|Coordinate||46,311,626 bp (GRCm38)|
|Base Change||A ⇒ T (forward strand)|
|Gene Name||nuclear factor of kappa light polypeptide gene enhancer in B cells 2, p49/p100|
|Synonym(s)||NF kappaB2, p52|
|Chromosomal Location||46,304,737-46,312,090 bp (+)|
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a subunit of the transcription factor complex nuclear factor-kappa-B (NFkB). The NFkB complex is expressed in numerous cell types and functions as a central activator of genes involved in inflammation and immune function. The protein encoded by this gene can function as both a transcriptional activator or repressor depending on its dimerization partner. The p100 full-length protein is co-translationally processed into a p52 active form. Chromosomal rearrangements and translocations of this locus have been observed in B cell lymphomas, some of which may result in the formation of fusion proteins. There is a pseudogene for this gene on chromosome 18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
PHENOTYPE: Homozygotes for targeted null mutations exhibit gastric hyperplasia, enlarged lymph nodes, enhanced cytokine production by activated T cells, absence of Peyer's patches, increased susceptibility to Leishmania major, and early postnatal mortality. [provided by MGI curators]
|Amino Acid Change||Methionine changed to Leucine|
|Institutional Source||Beutler Lab|
|Gene Model||predicted gene model for protein(s): [ENSMUSP00000072859] [ENSMUSP00000107512]|
Crystal structure of the dimerization domains p52 homodimer [X-RAY DIFFRACTION]
Crystal structure of the dimerization domains p52 and RelB [X-RAY DIFFRACTION]
AA Change: M838L
|Predicted Effect||possibly damaging
PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
AA Change: M838L
|Predicted Effect||possibly damaging
PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
|Meta Mutation Damage Score||0.0605|
|Is this an essential gene?||Possibly essential (E-score: 0.592)|
|Candidate Explorer Status||CE: not good candidate; Verification probability: 0.087; ML prob: 0.128; human score: -3|
Linkage Analysis Data
|Alleles Listed at MGI|
|Mode of Inheritance||Autosomal Recessive|
|Last Updated||2019-09-04 9:46 PM by Diantha La Vine|
|Record Created||2015-01-10 2:16 PM by Bruce Beutler|
The pale_fire phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R0270, some of which exhibited an increased frequency of B1a cells in the peripheral blood (Figure 1).
|Nature of Mutation|
Whole exome HiSeq sequencing of the G1 grandsire identified 110 mutations. The increased B1a cell frequency in the peripheral blood was linked by continuous variable mapping to a mutation in Nfkb2: an A to T transversion at base pair 46,311,626 (v38) on chromosome 19, or base pair 8,015 in the GenBank genomic region NC_000085. Linkage was found with a recessive model of inheritance (P = 2.53 x 10-4), wherein 10 variant homozygotes departed phenotypically from 15 homozygous reference mice and 20 heterozygous mice (Figure 2).
The mutation corresponds to residue 2,821 in the mRNA sequence NM_019408 (variant 1) within exon 21 of 22 total exons, to residue 2,670 in the mRNA sequence NM_001177369 (variant 2) within exon 22 of 23 total exons, and residue 2,586 in the mRNA sequence NM_001177370 (variant 3) within exon 21 of 22 total exons.
Genomic numbering corresponds to NC_000085. The mutated nucleotide is indicated in red. The mutation results in a methionine (M) to leucine (L) substitution at position 838 (M838L) in all isoforms of the NF-κB2 protein, and is strongly predicted by PolyPhen-2 to cause loss of function (score = 0.956) (1).
|Illustration of Mutations in
Gene & Protein
The Nfkb2 gene encodes a roughly 100 kD 899 amino acid protein (p100), which is cleaved at amino acids 454-455 to produce an active 52-kD transcription factor (p52) that is a member of the NF-κB family of transcription factors [Figure 3; reviewed in (2)]. The members of the NF-κB family (i.e., NF-κB1 (p50 and its precursor p105; see the record for Finlay), RelA (also known as p65), c-Rel, and RelB) are characterized by the presence of an N-terminal Rel homology domain (RHD) that is responsible for homo- and heterodimerization as well as for sequence-specific DNA binding. Unlike RelA, c-Rel, and RelB, p52 and p50 do not contain a C-terminal transcription activation domain (TAD). p52 is able to heterodimerize with most other NF-κB proteins, but preferentially binds to RelB, as does the p100 precursor (3-5). p52 homodimers likely repress transcription by competing with other NF-κB dimers for binding sites in the promoters of NF-κB activated genes. Both the p100 and p105 proteins contain multiple C-terminal ankyrin repeats (seven in p100), a common feature shared by IκB family members (Figure 4). Between the RHD and the ankyrin repeats is a glycine-rich region (GRR) that is essential for determining the site of p100 cleavage into the p52 subunit. p100 also contains a C-terminal death domain (DD) at amino acids 764-851 that associates with the S9 subunit of the 19 S protease (6). Death domains are conserved regions that are usually involved in homotypic protein interactions, and are composed of a bundle of six α-helices.
The pale_fire mutation results in a methionine (M) to leucine (L) substitution at position 838 (M838L) within the DD.
Please see the record xander for more information about Nfkb2.
The NF-κB signaling pathway functions in essentially all mammalian cell types and is activated in response to injury, infection, inflammation and other stressful conditions requiring rapid reprogramming of gene expression. The non-canonical NF-κB pathway drives the post-translational processing of p100 to mature p52 through IKK-1 and NIK, and results in the activation of p52/RelB heterodimers (2;4;5;7), and appears to be mostly restricted to a subset of tumor necrosis factor (TNF) receptors including lymphotoxin-β receptor (LTβR), B cell activating receptor (BAFFR), CD40, receptor activator of NF-κB (RANK) and TNF-related weak inducer of apoptosis (TWEAK) (8-12). These receptors are involved in secondary lymphoid organogenesis (SLO), B cell differentiation, survival and homeostasis, osteoclastogenesis, and angiogenesis (7). Mice homozygous for targeted null mutations of Nfkb2 exhibit absence of Peyer's patches (PPs) and reduced lymph nodes, increased susceptibility to certain pathogens, impaired B cell maturation, aberrant T cell function, and early postnatal mortality [reviewed by (13)]. They also exhibit disruption of splenic architecture that includes an absence of the splenic follicular marginal zone and marked depletion of B cell follicular areas or germinal centers (14-16).
Although Nfkb2 function is required for conventional B cell maturation, the analysis of xander mice and pale_fire mice demonstrates that Nfkb2 is not required for peritoneal B cells. Instead, xander and pale_fire animals display increased numbers of B1 cells, a phenotype that is similar to that seen in alymphoplasia (aly) mice with a point mutation in NIK (17). The increased numbers of B1 cells in the peritoneum is suggested to arise from a migration defect in aly/aly peritoneal B cells caused by a defect in SLO chemokine receptor signaling (18). It is possible that NIK activation of NF-κB2 in response to chemokine receptor signaling plays a role in peritoneal B cell migration.
1) 94°C 2:00
The following sequence of 654 nucleotides is amplified (chromosome 19, + strand):
1 gttgagaagc ctggtggaca catacaggaa gaccccgtct cccagcggca gtctccttcg
Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.
1. Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., and Sunyaev, S. R. (2010) A Method and Server for Predicting Damaging Missense Mutations. Nat Methods. 7, 248-249.
2. Vallabhapurapu, S., and Karin, M. (2009) Regulation and Function of NF-kappaB Transcription Factors in the Immune System. Annu Rev Immunol. 27, 693-733.
3. Dobrzanski, P., Ryseck, R. P., and Bravo, R. (1995) Specific Inhibition of RelB/p52 Transcriptional Activity by the C-Terminal Domain of p100. Oncogene. 10, 1003-1007.
4. Senftleben, U., Cao, Y., Xiao, G., Greten, F. R., Krahn, G., Bonizzi, G., Chen, Y., Hu, Y., Fong, A., Sun, S. C., and Karin, M. (2001) Activation by IKKalpha of a Second, Evolutionary Conserved, NF-Kappa B Signaling Pathway. Science. 293, 1495-1499.
5. Yilmaz, Z. B., Weih, D. S., Sivakumar, V., and Weih, F. (2003) RelB is Required for Peyer's Patch Development: Differential Regulation of p52-RelB by Lymphotoxin and TNF. EMBO J. 22, 121-130.
6. Fong, A., and Sun, S. C. (2002) Genetic Evidence for the Essential Role of Beta-Transducin Repeat-Containing Protein in the Inducible Processing of NF-Kappa B2/p100. J Biol Chem. 277, 22111-22114.
7. Dejardin, E. (2006) The Alternative NF-kappaB Pathway from Biochemistry to Biology: Pitfalls and Promises for Future Drug Development. Biochem Pharmacol. 72, 1161-1179.
8. Xiao, G., Harhaj, E. W., and Sun, S. C. (2001) NF-kappaB-Inducing Kinase Regulates the Processing of NF-kappaB2 p100. Mol Cell. 7, 401-409.
9. Luftig, M. A., Cahir-McFarland, E., Mosialos, G., and Kieff, E. (2001) Effects of the NIK Aly Mutation on NF-kappaB Activation by the Epstein-Barr Virus Latent Infection Membrane Protein, Lymphotoxin Beta Receptor, and CD40. J Biol Chem. 276, 14602-14606.
10. Kayagaki, N., Yan, M., Seshasayee, D., Wang, H., Lee, W., French, D. M., Grewal, I. S., Cochran, A. G., Gordon, N. C., Yin, J., Starovasnik, M. A., and Dixit, V. M. (2002) BAFF/BLyS Receptor 3 Binds the B Cell Survival Factor BAFF Ligand through a Discrete Surface Loop and Promotes Processing of NF-kappaB2. Immunity. 17, 515-524.
11. Coope, H. J., Atkinson, P. G., Huhse, B., Belich, M., Janzen, J., Holman, M. J., Klaus, G. G., Johnston, L. H., and Ley, S. C. (2002) CD40 Regulates the Processing of NF-kappaB2 p100 to p52. EMBO J. 21, 5375-5385.
12. Saitoh, T., Nakayama, M., Nakano, H., Yagita, H., Yamamoto, N., and Yamaoka, S. (2003) TWEAK Induces NF-kappaB2 p100 Processing and Long Lasting NF-kappaB Activation. J Biol Chem. 278, 36005-36012.
13. Gerondakis, S., Grumont, R., Gugasyan, R., Wong, L., Isomura, I., Ho, W., and Banerjee, A. (2006) Unravelling the Complexities of the NF-kappaB Signalling Pathway using Mouse Knockout and Transgenic Models. Oncogene. 25, 6781-6799.
14. Caamano, J. H., Rizzo, C. A., Durham, S. K., Barton, D. S., Raventos-Suarez, C., Snapper, C. M., and Bravo, R. (1998) Nuclear Factor (NF)-Kappa B2 (p100/p52) is Required for Normal Splenic Microarchitecture and B Cell-Mediated Immune Responses. J Exp Med. 187, 185-196.
15. Franzoso, G., Carlson, L., Poljak, L., Shores, E. W., Epstein, S., Leonardi, A., Grinberg, A., Tran, T., Scharton-Kersten, T., Anver, M., Love, P., Brown, K., and Siebenlist, U. (1998) Mice Deficient in Nuclear Factor (NF)-Kappa B/p52 Present with Defects in Humoral Responses, Germinal Center Reactions, and Splenic Microarchitecture. J Exp Med. 187, 147-159.
16. Carragher, D., Johal, R., Button, A., White, A., Eliopoulos, A., Jenkinson, E., Anderson, G., and Caamano, J. (2004) A Stroma-Derived Defect in NF-kappaB2-/- Mice Causes Impaired Lymph Node Development and Lymphocyte Recruitment. J Immunol. 173, 2271-2279.
17. Shinkura, R., Kitada, K., Matsuda, F., Tashiro, K., Ikuta, K., Suzuki, M., Kogishi, K., Serikawa, T., and Honjo, T. (1999) Alymphoplasia is Caused by a Point Mutation in the Mouse Gene Encoding Nf-Kappa b-Inducing Kinase. Nat Genet. 22, 74-77.
18. Fagarasan, S., Shinkura, R., Kamata, T., Nogaki, F., Ikuta, K., Tashiro, K., and Honjo, T. (2000) Alymphoplasia (Aly)-Type Nuclear Factor kappaB-Inducing Kinase (NIK) Causes Defects in Secondary Lymphoid Tissue Chemokine Receptor Signaling and Homing of Peritoneal Cells to the Gut-Associated Lymphatic Tissue System. J Exp Med. 191, 1477-1486.
|Science Writers||Anne Murray|