TNFB (Danio rerio)
Description [+]
- Synonyms: TNFB, TUMOR NECROSIS FACTOR B (TNF SUPERFAMILY, MEMBER 2), TNF-ALPHA, TNF , TNF2, TNF-A_V2, TNFA-LIKE
- Species: Metazoa;Bilateria;Deuterostoma;Chordata;Vertebrata;Pisces; Danio rerio
- Short gene description: tumor necrosis factor (TNF superfamily, member 2) [Source:RefSeq_peptide;Acc:NP_001019618]
- Family: Death ligand
- Process: undefined,
- Pathways: extrinsic pathway,
- Criteria: manually curated
- Curator comment:
- Human ortholog(s): TNF LTA LTA LTA
- WIKI: TNFB-D_rerio
References [+]
- Molecular cloning and expression of a TNF receptor and two TNF ligands in the fish ovary.
- Bobe J, Goetz FW
- Using degenerative primers, partial cDNAs of a TNF (tumor necrosis factor) receptor and two TNF ligands were obtained by PCR of zebrafish and trout cDNAs, or cDNA libraries. These fragments were then used to screen cDNA libraries of appropriate tissues to obtain clones containing full coding sequences. A zebrafish cDNA was obtained that presumably codes for a 438 amino acid ovarian TNF receptor (OTR) that was identified as a death-domain-containing member of the TNF receptor family. On Northern blots, the OTR cDNA hybridized with a 3.4-kb transcript that is abundant in the zebrafish ovary but lightly detected in all other tissues tested. A zebrafish cDNA presumably coding for a 214 amino acid protein with sequence similarity to mammalian TRAIL (TNF-related apoptosis inducing ligand), was also isolated. In addition, a fragment of the brook trout TRAIL homologue was obtained. Finally, a full-length brook trout cDNA, that presumably codes for a 255 amino acid protein with sequence similarity to mammalian TNF-alpha and lymphotoxin-alpha, was isolated. This study is the first report of a death-domain-containing TNF receptor and the first published report of a TNF ligand in fish. Comp Biochem Physiol B Biochem Mol Biol. 2001 Jun;129(2-3):475-81.
- Delineation of the cell-extrinsic apoptosis pathway in the zebrafish.
- Eimon PM, Kratz E, Varfolomeev E, Hymowitz SG, Stern H, Zha J, Ashkenazi A
- The mammalian extrinsic apoptosis pathway is triggered by Fas ligand (FasL) and Apo2 ligand/tumor necrosis factor (TNF)-related apoptosis-inducing ligand (Apo2L/TRAIL). Ligand binding to cognate receptors activates initiator caspases directly in a death-inducing signaling complex. In Drosophila, TNF ligand binding activates initiator caspases indirectly, through JNK. We characterized the extrinsic pathway in zebrafish to determine how it operates in a nonmammalian vertebrate. We identified homologs of FasL and Apo2L/TRAIL, their receptors, and other components of the cell death machinery. Studies with three Apo2L/TRAIL homologs demonstrated that they bind the receptors zHDR (previously linked to hematopoiesis) and ovarian TNFR (zOTR). Ectopic expression of these ligands during embryogenesis induced apoptosis in erythroblasts and notochord cells. Inhibition of zHDR, zOTR, the adaptor zFADD, or caspase-8-like proteases blocked ligand-induced apoptosis, as did antiapoptotic Bcl-2 family members. Thus, the extrinsic apoptosis pathway in zebrafish closely resembles its mammalian counterpart and cooperates with the intrinsic pathway to trigger tissue-specific apoptosis during embryogenesis in response to ectopic Apo2L/TRAIL expression. Cell Death Differ. 2006 Oct;13(10):1619-30. Epub 2006 Aug 4.
- References from Human ortholog(s):
- Human tumour necrosis factor: precursor structure, expression and homology to lymphotoxin.
- Pennica D, Nedwin GE, Hayflick JS, Seeburg PH, Derynck R, Palladino MA, Kohr WJ, Aggarwal BB, Goeddel DV
- Human tumour necrosis factor has about 30% homology in its amino acid sequence with lymphotoxin, a lymphokine that has similar biological properties. Recombinant tumour necrosis factor can be obtained by expression of its complementary DNA in Escherichia coli and induces the haemorrhagic necrosis of transplanted methylcholanthrene-induced sarcomas in syngeneic mice. Nature. 1984 Dec 20-1985 Jan 2;312(5996):724-9.
Structure & Sequence [+]
Pfam domains:
(Pfam is a large collection of protein families.)
| Source | Domain Name | Start | End |
|---|---|---|---|
| PFAM A | TNF | 113 | 242 |
Protein sequence [+]
tnfb | Danio rerio | 7955 | length:242
MVRYETTLVDMEAGVGGVYQTTVAPVPVNSSRSWIWKTLAAVAFVGLCVVAAFFFTWHVM
KPNEEGQKPNREHLKQQITTPSASSDHGKVLKQIAQSTKAAIHLHGDPSGQSLKWVGGVD
QAFQQGGLRLENNEIIIPKDGLYFVYSQVSYETLCVEDVEGDGQKYLSHTINRYTDAVRE
KMPLQNSANSVCQSLDGKTSYSTIYLGAVFDLFGDDRLSTHTTRVGDIENNYAKTFFGVF
AL
KPNEEGQKPNREHLKQQITTPSASSDHGKVLKQIAQSTKAAIHLHGDPSGQSLKWVGGVD
QAFQQGGLRLENNEIIIPKDGLYFVYSQVSYETLCVEDVEGDGQKYLSHTINRYTDAVRE
KMPLQNSANSVCQSLDGKTSYSTIYLGAVFDLFGDDRLSTHTTRVGDIENNYAKTFFGVF
AL
Structure links:
- Smartdomain prediction information: SM00207
Evolution [+]
View protein alignment and tree with Jalview:
Explore tree at phylomeDB: Click here.
Homologs list [+]
| Name | Relationship | Species |
|---|---|---|
| TNFA_PANTR | orthology | Chimpanzee |
| TNFB_PANTR | orthology | Chimpanzee |
| TNFB_BOVIN | orthology | Cow |
| TNFA_BOVIN | orthology | Cow |
| TNFB_CANFA | orthology | Dog |
| TNFA_CANFA | orthology | Dog |
| NP_001033074.1 | orthology | Fugu |
| G_aculeatus_ENSGACP00000017676 | orthology | Gasterosteus |
| Q8HZD8_9PRIM | orthology | Gorilla |
| LTA | orthology | Gorilla |
| LTA | orthology | Horse |
| TNFA_HORSE | orthology | Horse |
| H_sapiens_ENSP00000372988 | orthology | Human |
| LTA | orthology | Human |
| TNF | orthology | Human |
| LTA | orthology | Human |
| H_sapiens_ENSP00000372790 | orthology | Human |
| LTA | orthology | Human |
| TNFA_MACMU | orthology | Macaca |
| TNFB_MACMU | orthology | Macaca |
| O_latipes_ENSORLP00000020071 | orthology | Medaka |
| TNF | orthology | Monodelphis |
| LTA | orthology | Monodelphis |
| Tnf | orthology | Mouse |
| Lta | orthology | Mouse |
| LTA | orthology | Orangutan |
| Q8HZD7_PONPY | orthology | Orangutan |
| TNFB_RABIT | orthology | Rabbit |
| TNFA_RABIT | orthology | Rabbit |
| Tnf | orthology | Rat |
| Lta | orthology | Rat |
| TNF | orthology | Tetraodon |
| X_tropicalis_ENSXETP00000005341 | orthology | Xenopus |
| NP_989710.1 | paralogy | Chicken |
| NP_001019749.1 | paralogy | Chicken |
| NP_001026730.1 | paralogy | Chicken |
| FASLG | paralogy | Chimpanzee |
| TNFSF15 | paralogy | Chimpanzee |
| TNFSF10 | paralogy | Chimpanzee |
| NP_001092329.1 | paralogy | Cow |
| NP_001092329.1 | paralogy | Cow |
| IPI00701832.3 | paralogy | Cow |
| IPI00694513.2 | paralogy | Cow |
| Q9TTJ2_BOVIN | paralogy | Cow |
| FASLG | paralogy | Dog |
| TNFSF15 | paralogy | Dog |
| TNFSF10 | paralogy | Dog |
| G_aculeatus_ENSGACP00000004738 | paralogy | Gasterosteus |
| G_aculeatus_ENSGACP00000000611 | paralogy | Gasterosteus |
| TNFSF15 | paralogy | Gorilla |
| TNFSF10 | paralogy | Gorilla |
| TNFSF10 | paralogy | Horse |
| FASLG | paralogy | Horse |
| TNFSF15 | paralogy | Horse |
| FASL | paralogy | Human |
| TNFSF15 | paralogy | Human |
| TNFSF10 | paralogy | Human |
| A_carolinensis_ENSACAP00000006055 | paralogy | Lyzard |
| TNFSF10 | paralogy | Lyzard |
| TNFSF10 | paralogy | Macaca |
| TNFL6_MACMU | paralogy | Macaca |
| TNFSF15 | paralogy | Macaca |
| TNFSF10 (1 of 2) | paralogy | Medaka |
| O_latipes_ENSORLP00000013121 | paralogy | Medaka |
| TNFSF15 | paralogy | Monodelphis |
| Tnfsf15 | paralogy | Mouse |
| Fasl | paralogy | Mouse |
| TRAIL | paralogy | Mouse |
| TNFSF15 | paralogy | Orangutan |
| TNFSF10 | paralogy | Orangutan |
| FASLG | paralogy | Orangutan |
| TNFSF10 | paralogy | Ornithorhynchus |
| FASLG | paralogy | Ornithorhynchus |
| TNFSF15 | paralogy | Ornithorhynchus |
| O_cuniculus_ENSOCUP00000004879 | paralogy | Rabbit |
| TNFSF15 | paralogy | Rabbit |
| O_cuniculus_ENSOCUP00000012761 | paralogy | Rabbit |
| Tnfsf10 | paralogy | Rat |
| Tnfsf15 | paralogy | Rat |
| Faslg | paralogy | Rat |
| FASLG | paralogy | Xenopus |
| TNFSF15 | paralogy | Xenopus |
| TNFSF10 | paralogy | Zebra finch |
| CD40LG | paralogy | Zebra finch |
| TNFSF15 | paralogy | Zebra finch |
| FASLG | paralogy | Zebra finch |
| tnfa | paralogy | Zebrafish |
| tnfsf10l4 | paralogy | Zebrafish |
| tnfsf10l2 | paralogy | Zebrafish |
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Gene Ontology [+]
| GO id | Name | Ontology type | Evidence |
|---|---|---|---|
| GO:0006955 | immune response | biological_proccess | IEA |
| GO:0005164 | tumor necrosis factor receptor binding | mollecular_function | IEA |
| GO:0005125 | cytokine activity | mollecular_function | IEA |
| GO:0016020 | membrane | cell_component | IEA |
| GO:0005615 | extracellular space | cell_component | IEA |
Check GO Evidence Codes here
Information from other databases [+]
- Gene info from ZFIN [?] ZDB-GENE-050601-2
- Ensembl genome browser [?] : ENSDARG00000013598
- Expression info from Arrayexpress [?] : ENSDARG00000013598
- Protein expression from Protein Atlas: [?] ENSDARG00000013598
- Community gene edition from Wikigenes: [?] 554167
- entrezgene: 554167
- refseq_dna: NM_001024447
- refseq_peptide: NP_001019618
Click on [?] for more information.
