TRAF2

These structural differences prevent TRAF2 from interacting with Ubc13 and other related E2s via steric clash and unfavorable interfaces.

PMID:20577214

Remarkably however, addition of S1P induced efficient TRAF2-mediated ubiquitination of RIP1 (Fig. 3a).

Keratinocyte-specific deletion of Traf2, but not Sphk1 deficiency, disrupted TNF mediated NF-κB and MAP kinase signalling

support the idea that the main function of TRAF2 in TNF-induced NF-κB is to recruit cIAPs to the TNFR1-SC

GO:0005164 tumor necrosis factor receptor binding

IEA
GO_REF:0000120

Summary: The TRAF2 MATH domain binds the cytoplasmic tails of TNF receptor superfamily members. Recombinant human TRAF2 binds the CD40 cytoplasmic domain directly. In horse F7BIV4 the MATH domain is 142/146 identical to the human one.

Reason: Receptor binding is the defining activity of the TRAF-C/MATH domain. The PAINT curators also placed GO:0005164 at the eumetazoan node PTN000805720, which is ancestral to the TRAF2 subfamily (PTHR10131:SF21) that contains F7BIV4. The term means binding the intracellular part of the receptor, not binding the TNF cytokine.

Supporting Evidence:

PMID:9718306

TRAF1, TRAF2, TRAF3, and TRAF6, but not TRAF4 or TRAF5, bound directly to the CD40 cytoplasmic domain.

file:HORSE/TRAF2/TRAF2-bioinformatics/RESULTS-rereview.md

MATH domain (human 351-496): 142/146 identical, with all 5 Cys/His positions identical.

GO:0005737 cytoplasm

IEA
GO_REF:0000044

Summary: TRAF2 is a soluble cytoplasmic adaptor that is recruited to the cytoplasmic face of ligand-engaged receptors and to IRE1 at the ER.

Reason: Cytoplasm is the right compartment. The PAINT curators placed GO:0005737 at the deep node PTN008938480 (PTHR10131), which includes the TRAF2 subfamily. Experimental human TRAF2 localisation (UniProt Q12933, PubMed:15383523 and PubMed:19150425) agrees. Cytosol, the more specific term, is also annotated and accepted. Cytoplasm is kept as well, because TRAF2 also acts at the cytoplasmic face of membranes.

Supporting Evidence:

PMID:20447407

To fulfill this role, cIAPs must be recruited to the receptor complex by TNF-receptor-associated factor (TRAF) 2.

PMID:10650002

The cytoplasmic part of IRE1 bound TRAF2, an adaptor protein that couples plasma membrane receptors to JNK activation.

GO:0005829 cytosol

IEA
GO_REF:0000002

Summary: TRAF2 has no transmembrane or signal sequence. It is a soluble cytosolic adaptor that is recruited from the cytosol to receptor complexes.

Reason: This InterPro-based term is consistent with human TRAF2, which has experimental and Reactome cytosol annotations accepted in the human review. Horse F7BIV4 keeps the same domain architecture.

Supporting Evidence:

PMID:20447407

To fulfill this role, cIAPs must be recruited to the receptor complex by TNF-receptor-associated factor (TRAF) 2.

file:HORSE/TRAF2/TRAF2-bioinformatics/RESULTS-rereview.md

Every human residue has an aligned horse partner (0 unaligned human residues), so F7BIV4 is not a fragment.

GO:0007165 signal transduction

IEA
GO_REF:0000002

TOO GENERAL

Summary: The term is true but very broad. TRAF2 acts in TNF-family receptor signaling, which is captured by the accepted tumor necrosis factor-mediated signaling pathway (GO:0033209).

Reason: GO:0033209 tumor necrosis factor-mediated signaling pathway is accepted on this gene and is a descendant of GO:0007165 (through cell surface receptor signaling pathway; checked in OLS), so this term adds nothing. The claim itself is correct.

Supporting Evidence:

TRAF2 is required for TNF-alpha-mediated activation of c-Jun N-terminal kinase (JNK), contributes to activation of NF-kappaB, and mediates anti-apoptotic signals

GO:0008270 zinc ion binding

IEA
GO_REF:0000120

KEEP AS NON CORE

Summary: The TRAF2 RING and TRAF-type zinc fingers coordinate zinc structurally. The crystal structure of the human RING and first zinc finger resolves these sites, and all 8 RING Cys/His positions are conserved in F7BIV4.

Reason: Zinc binding is real and is the precise metal-binding term. It is structural and does not by itself establish catalysis, so it is non-core to the adaptor function.

Supporting Evidence:

Here we report the crystal structure of the RING and the first zinc finger domains of TRAF2.

file:HORSE/TRAF2/TRAF2-bioinformatics/RESULTS-rereview.md

RING window (human 34-73): 37/40 identical; all 8 Cys/His positions are identical.

GO:0033209 tumor necrosis factor-mediated signaling pathway

IEA
GO_REF:0000002

Summary: TRAF2 is a core component of TNFR1 and TNFR2 signaling complexes. It recruits cIAPs and is required in mice for full TNF-induced NF-kappaB and MAP kinase activation in fibroblasts and keratinocytes.

Reason: This is a core process. The PAINT curators placed GO:0033209 at node PTN000805720, which includes the TRAF2 subfamily (PTHR10131:SF21) that contains F7BIV4. TRAF2 takes part directly, as the scaffold that recruits the E3 ligases to the receptor complex.

Supporting Evidence:

TRAF2 is required for TNF-alpha-mediated activation of c-Jun N-terminal kinase (JNK), contributes to activation of NF-kappaB, and mediates anti-apoptotic signals

Keratinocyte-specific deletion of Traf2, but not Sphk1 deficiency, disrupted TNF mediated NF-κB and MAP kinase signalling

GO:0042981 regulation of apoptotic process

IEA
GO_REF:0000002

Summary: TRAF2 limits TNF-induced apoptosis. Traf2-deficient cells are more sensitive to TNF killing, and TRAF2-cIAP recruitment supports survival signaling. TRAF2 can also promote death in other contexts, such as ER-stress-driven ASK1-JNK signaling, so regulation in both directions applies.

Reason: Because TRAF2 regulates apoptosis in both directions depending on the signal, the general regulation term is the right level of precision. The anti-apoptotic role in TNF signaling is a major, conserved output of the receptor complex that TRAF2 organises.

Supporting Evidence:

TRAF2 is required for TNF-alpha-mediated activation of c-Jun N-terminal kinase (JNK), contributes to activation of NF-kappaB, and mediates anti-apoptotic signals

In these cell types, absence of TRAF2 caused a delay in TNF-induced activation of NF-κB and MAPK, and sensitivity to killing by TNF was increased.

GO:0046328 regulation of JNK cascade

IEA
GO_REF:0000002

MODIFY

Summary: The evidence gives a direction. TRAF2 is required for TNF-induced JNK activation, and dominant-negative TRAF2 blocks IRE1-induced JNK activation.

Reason: The general regulation term is correct, but the evidence specifically supports positive regulation of the JNK cascade (GO:0046330), from both TNF receptors and IRE1. No evidence was found that TRAF2 negatively regulates JNK.

Proposed replacements: positive regulation of JNK cascade

Supporting Evidence:

TRAF2 is required for TNF-alpha-mediated activation of c-Jun N-terminal kinase (JNK)

PMID:10650002

Dominant-negative TRAF2 inhibited activation of JNK by IRE1.

GO:0046872 metal ion binding

IEA
GO_REF:0000002

TOO GENERAL

Summary: True but uninformative, because the more specific zinc ion binding (GO:0008270) is kept on this gene.

Reason: GO:0008270 zinc ion binding, kept as non-core, is a descendant of GO:0046872 (checked in OLS). The metals coordinated by the TRAF2 RING and zinc fingers are zinc.

Supporting Evidence:

Here we report the crystal structure of the RING and the first zinc finger domains of TRAF2.

GO:0051865 protein autoubiquitination

IEA
GO_REF:0000002

UNDECIDED

Summary: Recombinant TRAF2 autoubiquitination has been reported only with an S1P cofactor. TRAF2 is also a known cIAP1 substrate, so ubiquitinated TRAF2 does not prove self-catalysis.

Reason: This term depends on intrinsic E3 activity, which is disputed (see GO:0004842). The S1P-cofactor model is not supported by Sphk1 genetics. The human review keeps the same term UNDECIDED.

Supporting Evidence:

PMID:20577214

S1P also stimulated in vitro autoubiquitination of recombinant TRAF2 (Supplementary Fig. 8d).

Although c-IAP1 bound TRAF2 and TRAF1 in vitro, it ubiquitinated only TRAF2.

the role of the TRAF2 RING is controversial.

GO:0061630 ubiquitin protein ligase activity

IEA
GO_REF:0000003

UNDECIDED

Summary: This term comes from the EC 2.3.2.27 number that the PIRNR family rule assigns to the horse record. Whether TRAF2 is itself a ligase or only recruits the cIAPs is disputed.

Reason: The same considerations as for GO:0004842 apply. The EC number on the horse record is a family-level assignment and adds no independent evidence. The human review keeps the same term UNDECIDED.

Supporting Evidence:

These structural differences prevent TRAF2 from interacting with Ubc13 and other related E2s via steric clash and unfavorable interfaces.

PMID:20577214

Remarkably however, addition of S1P induced efficient TRAF2-mediated ubiquitination of RIP1 (Fig. 3a).

Keratinocyte-specific deletion of Traf2, but not Sphk1 deficiency, disrupted TNF mediated NF-κB and MAP kinase signalling

GO:0035591 signaling adaptor activity

IBA
GO_REF:0000033

NEW

Summary: TRAF2 links activated receptors to downstream effectors by recruiting cIAP1/2 through its coiled-coil region. This adaptor activity is the core molecular function of TRAF2.

Reason: The PAINT curators placed GO:0035591 (IBD) at the TRAF-family node PTN008301857. Human TRAF2 in the same subfamily (PTHR10131:SF21) inherits it as IBA, and the curators negated it (IRD) only on separate subclades. F7BIV4 carries no IBA rows in GOA. All three cIAP-binding residues are conserved in the horse protein.

Supporting Evidence:

PMID:20447407

In this study, we reconstituted the complex between baculoviral IAP repeat (BIR) 1 of cIAP1 and the coiled-coil region of TRAF2

file:HORSE/TRAF2/TRAF2-bioinformatics/RESULTS-rereview.md

cIAP-binding residues: human I285, V288 and E292 align to identical horse I300, V303 and E307.

GO:0043123 positive regulation of canonical NF-kappaB signal transduction

IBA
GO_REF:0000033

NEW

Summary: TRAF2 promotes TNF-induced canonical NF-kappaB activation by recruiting cIAPs to the TNFR1 signaling complex. Traf2 loss delays NF-kappaB activation in fibroblasts and keratinocytes.

Reason: The PAINT curators placed GO:0043123 (IBD) at the vertebrate TRAF2-clade node PTN002562154, seeded by human and mouse TRAF2. F7BIV4 falls within this clade. TRAF2 takes part directly, as the receptor-complex scaffold for the E3 ligases. Note that TRAF2 also suppresses non-canonical NF-kappaB, which is a different pathway.

Supporting Evidence:

support the idea that the main function of TRAF2 in TNF-induced NF-κB is to recruit cIAPs to the TNFR1-SC