More than just an IκB kinase: the IKK complex coordinates mRNA stability and transcription

Abstract

The IκB kinase (IKK) complex is best known as the core regulator of NF‐κB signalling. Recent work from Mikuda et al reveals a new and unexpected function for IKK in the regulation of mRNA stability. Through interacting with and phosphorylating EDC4, a key component of the mRNA decapping complex, IKK regulates P‐body formation and the stability of numerous mRNAs, including many encoding inflammatory cytokines. Activation of IKK can therefore be more generally thought of as programming the cellular response to stress and infection through both mRNA stability and transcription.

The complexity of the numerous signals leading to activation of the NF‐κB transcription factor and the diversity of its roles as a regulator of gene expression can appear bewildering. However, a common feature of almost all stimuli that activate this pathway, be they inflammatory cytokines, pathogen‐associated molecular patterns (PAMPs) or cellular stresses such as DNA damage, is convergence on the IκB kinase (IKK) complex (Hinz & Scheidereit, 2014). IKK activation typically results from its proximity‐induced phosphorylation by a kinase such as transforming growth factor β‐activated kinase 1 (TAK1), facilitated through recruitment by linear and lysine 63 (K63)‐linked ubiquitin chains (Hinz & Scheidereit, 2014). In the case of IKK, this is mediated by ubiquitin binding motifs present in its regulatory subunit IKKγ (NEMO; Hinz & Scheidereit, 2014). In addition, the IKK complex contains two catalytic subunits IKKα and IKKβ. Of these, IKKβ is primarily responsible for activating the “classical” NF‐κB pathway, through phosphorylation and subsequent lysine 48 (K48)‐linked ubiquitin‐dependent proteasomal degradation of the inhibitor of NF‐κB, IκBα (Hinz & Scheidereit, 2014).

In addition to the biochemical evidence characterising this pathway, studies using mouse models confirmed the central importance of the IKK/NF‐κB signalling axis. For example, mice with knockouts of the genes encoding IKKγ, IKKβ and the NF‐κB subunit RelA(p65) all die in utero due to tumour necrosis factor (TNF) α‐induced hepatocyte death (Gerondakis et al, 2006). A consequence of this was the establishment of a dogma that led to IKK subunit mutant mice or specific IKKβ inhibitors often being used as proxies for the analysis of NF‐κB pathway signalling. However, in the years since these first studies it has become clear that IKKβ has many targets other than IκBα and can therefore better be thought of as a kinase that programmes the wider cellular response to infection and stress, of which NF‐κB activation is a critical but not sole component (Hinz & Scheidereit, 2014).

Adding to the growing evidence for the IKK complex being a pleiotropic regulator of inflammatory and stress responses is the report from Mikuda et al (2018). This article defines a new role for the IKK complex as a regulator of mRNA stability. Significantly, many of the mRNAs identified as being IKK regulated are not NF‐κB targets, further establishing that the consequences of IKKβ inhibition go far beyond its originally assigned role.

Mikuda et al (2018) used SILAC proteomics to identify novel IKKγ‐associated proteins following treatment with ionising radiation (IR), a known inducer of IKK activity and NF‐κB signalling (McCool & Miyamoto, 2012). Unexpectedly, the authors found that DNA damage induced the association of IKKγ with a number of RNA binding proteins (RBPs). This study has focussed on just one of these RBPs, EDC4, although an implication of these data is that the role of IKK as an RNA regulator goes far beyond the results described here. EDC4 is a component of the mRNA decapping complex where it acts as a scaffold for the assembly of the decapping enzyme DCP2 and its coactivator DCP1a. Removal of the 5′ mRNA cap by DCP1a and DCP2 then allows 5′–3′ mRNA degradation by the exonuclease XRN1 (Chang et al, 2014). Mikuda et al (2018) established that both IKKγ and IKKβ inducibly interact with EDC4 in response not only to IR treatment but also to TNFα, establishing the relevance of this complex to inflammatory signalling. Importantly, EDC4 is a substrate of IKKβ and mutation of these IKK phosphorylation sites abolished both its interaction with DCP1a and DCP2 as well as the stimulus‐induced increase in P‐body numbers, the sites of mRNA degradation and storage within the cytoplasm. Moreover, IKKβ associates with EDC4 in P bodies and inhibition of IKK activity abolishes the increase in P‐body numbers seen after IR treatment.

IκB kinase and EDC4 together regulate a large number of target mRNAs. Mikuda et al (2018) demonstrated that these include both NF‐κB‐dependent and NF‐κB‐independent transcripts. Interestingly, the IKK/EDC4 complex differentially regulates mRNA stability both before and after cell stress. Notably, in unstimulated cells, IKK and EDC4 act to destabilise a group of genes that include many inflammatory cytokines. However, after IR treatment this changes and IKK/EDC4 now function to promote their stability. As the authors suggest, such a switch would act to dampen inappropriate transcriptional noise but then provide a rapid mechanism to turn on the inflammatory response after stress (Fig 1). It will be interesting to learn whether a converse process plays a role in the resolution of the inflammatory response. The mechanistic basis for IKK and EDC4 regulation of mRNA stability in the absence of stimulation is not yet clear. Both proteins are present in P bodies under these conditions, and this could be a consequence of a low level of basal IKKβ activity present in the cell lines used. Alternatively, in the absence of stimulation IKKβ might fulfil a kinase‐independent scaffold function, as has been shown previously (Tsuchiya et al, 2010). Moreover, whether the decapping complex is actually responsible for the IKK‐dependent effects, either before or after cell stimulation, was not formally established by Mikuda et al (2018). Indeed, it is possible that phosphorylation of EDC4 by IKKβ may have other effects, possibly involving the other IKK‐associated RBPs (which did not include the other members of the decapping complex). EDC4 and the other members of the decapping complex have also been found associated with miRNAs (Treiber et al, 2017), providing a potentially indirect route through which they and IKK might influence mRNA stability and translation. Phosphorylation of EDC4 by IKK could also conceivably have other effects. For example, EDC4 has been described as chromatin associated, where it interacts with the BRCA1‐BRIP1‐TOPBP1 complex and can regulate DNA repair following DNA damage in a manner independent of its role in P bodies and mRNA stability (Hernandez et al, 2018).

Figure 1. IKK/EDC4 regulation of cytokine mRNA stability during the inflammatory response.

Diagram depicting the model proposed by Mikuda et al (2018), in which IKK/EDC4 function switches upon cell stress from promoting the destabilisation of cytokine‐encoding mRNAs to increasing their stability. Such a change in activity allows transcriptional noise to be suppressed when the cell is in an unstimulated state but then ensures that inflammatory signals are rapidly turned on when required. Also shown is how hypothetically this process could be reversed during resolution of inflammation. This issue was not, however, explored by Mikuda et al (2018). Not shown, for simplicity, are the roles of IKK and EDC4 in regulating the stability of other classes of mRNA nor the parallel role of IKK‐activated NF‐κB in driving pro‐inflammatory gene expression.

Although the core components of the IKK complex have been known for some time, it has been established that different subcomplexes targeting the IKKs to different substrates (e.g. Teo et al, 2010) do exist, although they remain poorly defined. Mikuda et al (2018) demonstrated that the amount of IKK complex localising to P bodies with EDC4 represents only a small proportion of the total. However, their data also imply that a number of different IKK subcomplexes regulating RNA biology could form after cell stress, creating a complex network regulating mRNA stability in parallel with nuclear transcription. It is likely therefore that the data presented here are only the tip of a large iceberg through which the IKKs act to coordinate the cellular response to stress and infection.

The EMBO Journal (2018) 37: e101084