Cellular responses to stress-like stimuli require the IκB kinase (IKK) signalsome (IKKα, IKKβ, and NEMO/ IKKγ) to activate NF-κB-dependent genes. IKKβ and NEMO/IKKγ are required to release NF-κB p65/p50 heterodimers from IκBα, resulting in their nuclear migration and sequence-specific DNA binding; but IKKα was found to be dispensable for this initial phase of canonical NF-κB activation. Nevertheless, IKKα(-/-) mouse embryonic fibroblasts (MEFs) fail to express NF-κB targets in response to proinflammatory stimuli, uncovering a nuclear role for IKKα in NF-κB activation. However, it remains unknown whether the global defect in NF-κB-dependent gene expression of IKKα(-/-) cells is caused by the absence of IKKα kinase activity. We show by gene expression profiling that rescue of near physiological levels of wild type IKKα in IKKα(-/-) MEFs globally restores expression of their canonical NF-κB target genes. To prove that the kinase activity of IKKα was required on a genomic scale, the same physiological rescue was performed with a kinase-dead, ATP binding domain IKKα mutant (IKKα(K44M)). Remarkably, the IKKa(K44M) protein rescued ∼28% of these genes, albeit in a largely stimulus-independent manner with the notable exception of several genes that also acquired tumor necrosis factor-α responsiveness. Thus the IKKα-containing signalsome unexpectedly functions in the presence and absence of extracellular signals in both kinase-dependent and -independent modes to differentially modulate the expression of five distinct classes of IKKα/NF-κB-dependent genes.
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