Ubiquitin signals are decoded in cells by at least 200 ubiquitin binding proteins, which interact with different types of polyubiquitin chains and ubiquitin-like modifiers. These interactions induce conformational changes that allow these proteins to transmit the ubiquitin signal to effector proteins (Dikic et al., 2009). NEMO (NFκB Essential Modifier) is the protypic member of a family of proteins that interact with Lys63-linked and linear polyubiquitin chains (Nanda et al.,2011). NEMO functions as a high affinity receptor for linear ubiquitin chains and a low affinity receptor for long lysine-linked ubiquitin chains. It is thought that this phenomenon could explain quantitatively distinct NF-κB activation patterns in response to numerous cell stimuli (Kensche et al., 2012). NEMO is an integral component of the canonical IκB kinase (IKK) complex and is essential for the activation of IKKα and IKKβ, the protein kinase components of the complex. Mutations that abrogate binding of polyubiquitin chains to NEMO do not activate the IKK complex(Ea et al., 2006; Wu et al.,2006) and cause a severe immunodeficiency disease and greatly increased susceptibility to infection by bacteria of the tuberculosis family (Doffinger et al.,2001). NEMO also interacts with TANK, a component of the IKK-related kinases TBK1 and IKKε (Chariot et al., 2002).
The NEMO-TANK interaction is essential for effective cross-talk between thecanonical IKK complex and the IKK-related kinases which, if disrupted by the loss of TANK, leads to the hyperactivation of the innate immune system and to autoimmune disease (Clark et al., 2011; Kawagoe et al., 2009). NEMO is a powerful reagent for capturing the Lys63linked and linear polyubiquitin chains and their binding partners present in cell extracts. It is recommended that the NEMO [D311N] mutant, which is unable to bind polyubiquitin chains, is used as a control in such experiments (Windheim et al., 2008).
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