Araf encodes A-Raf, a serine/threonine protein kinase of the RAF family (with B-Raf and Raf-1/C-Raf). It has an N-terminal RAS-binding domain, a cysteine-rich zinc-binding domain and a C-terminal kinase domain. Inactive A-Raf monomers are cytosolic; RAS-GTP recruits them to the plasma membrane, where they form active dimers and phosphorylate and activate the MAP kinase kinases MEK1/2, relaying mitogenic signals to ERK. A-Raf has weaker intrinsic MEK kinase activity than B-Raf. It also has kinase-independent roles, including binding MST2 to restrain MST2-driven apoptosis and competing with NF1 for RAS to sustain RAS-GTP. Human ARAF also acts downstream of Galpha12 to promote degradation of the mTORC2 subunit PRR5L, which regulates mTORC2 signaling.
Definition: A kinase-independent function of A-Raf in which A-Raf binds RAS and competes with NF1 (a RasGAP) for RAS, reducing NF1-stimulated GTP hydrolysis and thereby increasing RAS-GTP levels and positively regulating Ras protein signal transduction. This activity requires the A-Raf RAS-binding capacity and its unique N-terminus, but not dimerization or kinase activity.
Justification: The falcon deep research report (anchored on Su et al. 2022, Molecular Cell) documents a non-catalytic mechanism by which ARAF antagonizes NF1 binding to RAS to increase RAS-GTP. This RAS-node regulatory function is not captured by any of the existing GOA annotations (none cover regulation of Ras GTPase activity or RasGAP antagonism). The existing GO term GO:0046579 (positive regulation of Ras protein signal transduction) already exists and is an appropriate fit, so this is a candidate missing annotation rather than a genuinely novel ontology term. Cross-species (human/mouse) mechanistic inference for the rat ortholog.
Parent term: intracellular signal transduction
Mappings:
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Cytoplasmic localization of Araf, inferred phylogenetically from RAF-family members with experimental cytoplasmic localization. Reason: RAF kinases sit in the cytoplasm as inactive monomers and are recruited to membranes by RAS-GTP. Rat Araf lies within the RAF clade with no sign of divergence, so the IBA is sound. The term is a broad location rather than a functional site, so it is kept as non-core. Supporting Evidence: file:rat/Araf/Araf-deep-research-falcon.md In resting cells, RAFs are commonly described as **inactive cytosolic monomers**; upon RAS activation they become recruited to membranes and form active dimers. |
| GO:0000165 MAPK cascade | IBA GO_REF:0000033 | ACCEPT | Summary: MAPK cascade is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (IBA, GO_REF:0000033). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md Araf encodes a RAF-family serine/threonine kinase that functions as an upstream node in the canonical **RASβRAFβMEKβERK** MAPK cascade. |
| GO:0004709 MAP kinase kinase kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: MAP kinase kinase kinase activity is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (IBA, GO_REF:0000033). Falcon notes A-Raf is a comparatively weak MEK kinase relative to B-Raf, but still functions as a RAF-family MEK kinase in the cascade. Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md At the pathway level, RAF kinases act as **MEK kinases**, phosphorylating/activating MEK1/2, which then phosphorylates ERK to drive transcriptional programs. file:rat/Araf/Araf-deep-research-falcon.md However, multiple sources emphasize that **AβRaf has comparatively low MEK kinase activity** relative to BβRaf UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0005829 cytosol | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: cytosol is retained for Araf as supported contextual biology, but it is not the defining core function (IBA, GO_REF:0000033). Falcon supports cytosolic localization of inactive RAF monomers prior to RAS-driven membrane recruitment. Reason: This term describes localization, ATP/cofactor binding, or a secondary signaling context rather than the defining MAPKKK activity. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md In resting cells, RAFs are commonly described as **inactive cytosolic monomers**; upon RAS activation they become recruited to membranes and form active dimers. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: mitochondrion is retained for Araf as supported contextual biology, but it is not the defining core function (IBA, GO_REF:0000033). Falcon reports context-dependent A-Raf mitochondrial localization (with MST2) in tumor contexts, treated as inference for the rat ortholog. Reason: This term describes localization, ATP/cofactor binding, or a secondary signaling context rather than the defining MAPKKK activity. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md AβRaf has been reported to localize to **mitochondria** (together with MST2) in tumor contexts |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: protein kinase activity captures part of Araf biology, but a more specific or better-aspected GO term should replace it (IEA, GO_REF:0000002). Reason: The current term is too generic or indirect; replace it with the supported MAPKKK/serine-threonine kinase activity or direct protein phosphorylation process. Proposed replacements: MAP kinase kinase kinase activity protein serine/threonine kinase activity Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000003 | ACCEPT | Summary: protein serine/threonine kinase activity is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (IEA, GO_REF:0000003). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0004709 MAP kinase kinase kinase activity | IEA GO_REF:0000117 | ACCEPT | Summary: MAP kinase kinase kinase activity is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (IEA, GO_REF:0000117). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding mapped from the protein kinase domain signatures. Reason: Araf has a canonical protein kinase domain with a glycine-rich ATP-binding loop and the catalytic lysine, so ATP binding is real but is a component of its kinase activity, not a separate function. Kept as non-core. Supporting Evidence: UniProtKB:P14056 Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. RAF subfamily. |
| GO:0007165 signal transduction | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: signal transduction (GO:0007165) is the direct parent of intracellular signal transduction (GO:0035556), which is already retained as an accepted TAS annotation (PMID:9779826). The broad automated parent term is redundant with the more specific child annotation (IEA, GO_REF:0000002). Reason: GO:0007165 signal transduction is a parent of the more specific GO:0035556 intracellular signal transduction, which is already accepted (TAS, PMID:9779826). Retaining the broad automated (IEA) parent alongside the retained specific child is redundant over-annotation. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md AβRaf is a RAF-family Ser/Thr kinase upstream of MEK/ERK, participating in growth-factor/RAS-driven signaling. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: protein serine kinase activity is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (IEA, GO_REF:0000116). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0005739 mitochondrion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Mitochondrial localization transferred electronically from mouse Araf (UniProtKB:P04627). Reason: A-Raf has been reported at mitochondria in some contexts, including with MST2, but this is a conditional location rather than its main signaling site at the RAS-bound plasma membrane. Kept as non-core. Supporting Evidence: file:rat/Araf/Araf-deep-research-falcon.md AβRaf has been reported to localize to **mitochondria** (together with MST2) in tumor contexts |
| GO:0005886 plasma membrane | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: plasma membrane is retained for Araf as supported contextual biology, but it is not the defining core function (ISO, GO_REF:0000121). Falcon supports plasma membrane recruitment of RAFs upon RAS-GTP engagement as part of the activation cycle. Reason: This term describes localization, ATP/cofactor binding, or a secondary signaling context rather than the defining MAPKKK activity. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md RAF family members are described as cytosolic in the inactive state and recruited to the **plasma membrane** upon RASβGTP engagement as part of activation. |
| GO:0032006 regulation of TOR signaling | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Regulation of TOR signaling, inferred by sequence similarity to human ARAF (UniProtKB:P10398), based on the Galpha12-ARAF-RFFL-PRR5L pathway that controls mTORC2. Reason: In human cells, Galpha12 activates ARAF, which via ERK upregulates the E3 ligase RFFL; RFFL degrades the mTORC2 subunit PRR5L, increasing mTORC2-mediated PKC-delta phosphorylation. ARAF knockdown, but not BRAF or CRAF knockdown, blocked this, so the regulatory role is specific to ARAF. It is an upstream, indirect input into mTORC2 rather than the core MAPKKK function, so it is kept as non-core. Supporting Evidence: UniProtKB:P14056 May also regulate the TOR signaling cascade (By similarity). PMID:22609986 Knockdown of ARAF, but not BRAF or CRAF, by siRNAs inhibited GΞ±12QL-mediated upregulation of RFFL expression and polyubiquitination of PRR5L |
| GO:0032006 regulation of TOR signaling | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: Regulation of TOR signaling transferred from human ARAF (UniProtKB:P10398) by orthology. Reason: Same basis as the ISS row: the human ARAF-RFFL-PRR5L axis regulates mTORC2. Indirect and context-specific, so kept as non-core. Supporting Evidence: PMID:22609986 Knockdown of ARAF, but not BRAF or CRAF, by siRNAs inhibited GΞ±12QL-mediated upregulation of RFFL expression and polyubiquitination of PRR5L |
| GO:0032434 regulation of proteasomal ubiquitin-dependent protein catabolic process | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Regulation of proteasomal ubiquitin-dependent protein catabolic process, inferred by sequence similarity to human ARAF (UniProtKB:P10398) from the PRR5L degradation study. Reason: In the source study, ARAF acts through ERK to raise expression of the E3 ligase RFFL, which then ubiquitinates PRR5L. ARAF is several steps upstream: it changes the abundance of an E3 ligase and has no direct part in ubiquitination or proteasomal targeting. Annotating the kinase to regulation of proteasomal catabolism overstates its role; the finding is better represented by the regulation of TOR signaling rows. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:P10398 Β· ARAF SUPPORTS SOURCE BUT NOT TARGET The human ARAF donor annotation (IMP, PMID:22609986) records that ARAF knockdown blocked RFFL upregulation and PRR5L polyubiquitination. The ortholog transfer itself is sound, but ARAF acts upstream through ERK-driven RFFL expression, so a regulation of proteasomal catabolism term overstates the kinase's role. Supporting Evidence: PMID:22609986 Knockdown of ARAF, but not BRAF or CRAF, by siRNAs inhibited GΞ±12QL-mediated upregulation of RFFL expression and polyubiquitination of PRR5L |
| GO:0032434 regulation of proteasomal ubiquitin-dependent protein catabolic process | ISO GO_REF:0000121 | MARK AS OVER ANNOTATED | Summary: Regulation of proteasomal ubiquitin-dependent protein catabolic process transferred from human ARAF (UniProtKB:P10398) by orthology. Reason: Same basis as the ISS row. ARAF regulates RFFL expression through ERK and is several steps upstream of PRR5L ubiquitination, so the term overstates its involvement. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:P10398 Β· ARAF SUPPORTS SOURCE BUT NOT TARGET The human ARAF donor annotation (IMP, PMID:22609986) records that ARAF knockdown blocked RFFL upregulation and PRR5L polyubiquitination. The ortholog transfer itself is sound, but ARAF acts upstream through ERK-driven RFFL expression, so a regulation of proteasomal catabolism term overstates the kinase's role. Supporting Evidence: PMID:22609986 Knockdown of ARAF, but not BRAF or CRAF, by siRNAs inhibited GΞ±12QL-mediated upregulation of RFFL expression and polyubiquitination of PRR5L |
| GO:0005739 mitochondrion | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: Mitochondrial localization transferred from mouse Araf (MGI:MGI:88065). Reason: A conditional location reported for A-Raf, including with MST2, and secondary to its RAS-dependent membrane signaling site. Kept as non-core. Supporting Evidence: file:rat/Araf/Araf-deep-research-falcon.md AβRaf has been reported to localize to **mitochondria** (together with MST2) in tumor contexts |
| GO:0004674 protein serine/threonine kinase activity | ISO GO_REF:0000121 | ACCEPT | Summary: protein serine/threonine kinase activity is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (ISO, GO_REF:0000121). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0033138 positive regulation of peptidyl-serine phosphorylation | ISO GO_REF:0000121 | MODIFY | Summary: positive regulation of peptidyl-serine phosphorylation captures part of Araf biology, but a more specific or better-aspected GO term should replace it (ISO, GO_REF:0000121). Reason: The current positive-regulation term is indirect for a kinase. Replace it with direct peptidyl-serine phosphorylation, which better matches Araf serine/threonine kinase activity than generic protein phosphorylation. GOA no longer carries this row (retired); the review is kept for provenance. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: UniProtKB:P10398 Β· human ARAF SUPPORTS SOURCE BUT NOT TARGET The human ARAF donor annotation is a regulation-of-phosphorylation term; for a serine/threonine kinase the direct peptidyl-serine phosphorylation term is the better-scoped transfer. Proposed replacements: peptidyl-serine phosphorylation Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). |
| GO:0043066 negative regulation of apoptotic process | ISO GO_REF:0000121 | KEEP AS NON CORE | Summary: negative regulation of apoptotic process is retained for Araf as supported contextual biology, but it is not the defining core function (ISO, GO_REF:0000121). Falcon supports a kinase-independent A-Raf function - binding MST2 to suppress MST2-mediated apoptosis. Reason: The anti-apoptotic function via kinase-independent MST2 binding is real but represents a non-core scaffolding role distinct from the primary MAPKKK kinase activity that defines A-Raf. Supporting Evidence: UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade (By similarity). file:rat/Araf/Araf-deep-research-falcon.md AβRaf is described as binding **MST2** and suppressing MST2-mediated apoptosis, indicating kinase-independent pathway crosstalk. |
| GO:0004709 MAP kinase kinase kinase activity | IDA PMID:10648842 Hepatic epidermal growth factor-regulated mitogen-activated ... | ACCEPT | Summary: MAP kinase kinase kinase activity, from immunoprecipitation kinase assays of Raf isoforms, including A-Raf, from rat liver. Reason: The study detected A-Raf in fetal and adult rat liver and assayed immunoprecipitated Raf and MEKK isoforms for MEK-phosphorylating activity. The abstract reports that none of these accounted for the EGF-sensitive hepatic MEK kinase activity; it does not say A-Raf lacked MEK kinase activity. The cached record is abstract-only, the curator read the full text, and MEK kinase activity is the established function of RAF-family kinases, so the annotation is accepted. (Earlier review text called this evidence mismatched; that judgment cannot be made from the abstract.) Supporting Evidence: PMID:10648842 Western immunoblotting confirmed that Raf-1, A-Raf, B-Raf, MEKK1 and MEKK2 were present at similar levels in E19 and adult liver. file:rat/Araf/Araf-deep-research-falcon.md At the pathway level, RAF kinases act as **MEK kinases** UniProtKB:P14056 FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. |
| GO:0006468 protein phosphorylation | IDA PMID:10648842 Hepatic epidermal growth factor-regulated mitogen-activated ... | ACCEPT | Summary: Protein phosphorylation, from the same rat liver immunoprecipitation kinase assays (PMID:10648842). Reason: Araf is a serine/threonine kinase that phosphorylates MEK, so protein phosphorylation is correct. The abstract-only record does not contradict A-Raf kinase activity. GOA no longer carries this row (retired); the review is kept for provenance. (Earlier review text called the evidence mismatched; that judgment cannot be made from the abstract.) Supporting Evidence: UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) file:rat/Araf/Araf-deep-research-falcon.md At the pathway level, RAF kinases act as **MEK kinases** |
| GO:0005829 cytosol | TAS Reactome:R-RNO-188339 | KEEP AS NON CORE | Summary: Cytosolic localization from the Reactome RAF/MAP kinase cascade (R-RNO-188339). Reason: Inactive RAF monomers are cytosolic before RAS-driven recruitment to the membrane, so the location is correct. It is the resting rather than the signaling location, so it is kept as non-core. Supporting Evidence: file:rat/Araf/Araf-deep-research-falcon.md In resting cells, RAFs are commonly described as **inactive cytosolic monomers**; upon RAS activation they become recruited to membranes and form active dimers. |
| GO:0004709 MAP kinase kinase kinase activity | TAS PMID:9779826 Expression of mitogen-activated protein kinase pathways duri... | ACCEPT | Summary: MAP kinase kinase kinase activity is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (TAS, PMID:9779826). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: PMID:9779826 Expression of mitogen-activated protein kinase pathways during postnatal development of rat heart. UniProtKB:P14056 Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) |
| GO:0006468 protein phosphorylation | TAS PMID:9779826 Expression of mitogen-activated protein kinase pathways duri... | ACCEPT | Summary: protein phosphorylation is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (TAS, PMID:9779826). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. GOA no longer carries this row (retired); the review is kept for provenance. Supporting Evidence: PMID:9779826 Expression of mitogen-activated protein kinase pathways during postnatal development of rat heart. |
| GO:0035556 intracellular signal transduction | TAS PMID:9779826 Expression of mitogen-activated protein kinase pathways duri... | ACCEPT | Summary: intracellular signal transduction is retained for Araf because it matches the documented core molecular role or a direct pathway consequence (TAS, PMID:9779826). Reason: This term directly reflects Araf RAF-family serine/threonine kinase activity and its role in MAPK signal transduction. Supporting Evidence: PMID:9779826 Expression of mitogen-activated protein kinase pathways during postnatal development of rat heart. file:rat/Araf/Araf-deep-research-falcon.md Araf encodes a RAF-family serine/threonine kinase that functions as an upstream node in the canonical **RASβRAFβMEKβERK** MAPK cascade. |
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