The NF-Kb Family of Transcription Factors and Its Regulation

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The NF-kB Family of Transcription Factors and Its Regulation

Andrea Oeckinghaus1,2 and Sankar Ghosh1,2

1Department of Immunobiology and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520 2Department of Microbiology and Immunology, Columbia University, College of Physicians and Surgeons, New York 10032 Correspondence: [email protected]

Nuclear factor-kB (NF-kB) consists of a family of transcription factors that play critical roles in inflammation, immunity, cell proliferation, differentiation, and survival. Inducible NF-kB activation depends on phosphorylation-induced proteosomal degradation of the inhibitor of NF-kB proteins (IkBs), which retain inactive NF-kB dimers in the cytosol in unstimulated cells. The majority of the diverse signaling pathways that lead to NF-kB activation converge on the IkB kinase (IKK) complex, which is responsible for IkB phosphorylation and is essential for signal transduction to NF-kB. Additional regulation of NF-kB activity is achieved through various post-translational modifications of the core components of the NF-kB signaling pathways. In addition to cytosolic modifications of IKK and IkB 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-kB response. This has made the NF-kB pathway a paradigm for understanding general principles of signal transduction and gene regulation.

ollowing the identification of NF-kB responses to a remarkable diversity of external F(nuclear factor-kB) as a regulator of kB stimuli, and thus is a pivotal element in multiple light chain expression in mature B and plasma physiological and pathological processes. The cells by Sen and Baltimore, inducibility of its progress made in the past two decades in under- activity in response to exogenous stimuli was standing how different stimuli culminate in demonstrated in various cell types (Sen et al. NF-kB activation and how NF-kB activation is 1986b; Sen et al. 1986a). Years of intense translated into a cell-type- and situation-specific research that followed demonstrated that response has made the NF-kB pathway a para- NF-kB is expressed in almost all cell types and digm for understanding signaling mechanisms tissues, and specific NF-kB binding sites are and gene regulation. Coupled with the large present in the promoters/enhancers of a large number of diseases in which dysregulation of number of genes. It is now well-established NF-kB has been implicated, the continuing that NF-kB plays a critical role in mediating interest into the regulatory mechanisms that

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A. Oeckinghaus and S. Ghosh

govern the activity of this important transcrip- a process pivotal for survival. A large number tion factor can be easily explained. of diverse external stimuli lead to activation of Because of its ability to influence expression NF-kB and the genes whose expression is regu- of numerous genes, the activity of NF-kBis lated by NF-kB play important and conserved tightly regulated at multiple levels. The pri- roles in immune and stress responses, and mary mechanism for regulating NF-kBis impact processes such as apoptosis, prolifer- through inhibitory IkB proteins (IkB, inhibitor ation, differentiation, and development. of NF-kB), and the kinase that phosphorylates Bacterial and viral infections (e.g., through IkBs, namely, the IkB kinase (IKK) complex. recognition of microbial products by receptors A number of post-translational modifications such as the Toll-like receptors), inflamma- also modulate the activity of the IkB and IKK tory cytokines, and antigen receptor engage- proteins as well as NF-kB molecules themselves. ment, can all lead to activation of NF-kB, In this article, we introduce the major players confirming its crucial role in innate and adap- in the NF-kB signaling cascade and describe tive immune responses. In addition, NF-kB the key regulatory steps that control NF-kB activation can be induced upon physical activity. We highlight the basic principles that (UV- or g-irradiation), physiological (ischemia underlie NF-kB regulation, and many of these and hyperosmotic shock), or oxidative stresses topics are discussed in depth in other articles (Fig. 1) (Baeuerle and Henkel 1994; Hayden on the subject. et al. 2006). Consistent with the large number of signals that activate NF-kB, the list of target genes con- NF-kB STIMULI AND kB-DEPENDENT trolled by NF-kB is also extensive (Pahl 1999). TARGET GENES Importantly, regulators of NF-kB such as NF-kB transcription factors are crucial players IkBa, p105, or A20 are themselves NF-kB- in an elaborate system that allows cells to dependent, thereby generating auto-regulatory adapt and respond to environmental changes, feedback loops in the NF-kB response. Other

Antigen receptors Cytokines TCR TNFa BCR IL-1 Infection Genotoxic stress LPS UV-, g-radiation dsRNA reactive oxygen intermediates (ROI)

NF-kB

Immunregulatory proteins Regulators of apoptosis Serum amyloid protein, C3 complement Bcl-XL, Cyclins, Cytokines Rel/IkB IAPs VCAM, growth proteins ICAM TNFa, IL-1, factors IL-6, IL-12 IkBa, c-Rel, G-CSF, APOTOSIS/ TCRa, b p105 CELL SURVIVAL MHC I M-CSF

IMMUNE RESPONSE/INFLAMMATION NF-kB PROLIFERATION REGULATION Figure 1. NF-kB stimuli and target genes. NF-kB acts as a central mediator of immune and inﬂammatory responses, and is involved in stress responses and regulation of cell proliferation and apoptosis. The respective NF-kB target genes allow the organism to respond effectively to these environmental changes. Representative examples are given for NF-kB inducers and kB-dependent target genes.

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The NF-kB Family of Transcription Factors and Its Regulation

NF-kB target genes are central components of carboxy-terminal part of the RHD is mainly the immune response, e.g., immune receptor responsible for dimerization and interaction subunits or MHC molecules. Inflammatory with IkBs (Ghosh et al. 1995; Muller et al. processes are controlled through NF-kB-depen- 1995; Chen et al. 1998). dent transcription of cytokines, chemokines, In most unstimulated cells, NF-kB dimers cell adhesion molecules, factors of the comple- are retained in an inactive form in the cytosol ment cascade, and acute phase proteins. The through their interaction with IkB proteins. list of kB-dependent target genes can be Degradation of these inhibitors upon their further extended to regulators of apoptosis phosphorylation by the IkB kinase (IKK) (antiapoptotic Bcl family members and inhibi- complex leads to nuclear translocation of NF- tor of apoptosis proteins/IAPs) and prolifer- kB and induction of transcription of target ation (cyclins and growth factors), thereby genes. Although NF-kB activity is inducible in substantiating its role in cell growth, prolifer- most cells, NF-kB can also be detected as a con- ation, and survival (Chen and Manning 1995; stitutively active, nuclear protein in certain cell Kopp and Ghosh 1995; Wissink et al. 1997). types, such as mature B cells, macrophages, Furthermore, crucial functions of NF-kBin neurons, and vascular smooth muscle cells, as embryonic development and physiology of the well as a large number of tumor cells. bone, skin, and central nervous system add to Through combinatorial associations, the the importance of this pleiotropic transcription Rel protein family members can form up to 15 factor (Hayden and Ghosh 2004). different dimers. However, the physiological Because so many key cellular processes such existence and relevance for all possible dimeric as cell survival, proliferation, and immunity are complexes has not yet been demonstrated. The regulated through NF-kB-dependent transcrip- p50/65 heterodimer clearly represents the tion, it is not surprising that dysregulation of most abundant of Rel dimers, being found in NF-kB pathways results in severe diseases such almost all cell types. In addition, dimeric com- as arthritis, immunodeficiency, autoimmunity, plexes of p65/p65, p65/c-Rel, p65/p52, c-Rel/ and cancer (Courtois and Gilmore 2006). c-Rel, p52/c-Rel, p50/c-Rel, p50/p50, RelB/ p50, and RelB/p52 have been described, some of them only in limited subsets of cells THE NF-kB TRANSCRIPTION (Hayden and Ghosh 2004). RelB seems to be FACTOR FAMILY unique in this regard as it is only found in The NF-kB transcription factor family in p50- or p52-containing complexes (Ryseck mammals consists of five proteins, p65 (RelA), et al. 1992; Dobrzanski et al. 1994). p50/c-Rel RelB, c-Rel, p105/p50 (NF-kB1), and p100/52 dimers are the primary component of the con- (NF-kB2) that associate with each other to stitutively active NF-kB observed in mature B form distinct transcriptionally active homo- cells (Grumont et al. 1994b; Miyamoto et al. and heterodimeric complexes (Fig. 2). They 1994). The NF-kB family of proteins can be all share a conserved 300 amino acid long further divided into two groups based on their amino-terminal Rel homology domain (RHD) transactivation potential because only p65, (Baldwin 1996; Ghosh et al. 1998), and se- RelB, and c-Rel contain carboxy-terminal quences within the RHD are required for di- transactivation domains (TAD) (Fig. 2). RelB merization, DNA binding, interaction with is unique in that it requires an amino-terminal IkBs, as well as nuclear translocation. Crystal leucine zipper region in addition to its TAD to structures of p50 homo- and p50/p65 heterodi- be fully active (Dobrzanski et al. 1993). p50 mers bound to DNA revealed that the amino- and p52 are generated by processing of the pre- terminal part of the RHD mediates specific cursor molecules p105 and p100, respectively. DNA binding to the NF-kB consensus sequence The amino-termini of these precursors present in regulatory elements of NF-kB target contain the RHDs of p50 or p52, followed by genes (50 GGGPuNNPyPyCC-30), whereas the a glycine rich region (GRR) and multiple

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A. Oeckinghaus and S. Ghosh

p65 RHD TAD RelA RelB LZ RHD TAD

c-Rel RHD TAD B/Rel Family

k GRR ANK p100/p52 RHD DD NF- NF-kB2

p105/p50 GRR RHD DD NF-kB1

ANK IkBa PEST

IkBb PEST

IkBe

IkBz

B Family Bcl-3 k I GRR ANK p100 RHD DD

p105 GRR RHD DD

NBD IKKa Kinase domain LZ HLH NBD IKKb Kinase domain LZ HLH

IKK complex NEMO CC1 CC2 LZ Z IKKg

Figure 2. Members of the NF-kB, IkB, and IKK protein families. The Rel homology domain (RHD) is characteristic for the NF-kB proteins, whereas IkB proteins contain ankyrin repeats (ANK) typical for this protein family. The precursor proteins p100 and p105 can therefore be assigned to and fulﬁll the functions of both the NF-kB and IkB protein families. The domains that typify each protein are indicated schematically. CC, coiled-coil; DD, death domain; GRR, glycine-rich region; HLH, helix-loop-helix; IKK, IkB kinase; LZ, leucine-zipper; NBD, NEMO binding domain; PEST, proline-, glutamic acid-, serine-, and threonine-rich region; TAD, transactivation domain; ZF, zinc ﬁnger.

copies of ankyrin repeats that are characteristic recruitment of deacetylases to promoter for the IkB protein family. Therefore, not all regions (Zhong et al. 2002). An intriguing combinations of Rel dimers are transcription- feature of p50 and p52 is their ability to associ- ally active: DNA-bound p50 and p52 homo- ate with atypical IkB proteins such as IkBz and and heterodimers have been found to repress Bcl-3, which most likely provide transcriptional kB-dependent transcription, most probably activation properties. Because of their carboxy- by preventing trancriptionally active NF-kB terminal ankyrin repeats, the precursors p105 dimers from binding to kB sites, or through and p100 can also inhibit nuclear localization

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The NF-kB Family of Transcription Factors and Its Regulation

and transcriptional activity of NF-kB dimers IkBz, can be induced upon stimulation and that they are associated with, and hence can be regulate the activity of NF-kB dimers in the classified as IkB proteins. nucleus. Finally, an alternative transcript of The specific physiological role of individual the p105 gene, apparently only expressed in NF-kB dimers remains to be fully understood. some murine lymphoid cells, has been iden- Crystallographic structural analysis has helped tified and termed IkBg, but its physiological delineate some of the principles that govern function remains unclear (Inoue et al. 1992; selection of particular kB-sites by NF-kB Gerondakis et al. 1993; Grumont and Geron- dimers, and biochemical experiments revealed dakis 1994a). preferential affinities of individual dimers for All IkB proteins are characterized by the particular sites in vitro. However, knockout presence of five to seven ankyrin repeat motifs, studies demonstrated that biochemical affinity which mediate their interaction with the RHD data do not fully explain the specificity of NF- of NF-kB proteins (Fig. 2). In general, individ- kB dimers in vivo and it has become obvious ual IkB proteins are thought to preferentially that dimer selection cannot be reduced to the associate with a particular subset of NF-kB kB sequence alone (Udalova et al. 2002; dimers, however surprisingly little experimental Hoffmann et al. 2003; Hoffmann et al. 2006; evidence concerning this important subject Schreiber et al. 2006; Britanova et al. 2008). exists. IkBa and IkBb are primarily believed The complex structures of target promoters to inhibit c-Rel and p65-containing complexes, together with the potential of particular NF- with IkBa having a higher affinity for p65:p50 kB dimers to trigger specific protein–protein than for p65:p65 complexes (Malek et al. interactions at the promoter is likely to be 2003). RelB exclusively binds p100, whereas more important as transcriptional control Bcl-3 and IkBz preferentially associate with involves the concerted action of the transcrip- homodimers of p50 and p52 (Hoffmann et al. tion factor, coactivators, and corepressors in 2006). the context of nucleosomal chromatin. The kB sequence may also affect the conformation The Canonical IkBs of the bound NF-kB dimers and thus influence their ability to recruit coactivators. The amino-terminal signal responsive regions Furthermore, the kinetics of NF-kB dimer (SRR) of the typical IkB proteins IkBa,IkBb, binding and release from DNA is based on the and IkB1 contain conserved serine residues presence of sufficient IkBs, as well as the nature (e.g., Ser32 and Ser36 in IkBa) that are targeted of post-translational modifications of NF-kB by the IKKb subunit of the IKK complex in the subunits. The combinatorial diversity of the course of canonical signaling to NF-kB (see NF-kB dimers certainly adds to their ability to also paragraph: The IKK complex). Phosphor- regulate distinct but overlapping sets of genes ylated IkB proteins are then modified with by influencing all these aspects of kB site K48-linked ubiquitin chains by ubiquitin selection. ligases of the SCF or SCRF (Skp1-Culin-Roc1/ Rbx1/Hrt-1-F-box) family, upon recognition of the DSPGXXSP motif of phosphorylated IkB PROTEINS IkB proteins through their receptor subunit In most resting cells, the association of NF-kB b-TRCP (b-tranducin repeat containing dimers with one of the prototypical IkBpro- protein) (Yaron et al. 1998; Fuchs et al. 1999; teins IkBa,IkBb, and IkB1, or the precursor Hatakeyama et al. 1999; Kroll et al. 1999; Wu Rel proteins p100 and p105, determines their and Ghosh 1999). Ubiquitination of IkBs cytosolic localization, which makes the IkB ultimately results in their degradation by the proteins essential for signal responsiveness. proteasome. In addition, expression of two atypical mem- IkBa is the best-studied member of the bers of this protein family, namely Bcl-3 and IkB family of proteins and displays all defining

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A. Oeckinghaus and S. Ghosh

characteristics of an NF-kB inhibitor. The ca- IkBa promoter, leads to normal kinetics of nonical p65/p50 heterodimer is primarily NF-kB activation and termination despite the associated with IkBa and rapid, stimulus- fact that IkBb normally does not function in induced degradation of IkBa is critical for the early dampening of the NF-kB response nuclear translocation and DNA binding of (Cheng et al. 1998). This suggests that the func- NF-kB p65/p50. The traditional model of IkB tional characteristics of the different canonical function posits that IkB proteins sequester IkBs are at least in part caused by temporal dis- NF-kB in the cytosol; however, the actual situ- tinctions in their resynthesis based on the ation is more complex. Crystallographic struc- specific transcriptional regulation of their pro- tural analysis of an IkBa:p65:p50 complex moters (Hoffmann et al. 2002). revealed that the IkBa molecule masks only Similar to IkBb,IkB1 is also degraded and the nuclear localization sequence (NLS) of resynthesized in response to NF-kB signaling p65, whereas the NLS of p50 remains accessible with significantly delayed kinetics (Kearns et al. (Huxford et al. 1998; Jacobs and Harrison 2006). Besides, IkB1 expression and function 1998). This exposed NLS together with the seem to be limited to cells of the hematopoetic nuclear export sequence (NES) present in lineage, reinforcing the hypothesis that distinct IkBa leads to constant shuttling of IkBa: IkBs exert unique roles in NF-kB responses in NF-kB complexes between the nucleus and different cellular scenarios. cytosol, despite a steady-state localization that appears to be exclusively cytosolic. Degradation The Precursor IkBs of IkBa shifts this dynamic equilibrium because it eliminates contribution of the NES in The precursor proteins p100 and p105 are IkBa and exposes the previously masked NLS exceptional in their ability to function as Rel of p65. As active NF-kB promotes IkBa ex- protein inhibitors, because they can dimerize pression, an important negative feedback regu- with other NF-kB molecules via their RHDs, latory mechanism is generated that critically whereas their carboxy-terminal ankyrin repeats influences the duration of the NF-kB response. serve the function of IkB proteins (Rice et al. Consistent with such a role, termination of the 1992; Naumann et al. 1993; Solan et al. 2002). NF-kB response upon TNFa stimulation is Although their overall sequence and organi- notably delayed in the case of IkBa deficiency zation is similar, generation of p50 and (Klement et al. 1996). p52 from their respective precursors occurs The roles of the other IkB family members through distinct processing mechanisms. p105 are less well established. Although IkBb shows is constitutively processed, resulting in a preset NF-kB binding specificity similar to IkBa,it ratio of p105 and p50 containing Rel dimers in also possesses a number of unique properties. each cell. This constitutive processing has been In contrast to IkBa,IkBb:NF-kB complexes suggested to occur co- or post-translationally do not undergo nuclear-cytoplasmic shuttling (Lin et al. 1998; Moorthy et al. 2006) and (Tam and Sen 2001) and IkBb can associate depends on a GRR located carboxy-terminal to with NF-kB complexes bound to DNA, suggest- the RHD that serves as termination signal for ing a possible regulatory function in the nucleus the proteosomal proteolysis (Lin and Ghosh (Thompson et al. 1995; Suyang et al. 1996). Even 1996). However, p105 can, like IkBa, also though IkBb is degraded and resynthesized in a undergo complete degradation upon phos- stimulus-dependent manner—although with phorylation of carboxy-terminal serine residues considerably delayed kinetics compared to by IKKb, a process that is favored when p105 is IkBa—IkBb deletion does not affect the bound to other NF-kB subunits (Harhaj et al. kinetics of NF-kB responses significantly 1996; Heissmeyer et al. 1999; Cohen et al. 2001; (Hoffmann et al. 2002). Surprisingly, knocking Cohen et al. 2004; Perkins 2006). Interestingly, in of IkBb to replace IkBa, thereby placing this event has been suggested to be independent IkBb expression under the regulation of the of ubiquitination (Moorthy et al. 2006).

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The NF-kB Family of Transcription Factors and Its Regulation

p100 processing represents a predominantly et al. 2007). The potential of Bcl3 to either stimulus-dependent event that defines the non- promote or impede transcription has been canonical NF-kB activation pathway (see also shown to depend to some extent on different paragraph: The IKK complex). It is regulated post-translational modifications (Nolan et al. through phosphorylation of p100 by the IKKa 1993; Bundy and McKeithan 1997; Massoumi subunit of the IKK complex, which results in et al. 2006). ubiquitination and subsequent partial degra- Within the IkB family, IkBz is most similar dation of p100 by the proteasome, releasing to Bcl3. It is not constitutively expressed, but transcriptionally active p50/RelB complexes induced upon engagement of IL-1 and TLR4 (Senftleben et al. 2001). However, p100 can receptors and is localized to the nucleus also regulate p65-containing complexes down- (Yamazaki et al. 2005). For the most part, IkBz stream of IKKa and limit p65-dependent associates with p50 homodimers. Expression responses in T cells in a negative feedback loop of a subset of NF-kB target genes, including similar to IkBa, thereby acting as an inhibitor IL-6, is not induced in IkBz-deficient cells in canonical signaling pathways (Ishimaru upon IL-1 or LPS stimulation. IkBz is hy- et al. 2006; Basak et al. 2007). Constitutive pothesized to act as a coactivator of p50 homo- processing of p100 has only been described to dimers even though IkBz does not contain an occur at a low level in certain cell types apparent TAD (Yamamoto et al. 2004). IkBz (Heusch et al. 1999). The ability of p100 to regu- has also been suggested to negatively regulate late RelB is of particular importance, as RelB- p65-containing complexes and may thus also containing dimers exclusively associate with be able to selectively activate or impede p100 and require p100 binding for stabilization specific NF-kB activity (Yamamoto et al. 2004; (Solan et al. 2002). Therefore, p100 is able to Motoyama et al. 2005). affect NF-kB transcriptional responses at a level It is obvious that our perception of IkB that extends beyond its role as an IkBprotein. proteins has changed significantly over the years from relatively simple inhibitory molecules to complex regulators of NF-kB-driven The Atypical IkBs gene expression. As described previously, The role of the atypical IkB protein Bcl3 in IkBs can influence the makeup of cellular NF-kB signaling is not fully understood and NF-kB through specific stabilization of units mechanism of action is still unclear. Bcl3 stable dimers, stabilize DNA-bound dimers, contains a TAD and is found primarily in the thereby repressing or prolonging transcrip- nucleus, where it associates with p50 and p52 tional responses, or even act as transcriptional homo- or heterodimers. Bcl3 has been sug- coactivators. Therefore, it is probably more gested to provide transcriptional activation appropriate to consider IkBs as multifaceted function on otherwise repressive p50 or p52 NF-kB regulators. homodimers (Bours et al. 1993). Furthermore, Bcl3 may remove repressive dimers from pro- THE IKK COMPLEX: CANONICAL AND moters, thereby allowing transcriptionally NON-CANONICAL SIGNALING TO NF-kB active p65/50 to access and facilitate transcription in an indirect manner through release of The first biochemical experiments assigned the repression (Wulczyn et al. 1992; Hayden and cytosolic IkB kinase activity to a large protein Ghosh 2004; Perkins 2006). Conversely, induc- complex of 700–900 kDa capable of specifically tion of Bcl3 expression has been shown to phosphorylating IkBa on serines 32 and 36. inhibit subsequent NF-kB activation. In such Purification of this complex revealed the a model, Bcl3 may stabilize repressing dimers presence of two catalytically active kinases, at kB sites, thereby preventing access of TAD IKKa and IKKb, and the regulatory subunit containing NF-kB dimers and consequent IKKg (NEMO) (Chen et al. 1996; Mercurio transcription (Wessells et al. 2004; Carmody et al. 1997; Woronicz et al. 1997; Zandi et al.

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1997). IKKa and IKKb are ubiquitously ex- have established a role for IKKa in regulating pressed and contain an amino-terminal kinase gene expression by modifying the phosphory- domain, a leucine zipper, and a carboxy- lation status of histones and p65 (Anest et al. terminal helix-loop-helix domain (HLH) 2003; Yamamoto et al. 2003; Chen and Greene (Fig. 2). The leucine zipper is responsible for 2004). dimerization of the kinases and mutations in In contrast to the canonical pathway, the this region render the kinases inactive, whereas non-canonical pathway that is induced by speci- the HLH is dispensable for dimerization, but fic members of the TNF cytokine family, such as essential for optimal kinase activity (Zandi BAFF, lymphotoxin-b, or CD40 ligand relies et al. 1998). The carboxy-terminal portions on IKKa, but not IKKb or IKKg. IKKa is of IKKa and -b are critical for their interac- believed to selectively phosphorylate p100 tion with the regulatory subunit IKKg, which associated with RelB (Senftleben et al. 2001; is mediated by a hexapeptide sequence Scheidereit 2006). Although the upstream (LDWSWL) on IKKs termed the NEMO bind- signal propagation events are poorly under- ing domain (NBD) (May et al. 2000; May stood, IKKa clearly requires activation of NIK et al. 2002). Activation of the IKK complex is (NF-kB-inducing kinase), which seems to func- dependent on the phosphorylation of two tion as both an IKKa-activating kinase as well as serines in the sequence motif SLCTS of the a scaffold linking IKKa and p100 (Xiao et al. T-loopregionsinatleastoneoftheIkB kinases 2004). Phosphorylation of p100 entails recruit- (Mercurio et al. 1997; Ling et al. 1998). ment of SCFbTrCP and subsequent polyubiq- Whether these phosphorylation events occur uitination of Lys855, which is situated in a through trans-autophosphorylation or through peptide sequence homologous to that targeted phosphorylation by an upstream kinase con- in IkBa (Fong and Sun 2002; Amir et al. tinues to be debated (Hayden and Ghosh 2004; 2004). Similar to p105 processing, the GRR of Scheidereit 2006). p100 is required for partial processing to gener- The physiological significance of IKKa and ate p52. In addition to non-canonical signaling IKKb has been analyzed extensively in knock- to NF-kB, IKKa regulates developmental pro- out mice. These studies have revealed two cesses that are both dependent, as well as inde- general types of signal propagation pathways pendent, of NF-kB-induced gene transcription to NF-kB activation, which are distinct in (Sil et al. 2004). respect to the inducing stimuli, the IKK subunits involved, and the NF-kB/IkB substrates targeted (Fig. 3). In the canonical NF-kB POST-TRANSLATIONAL MODIFICATIONS pathway, which is induced by inflammatory OF NF-kB cytokines, pathogen-associated molecules, and antigen receptors, IKKb is both necessary and Given the wide range of biological processes that sufficient to phosphorylate IkBa or IkBb in are affected by NF-kB, and the disastrous conse- an IKKg-dependent manner. Thus, IKKb- quences of dysregulated NF-kB signaling, intri- deficient mice exhibit embryonic lethality cate and highly regulated mechanisms exist for caused by severe liver apoptosis because of controlling NF-kB activity. These added layers defective TNF signaling to NF-kB in the devel- of regulation involve a variety of posttrans- oping liver (Beg et al. 1995; Li et al. 1999a; lational modifications of various core com- Li et al. 1999b). Congruently, IKKb-deficient ponents of this signaling pathway, thereby cells were shown to be unable to activate influencing NF-kB activity at multiple levels. NF-kB upon stimulation with proinflamma- The critical phosphorylation and ubiquitina- tory cytokines such as TNFa or interleukin-1 tion events of IkB proteins and the IKK (IL-1) (Li et al. 1999a; Li et al. 1999b). The complex have been described previously. In role of IKKa in canonical NF-kB signaling addition, the NF-kB subunits themselves remains unclear; however, more recent studies are subject to a wide range of regulatory

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The NF-kB Family of Transcription Factors and Its Regulation

Canonical pathway Non-canonical pathway (TNFa, IL-1, LPS) (CD40, BAFF, lymphotoxin-b)

NIK

NEMO P IKKa IKKb

NEMO P IKKa IKKa

Ub Ub Ub P P P P

IkR Proteasome p50 p65 p100 RelB p52 RelB

RelB

p52 p50p65

Figure 3. Canonical and non-canonical signaling to NF-kB. The canonical pathway is, e.g., induced by TNFa, IL-1, or LPS and uses a large variety of signaling adaptors to engage IKK activity. Phosphorylation of serine residues in the signal responsive region (SRR) of classical IkBs by IKKb leads to IkB ubiquitination and subsequent proteosomal degradation. This results in release of the NF-kB dimer, which can then translocate to the nucleus and induce transcription of target genes. The non-canonical pathway depends on NIK (NF- kB-inducing kinase) induced activation of IKKa. IKKa phosphorylates the p100 NF-kB subunit, which leads to proteosomal processing of p100 to p52. This results in the activation of p52-RelB dimers, which target speciﬁc kB elements.

protein modifications, including phosphory- modification of p65 to be recognized and has lation, ubiquitination, or acetylation (Perkins since been demonstrated to be critical for p65- 2006). Some of these modifications also rep- driven gene expression of many but not all resent important means for cross talk between target genes (Naumann and Scheidereit 1994; different signaling pathways (Perkins 2007). Neumann et al. 1995; Chen and Greene 2004). Importantly, degradation of IkBs and The catalytic subunit of PKA (PKAc) exists in nuclear translocation of the NF-kB dimers complex with cytosolic IkB:NF-kB complexes alone are not sufficient in eliciting a maximal and is activated upon IkB degradation to phos- NF-kB response, which has been shown to phorylate Ser276 of p65. p50 and c-Rel are also also critically depend on protein modifications modified by PKAc at equivalent sites to RelA of NF-kB subunits. Post-translational modifi- (Perkins 2006). In p65, Ser 276 phosphory- cations of p65 have been most thoroughly lation is thought to break an intramolecular investigated in this context. Phosphorylation interaction between the carboxy-terminal part by protein kinase A (PKA) was the first of the protein and the RHD, thereby facilitating

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DNA binding and enabling interaction with the phosphorylation of Ser276, has been shown to transcriptional coactivators p300 and CBP augment transcriptional activity without affect- (CREB-binding protein) (Zhong et al. 1998; ing DNA or IkB binding, presumably through Zhong et al. 2002). In addition to PKA, MSK1 generating a binding site for a coactivator and MSK2 (mitogen- and stress-activated protein. In contrast, acetylated Lys221 impedes protein kinase) have been shown to target association with IkBa, thereby enhancing Ser276, and in doing so possibly mediating DNA binding (Chen et al. 2002; Chen and cross talk with the ERK and p38 MAPK path- Greene 2004). Different histone deacetylases ways (Vermeulen et al. 2003; Perkins 2006). (HDAC) such as HDAC-3 and SIRT1 have been Several additional phosphorylation events implicated in removing p65 acetylations (Chen have been described but the physiological and Greene 2004; Yeung et al. 2004). consequences in most cases remain less clear. Ser536 within the TAD of p65 seems to be a TERMINATION OF THE NF-kB RESPONSE phosphorylation site that is targeted by several kinases, including IKKb. Numerous effects Our knowledge about the mechanisms leading have been ascribed to this modification, includ- to NF-kB activation far exceeds what we know ing regulation of p65 nuclear localization and about the regulatory mechanisms that deter- CBP/p300 interaction (Chen et al. 2005; mine its inactivation. The best studied and Perkins 2006). CK2 has been shown to inducibly well accepted mechanism for termination of modify Ser529; however, it remains unclear the NF-kB response involves the resynthesis of whether this phosphorylation affects p65 tran- IkB proteins induced by activated NF-kB scriptional activity (Wang et al. 2000). Ser311 (Pahl 1999). Newly synthesized IkBa can can be phosphorylated by the atypical protein enter the nucleus, remove NF-kB from the kinase PKCz in response to TNF stimulation, DNA, and relocalize it to the cytosol (Hayden which has also been demonstrated to positively and Ghosh 2004). Also, the precursors p105 influence p65:CBP interaction (Duran et al. and p100, as well as c-Rel and RelB, are NF-kB 2003). Interestingly, of the four phosphory- inducible genes, and hence the composition of lation sites mentioned above, two are found in NF-kB complexes in a cell can vary over time. the RHD (Ser276 and Ser311), whereas the Significant progress has also been made in other two are located within the TAD (Ser529 understanding how negative regulators influ- and Ser 536). ence signaling upstream of the IKK complex The diversity of the p65 phosphorylation (Hayden and Ghosh 2004; Krappmann and sites detected so far suggests that possibly even Scheidereit 2005; Hacker and Karin 2006). In more modification sites will be discovered in the recent years, additional inhibitory mecha- the future, in particular in other NF-kB sub- nisms have been identified that function later units. It is likely that these modifications in the pathway and directly affect the active, would serve to fine-tune NF-kB transcriptional DNA-bound NF-kB. These include post- activity, e.g., in determining target-gene speci- translational modifications of NF-kB subunits ficity and timing of gene expression, rather and have been shown to participate in shutting than acting as simple on–off switches. off the NF-kB response by altering cofactor p65 can also be inducibly acetylated at binding or mediating displacement and degra- different sites (Lys122, 123, 218, 221, and 310) dation of NF-kB dimers. Because acetylation with variable effects on its activity, probably of p65 has been demonstrated to negatively by the action of CBP/p300 and associated impact its DNA-binding affinity (Kiernan histone acetyltransferases (HAT). While acety- et al. 2003), regulation of p65 association lation of lysines 218, 221, and 310 has been with HATs and HDACs influences termination shown to promote p65 transactivation, acety- of the NF-kB response (Ghosh and Hayden lated lysines 122 and 123 act in an inhibitory 2008). An alternative scenario involves manner. Acetylation at Lys310, promoted by ubiquitin-dependent proteosomal degradation

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The NF-kB Family of Transcription Factors and Its Regulation

of promoter-bound p65, facilitated by the ubiq- the complexity of NF-kB regulation remains a uitin ligase SOCS-1 (Ryo et al. 2003; Saccani major goal to help act on specific steps of the et al. 2004). In parallel, the nuclear ubiquitin NF-kB pathway, thereby avoiding the risk of ligase PDLIM2 has been shown to target p65 harmful side effects that could result from for ubiquitination and proteasomal degra- general inhibition of NF-kB. dation, as well as to transport p65 to promyelo- cytic leukemia (PML) nuclear bodies, thereby supporting transcriptional silencing (Tanaka et al. 2007). In addition, IKKa has been demon- REFERENCES strated to promote p65 and c-Rel turnover and Amir RE, Haecker H, Karin M, Ciechanover A. 2004. removal from proinflammatory gene promoters Mechanism of processing of the NF-k B2 p100 precursor: Identification of the specific polyubiquitin chain- in macrophages (Lawrence et al. 2005). Finally, anchoring lysine residue and analysis of the role of NF-kB subunits have been shown to be inhib- NEDD8-modification on the SCF(b-TrCP) ubiquitin ited by oxidation and alkylation of a redox- ligase. Oncogene 23: 2540–2547. sensitive cysteine located in the DNA-binding Anest V, Hanson JL, Cogswell PC, Steinbrecher KA, Strahl BD, Baldwin AS. 2003. A nucleosomal function for IkB loop (Perkins 2006). This list is far from being kinase-a in NF-kB-dependent gene expression. Nature complete and it seems that we have just begun 423: 659–663. to understand the complex network of modi- Baeuerle PA, Henkel T. 1994. Function and activation of fications regulating NF-kB transcriptional NF-k B in the immune system. Annu Rev Immunol 12: 141–179. activity in the nucleus. As a detailed knowledge Baldwin AS Jr. 1996. The NF-k B and I k B proteins: New of these mechanisms is crucial for our under- discoveries and insights. Annu Rev Immunol 14: standing of the function of NF-kB, this area of 649–683. investigation is likely to continue to attract sig- Basak S, Kim H, Kearns JD, TergaonkarV, O’Dea E, Werner SL, Benedict CA, Ware CF, Ghosh G, Verma IM, et al. nificant attention in the future. 2007. A fourth IkB protein within the NF-kB signaling module. Cell 128: 369–381. Beg AA, Sha WC, Bronson RT, Ghosh S, Baltimore D. 1995. CONCLUSIONS Embryonic lethality and liver degeneration in mice lacking the RelA component of NF-k B. Nature 376: The transcription factors of the NF-kB family 167–170. control the expression of a large number of Bours V,Franzoso G, Azarenko V,Park S, Kanno T,Brown K, target genes in response to changes in the Siebenlist U. 1993. The oncoprotein Bcl-3 directly trans- activates through k B motifs via association with environment, thereby helping to orchestrate DNA-binding p50B homodimers. Cell 72: 729–739. inflammatory and immune responses. As aber- Britanova LV, Makeev VJ, Kuprash DV. 2008. In vitro selec- rant NF-kB activation underlies various disease tion of optimal RelB/p52 DNA-binding motifs. Biochem states, precise activation and termination of Biophys Res Commun 365: 583–588. NF-kB is ensured by multiple regulatory pro- Bundy DL, McKeithan TW. 1997. Diverse effects of BCL3 phosphorylation on its modulation of NF-kB p52 cesses. It is fair to say that the IkB proteins rep- homodimer binding to DNA. J Biol Chem 272: resent one of the primary means of NF-kB 33132–33139. regulation, although their versatile effects on Carmody RJ, Ruan Q, Palmer S, Hilliard B, Chen YH. 2007. Negative regulation of toll-like receptor signaling by NF-kB activity make them more complex than NF-kB p50 ubiquitination blockade. Science 317: simple inhibitory proteins. A diverse array of 675–678. post-translational modifications of IKK, IkB, Chen CC, Manning AM. 1995. Transcriptional regulation and NF-kB proteins provides the means to fine- of endothelial cell adhesion molecules: A dominant role for NF-k B. Agents Actions Suppl 47: 135–141. tune the NF-kB response at multiple levels. Chen LF, Greene WC. 2004. Shaping the nuclear action of Tremendous progress has been made in under- NF-kB. Nat Rev Mol Cell Biol 5: 392–401. standing the regulatory mechanisms shaping Chen LF,Mu Y,Greene WC. 2002. Acetylation of RelA at dis- the NF-kB response, yet it is striking how crete sites regulates distinct nuclear functions of NF-kB. much still remains to be discovered. Because of EMBO J 21: 6539–6548. Chen ZJ, Parent L, Maniatis T. 1996. Site-specific phos- the well-characterized links between NF-kB phorylation of IkB by a novel ubiquitination-dependent and diseases like cancer or arthritis, unraveling protein kinase activity. Cell 84: 853–862.

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A. Oeckinghaus and S. Ghosh

Chen FE, Huang DB, Chen YQ, Ghosh G. 1998. Crystal Grumont RJ, Gerondakis S. 1994b. The subunit compo- structure of p50/p65 heterodimer of transcription sition of NF-k B complexes changes during B-cell devel- factor NF-kB bound to DNA. Nature 391: 410–413. opment. Cell Growth Differ 5: 1321–1331. Chen LF, Williams SA, Mu Y, Nakano H, Duerr JM, Hacker H, Karin M. 2006. Regulation and function of Buckbinder L, Greene WC. 2005. NF-kB RelA phos- IKK and IKK-related kinases. Sci STKE 2006: re13. phorylation regulates RelA acetylation. Mol Cell Biol 25: Harhaj EW,Maggirwar SB, Sun SC. 1996. Inhibition of p105 7966–7975. processing by NF-kB proteins in transiently transfected Cheng JD, Ryseck RP,Attar RM, Dambach D, Bravo R. 1998. cells. Oncogene 12: 2385–2392. Functional redundancy of the nuclear factor k B inhibi- Hatakeyama S, Kitagawa M, Nakayama K, Shirane M, tors I k B and I k B b. J Exp Med 188: 1055–1062. Matsumoto M, Hattori K, Higashi H, Nakano H, Cohen S, Orian A, Ciechanover A. 2001. Processing of p105 Okumura K, Onoe K, et al. 1999. Ubiquitin-dependent is inhibited by docking of p50 active subunits to the degradation of IkB is mediated by a ubiquitin ligase ankyrin repeat domain, and inhibition is alleviated by Skp1/Cul 1/F-box protein FWD1. Proc Natl Acad Sci signaling via the carboxyl-terminal phosphorylation/ 96: 3859–3863. ubiquitin-ligase binding domain. J Biol Chem 276: Hayden MS, Ghosh S. 2004. Signaling to NF-kB. Genes Dev 26769–26776. 18: 2195–2224. Cohen S, Achbert-Weiner H, Ciechanover A. 2004. Dual Hayden MS, West AP, Ghosh S. 2006. NF-kB and the effects of IkB kinase b-mediated phosphorylation on immune response. Oncogene 25: 6758–6780. p105 Fate: SCF(b-TrCP)-dependent degradation and SCF(b-TrCP)-independent processing. Mol Cell Biol 24: Heissmeyer V, Krappmann D, Wulczyn FG, Scheidereit C. 475–486. 1999. NF-kB p105 is a target of IkB kinases and controls signal induction of Bcl-3-p50 complexes. EMBO J 18: k Courtois G, Gilmore TD. 2006. Mutations in the NF- B 4766–4778. signaling pathway: Implications for human disease. Oncogene 25: 6831–6843. Heusch M, Lin L, Geleziunas R, Greene WC. 1999. The generation of nfkb2 p52: Mechanism and efficiency. Dobrzanski P, Ryseck RP, Bravo R. 1993. Both N- and Oncogene 18: 6201–6208. C-terminal domains of RelB are required for full transactivation: Role of the N-terminal leucine zipper-like motif. Hoffmann A, Leung TH, Baltimore D. 2003. Genetic analy- Mol Cell Biol 13: 1572–1582. sis of NF-kB/Rel transcription factors defines functional specificities. EMBO J 22: 5530–5539. Dobrzanski P, Ryseck RP, Bravo R. 1994. Differential interactions of Rel-NF-k B complexes with I k B determine Hoffmann A, Natoli G, Ghosh G. 2006. Transcriptional pools of constitutive and inducible NF-k B activity. regulation via the NF-kB signaling module. Oncogene EMBO J 13: 4608–4616. 25: 6706–6716. Duran A, Diaz-Meco MT, Moscat J. 2003. Essential role of Hoffmann A, Levchenko A, Scott ML, Baltimore D. 2002. RelA Ser311 phosphorylation by zetaPKC in NF-kB The IkB-NF-kB signaling module: Temporal control transcriptional activation. EMBO J 22: 3910–3918. and selective gene activation. Science 298: 1241–1245. Fong A, Sun SC. 2002. Genetic evidence for the essential role Huxford T, Huang DB, Malek S, Ghosh G. 1998. The crystal of b-transducin repeat-containing protein in the induci- structure of the IkB/NF-kB complex reveals mechanisms ble processing of NF-k B2/p100. J Biol Chem 277: of NF-kB inactivation. Cell 95: 759–770. 22111–22114. Inoue J, Kerr LD, Kakizuka A, Verma IM. 1992. I k B g,a Fuchs SY, Chen A, Xiong Y, Pan ZQ, Ronai Z. 1999. HOS, a 70 kd protein identical to the C-terminal half of p110 human homolog of Slimb, forms an SCF complex with NF-k B: A new member of the I k B family. Cell 68: Skp1 and Cullin1 and targets the phosphorylation- 1109–1120. dependent degradation of IkB and b -catenin. Oncogene Ishimaru N, Kishimoto H, Hayashi Y, Sprent J. 2006. 18: 2039–2046. Regulation of naive T cell function by the NF-kB2 Gerondakis S, Morrice N, Richardson IB, Wettenhall R, pathway. Nat Immunol 7: 763–772. Fecondo J, Grumont RJ. 1993. The activity of a 70 kilo- Jacobs MD, Harrison SC. 1998. Structure of an IkB/NF-kB dalton I k B molecule identical to the carboxyl terminus complex. Cell 95: 749–758. of the p105 NF-k B precursor is modulated by protein Kearns JD, Basak S, Werner SL, Huang CS, Hoffmann A. kinase A. Cell Growth Differ 4: 617–627. 2006. IkBepsilon provides negative feedback to control Ghosh S, Hayden MS. 2008. New regulators of NF-kBin NF-kB oscillations, signaling dynamics, and inflamma- inflammation. Nat Rev Immunol 8: 837–848. tory gene expression. J Cell Biol 173: 659–664. Ghosh S, May MJ, Kopp EB. 1998. NF-k B and Rel proteins: Kiernan R, Bres V, Ng RW, Coudart MP, El Messaoudi S, Evolutionarily conserved mediators of immune Sardet C, Jin DY, Emiliani S, Benkirane M. 2003. responses. Annu Rev Immunol 16: 225–260. Post-activation turn-off of NF-k B-dependent transcrip- Ghosh G, van Duyne G, Ghosh S, Sigler PB. 1995. Structure tion is regulated by acetylation of p65. J Biol Chem 278: of NF-k B p50 homodimer bound to a k B site. Nature 2758–2766. 373: 303–310. Klement JF, Rice NR, Car BD, Abbondanzo SJ, Powers GD, Grumont RJ, Gerondakis S. 1994a. Alternative splicing of Bhatt PH, Chen CH, Rosen CA, Stewart CL. 1996. IkB RNA transcripts encoded by the murine p105 NF-k B deficiency results in a sustained NF-kB response and gene generates I k B g isoforms with different inhibitory severe widespread dermatitis in mice. Mol Cell Biol 16: activities. Proc Natl Acad Sci 91: 4367–4371. 2341–2349.

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The NF-kB Family of Transcription Factors and Its Regulation

Kopp EB, Ghosh S. 1995. NF-k B and rel proteins in innate Muller CW, Rey FA, Sodeoka M, Verdine GL, Harrison SC. immunity. Adv Immunol 58: 1–27. 1995. Structure of the NF-k B p50 homodimer bound Krappmann D, Scheidereit C. 2005. A pervasive role of ubi- to DNA. Nature 373: 311–317. quitin conjugation in activation and termination of IkB Naumann M, Scheidereit C. 1994. Activation of NF-k Bin kinase pathways. EMBO Rep 6: 321–326. vivo is regulated by multiple phosphorylations. Embo J Kroll M, Margottin F, Kohl A, Renard P, Durand H, 13: 4597–4607. Concordet JP, Bachelerie F, Arenzana-Seisdedos F, Naumann M, Nieters A, Hatada EN, Scheidereit C. 1993. Benarous R. 1999. Inducible degradation of IkB by the NF-k B precursor p100 inhibits nuclear translocation proteasome requires interaction with the F-box protein and DNA binding of NF-k B/rel-factors. Oncogene 8: h-bTrCP. J Biol Chem 274: 7941–7945. 2275–2281. Lawrence T, Bebien M, Liu GY, Nizet V,Karin M. 2005. IKK Neumann M, Grieshammer T, Chuvpilo S, Kneitz B, Lohoff limits macrophage NF-kB activation and contributes to M, Schimpl A, Franza BR Jr, Serfling E. 1995. RelA/p65 is the resolution of inflammation. Nature 434: 1138–1143. a molecular target for the immunosuppressive action of protein kinase A. Embo J 14: 1991–2004. Li Q, Van Antwerp D, Mercurio F,Lee KF,Verma IM. 1999a. Severe liver degeneration in mice lacking the IkB kinase 2 Nolan GP,Fujita T, Bhatia K, Huppi C, Liou HC, Scott ML, gene. Science 284: 321–325. Baltimore D. 1993. The bcl-3 proto-oncogene encodes a nuclear I k B-like molecule that preferentially interacts Li ZW, Chu W, Hu Y, Delhase M, Deerinck T, Ellisman M, with NF-k B p50 and p52 in a phosphorylation- b k Johnson R, Karin M. 1999b. The IKK subunit of I B dependent manner. Mol Cell Biol 13: 3557–3566. kinase (IKK) is essential for nuclear factor kB activation and prevention of apoptosis. J Exp Med 189: 1839–1845. Pahl HL. 1999. Activators and target genes of Rel/NF-kB transcription factors. Oncogene 18: 6853–6866. Lin L, Ghosh S. 1996. A glycine-rich region in NF-kB p105 functions as a processing signal for the generation of the Perkins ND. 2006. Post-translational modifications regulating the activity and function of the nuclear factor k B p50 subunit. Mol Cell Biol 16: 2248–2254. pathway. Oncogene 25: 6717–6730. Lin L, DeMartino GN, Greene WC. 1998. Cotranslational Perkins ND. 2007. Integrating cell-signalling pathways with biogenesis of NF-kB p50 by the 26S proteasome. Cell NF-kB and IKK function. Nat Rev Mol Cell Biol 8: 49–62. 92: 819–828. Rice NR, MacKichan ML, Israel A. 1992. The precursor of Ling L, Cao Z, Goeddel DV. 1998. NF-kB-inducing kinase NF-k B p50 has I k B-like functions. Cell 71: 243–253. activates IKK- by phosphorylation of Ser-176. Proc Natl Acad Sci 95: 3792–3797. Ryo A, Suizu F, Yoshida Y, Perrem K, Liou YC, Wulf G, Rottapel R, Yamaoka S, Lu KP. 2003. Regulation of Malek S, Huang DB, Huxford T, Ghosh S, Ghosh G. 2003. NF-kB signaling by Pin1-dependent prolyl isomerization X-ray crystal structure of an IkBb NF-kB p65 homo- and ubiquitin-mediated proteolysis of p65/RelA. Mol dimer complex. J Biol Chem 278: 23094–23100. Cell 12: 1413–1426. Massoumi R, Chmielarska K, Hennecke K, Pfeifer A, Fassler Ryseck RP, Bull P, Takamiya M, Bours V, Siebenlist U, R. 2006. Cyld inhibits tumor cell proliferation by block- Dobrzanski P,Bravo R. 1992. RelB, a new Rel family tran- ing Bcl-3-dependent NF-kB signaling. Cell 125: scription activator that can interact with p50-NF-k B. 665–677. Mol Cell Biol 12: 674–684. May MJ, Marienfeld RB, Ghosh S. 2002. Characterization Saccani S, Marazzi I, Beg AA, Natoli G. 2004. Degradation of of the Ik B-kinase NEMO binding domain. J Biol Chem promoter-bound p65/RelA is essential for the prompt 277: 45992–46000. termination of the nuclear factor kB response. J Exp May MJ, D’Acquisto F, Madge LA, Glockner J, Pober JS, Med 200: 107–113. Ghosh S. 2000. Selective inhibition of NF-kB activation Scheidereit C. 2006. IkaB kinase complexes: Gateways to by a peptide that blocks the interaction of NEMO with NF-kB activation and transcription. Oncogene 25: the IkB kinase complex. Science 289: 1550–1554. 6685–6705. Mercurio F,Zhu H, Murray BW,Shevchenko A, Bennett BL, Schreiber J, Jenner RG, Murray HL, Gerber GK, Gifford DK, Li J, Young DB, Barbosa M, Mann M, Manning A, et al. Young RA. 2006. Coordinated binding of NF-kB family 1997. IKK-1 and IKK-2: Cytokine-activated IkB kinases members in the response of human cells to lipopolysac- essential for NF-kB activation. Science 278: 860–866. charide. Proc Natl Acad Sci 103: 5899–5904. Miyamoto S, Schmitt MJ, Verma IM. 1994. Qualitative Sen R, Baltimore D. 1986a. Inducibility of k immunoglobu- changes in the subunit composition of k B-binding com- lin enhancer-binding protein NF-k B by a posttransla- plexes during murine B-cell differentiation. Proc Natl tional mechanism. Cell 47: 921–928. Acad Sci 91: 5056–5060. Sen R, Baltimore D. 1986b. Multiple nuclear factors interact Moorthy AK, Savinova OV, Ho JQ, Wang VY, Vu D, Ghosh with the immunoglobulin enhancer sequences. Cell 46: G. 2006. The 20S proteasome processes NF-kB1 p105 705–716. into p50 in a translation-independent manner. EMBO J Senftleben U, Cao Y,Xiao G, Greten FR, Krahn G, Bonizzi G, 25: 1945–1956. Chen Y, Hu Y, Fong A, Sun SC, et al. 2001. Activation by Motoyama M, Yamazaki S, Eto-Kimura A, Takeshige K, IKK of a second, evolutionary conserved, NF-k B signal- Muta T. 2005. Positive and negative regulation of ing pathway. Science 293: 1495–1499. nuclear factor-kB-mediated transcription by IkB-zeta, Sil AK, Maeda S, Sano Y, Roop DR, Karin M. 2004. IkB an inducible nuclear protein. J Biol Chem 280: kinase- acts in the epidermis to control skeletal and 7444–7451. craniofacial morphogenesis. Nature 428: 660–664.

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A. Oeckinghaus and S. Ghosh

Solan NJ, Miyoshi H, Carmona EM, Bren GD, Paya CV. Wulczyn FG, Naumann M, Scheidereit C. 1992. Candidate 2002. RelB cellular regulation and transcriptional activity proto-oncogene bcl-3 encodes a subunit-specific inhibi- are regulated by p100. J Biol Chem 277: 1405–1418. tor of transcription factor NF-k B. Nature 358: 597–599. Suyang H, Phillips R, Douglas I, Ghosh S. 1996. Role Xiao G, Fong A, Sun SC. 2004. Induction of p100 processing of unphosphorylated, newly synthesized I k B b in by NF-kB-inducing kinase involves docking IkB kinase persistent activation of NF-k B. Mol Cell Biol 16: (IKK) to p100 and IKK-mediated phosphorylation. J 5444–5449. Biol Chem 279: 30099–30105. Tam WF, Sen R. 2001. IkB family members function by Yamamoto M, Yamazaki S, Uematsu S, Sato S, Hemmi H, different mechanisms. J Biol Chem 276: 7701–7704. Hoshino K, Kaisho T, Kuwata H, Takeuchi O, Takeshige Tanaka T, Grusby MJ, Kaisho T. 2007. PDLIM2-mediated K, et al. 2004. Regulation of Toll/IL-1-receptor-mediated termination of transcription factor NF-kB activation by gene expression by the inducible nuclear protein IkBzeta. intranuclear sequestration and degradation of the p65 Nature 430: 218–222. subunit. Nat Immunol 8: 584–591. Yamamoto Y, Verma UN, Prajapati S, Kwak YT, Gaynor RB. Thompson JE, Phillips RJ, Erdjument-Bromage H, Tempst 2003. Histone H3 phosphorylation by IKK- is critical for cytokine-induced gene expression. Nature 423: 655–659. P,Ghosh S. 1995. I k B-b regulates the persistent response in a biphasic activation of NF-k B. Cell 80: 573–582. Yamazaki S, Muta T, Matsuo S, Takeshige K. 2005. Stimulus-specific induction of a novel nuclear Udalova IA, Mott R, Field D, Kwiatkowski D. 2002. factor-kB regulator, IkB-zeta, via Toll/Interleukin-1 Quantitative prediction of NF-k B DNA-protein inter- receptor is mediated by mRNA stabilization. J Biol actions. Proc Natl Acad Sci 99: 8167–8172. Chem 280: 1678–1687. VermeulenL, De Wilde G, VanDamme P,VandenBerghe W, Yaron A, Hatzubai A, Davis M, Lavon I, Amit S, Manning Haegeman G. 2003. Transcriptional activation of the AM, Andersen JS, Mann M, Mercurio F, Ben-Neriah Y. k NF- B p65 subunit by mitogen- and stress-activated 1998. Identification of the receptor component of the protein kinase-1 (MSK1). EMBO J 22: 1313–1324. IkBa-ubiquitin ligase. Nature 396: 590–594. Wang D, Westerheide SD, Hanson JL, Baldwin AS Jr. 2000. Yeung F, Hoberg JE, Ramsey CS, Keller MD, Jones DR, Frye Tumor necrosis factor-induced phosphorylation of RA, Mayo MW. 2004. Modulation of NF-kB-dependent RelA/p65 on Ser529 is controlled by casein kinase II. transcription and cell survival by the SIRT1 deacetylase. J Biol Chem 275: 32592–32597. EMBO J 23: 2369–2380. Wessells J, Baer M, Young HA, Claudio E, Brown K, Zandi E, Chen Y, Karin M. 1998. Direct phosphorylation of Siebenlist U, Johnson PF. 2004. BCL-3 and NF-kB p50 IkB by IKK and IKKb: Discrimination between free and attenuate lipopolysaccharide-induced inflammatory NF-kB-bound substrate. Science 281: 1360–1363. responses in macrophages. J Biol Chem 279: Zandi E, Rothwarf DM, Delhase M, Hayakawa M, Karin M. 49995–50003. 1997. The IkB kinase complex (IKK) contains two kinase Wissink S, van de Stolpe A, Caldenhoven E, Koenderman L, subunits, IKK and IKKb, necessary for IkB phosphoryl- van der Saag PT. 1997. NF-k B/Rel family members reg- ation and NF-kB activation. Cell 91: 243–252. ulating the ICAM-1 promoter in monocytic THP-1 cells. Zhong H, VollRE, Ghosh S. 1998. Phosphorylation of NF-k Immunobiology 198: 50–64. B p65 by PKA stimulates transcriptional activity by pro- Woronicz JD, Gao X, Cao Z, Rothe M, Goeddel DV. 1997. moting a novel bivalent interaction with the coactivator IkB kinase-b:NF-kB activation and complex formation CBP/p300. Mol Cell 1: 661–671. with IkB kinase- and NIK. Science 278: 866–869. Zhong H, May MJ, Jimi E, Ghosh S. 2002. The phosphoryl- Wu C, Ghosh S. 1999. b-TrCP mediates the signal-induced ation status of nuclear NF-k B determines its association ubiquitination of IkBb. J Biol Chem 274: 29591–29594. with CBP/p300 or HDAC-1. Mol Cell 9: 625–636.

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The NF-κB Family of Transcription Factors and Its Regulation

Andrea Oeckinghaus and Sankar Ghosh

Cold Spring Harb Perspect Biol published online September 2, 2009

Subject Collection NF-kB

Use of Forward Genetics to Discover Novel Oncogenic Activation of NF-κB Regulators of NF- κB Louis M. Staudt Tao Lu and George R. Stark Selectivity of the NF-κB Response The Regulatory Logic of the NF-κB Signaling Ranjan Sen and Stephen T. Smale System Ellen O'Dea and Alexander Hoffmann NF-κB in the Nervous System Roles of the NF-κB Pathway in Lymphocyte Barbara Kaltschmidt and Christian Kaltschmidt Development and Function Steve Gerondakis and Ulrich Siebenlist Signaling to NF-κB: Regulation by Ubiquitination The IKK Complex, a Central Regulator of NF-κB Ingrid E. Wertz and Vishva M. Dixit Activation Alain Israël Ubiquitination and Degradation of the Inhibitors of NF-κB in the Nervous System NF- κB Barbara Kaltschmidt and Christian Kaltschmidt Naama Kanarek, Nir London, Ora Schueler-Furman, et al. A Structural Guide to Proteins of the NF-κB The Nuclear Factor NF-κB Pathway in Signaling Module Inflammation Tom Huxford and Gourisankar Ghosh Toby Lawrence NF-κB in the Immune Response of Drosophila NF-κB as a Critical Link Between Inflammation Charles Hetru and Jules A. Hoffmann and Cancer Michael Karin Control of NF-κB-dependent Transcriptional Specification of DNA Binding Activity of NF-κB Responses by Chromatin Organization Proteins Gioacchino Natoli Fengyi Wan and Michael J. Lenardo

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