id: A0A8C4MM62 gene_symbol: FLCN product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9793 label: Equus asinus description: Folliculin (FLCN) is a cytoplasmic DENN/longin-domain protein that, as a heterodimer with FNIP1 or FNIP2, acts as the GTPase-activating protein for the lysosomal Rag GTPases RagC and RagD. By converting RagC/D to the GDP-bound state in response to amino acids it activates mTORC1 toward its non-canonical substrates TFEB and TFE3, keeping these MiT/TFE transcription factors phosphorylated and in the cytoplasm. Under amino acid starvation FLCN-FNIP sits on the lysosomal membrane within the inactive lysosomal folliculin complex with the Rags and Ragulator. FLCN is also reported at primary cilia, centrosomes and the mitotic spindle, contributes to autophagy and lysosome positioning, and human FLCN has been reported to bind and inhibit lactate dehydrogenase A. Loss of FLCN in mammals causes early embryonic lethality and, in heterozygotes, renal tumours (Birt-Hogg-Dube syndrome in human), driven largely by constitutive nuclear TFEB. The donkey protein belongs to the same PANTHER subfamily as human and mouse folliculin (PTHR31441:SF2), is full length (578 aa, 94.6% identity to human), and conserves the catalytic arginine finger (Arg-164). existing_annotations: - term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: involved_in supporting_entities: - ARBA:ARBA00029133 - PANTHER:PTN009120754 review: summary: FLCN represses TFE3/TFEB-driven transcription indirectly, by activating mTORC1 so that these transcription factors are retained in the cytoplasm. action: KEEP_AS_NON_CORE reason: Human FLCN carries an IMP annotation to this term and the effect is real, but FLCN is a cytoplasmic Rag GAP that acts several steps upstream of transcription; it has no DNA-binding or co-regulator activity. The term is retained as a non-core, indirect consequence of its mTORC1-TFE3/TFEB signalling role (in the mouse BHD model, FLCN loss acts through constitutive TFEB activity). The transfer comes from PANTHER node PTN009120754 in subfamily PTHR31441:SF2, which contains the donkey protein together with the experimentally characterised human and mouse folliculins. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: In low-amino acid conditions, the lysosomal folliculin complex (LFC) is formed on the membrane of lysosomes, which inhibits the GTPase-activating activity of FLCN, inactivates mTORC1 and maximizes nuclear translocation of TFEB and TFE3 - reference_id: PMID:32612235 supporting_text: We found that constitutive activation of TFEB is the main driver of the kidney abnormalities and mTORC1 hyperactivity in a mouse model of Birt-Hogg-Dubé syndrome. - term: id: GO:0005096 label: GTPase activator activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - InterPro:IPR037520 - PANTHER:PTN009120754 review: summary: FLCN is the GAP for RagC/RagD; the catalytic Arg-164 is conserved in the donkey sequence. action: ACCEPT reason: Human FLCN-FNIP stimulates GTP hydrolysis by RagC/RagD (human IDA), and Arg-164, the residue essential for GAP activity, maps to Arg-164 of the donkey protein, which aligns to human at 94.64% identity over its full length. The donkey protein is in the same PANTHER subfamily (PTHR31441:SF2) as human and mouse folliculin, and the GAP term is carried by PANTHER node PTN009120754. This is the defining molecular activity of FLCN. A more specific Rag-GAP term does not exist in GO; the complex term GO:1990877 captures the RagC/D specificity. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Activates mTORC1 by acting as a GTPase-activating protein - reference_id: PMID:24095279 supporting_text: We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GAP activity for RagC/D, but not RagA/B. - reference_id: PMID:31704029 supporting_text: Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/RESULTS.md supporting_text: 'SITE (Essential for GTPase activation (GAP) activity): human [164] R -> donkey [164] R.' - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/RESULTS.md supporting_text: The donkey sequence A0A8C4MM62 (578 residues) aligns to human Q8NFG4 (579 residues) with 94.64% identity across 578 paired residues. - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0191 review: summary: A nuclear pool of FLCN has been reported for the human protein. action: KEEP_AS_NON_CORE reason: Human FLCN has IDA support for nuclear localization, but its characterized functions are at the lysosome and in the cytosol. Retained as a secondary location. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt supporting_text: Nucleus {ECO:0000269|PubMed:17028174, ECO:0000269|PubMed:18663353}. - term: id: GO:0005765 label: lysosomal membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0157 review: summary: FLCN-FNIP is recruited to the lysosomal membrane, where it forms the lysosomal folliculin complex with the Rags and Ragulator. action: ACCEPT reason: Lysosomal membrane recruitment is central to FLCN's regulation of RagC/D and mTORC1 and is supported by multiple human studies, including the cryo-EM structure of the starved-state lysosomal folliculin complex. supported_by: - reference_id: PMID:31672913 supporting_text: Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: Localizes to lysosome membrane in amino acid-depleted conditions and relocalizes to the cytosol upon refeeding - term: id: GO:0005813 label: centrosome evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0048 review: summary: Human FLCN has been observed at centrosomes. action: KEEP_AS_NON_CORE reason: Supported by a single human localization study; no centrosomal function is established, so it is kept as a secondary location. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: Also localizes to motile and non-motile cilia, centrosomes and the mitotic spindle - term: id: GO:0005819 label: spindle evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0251 review: summary: Human FLCN has been observed on the mitotic spindle. action: KEEP_AS_NON_CORE reason: Same single human localization study as the centrosome and cilium rows; no spindle function is established. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: Also localizes to motile and non-motile cilia, centrosomes and the mitotic spindle - term: id: GO:0005829 label: cytosol evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0091 - PANTHER:PTN009120754 review: summary: FLCN-FNIP is cytosolic in nutrient-replete cells and relocates to lysosomes on starvation. action: ACCEPT reason: Cytosol is a well-supported location for human FLCN (several IDA studies) and is consistent with its role as a soluble, lysosome-recruited GAP. The cytosol term is also carried by PANTHER node PTN009120754. supported_by: - reference_id: PMID:31672913 supporting_text: Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: Localizes to lysosome membrane in amino acid-depleted conditions and relocalizes to the cytosol upon refeeding - term: id: GO:0005929 label: cilium evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0066 review: summary: Human FLCN localizes to primary and motile cilia and has a flow-stress role through primary cilia. action: KEEP_AS_NON_CORE reason: Ciliary localization is supported for human FLCN and linked to LKB1/AMPK regulation under flow stress, but it is a secondary, context-specific role relative to lysosomal Rag regulation. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:SUBCELLULAR LOCATION"] supporting_text: Also localizes to motile and non-motile cilia, centrosomes and the mitotic spindle - term: id: GO:0009968 label: negative regulation of signal transduction evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027208 review: summary: Very broad ARBA term; FLCN's principal signalling role is positive regulation of TORC1. action: MARK_AS_OVER_ANNOTATED reason: Human FLCN has scattered single-study or ISS annotations to negative regulation of particular pathways (Rho, ERK, PI3K-AKT), but none is a defining activity, and the generic parent conveys no information while sitting awkwardly beside the well-established positive regulation of TORC1 signalling. The ARBA assertion is not independent evidence; it is retained only as an over-annotation. supported_by: - reference_id: PMID:31672913 supporting_text: The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase - term: id: GO:0030511 label: positive regulation of transforming growth factor beta receptor signaling pathway evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in supporting_entities: - PANTHER:PTN009120754 review: summary: Mouse Flcn has an IMP annotation to positive regulation of TGF-beta receptor signalling; the effect is indirect. action: UNDECIDED reason: The TreeGrafter transfer comes from PANTHER node PTN009120754 (subfamily PTHR31441:SF2), which places the donkey protein with mouse Flcn (IMP) and human FLCN (ISS), so the phylogenetic placement is sound. However, neither UniProt record contains curated text describing a TGF-beta signalling role, and the primary experimental paper behind the mouse IMP is not cached and could not be read in this re-review. Any effect is likely indirect (via TFE3/TFEB-dependent transcription) rather than a role within the receptor signalling pathway. The previous KEEP_AS_NON_CORE was based only on the GO line of the mouse record, which restates the annotation rather than supporting it, so this is changed to UNDECIDED until the primary evidence is checked. - term: id: GO:0032008 label: positive regulation of TOR signaling evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00092062 review: summary: Correct but general; FLCN activates mTORC1 (TORC1) specifically, through its RagC/D GAP activity. action: MODIFY reason: The claim is true, but the evidence supports the more specific child term positive regulation of TORC1 signaling (GO:1904263), which the gene already carries from the PANTHER node PTN009120754. FLCN acts on the amino acid-Rag-mTORC1 axis, not on mTORC2. Per the refinement rule, the general term is refined to that descendant rather than accepted as is. proposed_replacement_terms: - id: GO:1904263 label: positive regulation of TORC1 signaling supported_by: - reference_id: PMID:31672913 supporting_text: The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase - term: id: GO:1904263 label: positive regulation of TORC1 signaling evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in supporting_entities: - PANTHER:PTN009120754 review: summary: Core process; FLCN-FNIP GAP activity on RagC/D activates mTORC1 toward TFEB/TFE3. action: ACCEPT reason: Human FLCN is experimentally established (IDA) as a positive regulator of TORC1 signalling via its Rag GAP activity, and the donkey protein retains the catalytic arginine and full domain architecture. supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Activates mTORC1 by acting as a GTPase-activating protein - reference_id: PMID:24095279 supporting_text: Thus, we reveal a role for RagC/D in mTORC1 activation and a molecular function for the FLCN tumor suppressor. - reference_id: PMID:32612235 supporting_text: the phosphorylation of TFEB-unlike other substrates of mTORC1, such as S6K and 4E-BP1- is strictly dependent on the amino-acid-mediated activation of RagC and RagD GTPases - term: id: GO:1990877 label: FNIP-folliculin RagC/D GAP evidence_type: ISS original_reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt qualifier: part_of review: summary: FLCN acts as a heterodimer with FNIP1 or FNIP2; this complex is the RagC/D GAP. action: NEW reason: The FLCN-FNIP heterodimer is the functional unit of the GAP activity (human IDA), and the donkey GOA record has no complex annotation. The FNIP-interacting C-terminal DENN region is fully present in the donkey protein. supported_by: - reference_id: PMID:24095279 supporting_text: We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GAP activity for RagC/D, but not RagA/B. - reference_id: PMID:31704029 supporting_text: We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:SUBUNIT"] supporting_text: Interacts (via C-terminus) with FNIP1 or FNIP2 (via C-terminus) references: - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: file:EQUAS/FLCN/FLCN-uniprot.txt title: UniProt record for donkey FLCN (A0A8C4MM62) findings: [] - id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt title: UniProt Swiss-Prot record for human FLCN (Q8NFG4) findings: [] - id: file:EQUAS/FLCN/FLCN-bioinformatics/mouse_Q8QZS3-uniprot.txt title: UniProt Swiss-Prot record for mouse Flcn (Q8QZS3) findings: [] - id: file:EQUAS/FLCN/FLCN-bioinformatics/RESULTS.md title: 'FLCN: donkey-human sequence comparison' findings: [] - id: PMID:34381247 title: The tumor suppressor folliculin inhibits lactate dehydrogenase A and regulates the Warburg effect. findings: - statement: Human FLCN binds LDHA and acts as an uncompetitive inhibitor through an N-terminal flexible loop. supporting_text: we identify the human tumor suppressor folliculin (FLCN) as a binding partner and uncompetitive inhibitor of LDHA reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Cached full text checked. Single-study human finding; not propagated by PANTHER node PTN009120754, so it is not transferred to donkey as a GO annotation. The LDHA-binding region (human 210-220, UniProt ECO:0000269 PubMed:34381247) is identical in the donkey sequence (alignment.txt). - id: PMID:24095279 title: The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1. findings: - statement: FLCN-FNIP1/2 is a GAP for RagC/D but not RagA/B, and localizes to the lysosome on amino acid starvation. supporting_text: We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GAP activity for RagC/D, but not RagA/B. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Primary human study establishing the molecular function; full text cached. - id: PMID:31704029 title: Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex. findings: - statement: Structure of FLCN-FNIP2 bound to the Rags and Ragulator identifies a conserved catalytic arginine finger on FLCN. supporting_text: Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger reference_review: relevance: HIGH correctness: VERIFIED review_notes: Defines Arg-164 as the arginine finger; that residue is conserved in donkey. - id: PMID:31672913 title: Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex. findings: - statement: FLCN relocalizes from cytosol to lysosomes on starvation, where its RagC GAP activity is inhibited within the lysosomal folliculin complex. supporting_text: The RagC-GAP activity of FLCN was inhibited within the LFC, owing to displacement of a catalytically required arginine in FLCN from the RagC nucleotide. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Supports cytosol and lysosomal membrane localization and the LFC checkpoint model. - id: PMID:32612235 title: A substrate-specific mTORC1 pathway underlies Birt-Hogg-Dubé syndrome. findings: - statement: FLCN-dependent RagC/D activation is required specifically for mTORC1 phosphorylation of TFEB, and constitutive TFEB drives the kidney phenotype of the mouse BHD model. supporting_text: We found that constitutive activation of TFEB is the main driver of the kidney abnormalities and mTORC1 hyperactivity in a mouse model of Birt-Hogg-Dubé syndrome. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Establishes the substrate-specific (TFEB) arm of FLCN-dependent mTORC1 signalling. core_functions: - description: As a heterodimer with FNIP1/FNIP2, FLCN is the GTPase-activating protein for RagC/RagD at the lysosome, activating mTORC1 toward TFEB/TFE3 in response to amino acids. molecular_function: id: GO:0005096 label: GTPase activator activity directly_involved_in: - id: GO:1904263 label: positive regulation of TORC1 signaling locations: - id: GO:0005765 label: lysosomal membrane - id: GO:0005829 label: cytosol in_complex: id: GO:1990877 label: FNIP-folliculin RagC/D GAP supported_by: - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/human_Q8NFG4-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: Activates mTORC1 by acting as a GTPase-activating protein - reference_id: PMID:24095279 supporting_text: We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GAP activity for RagC/D, but not RagA/B. - reference_id: PMID:31704029 supporting_text: Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger - reference_id: file:EQUAS/FLCN/FLCN-bioinformatics/RESULTS.md supporting_text: 'SITE (Essential for GTPase activation (GAP) activity): human [164] R -> donkey [164] R.' suggested_questions: - question: Human FLCN is reported (single study) to bind and uncompetitively inhibit LDHA via a region (human residues 210-220) that is identical in donkey; is LDHA inhibition a conserved, physiological activity of mammalian folliculin, which would justify an enzyme inhibitor activity annotation beyond human? - question: Is the TGF-beta signalling effect of FLCN loss (mouse IMP) a direct role in the receptor pathway or an indirect consequence of deregulated TFE3/TFEB transcription? suggested_experiments: - description: Measure RagC/RagD GAP activity of recombinant donkey FLCN-FNIP2 and of an R164A mutant, to confirm that the conserved catalytic arginine supports the same activity as in human.