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1 Introduction

Nearly 25 years of intensive research have uncovered many diverse functions for the dimeric transcription factor known as NF-κB (nuclear factor-kappaB) (Hayden and Ghosh 2008). NF-κB affects most aspects of cellular physiology—from immunity and inflammation to apoptosis, cell survival, growth, and proliferation. Only five genes encode the entire family of mammalian NF-κB transcription factors: NFKB1, NFKB2, RELA, RELB, and REL (Ghosh et al. 1998). Their polypeptide products give rise to the mature NF-κB subunits p50, p52, RelA (p65), RelB, and c-Rel, respectively, which combine in pairs to produce 15 distinct functioning NF-κB dimers (Gilmore 2006). While most of the dimer combinations are abundant in diverse cell types, others are more rare. A few have not been detected directly, but it remains likely that every possible NF-κB dimer combination exists in some cells and that some as yet undetected NF-κB dimers might exist under limited but specific cellular conditions.

The activity of these NF-κB dimers is directly controlled by a small set of proteins known as IκB (inhibitor of NF-kappaB) through the formation of stable IκB:NF-κB complexes (Whiteside and Isräel 1997). The non-covalent association of IκB to NF-κB shifts the steady-state subcellular localization of NF-κB dimers to the cytoplasm. A complicated and fascinating kinase complex known as IKK (inhibitor of NF-kappaB kinase) is responsible for phosphorylating the complex-associated IκB leading to its targeted ubiquitination by a specific SCF-type E3 ubiquitin-protein ligase and degradation by the 26S proteasome (Chen 2005; Karin and Ben-Neriah 2000). Free NF-κB then rapidly accumulates in the nucleus where it binds to a class of related DNA sequences, known as κB DNA sites, present within the promoters and enhancers of hundreds of protein coding and non-coding genes and elevates their expression (Pahl 1999).

While this simple model for activation and inducible gene expression has not changed much since its outlines were first being sketched during the decade following the discovery of NF-κB, its connection by multiple investigations to diverse signal transduction pathways and signaling events have uncovered multiple layers of NF-κB regulation (Fig. 1). In this chapter, we will focus on regulation of transcription factor NF-κB at the levels of dimer formation, association with IκB inhibitors, and sequence-specific DNA binding by NF-κB. We will use as our guide the growing body of structural information together with biochemical investigations aimed at testing structure-based hypotheses. This analysis illustrates how functional specificity can be achieved within a family of functionally and structurally related factors through small sequence variations and modifications. Understanding how these subtle differences give rise to the specific events in NF-κB-mediated transcriptional regulation in response to distinct stimuli is key to our grasp of how NF-κB controls cell physiology.

Fig. 1
figure 1

Regulation of transcription factor NF-κB occurs at many levels. Several of these are numbered in this simplified representation of the canonical NF-κB activation pathway. These include: 1—receptor engagement, kinase cascades, and ubiquitin-mediated regulation of IKK activity; 2—phosphorylation of IκB in complex with inactive NF-κB; 3—Ubiquitin-dependent proteolysis of IκB by the 26 S proteasome; 4—nuclear accumulation of active NF-κB; 5—elevated expression of NF-κB target gene products; 6—the influence of NF-κB target gene products on cellular physiology; 7—expression of cytoplasmic factors that deactivate IKK; 8—the action of nuclear factors that influence NF-κB target gene expression; 9—nuclear accumulation of IκBα; 10—the export of inactive IκBα:NF-κB complexes from the nucleus and restoration of the pre-induction resting cell state

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2 NF-κB and IκB

Five polypeptide subunits, p50, p52, RelA (p65), c-Rel, and RelB, constitute the NF-κB family (Fig. 2). With the exception of RelA, transcription of the genes encoding the NF-κB polypeptides is upregulated by NF-κB, generating a positive feedback response upon cell stimulation.

Fig. 2
figure 2

Domain organization of NF-κB and IκB proteins. The five NF-κB polypeptides are depicted in schematic form with the arrangement of the elements and domains discussed in the text identified and human numbering indicated. The IκB proteins are divided into classical IκB, NF-κB precursors, and nuclear IκB

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Two of the family members, p50 and p52, are the processed products of NF-κB subunit precursors p105 and p100, respectively. Interestingly, the partial proteolytic processing of p105 is constitutive, whereas that of p100 is induced via specific signals. A small class of inducers, including BAFF ligand, lymphotoxin-β, and CD40, activates a distinct NF-κB activation pathway that leads to processing of p100 into p52. The cellular signaling that leads to p100 processing is referred to as the alternative or non-canonical NF-κB activation pathway (Senftleben et al. 2001). The primary NF-κB dimer that is activated through alternative NF-κB activation pathway is the p52:RelB heterodimer via activation of the IKKα subunit of the IKK complex. In contrast, the catalytic activity of the IKKβ subunit of IKK is activated in response to a separate class of inducers, which includes IL-1 (interleukin-1), TNF-α (tumor necrosis factor-α), and LPS (bacterial lipopolysaccharide), through signaling referred to as the canonical NF-κB activation pathway. Induction of NF-κB activity through the canonical pathway ultimately activates NF-κB dimers that contain RelA and c-Rel subunits.

NF-κB subunit polypeptides share sequence homology throughout an N-terminal portion of roughly 300 amino acid residues in length referred to as the Rel homology region (RHR). The RHR is responsible for subunit association into active NF-κB dimers, NF-κB nuclear localization and DNA binding, and the association of NF-κB with IκB inhibitor proteins. The RHR can be divided into three structural regions: the NTD (N-terminal domain), DD (dimerization domain), and NLS polypeptide (Fig. 3a). Together the NTD and DD are responsible for DNA binding. The DD alone mediates association of NF-κB subunits to form active dimers. The NLS polypeptide is flexible in solution allowing it to adopt different conformations when bound to distinct partners such as IκB or importin-α proteins (Conti and Kuriyan 2000). The entire RHR of NF-κB is contacted by IκB upon binding to the inhibitor and a significant fraction of binding energy is contributed by the NLS polypeptide. C-terminal to the RHR of RelA, RelB, and c-Rel is a region that conveys transcriptional activation potential and, consequently, NF-κB dimers that possess at least one of these subunits function as activators of transcription. This TAD (transcriptional activation domain) region is not conserved between the NF-κB subunits at the amino acid sequence level and is, therefore, defined functionally. Both the NF-κB p50 and p52 subunits lack a C-terminal TAD and instead contain within this region the glycine-rich remnants of their incomplete proteolytic processing from p105 and p100 precursors. As a consequence of their lack of a C-terminal TAD, NF-κB dimers composed only of p50 and/or p52 subunits fail to activate transcription in vitro or in vivo.

Fig. 3
figure 3

Ribbon structure diagrams of NF-κB RHR and dimerization. a The NF-κB p50 subunit RHR is depicted in green ribbon diagram with elements and domains labeled according to the discussion in the text. The dashed C-terminal element represents the NLS polypeptide, which is unstructured in its unbound state. b The assembled dimerization domains of the p50 (green) and RelA (red) subunits viewed orthogonal to their vertical axis of 2-fold pseudosymmetry. c A similar view of the RelB DD homodimer reveals that the two subunits (yellow and purple) form an intertwined dimer. d Close-up view of the dimer interface with amino acid side chains from the text depicted and labeled. e NF-κB p50 homodimer DD interface. f RelA DD homodimer interface

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Three polypetides, IκBα, IκBβ, and IκBε, mediate classical IκB activities as they relate to NF-κB binding in the nucleus and phosphorylation-dependent proteasome-mediated degradation in response to induction. IκBα, IκBβ, and IκBε preferentially bind to NF-κB dimers that contain at least one RelA or c-Rel subunit. These classical IκB proteins share a central ARD (ankyrin repeat domain) that contains six ankyrin repeats (Fig. 2). The ankyrin repeat is a roughly 33 amino acid tandem helical repeat motif that appears in multiple copies in numerous proteins (Bork 1993; Gaudet 2008). The ARD is flanked by sequences that are predicted to be unstructured. The N-terminal flexible regions in IκBα, IκBβ, and IκBε contain two serine residues within the consensus sequence DSGXXS that are sites for phosphorylation by the IKKβ subunit. Once phosphorylated, this N-terminal region serves as the recognition site for the E3 receptor subunit β-TrCP and, through the action of an SCF-type E3 ubiquitin-protein ligase and the 26S proteasome, leads directly to IκB proteolysis (Yaron et al. 1998). The importance of this N-terminal region for the inducible proteolysis of classical IκB proteins is illustrated by the fact that an IκBα molecule with its two IKK phosphorylation sites mutated to alanines functions as a “super-repressor” of NF-κB activation through the canonical NF-κB activation pathway (Muenchen et al. 2000). C-terminal to the ARD is a structurally flexible region rich in the amino acids proline, glutamic acid, serine, and threonine. This so-called PEST region is common to many proteins that exhibit rapid turnover in the cell (Rogers et al. 1986).

The unprocessed p105 and p100 also act as inhibitors of NF-κB (Hatada et al. 1993; Naumann et al. 1993). However, unlike the oligomerization exhibited by IκBα, IκBβ, and IκBε, where a monomeric IκB assembles with a single NF-κB dimer to form an inactive complex, p100 and p105 assemble into larger complexes wherein they integrate multiple inhibitor and NF-κB molecules (Savinova et al. 2009). We refer these larger complexes, which can be purified and biophysically analyzed, as “IκBsomes” and it has been shown computationally and experimentally that p100 and p105 function as legitimate IκB molecules (Basak et al. 2008). The complete degradation of p100 and p105 in IκBsomes could, in principle, release multiple NF-κB subunits, which then could initiate physiologic programs that are distinct from those regulated by the classical IκB inhibitors.

Three additional ARD-containing polypeptides have been shown to participate in NF-κB regulation. These are Bcl-3, IκBζ, and IκBNS (Fig. 2). Of these, Bcl-3 is the most well-studied because of its early discovery (Hatada et al. 1992; Ohno et al. 1990). Though they are grouped with other IκB proteins because of their structural similarity and abilities to bind NF-κB dimers, Bcl-3, IκBζ, and IκBNS exhibit significant differences from classical IκB proteins (Fiorini et al. 2002; Haruta et al. 2001; Kitamura et al. 2000; Yamazaki et al. 2001). First of all, they display binding specificity toward p50 and/or p52 subunits in NF-κB dimers. Furthermore, each of the three proteins migrates to the nucleus when over-expressed in cells, leading to their classification as “nuclear IκB proteins”. In the nucleus, it appears that these proteins play regulatory roles that may include chromatin rearrangement, NF-κB dimer exchange, and co-activation of specific NF-κB target gene expression. IκBζ, for example, was shown in mice knockout studies to be necessary for the NF-κB-induced activation of the inflammatory cytokine IL-6 (interleukin-6) in response to LPS treatment of peritoneal macrophages (Yamamoto et al. 2004). The functional consequences of Bcl-3 are particularly complicated as it has been shown that both the phosphorylation status and partner selection dictate whether Bcl-3 might act as a co-activator, a co-repressor, or an inhibitor (Palmer and Chen 2008).

3 NF-κB Structure and Dimer Formation

The DD (dimerization domain) consists of approximately 100 amino acids toward C-terminal one-third of the RHR. Sequence identity and homology within the DD across the family are roughly 20 and 50%, respectively. The molecular structure of the DD has been determined at high resolution by X-ray crystallography for all five NF-κB subunits (Huang et al. 1997, 2005). The NF-κB DD folds into an immunoglobulin-like (Ig-like) fold where two anti-parallel β-sheets form a sandwich (Fig. 3b). One of these sheets forms the dimer interface by interacting symmetrically with neighboring DD. Fourteen amino acid residues are involved in dimer formation. However, as revealed by alanine scanning mutagenesis in the p50 subunit and subsequent assessment of dimer formation, few of these amino acids make energetic contributions to dimer stability (Sengchanthalangsy et al. 1999).

The NF-κB DD X-ray crystal structures provide clues as to why some of the dimers form preferentially to others. For instance, the NF-κB p50:RelA heterodimer is more stable than the homodimer of p50, while the RelA homodimer is the weakest of the three. Furthermore, heterodimers such as p50:RelA and p52:RelB are, in general, stable dimers. The RelB homodimer has not been detected in vivo, whereas p50 and p52 heterodimers are abundant. Therefore, it is surprising that the RelB homodimer can be formed in vitro. The X-ray crystal structure of a RelB homodimer DD revealed that it adopts a distinct domain-swapped structure (Fig. 3c).

A close inspection of these structures reveals that differential selectivity and stability of NF-κB dimers are controlled in two different ways: the first is variation in the amino acid residues that directly contact the other subunit across the dimer interface; the second is variation in surface or core amino acid residues that influence folding stability of the DD. While the first seems obvious, this second class of residues that affects dimerization through an indirect manner is at least as important.

The p50 DD homodimer X-ray crystal structure, which was the first solved, indicated a relatively weak dimer interface in which water is barely excluded. The interface is alarmingly loose with inter-atomic contact distances that are consistently longer than optimum. A binding constant for dimer-monomer dissociation (K Dim) was determined by analytical ultracentrifugation at approximately 1.0 μM. This suggested that free NF-κB p50 subunit in solution at cellular concentrations (~0.1 μM) should exist both in monomeric and dimeric states.

3.1 Regulation of NF-κB Dimerization at the Interface

Although the inter-subunit distances in p50 and RelA homodimers are similar, suggesting overall similarity in their respective mechanisms of dimer formation, fewer hydrogen bonds at the RelA homodimer interface suggested that it would be weaker than the p50 homodimer. Three differences in the amino acids at the dimer interfaces of p50 and RelA homodimer suggest how the resulting dimerization of p50:p50, RelA:RelA, and p50:RelA dimers might be affected. Residues at positions 254 and 267 are an aspartic acid and a tyrosine, respectively, in p50. The equivalent positions in RelA are occupied by an asparagine and a phenylalanine. This results in the juxtaposition of an Asp-Asn pair in the p50:RelA heterodimer, which can form a hydrogen bond of nearly perfect length and geometry and stabilize dimerization (Fig. 3d). The analogous placement of Asp-Asp and Asn-Asn pairs decrease the stability of the p50 homodimer and RelA homodimer, respectively (Fig. 3e, f). The Tyr to Phe change accounts for the remaining difference in the number of hydrogen bonds at the dimer interface of p50 and RelA homodimers. The lack of a hydroxyl group on Phe makes RelA homodimer less stable than p50 homodimer, wherein the hydroxyl group of Tyr mediates several hydrogen bonds across the subunit interface.

Another example of a difference at the dimer interface that influences NF-κB dimer selectivity is the change from a Phe at position 307 in p50 to Val at the corresponding position at the dimer interface of RelA. The small valine side chains position themselves uncomfortably close as they approach one another at the p65 dimer interface. The aromatic phenylalanine ring in p50 orients itself differently optimizing Van der Waals interactions and avoiding a steric clash at the dimer interface of p50 homodimer.

The remaining amino acid residues at the NF-κB dimer interface are identical across the family. Therefore, the differences in affinity observed between different combinatorial dimers could be explained by the amino acid identity at these three positions only. However, this is not the case. Several inconsistencies, culminating with our observation of an unusual domain-swapped architecture of the RelB homodimer, indicated that non-interfacial amino acid residues also play a vital role in controlling assembly of active NF-κB dimers (Huang et al. 2005). In RelB, the three interfacial residues in question are Asn, Tyr, and Ile. Of these only Ile is distinct as equivalent Asn residues are present in RelA and c-Rel and an equivalent Tyr is present in p50 and p52. Mutation of Ile to either Val or Tyr, the residues present in p65 or p50, respectively, does not convert RelB into a regular side-by-side NF-κB homodimer. This suggests that subtle changes elsewhere in the domain are critical for the domain-swapping in the RelB DD homodimer structure.

3.2 Regulation of NF-κB Dimerization at a Distance

Understanding the role of surface and buried amino acid residues outside of the dimer interface that indirectly influence dimer selectivity and stability is more difficult to imagine. Furthermore, X-ray crystal structures do little to provide a clear explanation. The influence on dimerization of amino acid residues far from the subunit interface is more directly assessed by mutational analysis and measurement of dimerization affinity. In RelA, a cysteine at position 216 occupies a position in the core of the DD that is projected opposite to the dimer interface. When this cysteine is mutated to an alanine, p65 homodimer stability is significantly reduced. The simplest explanation for this reduced dimer stability is that removal of the sulfhydryl group destabilizes the DD core structure, which in turn affects the stability of interactions at the dimer interface.

Several amino acid residues located on the surface of RelB opposite to the dimer interface are hydrophobic. These surface-exposed hydrophobic amino acids are unique to RelB among the mammalian NF-κB family. Equivalent residues in other NF-κB subunit structures are polar and are involved in surface hydrogen bond formation to stabilize the DD structure. Mutation of these residues to polar residues decreases the affinity of RelB for dimerization with p52. It is likely that the mutant RelB forms a more stable homodimer, thereby decreasing its availability to heterodimer formation with p52. The importance of domain folding stability for NF-κB dimer assembly and subunit dimerization selectivity is further supported by the mutation of serine at position 319 of RelB. When this surface residue is mutated to Ala, RelB protein stability is dramatically reduced.

Stability of the NF-κB p50:RelA heterodimer is relatively high as judged by the fact that the heterodimer forms preferentially when p50 and RelA homodimers are mixed together. However, under similar conditions, p50:c-Rel heterodimer formation is not as efficient. This observation suggests that c-Rel homodimer might be more stable than RelA homodimer. This is particularly intriguing as RelA and c-Rel share greater than 70% sequence identity within their dimerization domains and inter-subunit contacting residues are identical in both proteins. We conclude that small variations in sequence can impact dimerization of two closely related proteins such as RelA and c-Rel. Finally, it is worth noting that despite its high degree of sequence and structural homology to the p50 subunit the NF-κB p52 homodimer is rarely observed in vivo. Although there exist many explanations for this negative result, it is possible that instability in the p52:p52 homodimer allows for its more stable assembly into functionally important NF-κB members such as the p52:RelA and p52:RelB heterodimers.

3.3 Conditional NF-κB Dimerization

Some of the NF-κB dimers are rarely observed in vivo such as RelA:RelB and c-Rel:RelB. It has been reported that phosphorylation of serine at position 276 of RelA allows the modified protein to form a heterodimer with RelB. It is clear from structural studies that phosphorylation of RelA at Ser276 cannot directly affect dimerization as the amino acid is positioned opposite to the dimer interface. What this observation suggests is that phosphorylation alters domain stability in a manner such that RelB is able to associate with RelA. Unpublished results from our laboratory suggest that RelB is largely unfolded in solution at physiological concentrations and that it becomes folded upon dimerization with p50 or p52. We also have found that the introduction of a glutamic acid or aspartic acid mutation at position 276 to mimic phosphorylation significantly decreases the folding stability of RelA. It is possible that phosphorylation-dependent destabilization of RelA functions to catalyze formation of a stable RelA:RelB heterodimer.

4 IκB Structure and Regulation of NF-κB

IκB proteins control induction of NF-κB in a stimulus-specific manner. In particular, the rapid and transient activation of NF-κB that is required to mount immune and inflammatory responses is mediated by the degradation of classical IκB proteins, IκBα, IκBβ, and IκBε, and the subsequent transcriptional upregulation of response genes. On the other hand, the non-classical IκB proteins, p105 and p100 induce a more prolonged gene activation program as these IκB proteins are co-opted for slow degradation processes.

4.1 IκBα Binding to the NF-κB p50:RelA Heterodimer

The primary functions of IκBα are to inhibit the DNA binding activity of NF-κB, to bias the steady-state localization of IκB:NF-κB complexes toward the cytoplasm, and to maintain an inhibited pool of NF-κB that is posed for rapid activation via fast IκBα degradation. The X-ray crystal structures of IκBα bound to the NF-κB p50:RelA heterodimer have provided insight into how IκBα inhibits NF-κB activity (Huxford et al. 1998; Jacobs and Harrison 1998). The binding surface is modular and can be divided into three distinct segments. First is the rigid body interaction between the ARD of IκBα and the p50:RelA dimer platform (Fig. 4). This interaction interface, which is mediated primarily by close-packed Van der Waals interactions, accounts for the greatest amount of buried surface area in the complex. The second mode of interaction is mediated by C-terminal NLS polypeptide region beyond the DD of RelA and the first two ankyrin repeats of the IκBα ARD. The C-terminal extended portion, which is flexible in its unbound state, binds to IκBα by forming two helices that mediate specific ion-pair and hydrophobic interactions between conserved amino acid side chains from both proteins. Indeed, the complementary interactions at this site are responsible for the majority of the binding energy of the complex. The third mode of interaction involves the C-terminal PEST region of IκBα, which binds the NTD of the RelA subunit through dynamic long-range electrostatic interactions. This interaction converts the RelA subunit NTD into a conformation relative to the DD that is distinct from that observed when RelA binds DNA (discussed in the next section). The structures explain why binding of NF-κB to IκBα inhibits its ability to bind DNA. In addition, they suggest that IκBα conceals the NLS (nuclear localization signal) of RelA explaining the shift toward cytoplasmic localization of the IκBα:p50:RelA complex.

Fig. 4
figure 4

Ribbon structure diagram of the IκBα inhibitor in complex with the NF-κB p50:RelA heterodimer. The helical ARD (ankyrin repeat domain) of IκBα is depicted in light blue. NF-κB p50 and p65 subunits are green and red, respectively. The complex is viewed similarly as in Fig. 3b (left) and then rotated 90° about the vertical axis (right)

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The IκBα:NF-κB complex crystal structure hints that IκB proteins might influence NF-κB dimer formation. IκBα sits atop the p50:p65 heterodimer interface forming a ternary interface suggesting that IκBα could function to further stabilize the NF-κB dimer. Since IκBα binding affinity is much higher than dimerization affinity (<1 nM compared to >0.1 μM), IκBα must bring together two NF-κB subunits at concentrations much lower than the K Dim. One possible functional advantage of this IκB-mediated NF-κB dimer stabilization is that different IκB proteins could catalyze the assembly of otherwise rare NF-κB dimers. For example, and as mentioned previously, the free NF-κB p52 homodimer has not been observed in vivo. However, the p52 homodimer bound to the nuclear IκB protein Bcl-3 has been detected. This suggests that, although p52 preferably forms heterodimers, interaction with a specific IκB molecule can induce formation the homodimer.

4.2 Regulation of IκBα:NF-κB Complex Formation

Biophysical analysis on free IκBα in solution revealed that only the first four ankyrin repeats adopt a stable folded structure while the two remaining C-terminal repeats and the contiguous PEST sequence remain mostly unfolded (Croy et al. 2004). This is rare for ARD-containing proteins, most of which display high folding stability in solution (Kohl et al. 2003). Upon binding to NF-κB, however, the six ankyrin repeats of IκBα stack as a continuous folded domain (Bergqvist et al. 2006). These observations suggest that as the disordered NLS polypeptide region of RelA adopts an ordered structure upon binding to the more stable portion of the ARD, the unfolded C-terminal portions of IκBα undergo a similar transition upon binding to the folded dimerization domains of the p50:RelA heterodimer. By introducing amino acid substitutions that render the IκBα ARD more similar to the ankyrin repeat consensus, mutant versions of IκBα have been engineered in order that their two C-terminal repeats adopt the ankyrin fold independent of NF-κB binding (Ferreiro et al. 2007). Surprisingly, these pre-folded mutants showed a measurably reduced binding affinity for the NF-κB p50:p65 heterodimer (Truhlar et al. 2008). Kinetic analyses revealed that an increased rate of dissociation of the pre-folded mutants was responsible for the observed decrease in NF-κB binding. Therefore, by coupling folding and binding, IκBα significantly decreases its rate of dissociation from NF-κB resulting in a high affinity protein–protein interaction (K D in the high pM range). These observations, based on structural studies and biophysical characterization, serve to explain why IκBα must be actively removed via 26 S proteasome-mediated proteolysis in order to supply free NF-κB for inducible gene expression. They also suggest that deviations from the consensus ankyrin repeat sequence endow IκBα with its signature NF-κB binding and regulatory properties.

4.3 The IκBβ:RelA Homodimer Complex

The X-ray crystal structure of the IκBβ:RelA homodimer complex revealed similar modes of interaction between IκB and NF-κB proteins (Malek et al. 2003). However, there are clear differences that are noteworthy. First, interactions between the ARD and an NLS are nearly identical. Interestingly, the NLS of the second RelA subunit also appears to interact weakly. Although IκBβ alone was shown to partially protect this second RelA subunit NLS polypeptide from proteolysis with limiting amounts of protease in vitro, it appears as if the IκBβ requires some other component to stabilize its complex with RelA homodimer. Second, the sixth and final ankyrin repeat of IκBβ appeared to be less intimately involved in the NF-kB binding as compared with the similar region of IκBα in the IκBκ:NF-κB complex structure. This may explain the why the C-terminal PEST sequence in IκBβ is not critical for interaction with the N-terminal domain of RelA as it appears to be positioned away from the protein–protein interface. Third, IκBβ contains a unique insertion of 42 amino acids in length located between ankyrin repeats 3 and 4. This insert, the majority of which is disordered in the X-ray structure, is projected into solution far from the protein–protein interface. It is likely that the insert is used for other purposes such as in binding to other factors.

The IκBβ:RelA complex also provides intriguing insights into how IκBβ might bind and regulate activity of the NF-κB c-Rel homodimer. It was previously reported that IκBβ interacts with c-Rel in a phosphorylation-dependent manner, whereby two serines in the IκBβ PEST sequence (amino acids 313 and 315 in murine IκBβ numbering) must be phosphorylated (Thompson et al. 1995). This suggests the intriguing possibility of two distinct modes of NF-κB inhibition by IκBβ: one that relies primarily on interactions between the IκBβ ARD and RelA DD and NLS polypeptide and another that involves the phosphorylated IκBβ PEST and c-Rel. The requirement of PEST phosphorylation for IκBβ:c-Rel homodimer complex formation further suggests that the c-Rel NTD may play a role in IκBβ complex formation in a manner analogous to interactions between the analogous NTD of Rel and IκBα in the IκBα:NF-κB complex structure. Alternative binding modes by IκBβ could explain why IκBβ is not a good inhibitor of DNA binding by the RelA homodimer as the unphosphorylated IκBβ PEST does not engage the RelA NTD. In contrast, a PEST-phosphorylated IκBβ might be able to inhibit DNA binding by the c-Rel homodimer. In contrast to IκBα, which can readily dissociate RelA homodimer or p50:RelA heterodimer from their complexes with target DNA, IκBβ appears to be unable to carry out this function. Future experiments will determine whether IκBβ is capable of stripping c-Rel from κB DNA.

Finally, it has been observed that deletion of the insert between ankyrin repeats 3 and 4 of IκBβ reduces its affinity for c-Rel homodimer. κB-Ras, a small GTPase, was shown to be involved in IκBβ-mediated inhibition of NF-κB and might interact with IκBβ:NF-κB complexes through this inter-repeat loop (Chen et al. 2004; Fenwick et al. 2000).

4.4 NF-κB Regulation by IκBε

IκBε was originally reported to inhibit homodimers of RelA and c-Rel (Li and Nabel 1997; Simeonidis et al. 1997; Whiteside et al. 1997). However, a recent study also suggested that IκBε negative feedback regulates RelA:p50 to dampen IκBα-mediated oscillations (Kearns et al. 2006). Significant differences in domain architecture between IκBε and other classical IκB proteins include the relative absence of acidic amino acid residues within the C-terminal PEST region and an extended N-terminus. These differences may allow IκBε to use these peripheral regions to specifically recognize features unique to RelA or c-Rel homodimers. More structural and in vitro biochemical studies are required in order to gain mechanistic insight into how IκBε regulates NF-κB activity.

4.5 The Non-Classical IκB Proteins p105 and p100

The paradigm of NF-κB regulation in the cytoplasm for the better part of the past 20 years has hinged upon stimulus-dependent rapid degradation of IκBα followed by nuclear translocation of the NF-κB p50:RelA heterodimer. Recently, it has become increasingly clear that the NF-κB precursors p105 and p100 also function as IκB inhibitors. The ability of p105 to function as an IκB molecule was demonstrated previously (Mercurio et al. 1992; Rice et al. 1992). Furthermore, the biological significance of the inhibitory activities of both p105 and p100 have been evident for many years since mouse studies revealed that chromosomal deletion of their C-terminal ARD leads to severe misregulation of NF-κB (Ishikawa et al. 1997, 1998). However, as p105 and p100 also function as the immature precursors of the NF-κB subunits p50 and p52, respectively, dissecting the specific consequences on NF-κB regulation due to modification or disruption of these proteins has been a challenge. The p105 protein binds and inhibits all NF-κB subunits including p50, its own processed product. This is in contrast to the NF-κB inhibitory activity demonstrated by classical IκB proteins, which is directed toward specific NF-κB subunits. Recent experiments have established that multiple copies of p100 and p105 can assemble to form large complexes wherein diverse NF-κB subunits are bound (Savinova et al. 2009). We have referred to these large NF-κB signaling complexes as “IκBsomes”. The observed differences in structural arrangement and binding specificity exhibited by non-classical inhibitors suggest that they might display distinct kinetic profiles of NF-κB activation and post-induction repression as compared to the classical inhibitors. Recent evidence suggests that over half of cellular RelA and c-Rel and all of RelB are bound to p100 and p105 in the steady state of most cells (Basak et al. 2007; Tergaonkar et al. 2005). Although their ability to function as IκB proteins is now firmly established, the unique physiological consequences of NF-κB regulation by p105 and p100 are just beginning to be determined (Chang et al. 2009; Sriskantharajah et al. 2009).

4.6 Post-Induction Repression of NF-κB by IκB

Most NF-κB activating signals, such as TNF-α and IL-1, lead to the elevated expression of the NF-κB-inducible IκB proteins IκBα, IκBε, p105, and p100. The newly synthesized inhibitors can then function to repress NF-κB activity. Most notably, free IκBα can enter the nucleus where it is capable of binding and disrupting NF-κB:DNA complexes (Bergqvist et al. 2009) before returning the inactive NF-κB to the cytoplasm. However, the differences in kinetics of IκB protein expression coupled with their varied rates of constitutive and signal-induced degradation results in the periodic mobilization of NF-κB in waves of activity (Hoffmann et al. 2002; Kearns and Hoffmann 2009). Computational modeling of IκB:NF-κB regulation using a systems biology approach has correctly predicted the temporal control of NF-κB in response to several stimuli. Signaling through the cytokine-responsive IKKβ subunit liberates NF-κB dimers that were associated with classical IκB proteins whereas p100, which responds specifically to signaling from IKKα:NIK complexes, remains intact. However, newly synthesized p100 (produced by the RelA-target gene nfkb2) can multimerize to form a novel “IκBδ” activity within IkκBsomes, and thus trap RelA:p50 NF-κB during the later stages of induction to provide negative feedback inhibition (Shih et al. 2009). This newly inhibited IκBδ complex can subsequently become the target for non-canonical signaling. Therefore, NF-κB signaling pathways are intricately intertwined and susceptible to alteration as cells respond continuously to their environment (Basak et al. 2008).

4.7 Kinetics of IκB Degradation

NF-κB activation kinetics correlate with the rates with which the proteasome degrades IκB proteins. This, in turn, depends upon the ability of the IKK complex to recognize and phosphorylate IκB proteins at specific sites. It is clear that the phosphorylation sites of classical IκB proteins are accessible to IKK when they are bound to NF-κB. Active IKK also phosphorylates unbound IκB proteins (Mathes et al. 2008). Phosphorylation of free IκBβ by IKK occurs at a slower rate compared to that of IκBα although the rate of IκBβ phosphorylation remains on the time scale of minutes. Small variations in the amino acid sequences at their respective phosphorylation sites account for the observed differences in the rates of IκBβ and IκBα phosphorylation by IKKβ (Wu and Ghosh 2003). Structural and biochemical studies indicate that phosphorylation sites of IκBβ remain accessible to IKK in the IκBβ:NF-κB complex and it is reasonable to assume that the same is true for IκBε (Malek et al. 2003). However, ubiquitin acceptors in IκBβ and -ε remain to be determined, as well as the molecular basis for distinct stimulus-induced degradation kinetics. The state of the IKK phosphorylation sites in p100 and p105 are unknown when the inhibitor proteins are multimerized within IκBsomes. Masking of these regions could serve as a mechanism for regulating the kinetics of phosphorylation of p100 and p105. Differences in the degradation kinetics of IκB may also arise from changes in the levels of ubiquitination, recognition by the proteasome, and unfolding of the IκB proteins prior to degradation. Detailed in vitro and cellular experiments to test these hypotheses are required in improve our understanding of NF-κB regulation arising from kinetic control of IκB degradation.

5 Recognition of DNA by NF-κB

NF-κB recognizes a double-stranded DNA element that is 9 to 11 bp (base pairs) long. Early comparisons of the first DNA sequences demonstrated to bind specifically to NF-κB dimers led to the following consensus sequence: 5′-GGGRNWYYCC-3′, where R = A or G; N = A, C, G, or T; W = A or T; and Y = C or T. The critical feature of this consensus is the presence of a series of G nucleotide bases the 5′ ends while the central portion of the sequence displays greater variation. DNA from gene enhancer regions that meet this consensus and can be shown to drive NF-κB-dependent reporter gene expression are termed “κB DNA” or “κB sites”. Hundreds of such sequences have been confirmed experimentally and the total number of unconfirmed κB sites detected by computational methods is in the thousands. Many of these newer sites reveal significantly greater variation than allowed by the original consensus κB DNA sequence.

5.1 NF-κB:DNA Complex Structures

The three-dimensional structures of several NF-κB RHR dimers in complex with diverse κB DNA have provided important insights into the DNA recognition mechanism of NF-κB (Berkowitz et al. 2002; Chen et al. 1998a, b, 2000; Chen-Park et al. 2002; Cramer et al. 1997; Escalante et al. 2002; Fusco et al. 2009; Ghosh et al. 1995; Huang et al. 2001; Moorthy et al. 2007; Müller et al. 1995; Panne et al. 2007). In general, the κB DNA is pseudo-symmetric and each NF-κB monomer binds to one DNA half site (Fig. 5). In its DNA-bound conformation, the NF-κB subunit NTD is positioned such that a conserved basic surface interacts with the acidic DNA. This represents a nearly 180° rotation for the NTD relative to its conformation in the RelA subunit of the IκBα:NF-κB complex crystal structures. Translation and rotation of the NTD relative to the DD is afforded by the short stretch of 10 amino acids that link the two domains.

Fig. 5
figure 5

Ribbon structure diagram of the NF-κB p50:RelA heterodimer in complex with κB DNA. Coloring as in Figs. 3 and 4 with DNA strands in magenta and orange. The view is as in Fig. 3b (left) and rotated 120° about the vertical axis (right) to show the interaction of loop L1 and the interdomain linker with DNA bases through the major groove

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Amino acid side chains from the immunoglobulin-like NTD of each NF-κB RHR mediate all of the direct contacts to DNA bases. The NF-κB dimer interface is maintained upon κB DNA binding and multiple additional non-specific DNA backbone interactions are made by the NTD and DD. The structure of NF-κB was unique at the time of its determination by virtue of the fact that all of the contacts with DNA were mediated by amino acids on loops that connect beta-strand elements of secondary structure. The arrangement of the NF-κB dimer about the major groove of one entire turn of DNA gives rise to a global structure that is reminiscent of a butterfly with a DNA “body” and a pair RHR “wings”. The C-terminal NLS polypeptide is disordered when it is included in the NF-κB RHR constructs used for X-ray crystal structure determination.

5.2 NF-κB Recognition of κB DNA at the 5′-end

A grouping of conserved amino acid residues that emanate from a large loop, referred to as the loop L1, directly contact bases within κB DNA. In p50 (murine numbering) these residues are Arg54, Arg56, Tyr57, Glu60, His64, and Lys241 (Fig. 6). The two Arg, the Tyr, and the Glu are invariant in all NF-κB subunits. His64 directly contacts the 5′ G. This residue is conserved in the NF-κB p52 subunit. However, substitution with Ala at this position in c-Rel, RelA, and RelB gives rise to differences in the half site length preferred by these two classes of NF-κB subunits as the Ala cannot compensate for the loss of this base-specific contact. As a consequence, the NF-κB p50 and p52 subunits prefer a 5′ half site that begins 5′-GGG and is five bp in length while the other subunits (RelA, RelB, or c-Rel) bind preferentially to 4 bp half sites that begin 5′-GG. A central bp, which is always A:T, is not contacted by either subunit suggesting that homodimers of p50 or p52 would bind optimally to an 11 bp κB DNA (two 5 bp half sites and a central A:T bp) while RelA, RelB, and c-Rel prefer 9 bp κB DNA. This also perfectly explains the original observation of NF-κB p50:RelA heterodimer bound to the 10 bp κB DNA from the enhancer of the immunoglobin kappa light chain gene (Sen and Baltimore 1986).

Fig. 6
figure 6

Schematic representation of base-specific contacts mediated by NF-κB p50 and RelA subunits and κB DNA. In this case, the κB DNA is that from the original immunoglobin kappa light chain gene and the contacts are those observed in its X-ray crystal structure with the NF-κB p50:RelA heterodimer. Bases are numbered as discussed in the text. Amino acid numbering comes from the murine sequences

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The central A:T bp serves as a convenient point of reference in studying base-specific interactions by NF-κB subunits and κB DNA. The 5′ G that is contacted by His64 of the p50 subunit occupies the position ±5 bp from this origin. The G:C bp at positions ±4 and ±3 are contacted similarly by each of the NF-κB subunits. The two invariant arginines (Arg56 and Arg54 in murine p50) make direct contact with these two G bases and the invariant glutamate contacts the paired C at the ±3 position. Recognition of both nucleotide bases at this position suggests a more important role of the G:C bp at position ±3 than either the G:C bp at the ±5 and ±4 positions.

5.3 NF-κB Binding to the Inner Bases of κB DNA

Base pairs at positions ±2 and ±1 in κB DNA exhibit more variability in sequence than the peripheral bases. In the crystal structure of the NF-κB p50:RelA heterodimer in complex with κB DNA from the immunoglobin kappa light chain gene, an Arg residue contained within the linker region that joins the NTD and DD in the RelA subunits crosses over and contacts the T of an A:T bp at position +2. An identical Arg is present in c-Rel. An analogous Lys residue at the corresponding position in p50 and p52 can interact with both T in an A:T bp or G from a G:C bp at the same position. Base pairs at position ±1 in κB DNA do not participate in any contacts with either RelA and c-Rel. However, the Lys residue within the interdomain linker of p50 and p52 can mediate contacts at this position dependent on the DNA sequence. The corresponding residue in RelB is also a lysine (Lys274 in murine RelB). However, rather than contact DNA this Lys projects inward to make an ion pair with Asp272. This suggests that RelB subunits might tolerate more sequence diversity at the inner positions of its κB DNA targets.

An invariant Tyr of loop L1 (Tyr57 in murine p50 and Tyr36 in murine RelA) participates in stacking interactions with bases at both ±1 and ±2 of the same strand. This stacking is favored by the presence of two successive T bases, as their exocyclic 5-methyl groups favor the interaction. Although a Phe at the same position could substitute for Tyr in maintain these stacking interactions, Tyr also participates in hydrogen bonds through its hydroxyl group making tyrosine an absolutely required residue for DNA recognition and binding. Either two C bases or any combination of T and C can also be accommodated at these positions, but an A or G at either position is unfavorable. The critical role played by this invariant Tyr is illustrated by the overrepresentation of the sequence AAATT or AATTT at the central 5 positions of the κB sequences recognized by RelA and c-Rel homodimers. It is likely that these Tyr base stacking interactions toward the center of the 9 bp κB sites preferred by RelA and c-Rel compensate for the fact that these NF-κB subunits contact fewer flanking GC bp.

It is not clear from structural analyses alone why A:T is by far the preferred central bp (position 0). It is likely that the presence of this base pair is necessary to convey DNA bending and/or dynamic characteristics necessary for optimum NF-κB:DNA complex formation.

5.4 Stabilization of NF-κB:DNA Complexes

The interaction of proteins can significantly alter binding affinity of NF-κB:DNA complexes. This can be true even if the protein binding is distal from the NF-κB:DNA interface. Both protein:DNA and protein:protein interactions are interdependent. This means that assembly of NF-κB into larger enhanceosome complexes and can be affected by subtle changes in DNA conformation.

This point is illustrated by two loops, one from the DD and the other from the NTD, which play particularly important roles. The βf-βg loop of the NF-κB DD projects toward κB DNA but does not directly contact it. Two conserved acidic residues (Asp267 and Glu269 in chicken c-Rel) are located within this loop and reside near the DNA in the complex between c-Rel homodimer and the IL2-CDRE κB DNA complex. These residues would be expected repel DNA and weaken binding (Huang et al. 2001). However, these negative charges are neutralized by an Arg in loop L1. Loop L1 is the same loop that contributes five of the six base contacting residues. Loop L1 can be divided into three parts: N-terminal front, N-terminal back, and C-terminal flexible part. The C-terminal portion of loop L1 is flexible and can contact the DNA backbone of nucleotides flanking the κB sequence. The N-terminal front and back end forms a rigid core structure that remain unchanged both in DNA bound and unbound forms. The surface residues projected from the front portion contribute the DNA base-contacting residues. An Arg on the back surface of the N-terminal portion contacts the acidic residues of the βf-βg loop. Interestingly, not all NF-κB:DNA complex crystallographic structures show this protein–protein interaction. We suggest that DNA conformation differences play a role in dictating RHR interdomain interactions. In the case of oncogenic v-Rel, a viral homologue of c-Rel, two core residues within the rigid part of Loop L1 are mutated. These two residues are at least partly responsible for altered DNA binding profiles by v-Rel as compared to c-Rel (Phelps and Ghosh 2004). Finally, these two loops also undergo modification, which also appears to regulate NF-κB DNA recognition as discussed below.

5.5 Post-Translational Modification and NF-κB:DNA Complex Regulation

A recent report has shown that monomethylation of RelA at Lys37 in response to induction by TNF-α and IL-1 is required for the expression of a subset of NF-κB target genes (Ea and Baltimore 2009). The methylated form of RelA displays extended gene activation as a result of prolonged DNA binding by RelA. Although a detailed mechanism to explain how modification of this residue might affect DNA binding is lacking, its position within of loop L1 suggests that the effect is likely indirect through altering the conformation the residues that directly contact DNA. It is important to mention here that some of the DNA contacting residues from loop L1 contact one another further stabilizing the loop L1 conformation and allowing them all to act as a unit. In p50, Glu60 bridges Arg54 and Arg56 as together they contact DNA as a structured module. The stability and utility of this folded polypeptide structure was illustrated when it was found to be exploited by RNA in selection binding experiments (Huang et al. 2003). In RelA and c-Rel, a similar Glu brings together one of the two Arg residues form the loop L1 and the Arg from the interdomain linker. These cooperative interactions between the amino acids side chains not only maintain a properly oriented conformation of the functional groups primed to contact DNA, but also contribute to differential base pair selectivity. Hence modification of lysine could affect orientation of these residues as well as residues that are involved in contact residues at loop βf-βg (discussed earlier).

Cells expressing a RelA Ser276Ala mutant show dramatically reduced transcriptional activity. This serine has been shown to undergo phosphorylation by two different kinases, MSK and cAMP-dependent protein kinase (PKA), and this post-translational modification is essential for RelA transcriptional activity (Dong et al. 2008; Reber et al. 2009; Vermeulen et al. 2003; Zhong et al. 1998). Although the RelA Ser276Ala appears to bind DNA, defects in DNA affinity cannot be completely ruled out in light of the importance of other residues in the same loop in the protein:DNA complex formation. Phosphorylation at position 276 has also been shown to be required for coactivator recruitment. Therefore, in addition to affinity modulation, phosphorylation may play a role in changing chromatin dynamics through acetylation activity of CBP/p300.

5.6 NF-κB Subunit Exchange in the Nucleus

One aspect of NF-κB regulation that has not yet been adequately addressed experimentally is the potential for exchange of subunits between active NF-κB dimers in the nucleus. The available structural and biochemical data suggest that this is likely to occur, especially in light of the relatively low dimerization affinity exhibited by many of the NF-κB dimer combinations and the preference of different κB DNA half sites toward specific NF-κB subunits. Functionally, it seems reasonable that such an exchange might coincide with the transition of a gene promoter from a repressed to an activated state. Homodimers of p50 and p52 are present in the nucleus of uninduced cells. Rapid mobilization of additional NF-κB subunits to the nucleus in response to IκB degradation could then lead to replacement of these repressive NF-κB with dimers that possess inherent transcription activation potential. It is not known whether the repressive p50 and p52 dimers are directly exchanged with p50:RelA or other activating homo- and heterodimers or, alternatively, if the individual p50 or p52 subunit monomers can exchange with a RelA monomer on κB DNA. Interestingly, analysis of the mice lacking the gene encoding IκBNS revealed a significant decrease in IL-2 (interleukin-2) production. ChIP assays on native cells revealed that IκBNS co-localizes with p50 homodimer at κB DNA and remains associated even after the p50 is dissociated (Touma et al. 2007). Therefore, it is possible that nuclear NF-κB subunit exchange on κB DNA falls under the purview of the nuclear IκB proteins.