NF-kB

# Overview
NF-B (nuclear factor-kappa B) is a protein complex which is a transcription factor.   NF-B is found in all cell types and is involved in cellular responses to stimuli such as stress, cytokines, free radicals, ultraviolet irradiation, and bacterial or viral antigens.  NF-B plays a key role in regulating the immune response to infection.  Consistent with this role, incorrect regulation of NF-B has been linked to cancer, inflammatory and autoimmune diseases, septic shock, viral infection and improper immune development. NF-B has also been implicated in processes of synaptic plasticity and memory.

# Discovery
NF-B was first discovered in the lab of Nobel Prize laureate David Baltimore via its interaction with an 11-base pair sequence in the immunoglobulin light-chain enhancer in B cells.

# Characterization
NF-B family members share structural homology with the retroviral oncoprotein v-Rel, resulting in their classification as NF-B/Rel proteins.
There are five proteins in the mammalian NF-B family:
- NF-B1 (also called p50) - NFKB1
- NF-B2 (also called p52) - NFKB2
- RelA (also named p65) - RELA
- RelB - RELB
- c-Rel  REL
In addition, there are NF-B proteins in lower organisms, such as the fruit fly Drosophila, sea urchins, sea anemones and sponges.
All proteins of the NF-B family share a Rel homology domain in their N-terminal halves.  A subfamily of NF-B proteins, including RelA, RelB and c-Rel, have a transactivation domain in their C-termini.  In contrast, the NF-B1 and NF-B2 proteins are synthesized as large precursors, p105 and p100, which undergo processing to generate the mature NF-B subunits, p50 and p52, respectively.  The processing of p105 and p100 is mediated by the ubiquitin/proteasome pathway and involves selective degradation of their C-terminal region containing ankyrin repeats.  While the generation of p52 from p100 is a tightly regulated process, p50 is produced from constitutive processing of p105.

# Activation of NF-B
Part of NF-B's importance in regulating cellular responses is that it  belongs to the category of "rapid-acting" primary transcription factors---i.e., transcription factors which are present in cells in an inactive state and do not require new protein synthesis to be activated (other members of this family include transcription factors such as c-Jun, STATs and nuclear hormone receptors).  This allows NF-B to act as a "first responder" to harmful cellular stimuli.  Stimulation of a wide variety of cell-surface receptors, such as RANK, TNFR, IL1R leads directly to NF-B activation and fairly rapid changes in gene expression.
Many bacterial products can activate NF-B. The identification of Toll-like receptors (TLRs) as specific pattern recognition molecules and the finding that stimulation of TLRs leads to activation of NF-B improved our understanding of how different pathogens activate NF-B. For example, studies have identified TLR4 as the receptor for the LPS component of Gram-Negative bacteria. TLRs are key regulators of both innate and adaptive immune responses.
Unlike RelA, RelB, and c-Rel, the p50 and p52 NF-B subunits do not contain transactivation domains in their C terminal halves.  Nevertheless, the p50 and p52 NF-B members play critical roles in modulating the specificity of NF-B function.  Although homodimers of p50 and p52 are generally repressors of B site transcription, both p50 and p52 participate in target gene transactivation by forming heterodimers with RelA, RelB or c-Rel.  Additionally, p50 and p52 homodimers also bind to the nuclear protein Bcl-3, and such complexes can function as transcriptional activators.

# Inhibitors of NF-B
In unstimulated cells, the NF-B dimers are sequestered in the cytoplasm by a family of inhibitors, called IBs (Inhibitor of kappa B), which are proteins that contain multiple copies of a sequence called ankyrin repeats.  By virtue of their ankyrin repeat domains, the IB proteins mask the nuclear localization signals (NLS) of NF-B proteins and keep them sequestered in an inactive state in the cytoplasm.
IBs are a family of related proteins that have an N-terminal regulatory domain, followed by six or more ankyrin repeats and a PEST domain near their C terminus.  Although the IB family consists of IB, IB, IB, IB and Bcl-3, the best studied and major IB protein is IB.  Due to the presence of ankyrin repeats in their C-terminal halves, p105 and p100 also function as IB proteins.  Of all the IB members, IB is unique in that it is synthesized from the nf-kb1 gene using an internal promoter, thereby resulting in a protein which is identical to the C-terminal half of p105.
Activation of the NF-B is initiated by the signal-induced degradation of IB proteins.  This occurs primarily via activation of a kinase called the IB kinase (IKK).  IKK is composed of a heterodimer of the catalytic IKK alpha and IKK beta subunits and a "master" regulatory protein termed NEMO (NF-kappa B essential modulator) or IKK gamma. When activated by signals, usually coming from the outside of the cell, the IB kinase phosphorylates two serine residues located in an IB regulatory domain.  When phosphorylated on these serines (e.g., serines 32 and 36 in human IB), the IB inhibitor molecules are modified by a process called ubiquitination which then leads them to be degraded by a cell structure called the proteasome.
With the degradation of the IB inhibitor, the NF-B complex is then freed to enter the nucleus where it can 'turn on' the expression of specific genes that have DNA-binding sites for NF-B nearby.  The activation of these genes by NF-B then leads to the given physiological response, for example, an inflammatory or immune response, a cell survival response, or cellular proliferation. NF-B turns on expression of its own repressor, IB.  The newly-synthesized IB then re-inhibits NF-B and thus forms an auto feedback loop, that results in oscillating levels of NF-B activity. In addition, several viruses, including the AIDS virus HIV, have binding sites for NF-B that controls the expression of viral genes, which in turn contribute to viral replication or viral pathogenicity.  In the case of HIV-1, activation of NF-B may, at least in part, be involved in activation of the virus from a latent, inactive state. YopJ is a factor secreted by Yersinia pestis, the causative agent of plague, that prevents the ubiquitination of IB. This causes this pathogen to effectively inhibit the NF-B pathway and thus block the immune response of a human infected with Yersinia.

# NF-B's Role in Cancer and Other Diseases
NF-B is widely used by eukaryotic cells as a regulator of genes that control cell proliferation and cell survival.  As such, many different types of human tumors have misregulated NF-B: that is, NF-B is constitutively active.  Active NF-B turns on the expression of genes that keep the cell proliferating and protect the cell from conditions that would otherwise cause it to die.  In tumor cells, NF-B is active either due to mutations in genes encoding the NF-B transcription factors themselves or in genes that control NF-B activity (such as IB genes); in addition, some tumor cells secrete factors that cause NF-B to become active.  Blocking NF-B can cause tumor cells to stop proliferating, to die, or to become more sensitive to the action of anti-tumor agents.  Thus, NF-B is the subject of much active research among pharmaceutical companies as a target for anti-cancer therapy.
Because NF-B controls many genes involved in inflammation, it is not surprising that NF-B is found to be chronically active in many inflammatory diseases, such as inflammatory bowel disease, arthritis, sepsis, among others.  Many natural products (including anti-oxidants) that have been promoted to have anti-cancer and anti-inflammatory activity have also been shown to inhibit NF-B.It has been shown that in vivo administration of Insulin also leads to anti inflammatory effects through inhibition of NF kB in mono-nuclear cells of obese patients.  There is a controversial US patent (US patent 6,410,516) that applies to the discovery and use of agents that can block NF-B for therapeutic purposes. This patent is involved in several lawsuits, including Ariad v. Lilly. Recent work by Karin, Ben-Neriah and others has highlighted the importance of the connection between NF-B, inflammation and cancer and underscored the value of therapies that regulate the activity of NF-B.
It has also been proposed that NF-B has a role in the growth and proliferation of myocardial cells infected with Trypanosoma cruzi.  In myocardial cells of normal mice it is normal to detect a low background of NF-B activity.  In mice infected with T. cruzi, the levels of NF-B DNA-binding activity become elevated.

# Signaling in Immunity
NF-kB is a major transcription factor which regulates genes responsible for both the innate immune response and the adaptive immune response. Upon activation of either the T- or B-cell receptor, NF-kB becomes activated through distinct signaling components. Upon ligation of the T-cell receptor, an adaptor molecule, ZAP70 is recruited via its SH2 domain to the cytoplasmic side of the receptor.  ZAP70 helps recruit both LCK and PLCgamma, which causes activation of PKC.  Through a cascade of phosphorylation events, the kinase complex is activated and NF-kB is able to enter the nucleus to upregulate genes involved in T-cell development, maturation and proliferation.

# Conserved in evolution
NF-kB is found in a number of simple organisms as well.  These include Cnidarians (such as sea anemones and coral), Porifera (sponges) and insects (such as moths, mosquitoes and fruitflies).  The sequencing of the genomes of Aedes aegypti, anopheles gambae, and the fruitfly Drosophila melanogaster has allowed comparative genetic and evolutionary studies on NF-kB.  In those insect species, activation of NF-kB is triggered by the Toll pathway (which evolved independently in insects and mammals) and by the Imd pathway.