Ntrk1 encodes TrkA, the high-affinity nerve growth factor (NGF) receptor: a single-pass type I plasma-membrane receptor tyrosine kinase built from an extracellular leucine-rich repeat and two immunoglobulin-like domains, a transmembrane helix, and an intracellular tyrosine kinase domain. NGF binding drives receptor dimerisation and trans-autophosphorylation of the activation-loop tyrosines, creating phosphotyrosine docking sites - an NPQY motif that recruits SHC1 and a C-terminal site that recruits PLCG1 - which couple the receptor to the ERK/MAPK, p38 and PI3K/AKT cascades. In sensory ganglia TrkA marks the peptidergic nociceptor population, where it supports neuronal survival and neurite outgrowth during development and, in most mammals, sensitises the heat-gated channel TRPV1 during inflammation. The naked mole-rat protein is a functionally distinctive variant: it carries one to three substitutions in the otherwise strictly conserved kinase domain, including a leucine-to-cysteine change at position 774, that leave ligand binding and the catalytic apparatus intact but reduce the efficiency with which ligand occupancy is converted into downstream signalling. NGF-driven ERK1/2 and p38 phosphorylation is weaker than in rat, and TRPV1 sensitisation is markedly reduced at 100 ng/mL NGF yet reaches rat-equivalent output at ten-fold higher ligand concentration. The receptor nonetheless remains competent for the outputs that matter developmentally: it is expressed on about half of naked mole-rat dorsal root ganglion neurons and drives robust neurite outgrowth in them, and it supports embryonic sensory neuron survival, although adult naked mole-rats show a marked paucity of unmyelinated C-fibres that emerges after birth. At the organismal level the reduced signalling output is associated with a complete absence of NGF- and inflammation-induced heat hyperalgesia, while NGF-dependent mechanical hyperalgesia is retained.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000104 | MODIFY | Summary: Correct but uninformative root-level term. The protein binds ATP specifically, and the ATP-binding residues are annotated in the UniProt feature table. Reason: The UniRule transfer is true - TrkA binds a nucleotide - but "nucleotide binding" is a broad parent that conveys nothing about the protein. UniProt places the P-loop at 518..526 and the beta-3 lysine at 546, both assigned the ATP ligand, and the entry carries the PROSITE protein kinase ATP-binding signature. The specific child GO:0005524 ATP binding is already present in this same GOA set, so the general term should be replaced rather than retained alongside it. Proposed replacements: ATP binding Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt FT BINDING 518..526 file:HETGA/Ntrk1/Ntrk1-uniprot.txt DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: True but under-specific: this is a receptor tyrosine kinase, not a generic protein kinase. Reason: The InterPro2GO mapping from the generic Ser/Thr-Tyr kinase catalytic domain (IPR001245) and the tyrosine kinase active-site signature (IPR008266) lands on the broad parent. The entry's own signatures resolve the specificity: it carries the NTRK1-specific InterPro entry and the PANTHER high-affinity NGF receptor subfamily, and UniProt assigns EC 2.7.10.1 (receptor protein-tyrosine kinase). The precise child GO:0004714 is already annotated. Naked mole-rat data give no reason to doubt catalytic competence: the kinase domain retains the complete catalytic apparatus and shows strong ligand-independent activation-loop autophosphorylation when overexpressed. Proposed replacements: transmembrane receptor protein tyrosine kinase activity Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt EC=2.7.10.1 {ECO:0000256|RuleBase:RU000312}; file:HETGA/Ntrk1/Ntrk1-uniprot.txt DR PANTHER; PTHR24416:SF370; HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR; 1. PMID:27732851 the Tyr674/675 residues in both chimeric TrkA and rat TrkA displayed strong basal receptor phosphorylation in the absence of NGF |
| GO:0004713 protein tyrosine kinase activity | IEA GO_REF:0000120 | MODIFY | Summary: Correct, but one level too general for a transmembrane receptor tyrosine kinase. Reason: The combined-IEA pipeline (InterPro IPR020635 plus UniRule) correctly identifies tyrosine kinase catalytic activity, and UniProt records the corresponding reaction. The protein is however specifically a single-pass receptor kinase, with a transmembrane helix at 418..441 separating the ligand-binding ectodomain from the kinase domain at 512..783, so the receptor-level child term GO:0004714 - already present in this GOA set - is the appropriate annotation. Proposed replacements: transmembrane receptor protein tyrosine kinase activity Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt Reaction=L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + file:HETGA/Ntrk1/Ntrk1-uniprot.txt FT TRANSMEM 418..441 |
| GO:0004714 transmembrane receptor protein tyrosine kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function, and positively supported in this species. The naked mole-rat receptor is hypofunctional in the sense of reduced signalling efficiency, but it retains the activity itself. Reason: This is the annotation the naked mole-rat literature is most likely to be misread as challenging, so the argument matters. Omerbasic et al. cloned nmrTrkA from sensory neuron mRNA and showed that at 100 ng/mL NGF it sensitises TRPV1 significantly less than rat TrkA - but at 1,000 ng/mL it reaches rat-equivalent output. A dose-response curve shifted to the right yet reaching the wild-type maximum is the signature of reduced efficiency, not of a lost molecular function. Independently, the kinase domain is catalytically competent: the chimeric receptor carrying the naked mole-rat intracellular domain shows strong basal activation-loop autophosphorylation, and all activation tyrosines are conserved. The sequence of A0AAX6QC09 carries the complete catalytic apparatus (P-loop 518..526, beta-3 Lys546, HRD Asp652 assigned as proton acceptor, DFG at 670, activation-loop Tyr pair at 682/683). REMOVE would assert that this protein cannot act as a receptor tyrosine kinase, which the data contradict; the quantitative deficit belongs in the annotation comment, not in the action. Supporting Evidence: PMID:27732851 When oocytes were stimulated with 1,000 ng/mL NGF, activation of the naked mole-rat TrkA receptor produced a degree of sensitization similar to that observed with rat TrkA PMID:27732851 All tyrosine residues important for receptor activation were conserved in all the species, including the naked mole-rat. PMID:27732851 the Tyr674/675 residues in both chimeric TrkA and rat TrkA displayed strong basal receptor phosphorylation in the absence of NGF file:HETGA/Ntrk1/Ntrk1-uniprot.txt FT ACT_SITE 652 |
| GO:0005030 neurotrophin receptor activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function. TrkA is the high-affinity NGF receptor, and naked mole-rat sensory neurons demonstrably transduce an NGF signal through it. Reason: The term requires combining with a neurotrophin and transmitting the signal to initiate a change in cell activity - both halves are satisfied in this species. Park et al. showed that cultured naked mole-rat sensory neurons that stain for TrkA elaborate extensive neurites in response to NGF, and explicitly used this to exclude absent or non-functional NGF receptors as the explanation for the missing thermal hyperalgesia. The InterPro NTRK1 signature and the PANTHER high-affinity NGF receptor subfamily assignment place the protein unambiguously in the TrkA orthology group. The reduced signalling efficiency documented by Omerbasic et al. refines this function; it does not abolish it. Supporting Evidence: PMID:18232734 The lack of NGF-induced thermal hyperalgesia cannot be explained by a lack of functional NGF receptors, because we were able to observe a robust stimulation of neurite-growth in cultured small and medium sensory neurons that were also stained positive for the NGF receptor TrkA PMID:18232734 In the presence of 500 ng/ml of NGF, sensory neurons elaborated extensive neurites and the same cells were positive for the trk A receptor file:HETGA/Ntrk1/Ntrk1-uniprot.txt DR InterPro; IPR020461; NTRK1. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: Accepted. The ATP-binding site is fully conserved and the kinase is catalytically active. Reason: UniProt annotates the glycine-rich P-loop at 518..526 and the beta-3 lysine at 546 as ATP-binding, and the entry carries the PROSITE protein kinase ATP-binding-region signature. Both features are present in the naked mole-rat sequence (position 546 is a lysine). Nothing in the naked mole-rat literature implicates the nucleotide pocket: the kinase-domain substitutions reported by Omerbasic et al. lie in the C-terminal lobe, and basal autophosphorylation of the activation loop demonstrates that the enzyme turns over ATP. Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt FT BINDING 546 file:HETGA/Ntrk1/Ntrk1-uniprot.txt Reaction=L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + |
| GO:0005770 late endosome | IEA GO_REF:0000117 | MODIFY | Summary: Redundant, less precise duplicate of the late endosome membrane annotation that the same UniProt record supports. Reason: TrkA is an integral membrane protein, so the compartment-level term "late endosome" is less accurate than the membrane-level term. UniProt's own subcellular location statement is specifically "Late endosome membrane; Single-pass type I membrane protein", and GO:0031902 late endosome membrane is already present in this GOA set from the SubCell mapping. There is no naked-mole-rat evidence bearing on endosomal residence either way; this is a conserved-trafficking transfer from the well-characterised human and rat receptor. Proposed replacements: late endosome membrane Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt type I membrane protein {ECO:0000256|ARBA:ARBA00004158}. Late endosome |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Core location. The receptor must be at the cell surface to bind extracellular NGF, and in naked mole-rat sensory neurons it demonstrably does. Reason: UniProt assigns Cell membrane with a single-pass type I topology, consistent with the predicted signal peptide (1..33) and transmembrane helix (418..441). Functionally, NGF applied to the bath sensitises TRPV1 and drives neurite outgrowth in naked mole-rat neurons, which requires surface-exposed receptor; and TrkA protein was detected in membranes isolated from oocytes expressing the naked mole-rat receptor, at levels comparable to rat TrkA, showing that the naked mole-rat variant traffics to the plasma membrane normally. Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004251}; PMID:27732851 Comparable amounts of rat and naked mole-rat TrkA protein were present in membranes isolated from X. laevis oocytes PMID:27732851 Immunohistochemistry confirmed that IB4-negative sensory neurons are TrkA positive in mouse and naked mole-rat |
| GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway | IEA GO_REF:0000120 | MODIFY | Summary: Correct umbrella term, but the ligand-specific child is known and already annotated. Reason: TrkA is the receptor for a defined ligand, NGF, and the signalling initiated by that ligand is what has actually been studied in this species. GO:0038180 nerve growth factor signaling pathway, present in this same GOA set, states the same claim at the informative level. Keeping the generic RTK-pathway parent adds nothing beyond what the NGF pathway term entails. Proposed replacements: nerve growth factor signaling pathway Supporting Evidence: PMID:32206859 Naked mole-rat sensory neurons also express the NGF receptor TrkA, but even in cultured DRG neurons NGF fails to induce sensitization of TRPV1 |
| GO:0010976 positive regulation of neuron projection development | IEA GO_REF:0000118 | ACCEPT | Summary: A PANTHER ancestral-node projection that is, unusually for this species, directly confirmed by naked-mole-rat experiments. Reason: Most annotations on this protein are untested electronic projections; this one is not. Park et al. cultured naked mole-rat dorsal root ganglion neurons and showed that in the absence of NGF they elaborate very few neurites, whereas with 500 ng/mL NGF the same TrkA-positive cells elaborate extensive neurites. Omerbasic et al. reiterate this result and note that the naked mole-rat receptor retains efficacy at high NGF concentrations. This is exactly the claim the term makes, demonstrated in the target species, and it is a core output of the receptor. Supporting Evidence: PMID:18232734 In the presence of 500 ng/ml of NGF, sensory neurons elaborated extensive neurites and the same cells were positive for the trk A receptor PMID:27732851 The maintained efficacy of the naked mole-rat TrkA receptor at very high NGF concentrations is consistent with our previous observation that NGF (500 ng/mL) promotes neurite outgrowth of both mouse and naked mole-rat sensory neurons in culture |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Correct but root-level; the specific membrane is known. Reason: The InterPro2GO mapping from the receptor tyrosine kinase class II signature yields the generic "membrane" term. UniProt specifies cell membrane with single-pass type I topology, and GO:0005886 plasma membrane is already annotated here. Replace the root term with the specific compartment. Proposed replacements: plasma membrane Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004251}; |
| GO:0016301 kinase activity | IEA GO_REF:0000104 | MODIFY | Summary: Correct but root-level parent of the known specific activity. Reason: UniRule keyword-derived terms of this generality do not discriminate this protein from any other kinase. UniProt assigns EC 2.7.10.1 and the receptor tyrosine kinase class II PROSITE signature, and GO:0004714 is already annotated, so the specific term should stand in its place. Proposed replacements: transmembrane receptor protein tyrosine kinase activity Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt DR PROSITE; PS00239; RECEPTOR_TYR_KIN_II; 1. |
| GO:0016740 transferase activity | IEA GO_REF:0000104 | MODIFY | Summary: Correct but two levels above the informative term. Reason: "Transferase activity" is a keyword-level grandparent of protein tyrosine kinase activity and carries no information about this protein. UniProt records the specific phosphotransfer reaction and EC 2.7.10.1; replace with the receptor tyrosine kinase term already present in this GOA set. Proposed replacements: transmembrane receptor protein tyrosine kinase activity Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt Reaction=L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + |
| GO:0030424 axon | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Plausible family-level projection resting on the mouse and rat retrograde-signalling literature; no naked-mole-rat evidence either way. Reason: TrkA in sensory and sympathetic neurons is internalised at axon terminals and retrogradely transported in signalling endosomes, which is the basis for the TreeGrafter projection from PTN000699860. In the naked mole-rat, TrkA-positive dorsal root ganglion neurons certainly exist and project axons in cutaneous nerves, but no one has localised the protein within naked mole-rat axons. Nothing contradicts the annotation, so it is retained; it is not a core claim about this protein and, given that the species shows a postnatal loss of unmyelinated axons that may reflect altered TrkA signalling, axonal trafficking is one of the places a species-specific difference could hide. Supporting Evidence: PMID:27732851 a hypofunctional TrkA receptor in the naked mole-rat is associated with a striking paucity of unmyelinated C-fibers in adult peripheral nerves |
| GO:0031175 neuron projection development | IEA GO_REF:0000117 | MODIFY | Summary: Right biology, wrong grain: a cell-surface receptor regulates neurite outgrowth rather than executing the developmental process. Reason: The ARBA transfer captures a real function, but TrkA acts upstream, converting an extracellular NGF signal into increased neurite elaboration; it is not itself part of the machinery that builds the projection. The regulatory child GO:0010976 is both more accurate and directly evidenced in this species by the demonstration that NGF drives extensive neurite outgrowth in TrkA-positive naked mole-rat sensory neurons. Proposed replacements: positive regulation of neuron projection development Supporting Evidence: PMID:18232734 In the presence of 500 ng/ml of NGF, sensory neurons elaborated extensive neurites and the same cells were positive for the trk A receptor |
| GO:0031901 early endosome membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Conserved trafficking annotation from UniProt SubCell and ARBA; untested in the naked mole-rat. Reason: Ligand-bound TrkA is internalised into early endosomes from which signalling continues, and UniProt records "Early endosome membrane; Single-pass type I membrane protein" for this entry. There is no naked-mole-rat measurement of receptor internalisation or endosomal residence. The annotation is retained because it is a well-supported property of the conserved receptor and the naked mole-rat protein reaches the plasma membrane normally, but it is not a core claim and it is one of the untested transfers flagged in the review notes. The judgement that the transfer is well founded at family level rests on the human-orthologue mechanistic record, which documents ligand-driven internalisation and endosomal signalling for NTRK1; that record is a conserved-mechanism baseline only and is cited here as context rather than quoted as species evidence. Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt Early endosome membrane {ECO:0000256|ARBA:ARBA00004158}; Single-pass |
| GO:0031902 late endosome membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Conserved trafficking annotation from the UniProt subcellular location vocabulary; untested in the naked mole-rat. Reason: Same standing as the early endosome membrane annotation. Late-endosomal and multivesicular-body compartments carry retrograde TrkA signalling endosomes and route the receptor to degradation in the characterised orthologues, and UniProt records the location for this entry. No naked-mole-rat data address it. Retained as a conserved-mechanism transfer, not as a core function; the human-orthologue mechanistic record is cited as the family-level baseline for that judgement, not as species evidence. Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt type I membrane protein {ECO:0000256|ARBA:ARBA00004158}. Late endosome file:HETGA/Ntrk1/Ntrk1-uniprot.txt Endosome {ECO:0000256|ARBA:ARBA00022753}; |
| GO:0038180 nerve growth factor signaling pathway | IEA GO_REF:0000120 | ACCEPT | Summary: Core biological process, retained in this species with reduced efficiency rather than lost. Reason: This is the annotation the naked mole-rat phenotype most tempts a reviewer to negate, and it should not be negated. The pathway operates: naked mole-rat sensory neurons respond to NGF with neurite outgrowth, the cloned receptor sensitises TRPV1 to rat-equivalent levels at 1,000 ng/mL NGF, and NGF still produces mechanical hyperalgesia in adult animals. What is reduced is the efficiency of the coupling at physiological NGF concentrations, mapped by chimeric receptors to the intracellular domain. A quantitative attenuation of an operative pathway is recorded in prose, not by REMOVE and not by a NOT qualifier - the latter would be positively false here, since the receptor does drive the pathway when NGF is high. Supporting Evidence: PMID:27732851 the naked mole-rat TrkA molecule is less efficient at initiating sensitization with NGF concentrations of βΌ100 ng/mL PMID:27732851 NGF signaling in adult naked mole-rat is still capable of producing mechanical hyperalgesia, a process that does not involve TRPV1 PMID:32206859 Indeed experiments using naked mole-rat TrkA and a chimeric TrkA (extracellular rat/intracellular naked mole-rat) further showed that activation of the naked mole-rat TrkA receptor is much less efficient at producing NGF-induced TRPV1 sensitization, thus indicating that the deficit lies in the intracellular domain |
| GO:0043121 neurotrophin binding | IEA GO_REF:0000118 | ACCEPT | Summary: Ligand binding is retained. The chimeric-receptor experiment specifically excluded the ectodomain as the site of the naked mole-rat defect. Reason: The naked mole-rat ectodomain has diverged, including the juxtamembrane NGF-binding region, which raises the obvious question of whether ligand binding is compromised. Omerbasic et al. tested precisely this: a chimera carrying the rat extracellular domain with the naked mole-rat transmembrane and kinase domains reproduced the signalling deficit, showing that the lesion is intracellular and that poor ligand binding is not the explanation. Functionally, NGF binding must occur for the receptor to drive neurite outgrowth in naked mole-rat neurons and to sensitise TRPV1 at high NGF. No direct binding measurement (Kd, SPR) has been made on the naked mole-rat protein - that limitation is recorded in the notes and as a suggested experiment - but the functional evidence supports the annotation. The general term is appropriate: TrkA family receptors bind more than one neurotrophin, and only NGF has been tested here. Supporting Evidence: PMID:27732851 There was significant sequence divergence in the extracellular TrkA domains, including the juxtamembrane NGF-binding domain; however, the intracellular sequences within the kinase domain were highly conserved PMID:32206859 Indeed experiments using naked mole-rat TrkA and a chimeric TrkA (extracellular rat/intracellular naked mole-rat) further showed that activation of the naked mole-rat TrkA receptor is much less efficient at producing NGF-induced TRPV1 sensitization, thus indicating that the deficit lies in the intracellular domain |
| GO:0043235 signaling receptor complex | IEA GO_REF:0000118 | ACCEPT | Summary: Accepted. TrkA signals as a ligand-induced dimer, and the naked mole-rat kinase domain supports dimerisation-driven trans-autophosphorylation. Reason: Receptor tyrosine kinases are annotated part_of a receptor complex because the signalling unit is a dimer, not a monomer; TrkA additionally associates with the co-receptor p75NTR in the characterised orthologues. For the naked mole-rat protein the relevant direct observation is that the receptor bearing its intracellular domain shows strong activation-loop phosphorylation in the absence of ligand when overexpressed, which the authors attribute to receptor dimerisation - trans-autophosphorylation within a receptor complex is therefore competent in this species. The PANTHER node projection is sound and nothing in the naked mole-rat data argues against it. Supporting Evidence: PMID:27732851 the Tyr674/675 residues in both chimeric TrkA and rat TrkA displayed strong basal receptor phosphorylation in the absence of NGF |
| GO:0043524 negative regulation of neuron apoptotic process | IEA GO_REF:0000117 | ACCEPT | Summary: Retained. Naked mole-rat TrkA signalling is explicitly stated to be sufficient for embryonic sensory neuron survival. Reason: Promotion of neuronal survival is the canonical neurotrophin-receptor output, and this ARBA transfer is one of the few whose species-specific status the primary paper addresses directly: Omerbasic et al. conclude that the signalling capacity of naked mole-rat TrkA suffices to support survival and functional development of sensory neurons during embryonic development. The countervailing observation - a two- to three-and-a-half fold excess of C-fibres at postnatal day 3 relative to adults, implying substantial postnatal axon loss - is presented by the authors as a postulate, is confounded by the Mashona mole-rat sharing two of the three kinase-domain variants without losing C-fibres, and was never shown to proceed by apoptosis. It therefore argues that this activity is weaker in the naked mole-rat, not that it is absent. Supporting Evidence: PMID:27732851 It thus appears that the signaling capacity of the naked mole-rat TrkA is sufficient to support the survival and functional development of sensory neurons during embryonic development PMID:27732851 the number of unmyelinated C-fibers counted in cross-sections from the purely cutaneous saphenous nerve and the mixed common peroneal nerve from naked mole-rats was between 2- and 3.5-fold higher than the number observed in adult nerves |
| GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Well-founded family-level projection that the naked mole-rat data neither confirm nor refute - and the one branch the primary paper singles out as most likely to be perturbed. Reason: The PANTHER node assertion rests on the characterised orthologues, where TrkA autophosphorylation recruits PI3K through IRS proteins and sustained AKT activation underlies NGF-dependent survival. The naked mole-rat measurements did not touch this branch: the SILAC phosphoproteomics and westerns quantified ERK1/2 and p38-alpha, not AKT or PI3K products. The only naked-mole-rat contact with PI3K is a speculation - that the leucine-to-cysteine change at 774 may alter phosphorylation or recognition of the flanking tyrosines, one of which (Tyr751) is the p85 docking site. That is a hypothesis about where the deficit might extend, not evidence for or against the annotation. Keeping it non-core records both that it is a sound conserved-mechanism transfer and that it is unverified in this species; a direct AKT phosphorylation assay on naked mole-rat TrkA is proposed in suggested_experiments. The human-orthologue mechanistic record supplies the family-level basis for the PI3K/AKT branch (IRS-mediated p85 recruitment, GGA3-dependent recycling sustaining NGF-induced AKT) and is cited as that baseline only. Supporting Evidence: PMID:27732851 Tyrosine 751 has been implicated in binding of the p85 subunit of phosphoinositide 3-kinase PMID:27732851 insertion of a cysteine for a leucine at position 774 in the naked mole-rat TrkA receptor may alter the efficiency of phosphorylation or recognition of the flanking |
| GO:0055038 recycling endosome membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Conserved trafficking annotation from the UniProt subcellular location vocabulary; untested in the naked mole-rat. Reason: Recycling of internalised TrkA back to the surface sustains NGF-induced signalling in the characterised orthologues, and UniProt records recycling endosome membrane with single-pass type I topology for this entry. No naked-mole-rat data address receptor recycling. Retained as a conserved-mechanism transfer; not core, and explicitly listed among the untested localisation claims in the notes. The human-orthologue mechanistic record documents GGA3/Arf6-dependent TrkA recycling and is cited as the family-level baseline for keeping this term, not as evidence about the naked mole-rat protein. Supporting Evidence: file:HETGA/Ntrk1/Ntrk1-uniprot.txt protein {ECO:0000256|ARBA:ARBA00037817}. Recycling endosome membrane |
| GO:1990090 cellular response to nerve growth factor stimulus | IEA GO_REF:0000118 | ACCEPT | Summary: Core process, and directly demonstrated in naked mole-rat cells. Reason: The term asks only that the cell change state in response to NGF, which naked mole-rat TrkA-expressing sensory neurons demonstrably do: they elaborate extensive neurites on NGF exposure. At the receptor level, NGF-driven phosphopeptide upregulation through the naked mole-rat intracellular domain was measured directly and was substantial (270 of 2,007 quantified class I sites), though smaller than with rat TrkA. The species-specific failure is confined to one downstream consequence - TRPV1 sensitisation at moderate NGF concentrations - and does not amount to an absence of cellular response to NGF. Supporting Evidence: PMID:18232734 The lack of NGF-induced thermal hyperalgesia cannot be explained by a lack of functional NGF receptors, because we were able to observe a robust stimulation of neurite-growth in cultured small and medium sensory neurons that were also stained positive for the NGF receptor TrkA PMID:27732851 significantly more phosphopeptides were upregulated in NGF-treated cells with rat TrkA (361/2,239 [16.8%]) compared to cells with chimeric TrkA (270/2,007 [13.5%] |
| GO:0070374 positive regulation of ERK1 and ERK2 cascade | IDA PMID:27732851 Hypofunctional TrkA Accounts for the Absence of Pain Sensiti... | NEW | Summary: Proposed new annotation. The one downstream branch for which direct measurements on the naked mole-rat TrkA intracellular domain exist: NGF stimulation increases ERK1/2 activation through it, less efficiently than through rat TrkA but unambiguously. Reason: The current GOA set annotates the PI3K/AKT branch, for which there is no naked-mole-rat measurement at all, but not the ERK branch, for which there is. Omerbasic et al. quantified ERK1 (MAPK3 pTyr-204) and ERK2 (MAPK1 pTyr-187) phosphopeptides by SILAC mass spectrometry and confirmed the result by anti-phospho-ERK western blotting; NGF raised phospho-ERK through the receptor bearing the naked mole-rat intracellular domain, to a lower level than through rat TrkA. Reduced is not absent, and positive regulation of the ERK1/2 cascade is therefore a demonstrated activity of this protein's intracellular domain. Caveat recorded honestly: the assay used a chimeric receptor with a rat ectodomain expressed in HEK293 cells, so the evidence is for the naked mole-rat intracellular domain rather than for the full-length native receptor in its own cells; the ectodomain was swapped precisely to isolate the intracellular contribution. Supporting Evidence: PMID:27732851 there was a stronger activation of specific phosphopeptides from Erk2 (MAPK1, pTyr-187) and Erk1 (MAPK3, pTyr-204) PMID:27732851 western blotting for phosphorylated Erk in HEK293 cells transfected with rat or chimeric TrkA after NGF stimulation revealed reduced levels of phospho-Erk protein after stimulation of the chimeric receptor PMID:27732851 We observed a stronger increase in the abundance of p38-Ξ± derived-phosphopeptides containing the pTyr182 residue after stimulation of rat TrkA compared to chimeric TrkA |
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Download this section (compressed HTML)Q: Is there any acceptable way to represent a receptor whose signalling output is quantitatively reduced but qualitatively intact? GO's action vocabulary offers ACCEPT or NOT, and neither expresses "same function, right-shifted dose-response"; the naked mole-rat TrkA is a clean test case for whether an efficiency annotation extension is warranted.
Q: Should the absence of NGF-induced heat hyperalgesia be captured anywhere in GO for this gene? It is an organismal phenotype, not a molecular function, and a NOT annotation would be false because the receptor does sensitise TRPV1 at high NGF - but it is the single most important fact about the gene in this species.
Q: Which of the one to three kinase-domain substitutions is causal? The paper could not resolve this, and the Mashona mole-rat shares two of the three without losing C-fibres, which points at the naked-mole-rat-specific leucine-to-cysteine change at 774 but does not prove it.
Suggested experts: Gary R. Lewin, Damir OmerbaΕ‘iΔ
Q: Do the endosomal and axonal localisation annotations hold for the naked mole-rat receptor? If the 774 substitution altered receptor trafficking, recycling, or turnover rather than only catalytic coupling, these untested transfers are where it would show.
Experiment: Measure NGF binding directly to purified naked mole-rat and rat TrkA ectodomains by surface plasmon resonance or isothermal titration calorimetry, and by saturation binding of labelled NGF to intact cells expressing each full-length receptor. The chimeric-receptor experiment excluded the ectodomain as the cause of the signalling deficit but did not measure affinity; the neurotrophin binding annotation currently rests on functional inference alone.
Hypothesis: Naked mole-rat TrkA binds NGF with affinity comparable to rat TrkA, and the hypofunction is entirely post-binding.
Type: quantitative ligand binding
Experiment: Stimulate cells expressing rat, full-length naked mole-rat, and chimeric TrkA with a range of NGF concentrations and quantify phospho-AKT (Ser473, Thr308), phospho-Tyr751, and p85 co-immunoprecipitation alongside phospho-ERK as an internal reference. This is the one annotated downstream branch for which no naked-mole-rat measurement exists.
Hypothesis: The PI3K/AKT branch downstream of naked mole-rat TrkA is attenuated to a similar degree as the ERK branch, because the 774 substitution perturbs recognition of the flanking Tyr751 p85 docking site.
Type: dose-resolved signalling assay
Experiment: Introduce the single 774 substitution into rat TrkA and the reciprocal reversion into naked mole-rat TrkA, then compare NGF dose-response curves for activation-loop autophosphorylation, ERK1/2 phosphorylation, and TRPV1 sensitisation. Include the other two kinase-domain variants singly and in combination to apportion the effect.
Hypothesis: The leucine-to-cysteine substitution at 774 is individually sufficient to reduce NGF-driven signalling output.
Type: site-directed mutagenesis and structure-function
Experiment: Follow surface-labelled TrkA in naked mole-rat and mouse dorsal root ganglion neurons by live imaging and endosomal-marker colocalisation after NGF stimulation, and measure receptor half-life and retrograde axonal transport in compartmented cultures. This tests the early, late and recycling endosome membrane annotations, and the axon annotation, none of which has ever been examined in this species.
Hypothesis: Naked mole-rat TrkA traffics, internalises and recycles like its orthologues, so the endosomal localisation annotations transfer correctly.
Type: receptor trafficking and live imaging
Experiment: Quantify apoptotic markers in naked mole-rat dorsal root ganglia across the postnatal window during which C-fibre number falls, and test whether exogenous NGF at high concentration, or expression of a wild-type mammalian TrkA, prevents the loss. The current negative regulation of neuron apoptotic process annotation rests on the conserved neurotrophic survival function plus a statement that embryonic survival is supported; the apoptotic mechanism of the adult deficit has never been demonstrated.
Hypothesis: The postnatal loss of C-fibres in naked mole-rats proceeds by apoptosis and is TrkA-dependent.
Type: developmental cell-death analysis
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