Biochemical Journal

Research article

Novel cross-talk within the IKK family controls innate immunity

Kristopher Clark, Mark Peggie, Lorna Plater, Ronald J. Sorcek, Erick R. R. Young, Jeffrey B. Madwed, Joanne Hough, Edward G. McIver, Philip Cohen

Abstract

Members of the IKK {IκB [inhibitor of NF-κB (nuclear factor κB)] kinase} family play a central role in innate immunity by inducing NF-κB- and IRF [IFN (interferon) regulatory factor]-dependent gene transcription programmes required for the production of pro-inflammatory cytokines and IFNs. However, the molecular mechanisms that activate these protein kinases and their complement of physiological substrates remain poorly defined. Using MRT67307, a novel inhibitor of IKKϵ/TBK1 (TANK {TRAF [TNF (tumour-necrosis-factor)-receptor-associated factor]-associated NF-κB activator}-binding kinase 1) and BI605906, a novel inhibitor of IKKβ, we demonstrate that two different signalling pathways participate in the activation of the IKK-related protein kinases by ligands that activate the IL-1 (interleukin-1), TLR (Toll-like receptor) 3 and TLR4 receptors. One signalling pathway is mediated by the canonical IKKs, which directly phosphorylate and activate IKKϵ and TBK1, whereas the second pathway appears to culminate in the autocatalytic activation of the IKK-related kinases. In contrast, the TNFα-induced activation of the IKK-related kinases is mediated solely by the canonical IKKs. In turn, the IKK-related kinases phosphorylate the catalytic subunits of the canonical IKKs and their regulatory subunit NEMO (NF-κB essential modulator), which is associated with reduced IKKα/β activity and NF-κB-dependent gene transcription. We also show that the canonical IKKs and the IKK-related kinases not only have unique physiological substrates, such as IκBα, p105, RelA (IKKα and IKKβ) and IRF3 (IKKϵ and TBK1), but also have several substrates in common, including the catalytic and regulatory (NEMO and TANK) subunits of the IKKs themselves. Taken together, our studies reveal that the canonical IKKs and the IKK-related kinases regulate each other by an intricate network involving phosphorylation of their catalytic and regulatory (NEMO and TANK) subunits to balance their activities during innate immunity.

  • inhibitor of nuclear factor κB kinase (IKK)
  • interferon
  • nuclear factor κB essential modifier (NEMO)
  • Toll-like receptor (TLR)
  • tumour necrosis factor-receptor-associated factor-associated nuclear factor κB activator-binding kinase 1 (TBK1)

INTRODUCTION

The production of inflammatory mediators in the innate immune system is triggered by the activation of a number of signalling pathways, including those that activate members of the IKK {IκB [inhibitor of NF-κB (nuclear factor κB)] kinase} family of protein kinases. Four IKKs have been identified, which can be divided into the canonical IKKs, IKKα and IKKβ, and the IKK-related kinases IKKϵ and TBK1 (TANK {TRAF [TNF (tumour-necrosis-factor)-receptor-associated factor]-associated NF-κB activator}-binding kinase 1) [1]. The canonical IKKs activate the transcription factor NF-κB, and hence NF-κB-dependent gene transcription, by phosphorylating IκBα and other IκB isoforms. Phosphorylation of IκBα licences it for Lys48-linked polyubiquitylation by SCFβTRCP (Skp1/cullin/F-box β-transducin repeat-containing protein) and subsequent destruction by the proteasome. This releases the NF-κB subunits RelA and c-Rel, which translocate to the nucleus and stimulate the transcription of genes encoding many inflammatory mediators. In contrast, IKKϵ and TBK1 phosphorylate IRF3 [IFN (interferon) regulatory factor 3), leading to nuclear translocation and transcription of genes that include IFNβ (reviewed in [2]).

The IL-1R [IL-1 (interleukin-1) receptor] and every TLR (Toll-like receptor), except for TLR3, signals via the adaptor protein MyD88 (myeloid differentiation factor 88) to activate the canonical IKKs. It is established that IL-1 cannot activate the canonical IKKs in MEFs (mouse embryonic fibroblasts) that do not express TRAF6 or do not express TAK1 (transforming growth factor-β-activated kinase 1) [35]. The E3 ubiquitin ligase activity of TRAF6 is required for signalling [6] and is thought to be needed to generate K63-pUb [Lys63-linked pUb (polyubiquitin)] chains, which bind to the TAB (TAK1-binding protein) 2 and TAB3 subunits of TAK1 [7,8]. This interaction is reported to induce a conformational change that allows TAK1 to phosphorylate and activate itself in vitro [8,9]. K63-pUb chains also interact with NEMO (NF-κB essential modulator; also called IKKγ), the regulatory component of the canonical IKK complex [10,11]. K63-pUb chains may therefore recruit and co-localize TAK1 and IKKα/IKKβ in cells, facilitating the direct phosphorylation and activation of the canonical IKKs by TAK1. However, NEMO also binds linear pUb chains as well as K63-pUb chains [12,13] and LUBAC (linear ubiquitin-chain-assembly complex), the E3 ligase that produces linear pUb chains specifically in vitro [14], appears to participate in the IL-1-stimulated activation of the canonical IKK complex, since activation by IL-1 was impaired in MEFs deficient in HOIL-1 (haem-oxidized iron-regulatory protein 2 ubiquitin ligase-1), a component of LUBAC [15]. Thus the relative importance of K63-pUb chains compared with linear pUb chains in activating the canonical IKK complex requires further investigation.

The activation of the IKK-related protein kinases requires their phosphorylation at Ser172 [16] and these kinases are a point of convergence of TRIF (Toll/IL-1R domain-containing adaptor protein inducing IFNβ)-dependent signalling pathways that are activated by TLR3 and TLR4 agonists [2]. The IKK-related kinases then phosphorylate and activate IRF3. Recently, we have shown that BX795, a potent inhibitor of the IKK-related kinases that suppresses the phosphorylation of IRF3 and the production of IFNβ in macrophages, enhances the phosphorylation of IKKϵ and TBK1 at Ser172 [17]. These findings indicated that a distinct protein kinase must be involved in the activation of the IKK-related kinases by poly(I:C) and LPS (lipopolysaccharide) and that IKKϵ/TBK1 control a feedback loop that limits the extent to which they can be activated.

Although the IKK-related kinases are widely believed to be activated solely by ligands that lead to the activation of IRF3 and the production of IFNβ, we found that IL-1 and TNFα activated IKKϵ and TBK1 in MEFs without inducing the phosphorylation of IRF3 or IRF3-dependent gene transcription [17]. Those findings raised the question of how these different agonists [IL-1, TNFα, LPS and poly(I:C)] activate the IKK-related kinases and the roles they play that are independent of IRF3. Since the specificity of signalling can frequently break down when components of signal transduction pathways are overexpressed, we decided to use a genetic and a pharmacological approach to study the activation of the endogenous IKK complexes. Our results demonstrate that MyD88-dependent (IL-1) and TRIF-dependent agonists [LPS and poly(I:C)] use two signalling pathways to activate the IKK-related kinases, one of which is mediated by the canonical IKKs. In contrast, TNFα only employs the canonical IKK-mediated pathway to activate the IKK-related kinases. We show further that the IKK-related kinases negatively regulate the canonical IKKs and identify several proteins that are physiological substrates for all the IKK family members. Our results reveal a complex interlocking network by which the IKK family members regulate one another to ensure that their activities are tightly coupled.

MATERIALS AND METHODS

Materials

The chemical synthesis of MRT67307 and BI605906 will be described elsewhere. 5Z-7-Oxozeaenol was purchased from BioAustralis Fine Chemicals. The Tpl2 (tumour progression locus 2) inhibitor called C1 (Compound 1) was synthesized by Dr Natalia Shpiro in the MRC Protein Phosphorylation Unit, University of Dundee, Dundee, Scotland, U.K. [18]. These pharmacological inhibitors were dissolved in DMSO and stored as 10 mM solutions at −20 °C. Mouse IL-1α and TNFα were purchased from Sigma, poly(I:C) was from Invivogen and LPS (Escherichia coli strain O5:B55) was from Alexis Biochemicals.

DNA constructs

DNA vectors expressing GST (glutathione transferase)–IRF3, FLAG–TBK1[K38A], GST–TBK1 and GST–IKKϵ have been described previously [17]. IKKα [NCBI (National Center for Biotechnology Information) accession no. O15111] was amplified from IMAGE EST 5275799 using KOD Hot Start DNA Polymerase (Novagen), cloned into pSC-b (Stratagene) and sequenced to completion. The insert was excised using NotI and inserted into pEBG6P to generate a DNA vector expressing GST–IKKα. IKKβ (GenBank® accession no. AF080158) was cloned in a similar manner using IMAGE EST 5784717. TANK (NCBI accession no. AAH67779) and NEMO (NCBI accession no. AAH50612) were amplified from IMAGE EST 5296558 and IMAGE EST 2820134 respectively and cloned into the BamHI and NotI sites of pCMVHA-1. Point mutations were created using the QuikChange® mutagenesis kit (Stratagene), but using KOD Hot Start DNA Polymerase. PRDII (NF-κB) elements from the IFNβ promoter cloned into the pLuc-MCS vector were generously provided by Dr Katherine Fitzgerald (School of Medicine, University of Massachusetts, North Worcester, MA, U.S.A.). pTK-RL was obtained from Stratagene.

Antibodies

Antibodies against human TBK1 (sheep S041C, bleed 2) and the C-terminal peptide of mouse IKKϵ (NRLIERLHRVPSAPDV) (sheep S277C, bleed 2), which were used to immunoprecipitate TBK1 and IKKϵ respectively [17], and an antibody raised against the Ser172-phosphorylation site of IKKϵ (CEKFVS*VYGTE, where S* indicates phosphoserine) (sheep S051C, bleed 2), which was used to immunoprecipitate the phosphorylated forms of both IKKϵ and TBK1 [17], anti-NEMO (sheep S527C, bleed 2) and anti-GST were provided by the Division of Signal Transduction Therapy, University of Dundee, Dundee, Scotland, U.K., and have been described previously. The following antibodies were used for immunoblotting: HRP (horseradish peroxidase)-conjugated secondary antibodies (Pierce), anti-FLAG, anti-IKKϵ (Sigma), anti-HA (haemagglutinin) (Roche), anti-RelA, anti-TRAF3, anti-TRAF6, anti-NEMO (Santa Cruz Biotechnology), anti-IKKβ (Upstate) anti-GAPDH (glyceraldehyde-3-phosphate dehydrogenase), anti-TBK1, anti-IKKα, anti-p38α MAPK (mitogen-activated protein kinase), anti-TANK and anti-IκBα (Cell Signaling Technology). Antibodies recognizing phospho-Ser933 of p105 (NF-κB1), phospho-Ser176/Ser180 of IKKα and phospho-Ser177/Ser181 of IKKβ, phospho-Ser468 of RelA, phospho-Ser536 of RelA, phospho-Ser396 of IRF3 and the phospho-Thr-Gly-phospho-Tyr sequence of ERK1/2 (extracellular-signal-regulated kinase 1/2) and p38 MAPK were also from Cell Signaling Technology. The antibody recognizing the phospho-Thr-Pro-phospho-Tyr sequence of JNK1/2 (c-Jun N-terminal kinase 1/2) was from Biosource, whereas that recognizing phospho-Ser172 of TBK1 was from Becton Dickinson.

Cell culture

HEK (human embryonic kidney)-293 cells stably expressing TLR3–FLAG (termed HEK-293-TLR3 cells) were provided by Dr Katherine Fitzgerald. Immortalized MEFs from mice expressing a truncated inactive form of TAK1 (Dr Shizuo Akira, Department of Host Defense, Osaka University, Osaka, Japan), immortalized MEFs from IKKα-deficient and IKKβ-deficient mice (Professor Inder Verma, Salk Institute, La Jolla, CA, U.S.A.), immortalized MEFs from TRAF6-deficient mice (Dr Tak Mak, Department of Medical Biophysics, Toronto, Canada), immortalized MEFs from TRAF3-knockout mice (Professor Genhong Chen, Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, CA, U.S.A.) and immortalized MEFs from NEMO-deficient mice (Professor Manolis Pasparakis, Institute of Genetics, University of Cologne, Cologne, Germany) were generously provided by these investigators. HEK-293-TLR3 cells, RAW264.7 cells and MEFs were maintained in DMEM (Dulbecco's modified Eagle's medium) supplemented with 2 mM glutamine, 10% (v/v) FBS (foetal bovine serum) and the antibiotics penicillin and streptomycin. HEK-293 cells were grown in suspension in Pro-293S medium supplemented with 2% (v/v) FBS in a humidified incubator maintained at 37 °C and 8% CO2. BMDMs (bone-marrow-derived macrophages) were generated from mice as described previously [19]. HEK-293 cells were transfected using PEI (polyethylenimine; Polysciences) [20], whereas immortalized MEFs were transfected using the Amaxa Nucleofection MEF2 kit.

Immunoprecipitation and immunoblotting

Pharmacological inhibitors dissolved in DMSO, or an equivalent volume of DMSO for control incubations, were added to the culture medium of cells grown as monolayers. After 1 h at 37 °C, the cells were stimulated with LPS, poly(I:C), IL-1α or TNFα as described in the Figure legends. Thereafter, the cells were rinsed in ice-cold PBS and extracted in lysis buffer [50 mM Tris/HCl (pH 7.4), 1 mM EDTA, 1 mM EGTA, 50 mM NaF, 5 mM sodium pyrophosphate, 10 mM sodium 2-glycerol 1-phosphate, 1 mM dithiothreitol, 1 mM sodium orthovanadate, 0.27 M sucrose, 1% (v/v) Triton X-100, 1 mg/ml aprotinin, 1 mg/ml leupeptin and 1 mM PMSF]. Cell extracts were clarified by centrifugation at 14000 g for 10 min at 4 °C and protein concentrations were determined using the Bradford assay. For immunoprecipitation of the phosphorylated forms of IKKϵ and TBK1, 1 mg of cell extract protein was incubated with 5 μg of antibody for 90 min at 4 °C, followed by the addition of Protein G–Sepharose. After mixing for 15 min at 4 °C and brief centrifugation, the immunocomplexes were washed three times in lysis buffer, denatured in SDS and subjected to SDS/PAGE. To detect proteins in cell lysates, 20 μg of protein extract was separated by SDS/PAGE. After transfer to PVDF membranes, proteins were detected by immunoblotting and visualized by treating the blots with ECL (enhanced chemiluminescence) (Amersham), followed by autoradiography.

Purification of recombinant protein kinases

Protein kinases were expressed as GST-fusion proteins for 48 h in HEK-293 cells (0.5 litres) grown in suspension. Cells were extracted in 25 ml of lysis buffer, clarified by centrifugation (14000 g for 10 min at 4 °C) and protein concentrations were determined using the Bradford assay. GST-fusion proteins were isolated from 200 mg of extract protein by affinity chromatography on glutathione–Sepharose beads (1 ml of packed volume) and, after washing three times with lysis buffer containing 0.5 M NaCl, were released from GST and glutathione–Sepharose by cleavage with PreScission protease. Specific activities of the kinases were determined as described previously [17,21].

Protein kinase assays

Substrates and kinases were diluted in 50 mM Tris/HCl (pH 7.5), 0.1% 2-mercaptoethanol, 0.1 mM EGTA and 10 mM magnesium acetate. Reactions were initiated with [γ-32P]ATP (2500 c.p.m./pmol) to a final concentration of 0.1 mM and terminated after 15 min at 30 °C by the addition of SDS and EDTA (pH 7.0) to final concentrations of 1.0% (w/v) and 20 mM respectively. After heating for 5 min at 100 °C and separation by SDS/PAGE, the phosphorylated proteins were detected by autoradiography.

Phosphomapping by LC (liquid chromatography)-MS/MS (tandem MS)

Colloidal Coomassie-Blue-stained protein bands were excised and digested with trypsin. Protein phosphorylation site analysis was performed by precursor 79 scanning on a 4000 Q-Trap mass spectrometer system [22] and on an LTQ-orbitrap velos [23].

Statistical analysis

Quantitative data are presented as the means±S.E.M. Statistical significance of differences between experimental groups was assessed using the Student's t test. Differences in means were considered significant if P< 0.05.

RESULTS

Characterization of novel pharmacological inhibitors of the IKK family

In earlier studies, we identified BX795 as a potent inhibitor of the IKK-related kinases (IKKϵ and TBK1) [17,21] that suppressed the LPS- or poly(I:C)-stimulated phosphorylation of IRF3 and production of IFNβ, without inhibiting the activation of NF-κB by the canonical IKKs [17]. However, BX795 did suppress the activation of JNK and p38α MAPK by inflammatory stimuli, an off-target effect which limited its use as a probe for the functions of IKKϵ and TBK1. We therefore modified BX795 to generate the improved inhibitor MRT67307 (Figure 1A), which inhibited IKKϵ and TBK1 with IC50 values of 160 and 19 nM when assayed at 0.1 mM ATP in vitro, but did not inhibit IKKα or IKKβ even at 10 μM. MRT67307 prevented the phosphorylation of IRF3 and the production of IFNβ in macrophages (Figures 1B and 1C), but no longer suppressed the activation of JNK or p38 MAPK by poly(I:C) (Figure 1B) or other agonists (see later Figures).

Figure 1 MRT67307 and BI605906, novel pharmacological inhibitors of the IKK family

(A) Structure of MRT67307. (B) BMDMs were incubated without or with 2 μM MRT67307 for 1 h and then stimulated with 10 μg/ml poly(I:C) for the times indicated. Cell extracts (20 μg of protein) were immunoblotted with the antibodies indicated. p-, phospho-. (C) Inhibition of IFNβ secretion in response to LPS. RAW264.7 macrophages were incubated for 1 h at the indicated concentrations of MRT67307 and then stimulated for 6 h with 100 ng/ml LPS. The concentration of IFNβ released into the culture medium was measured using an ELISA kit from R&D Systems. Values are means±S.E.M., n=3. (D) Structure of BI605906.

In the present study, we also used BI605906 (Figure 1D), an inhibitor of IKKβ with improved selectivity. This compound inhibited IKKβ in vitro with an IC50 value of 380 nM when assayed at 0.1 mM ATP. The only other protein kinase that was inhibited of over 100 tested, which included IKKα, IKKϵ and TBK1, was the IGF1 (insulin-like growth factor 1) receptor (IC50=7.6 μM).

Identification of signalling pathways that mediate the IL-1stimulated activation of IKKϵ/TBK1

To investigate the signalling pathways by which IL-1 activates the different IKK subfamily members, we studied their activation in MEFs that do not express TRAF6 or TAK1, both of which are required for the IL-1-stimulated activation of the canonical IKKs. These studies showed that, like IKKα and IKKβ, IKKϵ and TBK1 could not be activated by IL-1 in TRAF6−/− MEFs (Figure 2A). In contrast, all of the IKK family members were activated by IL-1 in TRAF3−/− MEFs (Figure 2B). However, and in contrast with the canonical IKKs, IL-1 activated the IKK-related kinases similarly in TAK1−/− and wild-type MEFs (Figure 2C). Thus the IL-1-dependent pathways that activate the canonical IKKs and the IKK-related kinases diverge ‘downstream’ of TRAF6. We therefore expected that the IKK-related kinases would be activated normally in MEFs that do not express NEMO, an essential regulatory component of the canonical IKKs. However, there was no activation of either the canonical IKKs or the IKK-related kinases in NEMO−/− MEFs, despite unimpaired activation of p38 MAPK and JNK (Figure 2D). These observations led us to investigate the role of the canonical IKK complex in the activation of the IKK-related kinases.

Figure 2 Activation of IKKϵ and TBK1 in response to IL-1 requires TRAF6 and NEMO, but not TAK1 or TRAF3

(A) TRAF6+/+ and TRAF6−/− MEFs, (B) TRAF3+/+ and TRAF3−/− MEFs, (C) TAK1+/+ and TAK1−/− MEFs or (D) NEMO+/+ and NEMO−/− MEFs were stimulated for 10 min with 5 ng/ml IL-1α. The Ser172-phosphorylated forms of IKKϵ and TBK1 were immunoprecipitated from cell extracts (1 mg) using the anti-(phospho-Ser172 IKKϵ) antibody (5 μg) as described previously [17], and the presence of IKKϵ and TBK1 were revealed by immunoblotting using antibodies recognizing all forms of IKKϵ and TBK1 (top panel). In the other panels, cell extracts were immunoblotted with the antibodies indicated. p-, phospho.

Although IKKβ plays a major role in the IL-1-stimulated phosphorylation of proteins such as p105 (also called NF-κB1) and the NF-κB subunit RelA in MEFs, IKKα also contributes to the phosphorylation of these substrates (Supplementary Figure S1A at http://www.BiochemJ.org/bj/434/bj4340093add.htm). Therefore, as no specific inhibitors of IKKα are currently available, we studied the effects of the IKKβ inhibitor BI605906 in IKKα−/− MEFs in the presence and absence of the IKKϵ/TBK1 inhibitor MRT67307. These studies revealed that BI605906 partially inhibited the IL-1-stimulated activation of IKKϵ/TBK1, whereas MRT67307 had little effect. However, the combined addition of both inhibitors completely prevented the activation of the IKK-related kinases by IL-1 (Figure 3A). These results suggested that two different pathways contribute to the IL-1-induced activation of the IKK-related kinases in IKKα−/− MEFs, one dependent on IKKβ activity and the other dependent on IKKϵ/TBK1 activity. Since IL-1 cannot activate the canonical IKKs in TAK1−/− MEFs (Figure 2C), we reasoned that the IL-1-stimulated activation of the IKK-related kinases should be completely blocked by the IKKϵ/TBK1 inhibitor MRT67307 in these cells, which indeed proved to be the case (Figure 3B).

Figure 3 Cross-talk between the canonical IKKs and IKK-related kinases during IL-1 signalling

(A) IKKα−/− MEFs were incubated for 1 h with 10 μM BI605906, 2 μM MRT67307 or both compounds, and then stimulated for 10 min with 5 ng/ml IL-1α. Phosphorylation of IKKϵ and TBK1 at Ser172 was monitored as described in the legend to Figure 2. In the other panels, cell extracts were immunoblotted with the antibodies indicated. (B) MEFs expressing a truncated inactive form of TAK1 were treated for 1 h with 2 μM MRT67307, and then stimulated for 10 min with 5 ng/ml IL-1α. Proteins were detected as described in (A). (C) Purified GST–IKKϵ[K38A] or GST–TBK1[K38A] proteins were incubated with 2 units/ml recombinant IKKα and IKKβ in the presence of MgATP for 30 min at 30 °C. Phosphorylation of the activation loop was monitored by immunoblotting using the anti-phospho-Ser172 TBK1 antibody. Blots were stripped and reprobed with anti-GST as a loading control. (D) Wild-type MEFs were incubated for 1 h without (control) or with 2 μM MRT67307, and then stimulated for the times indicated with 5 ng/ml IL-1α. Cells extracts were immunoblotted with the antibodies indicated. (E) Wild-type MEFs were co-transfected with DNA encoding an NF-κB luciferase reporter construct and pTK-RL plasmid DNA. At 24 h post-transfection, the cells were incubated for 1 h without (●) or with (○) 2 μM MRT67307 prior to stimulation with 5 ng/ml IL-1α for the times indicated. Luciferase activity was measured with a dual-luciferase assay system (Promega) and was normalized to Renilla luciferase activity. Values are means±S.E.M., n=3. *P< 0.05 compared with cells without treatment. (F) Purified IKKα[S176A/S180A] or IKKβ[S177A/S181A] were incubated with Mg[γ-32P]ATP with or without 2 units/ml IKKϵ or TBK1. Reactions were terminated in SDS, the proteins resolved by SDS/PAGE, stained with Coomassie Blue (lower panel) and the gel autoradiographed (upper panel). See also Supplementary Figure S1 at http://www.BiochemJ.org/bj/434/bj4340093add.htm.

The activation of the IKK-related kinases by the canonical IKKs could be mediated either directly or indirectly via another intervening protein kinase. Unequivocal evidence for a direct phosphorylation of IKKϵ and TBK1 by the canonical IKKs was obtained by reconstituting the kinase reaction in vitro using purified proteins. Incubation of purified IKKα and IKKβ with recombinant catalytically inactive mutants of IKKϵ and TBK1 led to the phosphorylation of Ser172 within the activation loop of the IKK-related kinases (Figure 3C). Similar results were obtained in co-transfection experiments (Supplementary Figure S1B).

Inhibition of the canonical IKKs by IKKϵ/TBK1

We noticed that MRT67307 not only failed to suppress the IL-1-stimulated phosphorylation of p105 at Ser933, but actually enhanced phosphorylation in IKKα−/− MEFs (Figure 3A), suggesting that the IKK-related kinases might negatively regulate IKKβ. To investigate this point, we studied the phosphorylation of RelA. The IL-1-stimulated phosphorylation of RelA at Ser468 was prevented by the IKKβ inhibitor BI605906 in IKKα−/− MEFs, whereas MRT67307 enhanced phosphorylation (Figure 3A). Similar results were obtained in wild-type MEFs, where MRT67307 enhanced the IL-1-stimulated phosphorylation of p105 at Ser933 and RelA at both Ser468 and Ser536 (Figure 3D). MRT67307 also enhanced IL-1-stimulated activation of NF-κB-dependent gene transcription in wild-type MEFs (Figure 3E), again indicating that the IKK-related protein kinases function as negative regulators of IKKβ in MEFs.

IL-1-stimulation decreased the electrophoretic mobility of IKKβ in IKKα−/− MEFs as a result of phosphorylation (Supplementary Figure S1C), which was partially suppressed by BI605906, partially suppressed by MRT67307 and completely suppressed by a combination of both inhibitors (Figure 3A). This experiment showed that the phosphorylation of IKKβ was partially dependent on IKKϵ/TBK1 activity and partly dependent on autophosphorylation. However, in contrast with BI605906, MRT67307 did not inhibit the phosphorylation of IKKβ at Ser177 and Ser181, the amino acid residues whose phosphorylation is required for activation (Figure 3A), demonstrating that the IKK-related kinases phosphorylate IKKβ at other sites. These conclusions were supported by further experiments in TAK1−/− MEFs. In these cells, IL-1 did not induce the phosphorylation of the activating serine residues on IKKα (Ser176/Ser180) and IKKβ (Ser177/Ser181), but still decreased the electrophoretic mobility of the canonical IKKs, an effect that was completely suppressed by MRT67307 (Figure 3B). Taken together, our results establish that the IKK-related kinases phosphorylate the canonical IKKs at sites outwith the activation loops.

To establish that IKKϵ and TBK1 can phosphorylate the canonical IKKs directly, we expressed mutants in which Ser176 and Ser180 of IKKα or Ser177 and Ser181 of IKKβ were changed to alanine to prevent their phosphorylation and the activation of IKKα and IKKβ. These mutants were phosphorylated by purified IKKϵ and TBK1 in vitro to ~1–2 mol/mol of protein, demonstrating that IKKϵ and TBK1 can phosphorylate the canonical IKKs at residues distinct from those that trigger their activation (Figure 3F).

Cross-talk between canonical IKKs and IKK-related kinases during TLR3 and TLR4 signalling

Since the IKK-related kinases play key roles in anti-viral immunity, we also investigated the regulation of IKKϵ and TBK1 by ligands that activate TLR3 and TLR4 in macrophages. Treatment of macrophages with MRT67307 enhanced the poly(I:C)-stimulated phosphorylation of TBK1 at Ser172 (Figure 4A, top panel) and enhanced the catalytic activity of IKKϵ and TBK1 as judged by immunoprecipitation from extracts of poly(I:C)-stimulated cells followed by enzymatic assay in the absence of MRT67307 (Figure 4A, middle two panels). Similar results were obtained in LPS-stimulated macrophages (Supplementary Figure S2B at http://www.BiochemJ.org/bj/434/bj4340093add.htm). This confirms our previous observations using the less-specific inhibitor BX795 [17]. Thus, as with the IL-1-stimulated MyD88-dependent pathway, the TLR3/TLR4–TRIF-dependent pathway also utilizes a distinct upstream protein kinase for the activation of the IKK-related kinases.

Figure 4 Cross-talk between IKK subfamily members also occurs during TLR3 signalling in macrophages

(A) BMDMs were incubated without or with 2 μM MRT67307 for 1 h then stimulated with 10 μg/ml poly(I:C) for the times indicated. IKKϵ and TBK1 were immunoprecipitated from 50 μg of cell extract protein and their catalytic activity was measured in the absence of MRT67307 by incubation with GST–IRF3 and Mg[γ-32P]ATP. Cell extracts were immunoblotted with the antibodies indicated. KA, autoradiogram. (B) RAW264.7 cells were treated with vehicle control, 1 μM 5Z-7-oxozeaenol, 2 μM MRT67307 or a combination of both for 1 h prior to stimulation with 10 μg/ml poly(I:C) for 45 min. The phosphorylation of Ser172 of IKKϵ and TBK1 was monitored as described in the legend for the top panels in Figure 2. For the other panels, cell extracts were immunoblotted with the indicated antibodies. (C) RAW264.7 cells were treated with vehicle control or 2 μM MRT67307 for 1 h prior to stimulation with 10 μg/ml poly(I:C) for the indicated times, and extracts were immunoblotted with the indicated antibodies. p-, phospho-. (D) The effect of MRT67307 on NF-κB-dependent gene transcription was measured in HEK-293-TLR3 cells in response to 25 μg/ml poly(I:C), as described in the legend to Figure 3(E). Values are means±S.E.M., n=3. *P< 0.05 compared with cells without treatment. See also Supplementary Figure S2 at http://www.BiochemJ.org/bj/434/bj4340093add.htm.

We found that incubation of macrophages with the IKKβ inhibitor BI605906 in the presence of MRT67307 only inhibited LPS- or poly(I:C)-stimulated phosphorylation of IKKϵ and TBK1 partially (results not shown), presumably because IKKα (which is not inhibited by BI605906) also contributes to the activation of the IKK-related kinases. Therefore, to investigate whether the TAK1–IKKα/β signalling pathway was also involved in the activation of IKKϵ and TBK1 by the TRIF-dependent pathway, we treated macrophages with a potent inhibitor of TAK1 called 5Z-7-oxozeaenol to inhibit the activation of IKKα as well as IKKβ [24]. At 1 μM, 5Z-7-oxozeaenol inhibited the LPS-mediated activation of IKKα/β, the phosphorylation of p105 and the activation of p38 MAPK without affecting an upstream signalling event, namely the modification of IRAK1 (IL-1R-associated kinase 1) by phosphorylation and polyubiquitination [25] (Supplementary Figure S2A). However, 5Z-7-oxozeaenol had little effect on poly(I:C)- or LPS-induced activation of IKKϵ and TBK1 (Figure 4B and Supplementary Figure S2B). Complete blockade of the activation of IKKϵ and TBK1 by poly(I:C) or LPS required incubation of macrophages with a combination of 5Z-7-oxozeaenol and MRT67307 (Figure 4B and Supplementary Figure S2B), demonstrating that TLR3- and TLR4-mediated activation of the IKK-related kinases involves the two signalling pathways described above for IL-1.

The phosphorylation of p105 by the canonical IKKs is required for activation of the protein kinase Tpl2 [26,27], which lies at the head of the protein kinase cascade that activates the MAPKs ERK1 and ERK2. It could therefore be argued that Tpl2, or a protein kinase activated by Tpl2, and not the canonical IKKs themselves, are the direct activators of the IKK-related kinases. However, C1, a relatively specific inhibitor of Tpl2 [18], did not affect the LPS-stimulated activation of IKKϵ or TBK1 in the absence or presence of MRT67307 under conditions where it blocked the activation of ERK1 and ERK2 (Supplementary Figure S2C). Thus Tpl2 and/or the protein kinases that it activates are not required for the activation of the IKK-related kinases.

Treatment of macrophages with MRT67307 led to an increase in the poly(I:C)- and LPS-stimulated phosphorylation of p105 and RelA (Figure 4C and Supplementary Figure S2C) and enhanced NF-κB transcriptional activity (Figure 4D), indicating that the negative regulation of the canonical IKKs by the IKK-related kinases also operates in the TLR3/TLR4 signalling pathways.

Regulation of IKKϵ and TBK1 by TNFα

We reported previously that, in contrast with the IL-1-stimulated activation of IKKϵ/TBK1, the TNFα-stimulated activation of these IKK-related kinases did not occur in TAK1−/− MEFs [17]. This result initially suggested that IL-1 and TNFα employ distinct signalling pathways to activate the IKK-related kinases. However, the present study suggested an alternative explanation, namely that TNFα may only be able to activate the IKK-related kinases using the TAK1–IKKα/IKKβ-dependent arm of the signalling pathway. We therefore studied the effects of BI605906 and MRT67307 on the TNFα-stimulated phosphorylation of the IKK-related kinases. These experiments showed that the TNFα-induced phosphorylation of IKK-related kinases at Ser172 was suppressed by BI605906, in IKKα−/− MEFs, but not by MRT67307 (Figure 5A), establishing that TNFα only activates IKKϵ/TBK1 via the canonical IKKs. Similar to the IL-1 signalling pathway, the IKK-related kinases inhibited the canonical IKKs in TNFα-stimulated MEFs, since MRT67307 enhanced the TNFα-induced phosphorylation of p105 in either IKKα−/− (Figure 5A) or wild-type MEFs (Figure 5B). MRT67307 also enhanced TNFα-stimulated NF-κB-dependent gene transcription (Figure 5C).

Figure 5 TNFα-induced activation of IKKϵ/TBK1 is controlled solely by the canonical IKK complex

(A) IKKα−/− MEFs were treated with 10 μM BI605906, 2 μM MRT67307 or a combination of both inhibitors, and then stimulated for 10 min with 10 ng/ml TNFα. Phosphorylation of IKKϵ and TBK1 was measured as described in the legend to Figure 2. In all other panels, cell extract protein (20 μg) was immunoblotted with the antibodies indicated. (B) Wild-type MEFs were incubated for 1 h without (control) or with 2 μM MRT67307 prior to stimulation with 10 ng/ml TNFα for the times indicated, and extracts were immunoblotted with the antibodies indicated. p-, phospho-. (C) The effect of MRT67307 on NF-κB-dependent gene transcription was measured in wild-type MEFs stimulated with 10 ng/ml TNFα as described in the legend to Figure 3(E). Values are means±S.E.M., n=3. *P< 0.05 compared with cells without treatment.

Identification of proteins targeted by both the canonical IKKs and the IKK-related kinases

To date, the canonical IKKs and the IKK-related kinases have been widely believed to operate in separate pathways and to phosphorylate unique substrates. Thus the canonical IKKs, but not the IKK-related kinases, phosphorylate p105, RelA and IκBα (Figures 3D and 6A), whereas the IKK-related kinases phosphorylate IRF3 specifically (Figure 1B). In the present study, we identify proteins that are substrates for both the canonical IKKs and the IKK-related kinases.

Pro-inflammatory stimuli induce the phosphorylation of NEMO [28,29], which can be monitored by a decrease in its electrophoretic mobility (Figure 2D). In the present study, we found that BI605906 or MRT67307 did not prevent the IL-1-stimulated phosphorylation of NEMO in IKKα−/− MEFs, but the combined addition of both compounds completely prevented phosphorylation (Figure 6B). Thus IKKβ and the IKK-related kinases are both involved in the IL-1-stimulated phosphorylation of NEMO. Consistent with this finding, MRT67307 completely suppressed the IL-1-stimulated decrease in the mobility of NEMO in TAK1−/− MEFs where the canonical IKKs are not activated (Figure 6C).

Figure 6 Selective and shared substrates within the IKK family

(A) IKKα−/− MEFs were incubated for 1 h with the indicated concentrations of BI605906, stimulated for 10 min with 5 ng/ml IL-1α and cell extracts immunoblotted with the antibodies indicated. p-, phospho-. (B) IKKα−/− MEFs were incubated for 1 h with 10 μM BI605906, 2 μM MRT67307 or with a combination of both, stimulated for 10 min with 5 ng/ml IL-1α and cell extracts were immunoblotted with the antibodies shown. (C) TAK1−/− cells were treated for 1 h without or with 2 μM MRT67307, stimulated for 10 min with 5 ng/ml IL-1α and immunoblotted as described in (B). (D) HEK-293 cells were co-transfected with DNA vectors encoding HA-tagged NEMO and GST, GST–IKKα, GST–IKKβ, GST–IKKϵ or GST–TBK1. Cell extracts (20 μg of protein) were then immunoblotted with either anti-HA or anti-GST antibodies. (E) The experiment was performed as described in (D), except that NEMO was replaced by TANK. (F) Summary of the sites on NEMO and TANK that became phosphorylated after co-transfection with IKK family members. Sites phosphorylated only after co-transfection with IKKϵ or TBK1 and not after co-transfection with IKKα or IKKβ are shown in bold-face type. Single-letter amino-acid notation is used.

LPS also stimulates the phosphorylation of TANK, a component of the TBK1 and IKKϵ complexes [30]. The IL-1stimulated phosphorylation of TANK in IKKα−/− MEFs was unaffected by MRT67307, was largely suppressed by BI605906 and was completely prevented in the presence of both inhibitors (Figure 6B). However, in TAK1−/− MEFs, where the canonical IKKs are not activated, the IL-1-stimulated phosphorylation of TANK was completely suppressed by MRT67307 (Figure 6C). Thus TANK, like NEMO, is phosphorylated in MEFs by both the canonical IKKs and the IKK-related kinases.

To identify the residues on NEMO and TANK that are phosphorylated by different members of the IKK subfamily, we co-transfected these proteins in HEK-293 cells, which decreased the electrophoretic mobilities of NEMO and TANK (Figures 6D and 6E). Tryptic digestion followed by mass spectrometric analysis identified a number of serine/threonine residues that became phosphorylated. All four members of the IKK subfamily phosphorylated NEMO at Ser141, Ser148 and Ser195, whereas Thr50 and Ser208 only became phosphorylated when NEMO was co-transfected with IKKϵ or TBK1. All of the IKKs phosphorylated TANK at Ser49, Ser126, Ser208 and Ser228, but only IKKϵ and TBK1 phosphorylated Ser178 and Ser257 (Figure 6F). Thus the different members of the IKK family members possess overlapping but not identical substrate specificities.

DISCUSSION

In an earlier study, we obtained evidence that the activation of the IKK-related kinases involves a separate ‘upstream’ kinase(s) [17], which we identify in the present study as the canonical IKKs, IKKα and IKKβ. We further show that two signalling pathways are involved in the IL-1-induced activation of the IKK-related protein kinases. They both require the E3 ubiquitin ligase TRAF6 but then diverge, one pathway requiring TAK1 and the canonical IKKs, and the second being independent of these protein kinases. The IKKα/β-independent pathway is suppressed by the IKKϵ/TBK1 inhibitor MRT67307, suggesting that it culminates in the autophosphorylation and autoactivation of the IKK-related kinases. However, it cannot be excluded that, like IKKβ, IKKϵ and TBK1 require another protein kinase (denoted as PKX in Figure 7A) to initiate the autophosphorylation reaction. Similar to IL-1, the poly(I:C)–TLR3 and LPS–TLR4-stimulated activation of the IKK-related kinases also involves IKKα/β-dependent and -independent pathways (Figure 7A). In contrast with IL-1, TNFα activates the IKK-related kinases solely through the canonical IKKs (Figure 7B), explaining our earlier observation that the TNFα-stimulated activation of IKKϵ/TBK1 did not occur in TAK1−/− MEFs [17].

Figure 7 Model for how different IKK family members are regulated in response to pro-inflammatory stimuli

(A) Agonists that engage the IL-1R, TLR3 or TLR4 activate IKKϵ and TBK1 by IKKα/β-dependent and -independent mechanisms. When the canonical IKK complex is inactive, IKKϵ and TBK1 are activated by a pathway that is suppressed by MRT67307. In this pathway, the binding of MRT67307 to IKKϵ/TBK1 may prevent phosphorylation of the activation loops of IKKϵ/TBK1 by an as yet unidentified protein kinase(s), denoted as PKX. Alternatively, PKX may be identical with IKKϵ/TBK1 and the pathway may culminate in autoactivation of these protein kinases. NEMO is required for activation of the IKK-related kinases by both the IKKα/β-dependent and -independent pathways. NEMO is known to interact with TANK, a regulatory component of the IKK-related kinases. Whether TANK binds to a separate pool of NEMO (as indicated in the diagram) or to the NEMO that is already complexed with the canonical IKKs is unknown. Once activated, IKKϵ and TBK1 phosphorylate IKKα/β, decreasing the activity of the canonical IKK complex. In addition, IKKα/β induce the expression of IKKϵ after several hours through an NF-κB-dependent transcriptional mechanism that may reinforce the negative control of the canonical IKKs. (B) TNFα activates IKKϵ/TBK1 solely by the IKKα/β-dependent pathway. (C) A Venn diagram of the substrates phosphorylated in cells by the different members of the IKK family.

The canonical IKKs phosphorylated IKKϵ and TBK1 at Ser172 in vitro, indicating that they activate the IKK-related kinases directly and not through an intervening kinase. However, we also found that the IKK-related kinases inhibit the canonical IKKs, since MRT67307 enhanced the phosphorylation of several physiological substrates of the canonical IKKs by all inflammatory stimuli tested. Thus the IKK-related kinases play an important role in limiting the extent of activation of the canonical IKKs and hence the activation of NF-κB. To our knowledge, this represents the first role for the IKK-related kinases in the MyD88-dependent signalling pathway to be identified, as well as the first general function of these protein kinases that is common to the IL-1, TNFα, poly(I:C) and LPS signalling pathways. In contrast, other known functions of IKKϵ and TBK1 are restricted to specific signalling events. For instance, the regulation of IRF3-dependent gene transcription by IKKϵ and TBK1 is associated with the TRIF-dependent production of IFNβ [2]. Another example is the pro-survival function of TBK1, which protects foetal hepatocytes from TNF-induced apoptosis [31].

The negative regulation of the canonical IKKs by the IKK-related kinases is likely to be effected at multiple levels because the IKK-related kinases not only phosphorylate the catalytic subunits of IKKα and IKKβ at sites distinct from those that trigger activation, but also phosphorylate NEMO. It has been reported that prolonged stimulation with TNFα leads to the deactivation of IKKβ due to phosphorylation of a cluster of serine residues near its C-terminus [32]. The phosphorylation of these sites was attributed to autophosphorylation, but the results of the present study suggest that the IKK-related kinases contribute to the phosphorylation of these inhibitory sites. Moreover, the IKKβ-catalysed phosphorylation of NEMO, on residues that were also identified in the present study as sites phosphorylated by IKKϵ/TBK1, dampens IKKβ activity and NF-κB-dependent gene transcription [21]. The mechanism may involve the dissociation of NEMO from the IKKα/β catalytic subunits leading to their inactivation [28,33].

The phosphorylation of TANK may also be important in the ‘cross-talk’ between the IKK-related kinases and the canonical IKKs. Mice that do not express TANK show increased TLR7-dependent activation of NF-κB and develop autoimmune disease due to enhanced signalling ‘downstream’ of MyD88, but produce normal levels of Type 1 IFNs during viral infection, presumably because the loss of TANK is compensated for by other TBK1/IKKϵ-binding proteins, such as NAP1 (NF-κB-activating kinase-associated protein kinase 1) and SINTBAD (similar to NAP1 TBK1 adaptor) [34]. Since TANK interacts with TRAF6, and TRAF6 polyubiquitylation was slightly enhanced in TLR7-stimulated macrophages from TANK−/− mice, it was suggested that TANK suppresses the activation of NF-κB by inhibiting TRAF6 polyubiquitylation [34]. This explanation may well be correct, but an additional possibility is that the NEMO–TANK interaction is critical for the negative regulation of the canonical IKKs by the IKK-related kinases, so that this negative regulation is lost in TANK−/− mice (Figure 7). It would therefore clearly be of interest to study how the IKK-related kinases are regulated and how they control the canonical IKKs in TANK−/− cells. Dissecting the precise molecular mechanisms by which the IKK-related kinases negatively regulate the canonical IKKs remains a challenging task for future research.

It is well established that inflammatory stimuli not only activate IKKϵ, but also increase the expression of the protein and, for this reason, it is also called IKKi (IKK inducible) [35]. It has been reported that IKKϵ expression is not induced in IKKβ−/− or RelA−/− MEFs [36]. These observations, together with the presence of functional NF-κB-binding sites in the promoter of the gene encoding IKKϵ [37], indicate that the canonical IKKs control the expression of IKKϵ as well as its activation. In the present study, we confirmed these results by demonstrating that the IKKβ inhibitor BI605906, but not MRT67307, suppresses the LPS-stimulated increase in IKKϵ expression (Supplementary Figure S2E). Thus IKKϵ, like IκBα and A20, represents an NF-κB-dependent gene that is induced in response to pro-inflammatory stimuli to negatively control the IKKβ–NF-κB signalling axis (Figure 7).

The IKK-related protein kinases are required for the phosphorylation and activation of IRF3 in a TRIF-dependent signalling pathway that is activated by agonists which engage TLR3 and TLR4 [2]. In these pathways, the phosphorylation of IRF3 requires the presence of TRAF3 and it has been inferred but, to our knowledge, never shown, that TRAF3 is required for the activation of the IKK-related kinases by these agonists [38,39]. In the present study, we found that the IL-1-stimulated activation of the IKK-related kinases was unimpaired in TRAF3−/− MEFs (Figure 2B). Moreover, the activation of the IKK-related kinases by IL-1 or TNFα [17], or by TLRs that signal via MyD88 (K. Clark and P. Cohen, unpublished work), does not induce the phosphorylation of IRF3 or significant production of IFNβ respectively. However, TLRs that signal via MyD88 can induce IFNβ production if they are co-localized with TRAF3 at the plasma membrane by expressing a fusion protein in which the phosphatidylinositol (4,5) bisphosphate-binding PH (pleckstrin homology) domain of PLC (phospholipase C)-δ1 is linked to TRAF3 [40]. These findings suggest that TRAF3 may not be required for the activation of the IKK-related kinases, but instead may be needed to couple the IKK-related kinases to the phosphorylation of IRF3.

In IKKα−/− MEFs, we noticed that the IKKβ inhibitor BI605906 not only prevented the phosphorylation of physiological substrates, such as p105 and RelA, but also the phosphorylation of the serine residues in IKKβ (Ser177 and Ser181) that trigger its activation. Similar results were obtained with PS1145, a structurally unrelated inhibitor of IKKβ (Supplementary Figures S1D and S1E). In contrast, BI605906 did not inhibit the phosphorylation of the equivalent residues of IKKα (Ser176 and Ser180) in IKKβ−/− MEFs (results not shown), demonstrating that BI605906 exerts its effect by binding to IKKβ and not by inhibiting a more upstream component of the pathway. These observations suggest that IKKβ may phosphorylate and activate itself in MEFs. This would be consistent with the finding that the inactive canonical IKK complex can phosphorylate and activate itself in vitro upon incubation with MgATP and pUb chains of undefined composition [9]. However, the canonical IKKs are not activated by IL-1 or TNFα in MEFs that do not express TAK1 or express a truncated inactive mutant [4,5]. It is therefore possible that TAK1 starts the activation of the canonical IKKs, which is then driven to completion autocatalytically by the canonical IKKs themselves.

A report that NEMO is required for the production of IFNβ ‘downstream’ of the cytoplasmic double-stranded RNA-receptor RIG-I (retinoic acid-inducible gene-I) in Sendai virus-infected cells [41] led us to study the activation of the IKK-related kinases by IL-1 in NEMO−/− MEFs. Since NEMO is required for the activity of the canonical IKKs, our expectation was that IL-1 would still activate the IKK-related kinases in NEMO−/− MEFs via the pathway that is independent of IKKα and IKKβ activity. However, the IL-1-stimulated activation of the IKK-related kinases was completely abolished in NEMO−/− MEFs, implying an essential role for NEMO in the activation of the IKK-related kinases independent of its role in regulating the canonical IKKs. NEMO does not bind directly to the catalytic subunits of IKKϵ and TBK1, but indirectly by binding to TANK [30,41]. Since activation of the canonical IKKs by IL-1 may be initiated by the binding of K63-pUb chains to NEMO, the IKK-related kinases could be activated in a similar manner [10,11]. For example, TRAF6-generated K63-pUb chains might bind to NEMO, inducing a conformational change in TANK that enables the IKK-related kinases to autophosphoryate and activate themselves. Consistent with this hypothesis, the NEMO[D311N] mutant that does not bind to K63-pUb chains was unable to restore IRF3-dependent gene transcription induced by overexpression of the MAVS (mitochondrial anti-viral signalling) protein, a pathway that requires the activation of IKKϵ and TBK1 [30,41]. Recent studies have begun to indicate that the TNFα-induced activation of the canonical IKKs may not be mediated by K63-pUb chains, as thought previously, but by other types of pUb chains [9,15,42]. The inability of TNFα to induce the formation of K63-pUb chains could explain why TNFα can only activate the IKK-related kinases through the canonical IKK-dependent pathway.

In the present study, we identified several proteins that are phosphorylated by both the canonical IKKs and the IKK-related kinases, namely, NEMO, TANK, IKKα, IKKβ, IKKϵ and TBK1, whereas IκBα, RelA and p105 are phosphorylated only by the canonical IKKs and IRF3 only by the IKK-related kinases (Figure 7C). Interestingly, the substrates we found that are common to all four members of the IKK subfamily of protein kinases are their regulatory and catalytic subunits, whose function is to co-ordinate the activities of the canonical and IKK-related kinases. In contrast, the substrates that are specific to either the canonical IKKs or the IKK-related kinases are components of transcription factors, which are dedicated to the expression of genes that encode particular inflammatory mediators. The finding that the canonical IKKs and the IKK-related kinases have overlapping substrate specificities in cells is consistent with studies on their preferences for synthetic peptide substrates [43,44]. Since IL-1 and TNFα activate IKKϵ and TBK1 without inducing the phosphorylation of IRF3, the identification of novel substrates for the IKK-related kinases in the present study provides new cell-based readouts for these kinases.

In summary, in the present study, we have identified a new role for the canonical IKKs in regulating the IKK-related kinases and established that the IKK-related kinases exert a negative regulation on the canonical IKKs that may be critical in preventing the overproduction of the inflammatory mediators that lead to inflammatory and autoimmune diseases. We have also identified new physiological substrates for the members of the IKK subfamily of protein kinases, through the introduction of improved pharmacological inhibitors of these enzymes. The wider exploitation of these compounds is likely to identify additional proteins that are targeted by both the canonical IKKs and IKK-related kinases.

AUTHOR CONTRIBUTION

Kristopher Clark performed all of the experiments presented in the Figures of the paper. Mark Peggie generated the constructs. Lorna Plater measured the IC50 values of MRT67307 and BI605906 against a large numbers of kinases. Ronald Sorcek, Erick Young and Jeffrey Madwed developed BI605906, while Joanne Hough and Edward McIver developed MRT67307. Kristopher Clark and Philip Cohen planned the experiments, analysed the data and wrote the manuscript.

FUNDING

K.C. is a recipient of a Long-Term Fellowship from EMBO, and P.C. is a Royal Society Research Professor. The work was supported by the U.K. Medical Research Council, and Boehringer Ingelheim.

Acknowledgments

We thank Katherine Fitzgerald, Shizuo Akira, Inder Verma, Tak Mak, Genhong Chen and Manolis Pasparakis for kindly providing the reagents and cell lines mentioned in the Materials and methods section. We also thank the National Centre for Protein Kinase Profiling, MRC Protein Phosphorylation Unit, University of Dundee, Dundee, Scotland, U.K. (http://www.kinase-screen.mrc.ac.uk) for analysing the specificities of BI605906 and MRT67307, Dr Nick Morrice for the identification of phosphorylation sites on NEMO and TANK, and the Protein and Antibody Production Teams of the Division of Signal Transduction Therapy at the University of Dundee, Dundee, Scotland, U.K. (co-ordinated by Hilary McLauchlan and James Hastie) for proteins and antibodies.

Abbreviations: BMDM, bone-marrow-derived macrophage; C1, Compound 1; ERK, extracellular-signal-regulated kinase; FBS, foetal bovine serum; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GST, glutathione transferase; HA, haemagglutinin; HEK, human embryonic kidney; IFN, interferon; IRF, IFN regulatory factor; IL-1, interleukin-1; IL-1R, IL-1 receptor; JNK, c-Jun N-terminal kinase; LPS, lipopolysaccharide; LUBAC, linear ubiquitin-chain-assembly complex; MAPK, mitogen-activated protein kinase; MEF, mouse embryonic fibroblast; MyD88, myeloid differentiation factor 88; NCBI, National Center for Biotechnology Information; NF-κB, nuclear factor κB; IκB, inhibitor of NF-κB; IKK, IκB kinase; NAP1, NF-κB-activating kinase-associated protein kinase 1; NEMO, NF-κB essential modulator; pUb, polyubiquitin; K63-pUb, Lys63-linked pUb; TAK1, transforming growth factor-β-activated kinase 1; TAB, TAK1-binding protein; TLR, Toll-like receptor; TNF, tumour necrosis factor; Tpl2, tumour progression locus 2; TRAF, TNF-receptor-associated factor; TANK, TRAF-associated NF-κB activator; TBK1, TANK-binding kinase 1; TRIF, Toll/IL-1R domain-containing adaptor protein inducing IFNβ

References

View Abstract