IκB kinase complex (IKK). Together, these three molecules form the NF-κB signaling module. Studies aimed at characterizing the molecular mechanisms of NF-κB, IκB, and IKK in terms of their three-dimensional structures have lead to a greater understanding of this vital transcription factor system.
Structural studies of the NF-κB transcription factor and its regulators I-κB and IKK provide insights into NF-κB dimerization, activation, and DNA binding.
doi:10.1101/cshperspect.a000075
PMCID: PMC2773632  PMID: 20066103
2.  IKKα Contributes to Canonical NF-κB Activation Downstream of Nod1-Mediated Peptidoglycan Recognition 
PLoS ONE  2010;5(10):e15371.
Background
During pathogen infection, innate immunity is initiated via the recognition of microbial products by pattern recognition receptors and the subsequent activation of transcription factors that upregulate proinflammatory genes. By controlling the expression of cytokines, chemokines, anti-bacterial peptides and adhesion molecules, the transcription factor nuclear factor-kappa B (NF-κB) has a central function in this process. In a typical model of NF-κB activation, the recognition of pathogen associated molecules triggers the canonical NF-κB pathway that depends on the phosphorylation of Inhibitor of NF-κB (IκB) by the catalytic subunit IκB kinase β (IKKβ), its degradation and the nuclear translocation of NF-κB dimers.
Methodology
Here, we performed an RNA interference (RNAi) screen on Shigella flexneri-induced NF-κB activation to identify new factors involved in the regulation of NF-κB following infection of epithelial cells by invasive bacteria. By targeting a subset of the human signaling proteome, we found that the catalytic subunit IKKα is also required for complete NF-κB activation during infection. Depletion of IKKα by RNAi strongly reduces the nuclear translocation of NF-κB p65 during S. flexneri infection as well as the expression of the proinflammatory chemokine interleukin-8. Similar to IKKβ, IKKα contributes to the phosphorylation of IκBα on serines 32 and 36, and to its degradation. Experiments performed with the synthetic Nod1 ligand L-Ala-D-γ-Glu-meso-diaminopimelic acid confirmed that IKKα is involved in NF-κB activation triggered downstream of Nod1-mediated peptidoglycan recognition.
Conclusions
Taken together, these results demonstrate the unexpected role of IKKα in the canonical NF-κB pathway triggered by peptidoglycan recognition during bacterial infection. In addition, they suggest that IKKα may be an important drug target for the development of treatments that aim at limiting inflammation in bacterial infection.
doi:10.1371/journal.pone.0015371
PMCID: PMC2955547  PMID: 20976174
3.  Oncogenic BRAF regulates β-Trcp expression and NF-κB activity in human melanoma cells 
Oncogene  2006;26(13):1954-1958.
Mutational activation of BRAF is a frequent event in human malignant melanomas suggesting that BRAF-dependent signaling is conducive to melanoma cell growth and survival. Previously published work reported that melanoma cells exhibit constitutive anti-apoptotic nuclear factor κB (NF-κB) transcription factor activation triggered by proteolysis of its inhibitor IκB. IκB degradation is dependent upon its phosphorylation by the IκB kinase (IKK) complex and subsequent ubiquitination facilitated by β-Trcp E3 ubiquitin ligase. Here, we report that melanocytes expressing a conditionally oncogenic form of BRAFV600E exhibit enhanced β-Trcp expression, increased IKK activity and a concomitant increase in the rate of IκBα degradation. Conversely, inhibition of BRAF signaling using either a broad-spectrum Raf inhibitor (BAY 43-9006) or by selective knock-down of BRAFV600E expression by RNA interference in human melanoma cells leads to decreased IKK activity and β-Trcp expression, stabilization of IκB, inhibition of NF-κB transcriptional activity and sensitization of these cells to apoptosis. Taken together, these data support a model in which mutational activation of BRAF in human melanomas contributes to constitutive induction of NF-κB activity and to increased survival of melanoma cells.
doi:10.1038/sj.onc.1209994
PMCID: PMC1903341  PMID: 17001349
BRAF; melanoma; β-Trcp; NF-κB; IκB kinase
4.  MicroRNA-30e* promotes human glioma cell invasiveness in an orthotopic xenotransplantation model by disrupting the NF-κB/IκBα negative feedback loop 
Constitutive activation of NF-κB is a frequent event in human cancers, playing important roles in cancer development and progression. In nontransformed cells, NF-κB activation is tightly controlled by IκBs. IκBs bind NF-κB in the cytoplasm, preventing it from translocating to the nucleus to modulate gene expression. Stimuli that activate NF-κB signaling trigger IκB degradation, enabling nuclear translocation of NF-κB. Among the genes regulated by NF-κB are those encoding the IκBs, providing a negative feedback loop that limits NF-κB activity. How transformed cells override this NF-κB/IκB negative feedback loop remains unclear. Here, we report in human glioma cell lines that microRNA-30e* (miR-30e*) directly targets the IκBα 3ι-UTR and suppresses IκBα expression. Overexpression of miR-30e* in human glioma cell lines led to hyperactivation of NF-κB and enhanced expression of NF-κB–regulated genes, which promoted glioma cell invasiveness in in vitro assays and in an orthotopic xenotransplantation model. These effects of miR-30e* were shown to be clinically relevant, as miR-30e* was found to be upregulated in primary human glioma cells and correlated with malignant progression and poor survival. Hence, miR-30e* provides an epigenetic mechanism that disrupts the NF-κB/IκBα loop and may represent a new therapeutic target and prognostic marker.
doi:10.1172/JCI58849
PMCID: PMC3248293  PMID: 22156201
5.  Inhibitor of Kappa B Epsilon (IκBε) Is a Non-Redundant Regulator of c-Rel-Dependent Gene Expression in Murine T and B Cells 
PLoS ONE  2011;6(9):e24504.
Inhibitors of kappa B (IκBs) -α, -β and -ε effect selective regulation of specific nuclear factor of kappa B (NF-κB) dimers according to cell lineage, differentiation state or stimulus, in a manner that is not yet precisely defined. Lymphocyte antigen receptor ligation leads to degradation of all three IκBs but activation only of subsets of NF-κB-dependent genes, including those regulated by c-Rel, such as anti-apoptotic CD40 and BAFF-R on B cells, and interleukin-2 (IL-2) in T cells. We report that pre-culture of a mouse T cell line with tumour necrosis factor-α (TNF) inhibits IL-2 gene expression at the level of transcription through suppressive effects on NF-κB, AP-1 and NFAT transcription factor expression and function. Selective upregulation of IκBε and suppressed nuclear translocation of c-Rel were very marked in TNF-treated, compared to control cells, whether activated via T cell receptor (TCR) pathway or TNF receptor. IκBε associated with newly synthesised c-Rel in activated cells and, in contrast to IκBα and -β, showed enhanced association with p65/c-Rel in TNF-treated cells relative to controls. Studies in IκBε-deficient mice revealed that basal nuclear expression and nuclear translocation of c-Rel at early time-points of receptor ligation were higher in IκBε−/− T and B cells, compared to wild-type. IκBε−/− mice exhibited increased lymph node cellularity and enhanced basal thymidine incorporation by lymphoid cells ex vivo. IκBε−/− T cell blasts were primed for IL-2 expression, relative to wild-type. IκBε−/− splenic B cells showed enhanced survival ex vivo, compared to wild-type, and survival correlated with basal expression of CD40 and induced expression of CD40 and BAFF-R. Enhanced basal nuclear translocation of c-Rel, and upregulation of BAFF-R and CD40 occurred despite increased IκBα expression in IκBε−/− B cells. The data imply that regulation of these c-Rel-dependent lymphoid responses is a non-redundant function of IκBε.
doi:10.1371/journal.pone.0024504
PMCID: PMC3167847  PMID: 21915344
6.  IκB Kinase α (IKKα) Regulation of IKKβ Kinase Activity 
Molecular and Cellular Biology  2000;20(10):3655-3666.
Two related kinases, IκB kinase α (IKKα) and IKKβ, phosphorylate the IκB proteins, leading to their degradation and the subsequent activation of gene expression by NF-κB. IKKβ has a much higher level of kinase activity for the IκB proteins than does IKKα and is more critical than IKKα in modulating tumor necrosis factor alpha activation of the NF-κB pathway. These results indicate an important role for IKKβ in activating the NF-κB pathway but leave open the question of the role of IKKα in regulating this pathway. In the current study, we demonstrate that IKKα directly phosphorylates IKKβ. Moreover, IKKα either directly or indirectly enhances IKKβ kinase activity for IκBα. Finally, transfection studies to analyze NF-κB-directed gene expression suggest that IKKα is upstream of IKKβ in activating the NF-κB pathway. These results indicate that IKKα, in addition to its previously described ability to phosphorylate IκBα, can increase the ability of IKKβ to phosphorylate IκBα.
PMCID: PMC85658  PMID: 10779355
7.  A homeostatic model of IκB metabolism to control constitutive NF-κB activity 
Cellular signal transduction pathways are usually studied following administration of an external stimulus. However, disease-associated aberrant activity of the pathway is often due to misregulation of the equilibrium state. The transcription factor NF-κB is typically described as being held inactive in the cytoplasm by binding its inhibitor, IκB, until an external stimulus triggers IκB degradation through an IκB kinase-dependent degradation pathway. Combining genetic, biochemical, and computational tools, we investigate steady-state regulation of the NF-κB signaling module and its impact on stimulus responsiveness. We present newly measured in vivo degradation rate constants for NF-κB-bound and -unbound IκB proteins that are critical for accurate computational predictions of steady-state IκB protein levels and basal NF-κB activity. Simulations reveal a homeostatic NF-κB signaling module in which differential degradation rates of free and bound pools of IκB represent a novel cross-regulation mechanism that imparts functional robustness to the signaling module.
doi:10.1038/msb4100148
PMCID: PMC2673708  PMID: 17486138
cross-regulation; homeostasis; mathematical modeling; robustness; signaling module
8.  UV as an amplifier rather than inducer of NF-κB activity 
Molecular cell  2008;30(5):632-641.
Summary
Inflammatory activation of NF-κB involves the stimulus-induced degradation of the NF-κB-bound inhibitor, IκB, via the IκB kinase (IKK). In response to UV irradiation, however, the mechanism and function of NF-κB activation remain unclear. Using a combined biochemical, genetic, and computational modeling approach, we delineate a dual requirement for constitutive IKK-dependent and IKK-independent IκB degradation pathways in conjunction with UV-induced translational inhibition. Interestingly, we find that the high homeostatic turnover of IκB in resting cells renders the NF-κB system remarkably resistant to metabolic stresses, but the two degradation pathways critically and differentially tune NF-κB responsiveness to UV. Indeed, in the context of low chronic inflammation that accelerates NF-κB-bound IκB degradation, UV irradiation results in dramatic NF-κB activation. Our work suggests that the human health relevance of NF-κB activation by UV lies with cellular homeostatic states that are associated with pathology rather than with healthy physiology.
doi:10.1016/j.molcel.2008.03.017
PMCID: PMC2682114  PMID: 18538661
9.  Structure-Function Relationship of Cytoplasmic and Nuclear IκB Proteins: An In Silico Analysis 
PLoS ONE  2010;5(12):e15782.
Cytoplasmic IκB proteins are primary regulators that interact with NF-κB subunits in the cytoplasm of unstimulated cells. Upon stimulation, these IκB proteins are rapidly degraded, thus allowing NF-κB to translocate into the nucleus and activate the transcription of genes encoding various immune mediators. Subsequent to translocation, nuclear IκB proteins play an important role in the regulation of NF-κB transcriptional activity by acting either as activators or inhibitors. To date, molecular basis for the binding of IκBα, IκBβ and IκBζ along with their partners is known; however, the activation and inhibition mechanism of the remaining IκB (IκBNS, IκBε and Bcl-3) proteins remains elusive. Moreover, even though IκB proteins are structurally similar, it is difficult to determine the exact specificities of IκB proteins towards their respective binding partners. The three-dimensional structures of IκBNS, IκBζ and IκBε were modeled. Subsequently, we used an explicit solvent method to perform detailed molecular dynamic simulations of these proteins along with their known crystal structures (IκBα, IκBβ and Bcl-3) in order to investigate the flexibility of the ankyrin repeat domains (ARDs). Furthermore, the refined models of IκBNS, IκBε and Bcl-3 were used for multiple protein-protein docking studies for the identification of IκBNS-p50/p50, IκBε-p50/p65 and Bcl-3-p50/p50 complexes in order to study the structural basis of their activation and inhibition. The docking experiments revealed that IκBε masked the nuclear localization signal (NLS) of the p50/p65 subunits, thereby preventing its translocation into the nucleus. For the Bcl-3- and IκBNS-p50/p50 complexes, the results show that Bcl-3 mediated transcription through its transactivation domain (TAD) while IκBNS inhibited transcription due to its lack of a TAD, which is consistent with biochemical studies. Additionally, the numbers of identified flexible residues were equal in number among all IκB proteins, although they were not conserved. This could be the primary reason for their binding partner specificities.
doi:10.1371/journal.pone.0015782
PMCID: PMC3009747  PMID: 21203422
10.  IκB Kinase (IKK)-Associated Protein 1, a Common Component of the Heterogeneous IKK Complex 
Molecular and Cellular Biology  1999;19(2):1526-1538.
Activation of the transcription factor NF-κB is controlled by the sequential phosphorylation, ubiquitination, and degradation of its inhibitory subunit, IκB. We recently purified a large multiprotein complex, the IκB kinase (IKK) signalsome, which contains two regulated IκB kinases, IKK1 and IKK2, that can each phosphorylate IκBα and IκBβ. The IKK signalsome contains several additional proteins presumably required for the regulation of the NFκB signal transduction cascade in vivo. In this report, we demonstrate reconstitution of IκB kinase activity in vitro by using purified recombinant IKK1 and IKK2. Recombinant IKK1 or IKK2 forms homo- or heterodimers, suggesting the possibility that similar IKK complexes exist in vivo. Indeed, in HeLa cells we identified two distinct IKK complexes, one containing IKK1-IKK2 heterodimers and the other containing IKK2 homodimers, which display differing levels of activation following tumor necrosis factor alpha stimulation. To better elucidate the nature of the IKK signalsome, we set out to identify IKK-associated proteins. To this end, we purified and cloned a novel component common to both complexes, named IKK-associated protein 1 (IKKAP1). In vitro, IKKAP1 associated specifically with IKK2 but not IKK1. Functional analyses revealed that binding to IKK2 requires sequences contained within the N-terminal domain of IKKAP1. Mutant versions of IKKAP1, which either lack the N-terminal IKK2-binding domain or contain only the IKK2-binding domain, disrupt the NF-κB signal transduction pathway. IKKAP1 therefore appears to mediate an essential step of the NF-κB signal transduction cascade. Heterogeneity of IKK complexes in vivo may provide a mechanism for differential regulation of NF-κB activation.
PMCID: PMC116081  PMID: 9891086
11.  IκB Is a Substrate for a Selective Pathway of Lysosomal Proteolysis 
Molecular Biology of the Cell  1998;9(8):1995-2010.
In lysosomes isolated from rat liver and spleen, a percentage of the intracellular inhibitor of the nuclear factor κ B (IκB) can be detected in the lysosomal matrix where it is rapidly degraded. Levels of IκB are significantly higher in a lysosomal subpopulation that is active in the direct uptake of specific cytosolic proteins. IκB is directly transported into isolated lysosomes in a process that requires binding of IκB to the heat shock protein of 73 kDa (hsc73), the cytosolic molecular chaperone involved in this pathway, and to the lysosomal glycoprotein of 96 kDa (lgp96), the receptor protein in the lysosomal membrane. Other substrates for this degradation pathway competitively inhibit IκB uptake by lysosomes. Ubiquitination and phosphorylation of IκB are not required for its targeting to lysosomes. The lysosomal degradation of IκB is activated under conditions of nutrient deprivation. Thus, the half-life of a long-lived pool of IκB is 4.4 d in serum-supplemented Chinese hamster ovary cells but only 0.9 d in serum-deprived Chinese hamster ovary cells. This increase in IκB degradation can be completely blocked by lysosomal inhibitors. In Chinese hamster ovary cells exhibiting an increased activity of the hsc73-mediated lysosomal degradation pathway due to overexpression of lamp2, the human form of lgp96, the degradation of IκB is increased. There are both short- and long-lived pools of IκB, and it is the long-lived pool that is subjected to the selective lysosomal degradation pathway. In the presence of antioxidants, the half-life of the long-lived pool of IκB is significantly increased. Thus, the production of intracellular reactive oxygen species during serum starvation may be one of the mechanisms mediating IκB degradation in lysosomes. This selective pathway of lysosomal degradation of IκB is physiologically important since prolonged serum deprivation results in an increase in the nuclear activity of nuclear factor κ B. In addition, the response of nuclear factor κ B to several stimuli increases when this lysosomal pathway of proteolysis is activated.
PMCID: PMC25451  PMID: 9693362
12.  Targeting IκB Proteins for HIV Latency Activation: the Role of Individual IκB and NF-κB Proteins 
Journal of Virology  2013;87(7):3966-3978.
Latently infected cell reservoirs represent the main barrier to HIV eradication. Combination antiretroviral therapy (cART) effectively blocks viral replication but cannot purge latent provirus. One approach to HIV eradication could include cART to block new infections plus an agent to activate latent provirus. NF-κB activation induces HIV expression, ending latency. Before activation, IκB proteins sequester NF-κB dimers in the cytoplasm. Three canonical IκBs, IκBα, IκBβ, and IκBε, exist, but the IκB proteins' role in HIV activation regulation is not fully understood. We studied the effects on HIV activation of targeting IκBs by single and pairwise small interfering RNA (siRNA) knockdown. After determining the relative abundance of the IκBs, the relative abundance of NF-κB subunits held by the IκBs, and the kinetics of IκB degradation and resynthesis following knockdown, we studied HIV activation by IκB knockdown, in comparison with those of known HIV activators, tumor necrosis factor alpha (TNF-α), tetradecanoyl phorbol acetate (TPA), and trichostatin A (TSA), in U1 monocytic and J-Lat 10.6 lymphocytic latently infected cells. We found that IκBα knockdown activated HIV in both U1 and J-Lat 10.6 cells, IκBβ knockdown did not activate HIV, and, surprisingly, IκBε knockdown produced the most HIV activation, comparable to TSA activation. Our data show that HIV reactivation can be triggered by targeting two different IκB proteins and that IκBε may be an effective target for HIV latency reactivation in T-cell and macrophage lineages. IκBε knockdown may offer attractive therapeutic advantages for HIV activation because it is not essential for mammalian growth and development and because new siRNA delivery strategies may target siRNAs to HIV latently infected cells.
doi:10.1128/JVI.03251-12
PMCID: PMC3624191  PMID: 23365428
13.  Activation of p38 Mitogen-Activated Protein Kinase by Sodium Salicylate Leads to Inhibition of Tumor Necrosis Factor-Induced IκBα Phosphorylation and Degradation 
Molecular and Cellular Biology  1998;18(1):78-84.
Many actions of the proinflammatory cytokines tumor necrosis factor (TNF) and interleukin-1 (IL-1) on gene expression are mediated by the transcription factor NF-κB. Activation of NF-κB by TNF and IL-1 is initiated by the phosphorylation of the inhibitory subunit, IκB, which targets IκB for degradation and leads to the release of active NF-κB. The nonsteroidal anti-inflammatory drug sodium salicylate (NaSal) interferes with TNF-induced NF-κB activation by inhibiting phosphorylation and subsequent degradation of the IκBα protein. Recent evidence indicated that NaSal activates the p38 mitogen-activated protein kinase (MAPK), raising the possibility that inhibition of NF-κB activation by NaSal is mediated by p38 MAPK. We now show that inhibition of TNF-induced IκBα phosphorylation and degradation by NaSal is prevented by treatment of cells with SB203580, a highly specific p38 MAPK inhibitor. Both p38 activation and inhibition of TNF-induced IκBα degradation were seen after only 30 s to 1 min of NaSal treatment. Induction of p38 MAPK activation and inhibition of TNF-induced IκBα degradation were demonstrated with pharmacologically achievable doses of NaSal. These findings provide evidence for a role of NaSal-induced p38 MAPK activation in the inhibition of TNF signaling and suggest a possible role for the p38 MAPK in the anti-inflammatory actions of salicylates. In addition, these results implicate the p38 MAPK as a possible negative regulator of TNF signaling that leads to NF-κB activation.
PMCID: PMC121454  PMID: 9418855
14.  Protein Kinase CK2 Mediates Inhibitor-Kappa B Kinase and Aberrant Nuclear Factor-κB Activation by Serum Factor(s) in Head and Neck Squamous Carcinoma Cells 
Cancer research  2006;66(13):6722-6731.
We previously showed that the signal transcription factor Nuclear Factor-kappaB (NF-κB) is aberrantly activated and that inhibition of NF-κB induces cell death and inhibits tumorigenesis in Head and Neck Squamous Cell Carcinomas (HNSCC). Thus, identification of specific kinases underlying the activation of NF-κB could provide targets for selective therapy. Inhibitor KappaB Kinase (IKK) is known to activate NF-κB by inducing N-terminal phosphorylation and degradation of its endogenous inhibitor, Inhibitor-κB (IκB). Casein Kinase II (CK2) was previously reported to be over expressed in HNSCC cells, and to be a C-terminal IκB kinase, but its relationship to NF-κB activation in HNSCC cells is unknown. In this study, we examined the contribution of IKK and CK2 in the regulation of NF-κB in HNSCC in vitro. NF-κB activation was specifically inhibited by kinase dead mutants of the IKK1 and IKK2 subunits or siRNA targeting the β subunit of CK2. CK2 and IKK kinase activity, as well as NF-κB transcriptional activity, were shown to be serum responsive, indicating that these kinases mediate aberrant activation of NF-κB in response to serum factor(s) in vitro. Recombinant CK2α was shown to phosphorylate rIKK2, as well as to promote immunoprecipitated IKK complex from HNSCC to phosphorylate the N-terminal S32/S36 of IκBα. We conclude that the aberrant NF-κB activity in HNSCC cells in response to serum is partially through a novel mechanism involving CK2 mediated activation of IKK2, making these kinases candidates for selective therapy to target the NF-κB pathway in HNSCC.
doi:10.1158/0008-5472.CAN-05-3758
PMCID: PMC1839920  PMID: 16818647
Casein Kinase 2; Inhibitor-KappaB Kinase; Nuclear Factor kappaB; squamous cell carcinoma; Serum
15.  Ubiquitination and Degradation of the Inhibitors of NF-κB 
The key step in NF-κB activation is the release of the NF-κB dimers from their inhibitory proteins, achieved via proteolysis of the IκBs. This irreversible signaling step constitutes a commitment to transcriptional activation. The signal is eventually terminated through nuclear expulsion of NF-κB, the outcome of a negative feedback loop based on IκBα transcription, synthesis, and IκBα-dependent nuclear export of NF-κB (Karin and Ben-Neriah 2000). Here, we review the process of signal-induced IκB ubiquitination and degradation by comparing the degradation of several IκBs and discussing the characteristics of IκBs’ ubiquitin machinery.
Ubiquitin-dependent degradation of IκB activates NF-κB. A single E3 ubiquitin ligase, β-TrCP, targets several IκB proteins for degradation.
doi:10.1101/cshperspect.a000166
PMCID: PMC2828279  PMID: 20182612
16.  Characterization of T-cell responses against IκBα in cancer patients 
Oncoimmunology  2012;1(8):1290-1296.
The nuclear factor κ light chain enhancer of activated B cells (NFκB) is constitutively active in most cancers, controlling multiple cellular processes including proliferation, invasion and resistance to therapy. NFκB is primarily regulated through the association with inhibitory proteins that are known as inhibitors of NFκB (IκBs). Increased NFκB activity in tumor cells has been correlated with decrease stability of IκB proteins, in particular IκBα. In responso to a large number of stimuli, IκB proteins are degraded by the proteasome. Cytotoxic T lymphocytes (CTLs) recognize HLA-restricted antigenic peptides that are generated by proteasomal degradation in target cells. In the present study, we demonstrate the presence of naturally occurring IκBα -specific T cells in the peripheral blood of patients suffering from several unrelated tumor types, i.e., breast cancer, malignant melanoma and renal cell carcinoma, but not of healthy controls. Furthermore, we show that such IBα-specific T cells are granzyme B-releasing, cytotoxic cells. Hence, the increased proteasomal degradation of IκBα in cancer induces IκBα-specific CTLs.
doi:10.4161/onci.21625
PMCID: PMC3518501  PMID: 23243592
CTL; NFκB; T cells; antigens; inhibitor of κB; proteasome
17.  A Novel NF-κB-inducing Kinase-MAPK Signaling Pathway Up-regulates NF-κB Activity in Melanoma Cells* 
The Journal of biological chemistry  2001;277(10):7920-7928.
Constitutive activation of NF-κB is an emerging hallmark of various types of tumors including breast, colon, pancreatic, ovarian, and melanoma. In melanoma cells, the basal expression of the CXC chemokine, CXCL1, is constitutively up-regulated. This up-regulation can be attributed in part to constitutive activation of NF-κB. Previous studies have shown an elevated basal IκB kinase (IKK) activity in Hs294T melanoma cells, which leads to an increased rate of IκB phosphorylation and degradation. This increase in IκB-α phosphorylation and degradation leads to an ~19-fold higher nuclear localization of NF-κB. However, the upstream IKK kinase activity is up-regulated by only about 2-fold and cannot account for the observed increase in NF-κB activity. We now demonstrate that NF-κB-inducing kinase (NIK) is highly expressed in melanoma cells, and IKK-associated NIK activity is enhanced in these cells compared with the normal cells. Kinase-dead NIK blocked constitutive NF-κB or CXCL1 promoter activity in Hs294T melanoma cells, but not in control normal human epidermal melanocytes. Transient overexpression of wild type NIK results in increased phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), which is inhibited in a concentration-dependent manner by PD98059, an inhibitor of p42/44 MAPK. Moreover, the NF-κB promoter activity decreased with overexpression of dominant negative ERK expression constructs, and EMSA analyses further support the hypothesis that ERK acts upstream of NF-κB and regulates the NF-κB DNA binding activity. Taken together, our data implicate involvement of IκB kinase and MAPK signaling cascades in NIK-induced constitutive activation of NF-κB.
doi:10.1074/jbc.M112210200
PMCID: PMC2668260  PMID: 11773061
18.  Activation of nuclear factor-κB is necessary for myotrophin-induced cardiac hypertrophy 
The Journal of Cell Biology  2002;159(6):1019-1028.
The transcription factor nuclear factor-κB (NF-κB) regulates expression of a variety of genes involved in immune responses, inflammation, proliferation, and programmed cell death (apoptosis). Here, we show that in rat neonatal ventricular cardiomyocytes, activation of NF-κB is involved in the hypertrophic response induced by myotrophin, a hypertrophic activator identified from spontaneously hypertensive rat heart and cardiomyopathic human hearts. Myotrophin treatment stimulated NF-κB nuclear translocation and transcriptional activity, accompanied by IκB-α phosphorylation and degradation. Consistently, myotrophin-induced NF-κB activation was enhanced by wild-type IκB kinase (IKK) β and abolished by the dominant-negative IKKβ or a general PKC inhibitor, calphostin C. Importantly, myotrophin-induced expression of two hypertrophic genes (atrial natriuretic factor [ANF] and c-myc) and also enhanced protein synthesis were partially inhibited by a potent NF-κB inhibitor, pyrrolidine dithio-carbamate (PDTC), and calphostin C. Expression of the dominant-negative form of IκB-α or IKKβ also partially inhibited the transcriptional activity of ANF induced by myotrophin. These findings suggest that the PKC–IKK–NF-κB pathway may play a critical role in mediating the myotrophin-induced hypertrophic response in cardiomyocytes.
doi:10.1083/jcb.200207149
PMCID: PMC2173971  PMID: 12486112
myotrophin; NF-κB; PKC; cardiac hypertrophy; signal transduction
19.  Klotho Depletion Contributes to Increased Inflammation in Kidney of the db/db Mouse Model of Diabetes via RelA (Serine)536 Phosphorylation 
Diabetes  2011;60(7):1907-1916.
OBJECTIVE
Klotho is an antiaging hormone present in the kidney that extends the lifespan, regulates kidney function, and modulates cellular responses to oxidative stress. We investigated whether Klotho levels and signaling modulate inflammation in diabetic kidneys.
RESEARCH DESIGN AND METHODS
Renal Klotho expression was determined by quantitative real-time PCR and immunoblot analysis. Primary mouse tubular epithelial cells were treated with methylglyoxalated albumin, and Klotho expression and inflammatory cytokines were measured. Nuclear factor (NF)-κB activation was assessed by treating human embryonic kidney (HEK) 293 and HK-2 cells with tumor necrosis factor (TNF)-α in the presence or absence of Klotho, followed by immunoblot analysis to evaluate inhibitor of κB (IκB)α degradation, IκB kinase (IKK) and p38 activation, RelA nuclear translocation, and phosphorylation. A chromatin immunoprecipitation assay was performed to analyze the effects of Klotho signaling on interleukin-8 and monocyte chemoattractant protein-1 promoter recruitment of RelA and RelA serine (Ser)536.
RESULTS
Renal Klotho mRNA and protein were significantly decreased in db/db mice, and a similar decline was observed in the primary cultures of mouse tubule epithelial cells treated with methylglyoxal-modified albumin. The exogenous addition of soluble Klotho or overexpression of membranous Klotho in tissue culture suppressed NF-κB activation and subsequent production of inflammatory cytokines in response to TNF-α stimulation. Klotho specifically inhibited RelA Ser536 phosphorylation as well as promoter DNA binding of this phosphorylated form of RelA without affecting IKK-mediated IκBα degradation, total RelA nuclear translocation, and total RelA DNA binding.
CONCLUSIONS
These findings suggest that Klotho serves as an anti-inflammatory modulator, negatively regulating the production of NF-κB–linked inflammatory proteins via a mechanism that involves phosphorylation of Ser536 in the transactivation domain of RelA.
doi:10.2337/db10-1262
PMCID: PMC3121423  PMID: 21593200
20.  Molecular Basis of NF-κB Signaling 
Annual review of biophysics  2013;42:443-468.
NF-κB (nuclear factor kappa B) family transcription factors are master regulators of immune and inflammatory processes in response to both injury and infection. In the latent state, NF-κBs are sequestered in the cytosol by their inhibitor IκB (inhibitor of NF-κB) proteins. Upon stimulations of innate immune receptors such as Toll-like receptors and cytokine receptors such as those in the TNF (tumor necrosis factor) receptor superfamily, a series of membrane proximal events lead to the activation of the IKK (IκB kinase). Phosphorylation of IκBs results in their proteasomal degradation and the release of NF-κB for nuclear translocation and activation of gene transcription. Here, we review the plethora of structural studies in these NF-κB activation pathways, including the TRAF (TNF receptor–associated factor) proteins, IKK, NF-κB, ubiquitin ligases, and deubiquitinating enzymes. Although these structures only provide snapshots of isolated processes, an emerging picture is that these signaling cascades coalesce into large oligomeric signaling complexes, or signalosomes, for signal propagation.
doi:10.1146/annurev-biophys-083012-130338
PMCID: PMC3678348  PMID: 23495970
TNF; Toll-like receptor; IKK; TRAF; ubiquitin; NEMO
21.  Molecular Determinants of NF-κB-Inducing Kinase Action 
Molecular and Cellular Biology  1998;18(10):5899-5907.
NF-κB corresponds to an inducible eukaryotic transcription factor complex that is negatively regulated in resting cells by its physical assembly with a family of cytoplasmic ankyrin-rich inhibitors termed IκB. Stimulation of cells with various proinflammatory cytokines, including tumor necrosis factor alpha (TNF-α), induces nuclear NF-κB expression. TNF-α signaling involves the recruitment of at least three proteins (TRADD, RIP, and TRAF2) to the type 1 TNF-α receptor tail, leading to the sequential activation of the downstream NF-κB-inducing kinase (NIK) and IκB-specific kinases (IKKα and IKKβ). When activated, IKKα and IKKβ directly phosphorylate the two N-terminal regulatory serines within IκBα, triggering ubiquitination and rapid degradation of this inhibitor in the 26S proteasome. This process liberates the NF-κB complex, allowing it to translocate to the nucleus. In studies of NIK, we found that Thr-559 located within the activation loop of its kinase domain regulates NIK action. Alanine substitution of Thr-559 but not other serine or threonine residues within the activation loop abolishes its activity and its ability to phosphorylate and activate IKKα. Such a NIK-T559A mutant also dominantly interferes with TNF-α induction of NF-κB. We also found that ectopically expressed NIK both spontaneously forms oligomers and displays a high level of constitutive activity. Analysis of a series of NIK deletion mutants indicates that multiple subregions of the kinase participate in the formation of these NIK-NIK oligomers. NIK also physically assembles with downstream IKKα; however, this interaction is mediated through a discrete C-terminal domain within NIK located between amino acids 735 and 947. When expressed alone, this C-terminal NIK fragment functions as a potent inhibitor of TNF-α-mediated induction of NF-κB and alone is sufficient to disrupt the physical association of NIK and IKKα. Together, these findings provide new insights into the molecular basis for TNF-α signaling, suggesting an important role for heterotypic and possibly homotypic interactions of NIK in this response.
PMCID: PMC109176  PMID: 9742107
22.  Cutting Edge 
Transcription factor NF-κB controls the expression of multiple genes involved in immunity and inflammation. The initial activation and duration of NF-κB signaling is regulated by posttranslational modifications to IκB kinase, which earmarks inhibitors of NF-κB for degradation. Prior studies suggest that K63-linked ubiquitination of NEMO (NF-κB essential modulator), an IκB kinase regulatory subunit, is critical for NF-κB and MAPK signaling following engagement of Ag receptors. We now demonstrate that NF-κB and MAPK pathways are largely unaffected in primary cells from mice harboring a ubiquitination-defective form of NEMO, NEMO-KR. TLR- but not Ag receptor-induced cellular responses are impaired in NEMO-KR mice, which are more resistant to LPS-induced endotoxic shock than wild-type animals. Thus, one function of NEMO ubiquitination is to fine tune innate immune responses under TLR control.
PMCID: PMC2601684  PMID: 18490708
23.  NF-κB as a target for oncogenic viruses 
Current topics in microbiology and immunology  2011;349:10.1007/82_2010_108.
NF-κB is a pivotal transcription factor that controls cell survival and proliferation in diverse physiological processes. The activity of NF-κB is tightly controlled through its cytoplasmic sequestration by specific inhibitors, IκBs. Various cellular stimuli induce the activation of an IκB kinase (IKK), which phosphorylates IκBs and triggers their proteasomal degradation, causing nuclear translocation of activated NF-κB. Under normal conditions, the activation of NF-κB occurs transiently, thus ensuring rapid but temporary induction of target genes. Deregulated NF-κB activation contributes to the development of various diseases, including cancers and immunological disorders. Accumulated studies demonstrate that the NF-κB signaling pathway is a target of several human oncogenic viruses, including the human T-cell leukemia virus type 1 (HTLV1), the Kaposi sarcoma-associated herpesvirus (KSHV), and the Epstein bar virus (EBV). These viruses encode specific oncoproteins that target different signaling components of the NF-κB pathway, leading to persistent activation of NF-κB. This chapter will discuss the molecular mechanisms by which NF-κB is activated by the viral oncoproteins.
doi:10.1007/82_2010_108
PMCID: PMC3855473  PMID: 20845110
24.  The NF-κB Family of Transcription Factors and Its Regulation 
Nuclear factor-κB (NF-κB) consists of a family of transcription factors that play critical roles in inflammation, immunity, cell proliferation, differentiation, and survival. Inducible NF-κB activation depends on phosphorylation-induced proteosomal degradation of the inhibitor of NF-κB proteins (IκBs), which retain inactive NF-κB dimers in the cytosol in unstimulated cells. The majority of the diverse signaling pathways that lead to NF-κB activation converge on the IκB kinase (IKK) complex, which is responsible for IκB phosphorylation and is essential for signal transduction to NF-κB. Additional regulation of NF-κB activity is achieved through various post-translational modifications of the core components of the NF-κB signaling pathways. In addition to cytosolic modifications of IKK and IκB proteins, as well as other pathway-specific mediators, the transcription factors are themselves extensively modified. Tremendous progress has been made over the last two decades in unraveling the elaborate regulatory networks that control the NF-κB response. This has made the NF-κB pathway a paradigm for understanding general principles of signal transduction and gene regulation.
NF-κB transcription factors regulate numerous physiological processes. Primarily regulated by I-κB, their activity is fine-tuned by various mechanisms.
doi:10.1101/cshperspect.a000034
PMCID: PMC2773619  PMID: 20066092
25.  Alternative nuclear functions for NF-κB family members 
The NF-κB signalling pathway regulates many different biological processes from the cellular level to the whole organism. The majority of these functions are completely dependent on the activation of the cytoplasmic IKK kinase complex that leads to IκB degradation and results in the nuclear translocation of specific NF-κB dimers, which, in general, act as transcription factors. Although this is a well-established mechanism of action, several publications have now demonstrated that some members of this pathway display additional functions in the nucleus as regulators of NF-κB-dependent and independent gene expression. In this review, we compiled and put in context most of the data concerning specific nuclear roles for IKK and IκB proteins.
PMCID: PMC3186045  PMID: 21984965
NF-κB (nuclear factor -κB); IκB (inhibitor of NF-κB); IKK (IκB kinases); chromatin; gene transcription

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