id: MODULE:hedgehog_signaling title: Pan-metazoan Hedgehog/Smoothened signaling pathway module description: >- A taxon-neutral decomposition of Hedgehog (Hh) signaling, the metazoan cell-cell communication system in which a dually lipidated Hedgehog ligand released by a signal-sending cell controls the activator/repressor balance of Ci/GLI zinc-finger transcription factors in a receiving cell. The module is written around the segments that are shared from cnidarians and insects to vertebrates: autocatalytic cholesterol-coupled processing and N-terminal palmitoylation of the ligand; reception by the twelve-pass Patched receptor and its Ig/fibronectin-domain co-receptors; relief of Patched-mediated restriction of sterol access to the class-F receptor Smoothened; kinase-driven proteolytic processing of Ci/GLI into a transcriptional repressor when the pathway is off; and Smoothened-dependent conversion of Ci/GLI into an activator through Suppressor of fused, Fused-family kinases, and a kinesin-4 scaffold. Where lineages differ they are modeled as variants on an explicit axis rather than as separate pathways: the vertebrate implementation runs the activation step in the primary cilium with GPR161, intraflagellar transport, and KIF7, while the Drosophila implementation runs the equivalent step on a cytoplasmic Hedgehog signaling complex nucleated by the Costal-2 kinesin at the plasma membrane. Sonic hedgehog (SHH) is the vertebrate exemplar ligand, but it is one of three vertebrate paralogs of the single ancestral Hedgehog ligand and is used here only as a representative member. status: DRAFT scope: CONCRETE evidence: - source_id: GO:0007224 title: smoothened signaling pathway statement: >- The module core is grounded in the GO biological-process term for Hedgehog signal transduction through Smoothened. - source_id: PMID:24311597 title: Structural basis of SUFU-GLI interaction in human Hedgehog signalling regulation. statement: Hedgehog signaling is a broadly conserved metazoan developmental pathway. supporting_text: >- Hedgehog signalling plays a fundamental role in the control of metazoan development, cell proliferation and differentiation - source_id: PMID:19592253 title: >- The mammalian Cos2 homolog Kif7 plays an essential role in modulating Hh signal transduction during development. statement: >- The pathway framework is conserved across animals while individual components differ between lineages, which is why lineage-specific steps are modeled here as variants of a shared core. supporting_text: >- The Hedgehog (Hh) signaling pathway regulates development in animals ranging from flies to humans. Although its framework is conserved, differences in pathway components have been reported. - source_id: PMID:31279575 title: Phosphorylation of Ci/Gli by Fused Family Kinases Promotes Hedgehog Signaling. statement: >- Fused-family kinase phosphorylation of Ci/GLI is a conserved activation mechanism shared by Drosophila Fu and the vertebrate kinases STK36 and ULK3, supporting a single pan-metazoan activation step. supporting_text: >- Hence, Fu-family kinase-mediated phosphorylation of Ci/Gli serves as a conserved mechanism that activates the Hh pathway transcription factor. - source_id: PMID:16204193 title: The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans. statement: >- The module is pan-metazoan but not universal in metazoans: nematodes lack recognizable Hedgehog and Smoothened while retaining expanded Patched-related and Hedgehog-related families. supporting_text: >- In Caenorhabditis elegans, the Hh signaling pathway has undergone considerable divergence. Surprisingly, obvious Smo and Hh homologs are absent whereas PTC, PTC-related (PTR), and a large family of nematode Hh-related (Hh-r) proteins are present. - source_id: PANTHER:PTN001726121 title: PAINT Hedgehog ligand ancestral node statement: >- Local PAINT IBD rows place patched binding and smoothened signaling pathway participation at a PTHR11889 node whose seeds span Drosophila hh (FB:FBgn0004644), mouse, zebrafish, and the three human Hedgehog ligands, which is the evolutionary anchor for treating the ligand step as ancestral. - source_id: PANTHER:PTN000885245 title: PAINT Smoothened ancestral node statement: >- Local PAINT IBD rows support smoothened signaling pathway participation, patched binding, and ciliary localization at a PTHR11309 node seeded by Drosophila smo (FB:FBgn0003444), mouse, zebrafish, and human SMO. - source_id: PANTHER:PTN000859153 title: PAINT Suppressor of fused ancestral node statement: >- Local PAINT IBD rows support protein sequestering activity and negative regulation of the smoothened signaling pathway at a PTHR10928 node whose seeds include Drosophila Su(fu) (FB:FBgn0005355), mouse, zebrafish, and human SUFU. - source_id: PANTHER:PTN001836086 title: PAINT Ci/GLI ancestral node statement: >- Local PAINT IBD rows support smoothened signaling pathway participation at a PTHR45718 node seeded by the mouse and human GLI paralogs and zebrafish gli genes; Drosophila ci belongs to the same family but is not among the seeds of this node. - source_id: Reactome:R-HSA-445448 title: HHIP binds Hedgehog statement: >- Secreted HHIP sequestration of Hedgehog ligand is curated as a distinct reception-tier event, modeled here in the vertebrate accessory variant. - source_id: Reactome:R-HSA-5610766 title: >- The intraflagellar transport A (IFT-A) complex is required for the transit of GLI:SUFU complexes to the ciliary base statement: >- Intraflagellar transport of GLI:SUFU complexes is specific to the cilium-based vertebrate implementation of the activation step. - source_id: Reactome:R-HSA-5610767 title: >- The intraflagellar transport B (IFT-B) complex is required for the transit of GLI:SUFU complexes to the ciliary tip statement: >- Anterograde intraflagellar transport delivers GLI:SUFU to the ciliary tip in the vertebrate variant. - source_id: Reactome:R-HSA-5635839 title: "ULK3:SUFU dissociates" statement: >- Release of GLI from SUFU downstream of a Fused-family kinase is curated as a discrete step of the activation segment. notes: >- Boundary decisions. This document replaces an earlier, explicitly vertebrate sketch of the same module id; the pan-metazoan scope is the requested change, so the ciliary machinery that was previously stated as module-level context now sits inside the vertebrate variant, where it belongs. Ligand biogenesis is kept inside the module because Hedgehog performs its own autoproteolysis and cholesterol transfer, so those are activities of a core participant rather than upstream biology. Transcriptional targets, tissue-level patterning outcomes, and pathway-level crosstalk (Wnt, BMP, primary-cilium assembly) are deliberately outside the boundary. HHIP, SCUBE2, and GAS1 are vertebrate accessories and are modeled as an optional reception-tier variant rather than as core steps; glypicans are modeled alongside them because the same heparan-sulfate proteoglycan role is documented in both flies (dally) and vertebrates. Taxon scope. "Pan-metazoan" here means the module is written for the animal clade in which ligand, receptor, transducer, and Ci/GLI effector co-occur, which includes cnidarians, most protostomes, and vertebrates. It is not a claim of universality: nematodes have lost recognizable Hedgehog and Smoothened while expanding Patched-related and Hedgehog-related families (PMID:16204193), and any realization in that lineage would be a different module, not a variant of this one. Grounding provenance. Every UniProt exemplar was taken from a local artifact rather than recalled: the PANTHER family entry tables under interpro/panther/ and the cached GO-CAM activity index gocams/index.tsv. PANTHER family and subfamily labels are copied verbatim from interpro/panther/panther.obo, and the four PTN ancestral nodes are resolved from the committed PAINT IBD slices. Where a genuine component could not be grounded, no identifier was invented (see knowledge_gaps). The Drosophila Patched, Dispatched and Fused exemplars and human DISP1 were left unasserted while UniProt was unreachable and were added once it was; Suppressor of fused, Slimb and Brother of Ihog are still named only in prose, because each has only unreviewed entries under more than one accession. The KIF7/Costal-2 grounding sits on a genuine disagreement between sources rather than on a settled id. PANTHER's own per-organism classification for release 19.0 places both in PTHR24115 (KIF7 at SF445, Costal-2 at SF949), while UniProt's PANTHER cross-reference, which is also what the cached per-family entry tables under interpro/panther/ record, places them in PTHR47969 (SF8 and SF15). The rebuilt member index carries both and treats either as acceptable. This module declares the PTHR24115 subfamilies, following PANTHER's classification as the more direct source for a PANTHER id, but the alternative is a real reading and not an error to be corrected away. Deep research. A module deep-research run was attempted with `just module-deep-research-openscientist hedgehog_signaling` and failed because the provider host is blocked by this environment's network egress policy (403). No deep-research file is therefore present, and none was hand-written in place of one. An ontology gap on the acyltransferase, recorded here rather than as a knowledge gap because a curator rather than an experiment would close it. No molecular-function term describes what the Hedgehog acyltransferase actually does. GO:0019706, which this module and the curated GO-CAM both give it, is defined as transfer of palmitate to a sulfur atom on a cysteine, producing an S-palmitoyl thioester; the enzyme instead forms an amide bond to the alpha-amino group of the ligand's N-terminal cysteine. The chemistry is not in doubt and the process side is already covered, since GO:0018009 names N-terminal peptidyl-L-cysteine N-palmitoylation explicitly and the HHAT gene review uses it. What is missing is the matching activity term: the N-palmitoyltransferase activities GO does have are all peptidyl-lysine, and the only chemically safe existing choice is the linkage-agnostic parent GO:0016409. The term this needs is protein-cysteine N-palmitoyltransferase activity under GO:0016409, the name UniProt and PANTHER already use for this enzyme, and the HHAT gene review carries that proposal as a proposed_new_terms entry. GO:0019706 is kept here because it is what GOA and the GO-CAM use, so the inaccuracy is inherited rather than introduced; a reader should know the term names the wrong bond. Gene-level grounding, which was an open curation gap when this module was written and is now largely closed. The module's leaf claims originally rested on PANTHER family membership, PAINT nodes and GO-CAM activities, with only SHH, SMO and GSK3B reviewed among the human exemplars and nothing on the Drosophila side, which mattered because the pan-metazoan claim is carried by the invertebrate members. Since then PTCH1, SUFU, GLI3, GLI2, KIF7, GPR161, HHAT and STK36 have been curated on the human side, and hh, ptc, smo and ci on the Drosophila side, so the protostome half of the pathway now has gene-level adjudication rather than family evidence alone. Several of those curations fed corrections back into this module and into the family reviews. Remaining participants are unreviewed but peripheral to the core segments. Three Drosophila participants are still named in prose without an accession: Suppressor of fused, Slimb and Brother of Ihog. Each exists only as unreviewed UniProt entries, and more than one accession carries the same gene symbol, so picking one would assert a canonical form UniProt has not designated. Every other participant is grounded: Drosophila ptc (P18502), disp (Q9VNJ5) and fu (P23647), and human DISP1 (Q96F81), are recorded as representative members. The Drosophila Su(fu) gene also appears as a PAINT seed (FB:FBgn0005355) for the SUFU ancestral node cited here, so that clade-level claim holds without a protein accession. Cite the three once UniProt designates reviewed entries, or record a chosen unreviewed accession together with the reason it was preferred over its siblings. This is a data-representation question, not a biological one. knowledge_gaps: - gap_statement: >- The biochemical mechanism by which ligand-free Patched restricts Smoothened remains undetermined: whether Patched depletes an activating sterol from the Smoothened-accessible leaflet, exports an inhibitor, or acts by direct contact is not settled. The molecular-function term this module gives the receptor, GO:0140303, is a vertebrate-grounded claim, and curating the Drosophila gene showed it does not carry over: the fly record contains no transport annotation of any kind, its lipid relationships are binding rather than flux (phosphatidylinositol-4-phosphate through the sterol-sensing domain, phosphatidic acid through the C-terminal tail), and two of them read as Patched sequestering a Smoothened activator, which is the opposite polarity to exporting an inhibitor. UniProt's cholesterol transporter statement for fly Patched is flagged by similarity from the human protein rather than observed in the fly. boundary: >- It is established that Patched is a twelve-pass RND-like protein with a sterol-sensing domain, that it binds the palmitoylated N-terminus of Hedgehog, that vertebrate Patched moves sterols, and that Hedgehog binding relieves its repression of Smoothened; what the transported species is in vivo, whether transport alone accounts for repression, and whether the transport model holds outside the vertebrates, are not. gap_kind: - BIOLOGY dark_aspect: MF_DARK status: OPEN significance: >- This is the one step of the core pathway with no agreed molecular mechanism, and it is the step targeted indirectly by every clinical Smoothened inhibitor. provenance: - reference_id: PMID:29995851 reference_section_type: INTRODUCTION supporting_text: >- How Patched inhibits Smo is enigmatic but there are studies showing that Patched may act indirectly by releasing a small molecule to regulate Smo - gap_statement: >- Which of the two Smoothened-to-PKA mechanisms dominates in vivo, direct pseudosubstrate inhibition of the PKA catalytic subunit or Gi-mediated lowering of cAMP, is not resolved, and whether the Drosophila pathway uses the pseudosubstrate route at all is untested here. boundary: >- Both mechanisms are demonstrated: Smoothened carries a PKA-inhibitor motif that blocks the PKA catalytic site, and Smoothened couples to Gi. gap_kind: - BIOLOGY dark_aspect: MF_DARK status: OPEN provenance: - reference_id: PMID:36202993 reference_section_type: ABSTRACT supporting_text: >- Here we show that SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity. module: id: hedgehog_signaling label: Pan-metazoan Hedgehog/Smoothened signaling pathway module_type: SIGNALING_PATHWAY description: >- Hedgehog ligand made in one cell is processed, lipidated, and released; reception by Patched on a second cell relieves Patched-mediated restriction of Smoothened; the resulting Smoothened activity switches Ci/GLI output from a proteolytically generated repressor to a full-length activator. concepts: - preferred_term: smoothened signaling pathway term: id: GO:0007224 label: smoothened signaling pathway description: >- The series of molecular signals generated as a consequence of activation of Smoothened by a Hedgehog ligand bound to Patched. - preferred_term: pattern specification process term: id: GO:0007389 label: pattern specification process description: >- The ancestral output of the pathway across animals: concentration- and duration-dependent Ci/GLI activity assigns positional cell fates. context: taxa: - preferred_term: metazoa term: id: NCBITaxon:33208 label: Metazoa description: >- Ligand, Patched receptor, Smoothened transducer, Suppressor of fused, and Ci/GLI effectors co-occur from cnidarians through insects to vertebrates. Nematodes are the well-documented exception. cellular_components: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane description: Where reception and transduction occur in every lineage. - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm description: Where the Ci/GLI processing and activation complexes assemble. - preferred_term: nucleus term: id: GO:0005634 label: nucleus description: Where the Ci/GLI activator and repressor forms act. parts: - order: 1 role: Hedgehog ligand biogenesis and release (signal-sending cell) node: id: hh_ligand_biogenesis label: Hedgehog autoprocessing, dual lipidation, and release module_type: BIOLOGICAL_PROCESS description: >- The Hedgehog precursor is its own processing enzyme. Its C-terminal Hint/Hog domain cleaves the protein and couples cholesterol to the new C-terminus of the N-terminal signaling domain; a membrane-bound O-acyltransferase (HHAT in vertebrates, Rasp/Skinny hedgehog in Drosophila) then palmitoylates the new N-terminus. The doubly lipidated product is membrane-tethered and requires a dedicated release transporter to leave the producing cell. evidence: - source_id: PMID:29995851 title: Structures of human Patched and its complex with native palmitoylated sonic hedgehog. statement: >- Autocatalytic cholesterol coupling in the endoplasmic reticulum followed by acyltransferase-mediated palmitoylation produces the mature, dually lipidated ligand. supporting_text: >- The Hh precursor undergoes autocatalytic processing in the endoplasmic reticulum to release an amino-terminal signaling domain (Hh-N) with cholesterol covalently coupled to its carboxyl terminus. - source_id: PMID:24342078 title: A new role for Hedgehogs in juxtacrine signaling. statement: >- The cholesterol-tethered product is actively released by Dispatched together with a secreted accessory protein in vertebrates, so release is a distinct step rather than passive diffusion. supporting_text: >- The processed N-terminal fragment would be retained in the cell by its cholesterol tail, except it is actively secreted by the synergistic actions of Disp and the secreted protein Scube2 annotons: - id: hh_autoprocessing label: Hedgehog precursor autoproteolysis participant: selector_type: FAMILY family: preferred_term: Hedgehog ligand family (Hint/Hog autoprocessing domain) term: id: PANTHER:PTHR11889 label: HEDGEHOG description: >- The single ancestral Hedgehog ligand family; vertebrates carry the SHH/IHH/DHH paralogs and Drosophila the single hh gene. representative_members: - preferred_term: SHH (human) term: id: UniProtKB:Q15465 label: Sonic hedgehog protein - preferred_term: hh (Drosophila melanogaster) term: id: UniProtKB:Q02936 label: Protein hedgehog function: preferred_term: intramolecular autoproteolysis of the Hedgehog precursor term: id: GO:0004175 label: endopeptidase activity substrates: - preferred_term: Hedgehog precursor protein products: - preferred_term: Hedgehog N-terminal signaling domain - preferred_term: Hedgehog C-terminal autoprocessing domain processes: - preferred_term: protein autoprocessing term: id: GO:0016540 label: protein autoprocessing locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- The ligand cleaves itself; no separate protease is required, which is why this step is inside the module rather than upstream of it. A note on the term, because this module deliberately disagrees with two of its own gene reviews. GO:0004175 is defined as hydrolysis of internal peptide bonds, and the Hint/Hog reaction is not a hydrolysis: the thioester intermediate is resolved by the 3-beta-hydroxyl of cholesterol, not by water, which is why the curated reviews of Drosophila hh and human SHH both move this annotation to GO:0140853. On that reading this annoton and hh_cholesterol_transfer are one reaction cycle rather than two activities, and collapsing them would be the tidier model. They are kept separate and this one keeps GO:0004175 because the typing is not this project's invention: GO-CAM gomodel:696022cd00000016 types its autocleavage activity GO:0004175 in the endoplasmic reticulum membrane, and the two annotons here mirror two activities of that model, each with its own gocam_association. Retyping them would silently overrule a GO curator on a mechanistic question they may have decided knowingly, using the cleavage framing for the half-reaction that does break the bond. The disagreement is recorded at family level instead, where PTHR11889 scopes GO:0140853 FAMILY_WIDE and leaves GO:0004175 UNRESOLVED with both arguments stated. A propagator should prefer GO:0140853 and read a GO:0004175 row on a Hedgehog ligand as the same event described the other way, not as a second activity. gocam_associations: - model: gomodel:696022cd00000016 activity: gomodel:696022cd00000016/696022cd00000036 title: Protein maturation of SHH by autocleavage, autocholesterylation and palmitoylation by HHAT (Human). - id: hh_cholesterol_transfer label: Hedgehog cholesterol transfer participant: selector_type: FAMILY family: preferred_term: Hedgehog ligand family (Hint/Hog autoprocessing domain) term: id: PANTHER:PTHR11889 label: HEDGEHOG representative_members: - preferred_term: SHH (human) term: id: UniProtKB:Q15465 label: Sonic hedgehog protein function: preferred_term: cholesterol transfer onto the Hedgehog signaling domain term: id: GO:0140853 label: cholesterol-protein transferase activity substrates: - preferred_term: cholesterol - preferred_term: Hedgehog N-terminal signaling domain products: - preferred_term: C-terminally cholesterylated Hedgehog signaling domain locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- Couples cholesterol to the signaling domain in the same reaction cycle as cleavage, tethering the ligand to the membrane and setting up the requirement for an active release step. gocam_associations: - model: gomodel:696022cd00000016 activity: gomodel:696022cd00000016/696022cd00000045 title: Protein maturation of SHH by autocleavage, autocholesterylation and palmitoylation by HHAT (Human). - id: hh_n_palmitoylation label: Hedgehog N-terminal palmitoylation participant: selector_type: FAMILY family: preferred_term: Hedgehog acyltransferase family (HHAT / Rasp) term: id: PANTHER:PTHR13285 label: ACYLTRANSFERASE description: >- Membrane-bound O-acyltransferase family containing vertebrate HHAT and Drosophila Rasp; the family term is broader than the Hedgehog-acylating role, which the two representative members pin down. representative_members: - preferred_term: HHAT (human) term: id: UniProtKB:Q5VTY9 label: Protein-cysteine N-palmitoyltransferase HHAT - preferred_term: rasp (Drosophila melanogaster) term: id: UniProtKB:Q9VZU2 label: Protein-cysteine N-palmitoyltransferase Rasp function: preferred_term: palmitoylation of the Hedgehog N-terminal cysteine term: id: GO:0019706 label: protein-cysteine S-palmitoyltransferase activity substrates: - preferred_term: cholesterylated Hedgehog signaling domain - preferred_term: palmitoyl-CoA products: - preferred_term: dually lipidated Hedgehog signaling domain locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- Required for high-activity ligand: the palmitate is the dominant contact in the Patched interface, so this step licenses reception rather than merely decorating the ligand. gocam_associations: - model: gomodel:696022cd00000016 activity: gomodel:696022cd00000016/696022cd00000024 title: Protein maturation of SHH by autocleavage, autocholesterylation and palmitoylation by HHAT (Human). - id: hh_release_transporter label: Dispatched-type Hedgehog release transporter participant: selector_type: FAMILY family: preferred_term: Dispatched RND-family Hedgehog release transporter term: id: PANTHER:PTHR45951 label: PROTEIN DISPATCHED-RELATED description: >- Twelve-pass RND-family transporter required to release cholesterol-tethered Hedgehog from the producing cell. Drosophila disp and vertebrate DISP1 are sister subfamilies of this family, so the release step is as conserved as the reception step it feeds. representative_members: - preferred_term: DISP1 (human) term: id: UniProtKB:Q96F81 label: Protein dispatched homolog 1 - preferred_term: disp (Drosophila melanogaster) term: id: UniProtKB:Q9VNJ5 label: Protein dispatched function: preferred_term: release of membrane-tethered lipidated Hedgehog ligand processes: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Conserved in flies and vertebrates; without it the processed ligand stays on the producing cell and long-range signaling fails. - id: mature_hh_ligand label: Mature dually lipidated Hedgehog ligand participant: selector_type: FAMILY family: preferred_term: Hedgehog ligand family (mature N-terminal signaling domain) term: id: PANTHER:PTHR11889 label: HEDGEHOG representative_members: - preferred_term: SHH (human) term: id: UniProtKB:Q15465 label: Sonic hedgehog protein - preferred_term: IHH (human) term: id: UniProtKB:Q14623 label: Indian hedgehog protein - preferred_term: DHH (human) term: id: UniProtKB:O43323 label: Desert hedgehog protein - preferred_term: hh (Drosophila melanogaster) term: id: UniProtKB:Q02936 label: Protein hedgehog ancestral_nodes: - preferred_term: PAINT Hedgehog ligand node PTN001726121 term: id: PANTHER:PTN001726121 label: PTN001726121 description: >- PTHR11889 node with IBD support for patched binding (F:GO:0005113), smoothened signaling pathway (P:GO:0007224), and extracellular localization (C:GO:0005576). Its seeds include Drosophila hh (FB:FBgn0004644) alongside mouse, zebrafish, chicken, and the three human ligands, so the ligand role is inferred to predate the protostome/deuterostome split. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN001726121 in PTHR11889. function: preferred_term: Hedgehog morphogen activity term: id: GO:0016015 label: morphogen activity targets: - preferred_term: Patched receptor processes: - preferred_term: smoothened signaling pathway term: id: GO:0007224 label: smoothened signaling pathway locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- The diffusible output of this part and the input to reception; acts over a concentration gradient, and in the DHH case largely by cell contact rather than at a distance. gocam_associations: - model: gomodel:696022cd00000016 activity: gomodel:696022cd00000016/696022cd00000017 title: Protein maturation of SHH by autocleavage, autocholesterylation and palmitoylation by HHAT (Human). connections: - source: hh_autoprocessing target: hh_cholesterol_transfer connection_type: PRECEDES description: >- Cleavage and cholesterol transfer are two activities of one autoprocessing cycle of the same molecule. chaining_status: NOT_APPLICABLE chaining_note: >- Protein-modification steps, not CoA-carrier metabolism; the reaction-continuity check does not apply. - source: hh_cholesterol_transfer target: hh_n_palmitoylation connection_type: PRECEDES description: The cholesterylated signaling domain is the acyltransferase substrate. chaining_status: NOT_APPLICABLE chaining_note: Protein-modification chain rather than a CoA-carrier metabolic chain. - source: hh_n_palmitoylation target: hh_release_transporter connection_type: PROVIDES_INPUT_FOR description: The dually lipidated ligand is the cargo of the release transporter. - source: hh_release_transporter target: mature_hh_ligand connection_type: CAUSES description: Release converts the membrane-tethered product into the diffusible signal. - order: 2 role: Ligand reception at the receiving-cell surface node: id: hh_reception label: Hedgehog reception by Patched and its co-receptors module_type: REGULATORY_STEP description: >- Patched is the ligand-binding receptor and, in the unliganded state, the pathway's brake: it restricts Smoothened activity and is relieved by ligand binding. Ig/fibronectin-domain co-receptors (Ihog and Boi in Drosophila, CDON and BOC in vertebrates) capture ligand and present it to Patched, raising sensitivity without themselves transducing. concepts: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway description: The unliganded state of this node is the pathway-off brake. evidence: - source_id: PMID:29995851 title: Structures of human Patched and its complex with native palmitoylated sonic hedgehog. statement: >- The ligand's palmitate dominates the Patched interface, and Patched carries a sterol-sensing domain resembling NPC1. supporting_text: >- The palmitoylated N terminus of SHH-N inserts into a cavity between the extracellular domains of PTCH1 and dominates the PTCH1-SHH-N interface - source_id: PMID:21931618 title: The hedgehog receptor patched is involved in cholesterol transport. statement: >- Patched moves cholesterol, which is the basis for modeling its molecular function as intramembrane lipid carrier activity rather than as a classical signaling receptor activity. annotons: - id: patched_receptor label: Patched receptor participant: selector_type: FAMILY family: preferred_term: Patched receptor family term: id: PANTHER:PTHR46022 label: PROTEIN PATCHED description: >- Twelve-pass RND-like Hedgehog receptor; Drosophila ptc and the vertebrate PTCH1/PTCH2 paralogs, which sit in the same PANTHER family. representative_members: - preferred_term: PTCH1 (human) term: id: UniProtKB:Q13635 label: Protein patched homolog 1 - preferred_term: PTCH2 (human) term: id: UniProtKB:Q9Y6C5 label: Protein patched homolog 2 - preferred_term: ptc (Drosophila melanogaster) term: id: UniProtKB:P18502 label: Protein patched function: preferred_term: sterol movement that keeps Smoothened off in the unliganded state term: id: GO:0140303 label: intramembrane lipid carrier activity substrates: - preferred_term: cholesterol targets: - preferred_term: Smoothened processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Binds the lipidated ligand and, when unoccupied, restricts sterol access to Smoothened; ligand binding inactivates this restriction. gocam_associations: - model: gomodel:696022cd00000812 activity: gomodel:696022cd00000812/696022cd00000880 title: Activation of the smoothened signaling pathway by SHH, which relieves SMO inhibition by PTCH1 (Human). - model: gomodel:696022cd00001416 title: Activation of the smoothened signaling pathway by SHH, which relieves SMO inhibition by PTCH2 (Human). - id: hh_coreceptor label: Ig/FNIII Hedgehog co-receptor participant: selector_type: FAMILY family: preferred_term: Ihog/CDON/BOC-type Hedgehog co-receptors term: id: PANTHER:PTHR44170 label: PROTEIN SIDEKICK description: >- Single-pass immunoglobulin/fibronectin-III cell-surface proteins. Drosophila Ihog and vertebrate CDON and BOC fall in this PANTHER family, which is the concrete evidence that the co-receptor tier is homologous across protostomes and deuterostomes; the family as a whole is broader than the Hedgehog role, so the representative members carry the specificity. representative_members: - preferred_term: CDON (human) term: id: UniProtKB:Q4KMG0 label: Cell adhesion molecule-related/down-regulated by oncogenes - preferred_term: BOC (human) term: id: UniProtKB:Q9BWV1 label: Brother of CDO - preferred_term: ihog (Drosophila melanogaster) term: id: UniProtKB:Q9VM64 label: Interference hedgehog function: preferred_term: capture and presentation of Hedgehog ligand to Patched term: id: GO:0140597 label: protein carrier activity cargo: - preferred_term: dually lipidated Hedgehog ligand processes: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Raises the effective ligand concentration at Patched; loss reduces sensitivity rather than abolishing transduction. gocam_associations: - model: gomodel:696022cd00000908 activity: gomodel:696022cd00000908/696022cd00000972 title: SCUBE2, CDON, BOC and GAS1 promote SHH transport to PTCH1 receptor (Human). variant_sets: - id: ligand_distribution_axis label: Extracellular ligand-distribution and tuning accessories axis: taxon / accessory complement acting on the ligand before reception selection: ZERO_OR_MORE notes: >- These tune how much ligand reaches Patched and over what range. They are not required for transduction, which is why the set is optional rather than an exactly-one choice. variants: - id: hspg_ligand_distribution label: Heparan-sulfate proteoglycan ligand distribution (pan-metazoan) module_type: REGULATORY_STEP description: >- Glypican-type GPI-anchored heparan-sulfate proteoglycans shape the extracellular movement and retention of Hedgehog in both flies (Dally, Dally-like) and vertebrates (GPC3, GPC5, GPC6). annotons: - id: glypican_ligand_distribution label: Glypican-mediated Hedgehog distribution participant: selector_type: FAMILY family: preferred_term: Glypican family heparan-sulfate proteoglycans term: id: PANTHER:PTHR10822 label: GLYPICAN representative_members: - preferred_term: dally (Drosophila melanogaster) term: id: UniProtKB:Q24114 label: Division abnormally delayed protein - preferred_term: GPC1 (human) term: id: UniProtKB:P35052 label: Glypican-1 function: preferred_term: extracellular retention and transfer of lipidated Hedgehog processes: - preferred_term: regulation of smoothened signaling pathway term: id: GO:0008589 label: regulation of smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Sets the shape and range of the ligand gradient rather than the on/off state of transduction. - id: vertebrate_secreted_accessories label: Vertebrate secreted and GPI-anchored accessories (SCUBE2, GAS1, HHIP) module_type: REGULATORY_STEP description: >- Vertebrates add a secreted carrier that solubilizes the lipidated ligand, a GPI-anchored presenting receptor, and a secreted antagonist that sequesters ligand. HHIP is explicitly vertebrate-specific. context: taxa: - preferred_term: vertebrates term: id: NCBITaxon:7742 label: Vertebrata evidence: - source_id: PMID:19561611 title: Structural insights into hedgehog ligand sequestration by the human hedgehog-interacting protein HHIP. statement: HHIP is a vertebrate-restricted secreted inhibitor of Hedgehog. supporting_text: >- Among these, the Hedgehog-interacting protein (Hhip) is a highly conserved, vertebrate-specific inhibitor of Hh signaling. annotons: - id: scube2_carrier label: SCUBE2 secreted ligand carrier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SCUBE2 (human) term: id: UniProtKB:Q9NQ36 label: Signal peptide, CUB and EGF-like domain-containing protein 2 function: preferred_term: solubilization and transport of lipidated Hedgehog term: id: GO:0140597 label: protein carrier activity cargo: - preferred_term: dually lipidated Hedgehog ligand processes: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: Works with Dispatched to release and carry the lipidated ligand. gocam_associations: - model: gomodel:696022cd00000908 activity: gomodel:696022cd00000908/696022cd00000954 title: SCUBE2, CDON, BOC and GAS1 promote SHH transport to PTCH1 receptor (Human). - id: gas1_presenting_receptor label: GAS1 GPI-anchored presenting receptor participant: selector_type: FAMILY family: preferred_term: GAS1 family presenting receptor term: id: PANTHER:PTHR16840 label: GROWTH ARREST-SPECIFIC PROTEIN 1 representative_members: - preferred_term: GAS1 (human) term: id: UniProtKB:P54826 label: Growth arrest-specific protein 1 function: preferred_term: presentation of Hedgehog ligand to Patched term: id: GO:0140597 label: protein carrier activity processes: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Acts with CDON and BOC as a partly redundant presenting tier in vertebrates. gocam_associations: - model: gomodel:696022cd00000908 activity: gomodel:696022cd00000908/696022cd00000963 title: SCUBE2, CDON, BOC and GAS1 promote SHH transport to PTCH1 receptor (Human). - id: hhip_antagonist label: HHIP secreted ligand sequestrant participant: selector_type: FAMILY family: preferred_term: Hedgehog-interacting protein family term: id: PANTHER:PTHR19328 label: HEDGEHOG-INTERACTING PROTEIN representative_members: - preferred_term: HHIP (human) term: id: UniProtKB:Q96QV1 label: Hedgehog-interacting protein function: preferred_term: sequestration of Hedgehog ligand away from Patched term: id: GO:0140311 label: protein sequestering activity targets: - preferred_term: Hedgehog ligand processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Hedgehog-induced negative feedback: a ligand-binding sink that limits the range of the signal. evidence: - source_id: Reactome:R-HSA-445448 title: HHIP binds Hedgehog statement: Curated as a distinct ligand-sequestration event. - order: 3 role: Smoothened activation node: id: smo_activation label: Smoothened de-repression and activation by sterols module_type: REGULATORY_STEP description: >- Relief of Patched restriction lets sterols occupy the Smoothened cysteine-rich domain and an intramolecular channel through its seven-transmembrane core, stabilizing the active conformation. Active Smoothened both couples to Gi and directly inhibits the catalytic subunit of protein kinase A through a pseudosubstrate motif. evidence: - source_id: PMID:32929279 title: Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling. statement: Sterol occupancy of a channel through Smoothened is the activation switch. supporting_text: >- These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated signaling. annotons: - id: smo_transducer label: Smoothened transducer participant: selector_type: FAMILY family: preferred_term: Smoothened subfamily of class-F receptors term: id: PANTHER:PTHR11309:SF35 label: PROTEIN SMOOTHENED description: >- The Smoothened subfamily within the Frizzled/class-F receptor family; one gene in Drosophila and one in most vertebrates. representative_members: - preferred_term: SMO (human) term: id: UniProtKB:Q99835 label: Protein smoothened - preferred_term: smo (Drosophila melanogaster) term: id: UniProtKB:P91682 label: Protein smoothened ancestral_nodes: - preferred_term: PAINT Smoothened node PTN000885245 term: id: PANTHER:PTN000885245 label: PTN000885245 description: >- PTHR11309 node with IBD support for the smoothened signaling pathway (P:GO:0007224), patched binding (F:GO:0005113), and cilium (C:GO:0005929), seeded by Drosophila smo (FB:FBgn0003444), mouse, zebrafish, and human SMO. The same node records Wnt receptor activity and canonical Wnt signaling as LOST on this lineage, which is the PAINT statement that Smoothened is not a Wnt receptor despite sitting inside the Frizzled family. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN000885245 in PTHR11309. function: preferred_term: sterol-activated class-F receptor activity term: id: GO:0004930 label: G protein-coupled receptor activity cofactors: - preferred_term: cholesterol - preferred_term: oxysterol targets: - preferred_term: heterotrimeric Gi protein - preferred_term: cAMP-dependent protein kinase catalytic subunit processes: - preferred_term: smoothened signaling pathway term: id: GO:0007224 label: smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- The obligate transducer: every lineage that has this pathway places Smoothened between Patched and the Ci/GLI machinery. gocam_associations: - model: gomodel:696022cd00000812 activity: gomodel:696022cd00000812/696022cd00000824 title: Activation of the smoothened signaling pathway by SHH, which relieves SMO inhibition by PTCH1 (Human). - model: gomodel:696022cd00000056 title: HSD11B2 and CYP27A1 generate oxysterols that activate SMO (Human). - id: smo_pka_inhibition label: Smoothened pseudosubstrate inhibition of protein kinase A participant: selector_type: FAMILY family: preferred_term: Smoothened subfamily of class-F receptors term: id: PANTHER:PTHR11309:SF35 label: PROTEIN SMOOTHENED representative_members: - preferred_term: SMO (human) term: id: UniProtKB:Q99835 label: Protein smoothened function: preferred_term: sequestration of the PKA catalytic subunit by a pseudosubstrate motif term: id: GO:0140311 label: protein sequestering activity targets: - preferred_term: cAMP-dependent protein kinase catalytic subunit processes: - preferred_term: smoothened signaling pathway term: id: GO:0007224 label: smoothened signaling pathway role_description: >- The direct route from receptor to effector: blocking PKA removes the phosphorylation that drives Ci/GLI processing. evidence: - source_id: PMID:36202993 title: A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. statement: Smoothened blocks the PKA catalytic site with a decoy substrate sequence. supporting_text: >- As a result, GLI is released from phosphorylation-induced inhibition. gocam_associations: - model: gomodel:693b3c0900001389 activity: gomodel:693b3c0900001389/696022cd00001031 title: >- Smoothened (SMO) activation by cholesterol triggers a signaling that promotes GLI1 transcription activator activity and inhibits the smoothened signaling inhibitor GPR161 (Human). - order: 4 role: Pathway-off state - kinase-driven Ci/GLI repressor production node: id: ci_gli_repressor_processing label: PKA-primed phosphorylation and limited proteolysis of Ci/GLI module_type: REGULATORY_STEP description: >- Without ligand, protein kinase A phosphorylates Ci/GLI at a cluster of sites, priming further phosphorylation by casein kinase 1 and glycogen synthase kinase 3. The phosphodegron recruits the F-box protein Slimb/beta-TrCP within an SCF complex, and partial proteasomal degradation removes the C-terminal activation domain, leaving an N-terminal DNA-binding repressor that shuts off target genes. This kinase cassette is shared by flies and vertebrates. concepts: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway annotons: - id: pka_priming_kinase label: Protein kinase A catalytic subunit participant: selector_type: FAMILY family: preferred_term: cAMP-dependent protein kinase catalytic subunit family description: >- PKA catalytic subunits; the vertebrate exemplar is recorded here, and Drosophila PKA-C1 plays the equivalent role. representative_members: - preferred_term: PRKACA (human) term: id: UniProtKB:P17612 label: cAMP-dependent protein kinase catalytic subunit alpha function: preferred_term: priming phosphorylation of Ci/GLI term: id: GO:0004691 label: cAMP-dependent protein kinase activity targets: - preferred_term: Ci/GLI transcription factor processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway role_description: >- The master off-switch kinase; its inhibition by Smoothened is what converts the pathway from repressor to activator output. gocam_associations: - model: gomodel:693b3c0900000157 activity: gomodel:693b3c0900000157/693b3c0900000265 title: >- GPR161 acts as a negative regulator of smoothened pathway by promoting protein processing of GLI3 into transcription repressor GLI3R (Human). - id: ck1_processive_kinase label: Casein kinase 1 participant: selector_type: FAMILY family: preferred_term: casein kinase 1 family representative_members: - preferred_term: CSNK1A1 (human) term: id: UniProtKB:P48729 label: Casein kinase I isoform alpha function: preferred_term: phosphorylation of PKA-primed sites on Ci/GLI term: id: GO:0004674 label: protein serine/threonine kinase activity targets: - preferred_term: PKA-primed Ci/GLI transcription factor processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway role_description: >- Extends the primed phosphorylation cluster; also acts on Smoothened itself, in the opposite direction, in Drosophila. - id: gsk3_processive_kinase label: Glycogen synthase kinase 3 participant: selector_type: FAMILY family: preferred_term: glycogen synthase kinase 3 family (GSK3 / Shaggy) representative_members: - preferred_term: GSK3B (human) term: id: UniProtKB:P49841 label: Glycogen synthase kinase-3 beta function: preferred_term: phosphorylation of PKA-primed sites on Ci/GLI term: id: GO:0004674 label: protein serine/threonine kinase activity targets: - preferred_term: PKA-primed Ci/GLI transcription factor processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway role_description: Completes the phosphodegron that the F-box protein reads. gocam_associations: - model: gomodel:693b3c0900000157 activity: gomodel:693b3c0900000157/693b3c0900000275 title: >- GPR161 acts as a negative regulator of smoothened pathway by promoting protein processing of GLI3 into transcription repressor GLI3R (Human). - id: btrc_slimb_adaptor label: Slimb/beta-TrCP SCF substrate adaptor participant: selector_type: FAMILY family: preferred_term: Slimb/beta-TrCP F-box substrate adaptor term: id: PANTHER:PTHR14604:SF5 label: F-BOX_WD REPEAT-CONTAINING PROTEIN 1A description: >- The adaptor is Slimb in Drosophila and beta-TrCP in vertebrates; only the vertebrate accession is recorded here. representative_members: - preferred_term: BTRC (human) term: id: UniProtKB:Q9Y297 label: F-box/WD repeat-containing protein 1A function: preferred_term: phosphodegron recognition on Ci/GLI term: id: GO:1990756 label: ubiquitin-like ligase-substrate adaptor activity targets: - preferred_term: phosphorylated Ci/GLI transcription factor processes: - preferred_term: protein processing term: id: GO:0016485 label: protein processing role_description: >- Couples the phosphorylation code to the proteasome; the outcome is partial proteolysis to a repressor, not full destruction. gocam_associations: - model: gomodel:693b3c0900000157 activity: gomodel:693b3c0900000157/693b3c0900000283 title: >- GPR161 acts as a negative regulator of smoothened pathway by promoting protein processing of GLI3 into transcription repressor GLI3R (Human). - id: ci_gli_repressor label: Ci/GLI repressor form participant: selector_type: FAMILY family: preferred_term: Ci/GLI zinc-finger transcription factor family (repressor form) term: id: PANTHER:PTHR45718 label: TRANSCRIPTIONAL ACTIVATOR CUBITUS INTERRUPTUS description: >- Drosophila Ci and the vertebrate GLI paralogs; GLI3 is the principal vertebrate repressor-forming paralog. representative_members: - preferred_term: GLI3 (human) term: id: UniProtKB:P10071 label: Transcription activator GLI3 - preferred_term: ci (Drosophila melanogaster) term: id: UniProtKB:P19538 label: Transcriptional activator cubitus interruptus function: preferred_term: repression of Hedgehog target genes by the processed N-terminal form term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: >- The default output of the pathway; much of Hedgehog biology is relief of this repression rather than gain of activation. gocam_associations: - model: gomodel:693b3c0900000157 activity: gomodel:693b3c0900000157/693b3c0900000307 title: >- GPR161 acts as a negative regulator of smoothened pathway by promoting protein processing of GLI3 into transcription repressor GLI3R (Human). connections: - source: pka_priming_kinase target: ck1_processive_kinase connection_type: PRECEDES description: PKA phosphorylation creates the priming site read by casein kinase 1. - source: ck1_processive_kinase target: btrc_slimb_adaptor connection_type: PROVIDES_INPUT_FOR description: The completed phosphodegron is the adaptor's substrate. - source: gsk3_processive_kinase target: btrc_slimb_adaptor connection_type: PROVIDES_INPUT_FOR description: GSK3 phosphorylation contributes to the same phosphodegron. - source: btrc_slimb_adaptor target: ci_gli_repressor connection_type: CAUSES description: Ubiquitin-dependent partial proteolysis generates the repressor form. - order: 5 role: Pathway-on state - conversion of Ci/GLI to the activator form node: id: ci_gli_activation label: SUFU release and Fused-family phosphorylation of Ci/GLI module_type: REGULATORY_STEP description: >- Active Smoothened blocks the processing cassette and drives the opposite reaction: Suppressor of fused releases full-length Ci/GLI, and Fused-family kinases phosphorylate it on conserved sites that promote activator function. The compartment in which this happens is the main lineage difference in the pathway and is modeled as a variant. concepts: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway evidence: - source_id: PMID:31279575 title: Phosphorylation of Ci/Gli by Fused Family Kinases Promotes Hedgehog Signaling. statement: >- Drosophila Fu phosphorylates Ci, and the vertebrate kinases ULK3 and STK36 phosphorylate GLI2 on conserved sites, making this a single conserved activation step with lineage-specific kinases. supporting_text: >- Furthermore, we provide evidence that Sonic hedgehog (Shh) activates Gli2 by stimulating its phosphorylation on conserved sites through the Fu-family kinases ULK3 and mFu/STK36 in a manner depending on Gli2 ciliary localization. annotons: - id: sufu_sequestration label: Suppressor of fused sequestration of Ci/GLI participant: selector_type: FAMILY family: preferred_term: Suppressor of fused family term: id: PANTHER:PTHR10928 label: SUPPRESSOR OF FUSED description: >- Single-copy negative regulator in flies and vertebrates; the Drosophila protein is a PAINT seed for the node below even though its accession is not recorded here. representative_members: - preferred_term: SUFU (human) term: id: UniProtKB:Q9UMX1 label: Suppressor of fused homolog ancestral_nodes: - preferred_term: PAINT Suppressor of fused node PTN000859153 term: id: PANTHER:PTN000859153 label: PTN000859153 description: >- PTHR10928 node with IBD support for protein sequestering activity (F:GO:0140311) and negative regulation of the smoothened signaling pathway (P:GO:0045879), seeded by Drosophila Su(fu) (FB:FBgn0005355), mouse, zebrafish, and human SUFU. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN000859153 in PTHR10928. function: preferred_term: sequestration of full-length Ci/GLI in the pathway-off state term: id: GO:0140311 label: protein sequestering activity targets: - preferred_term: full-length Ci/GLI transcription factor processes: - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- Holds full-length Ci/GLI inactive and is released on signaling; a brake inside the activation step rather than a separate pathway. gocam_associations: - model: gomodel:693b3c0900001389 activity: gomodel:693b3c0900001389/693b3c0900001460 title: >- Smoothened (SMO) activation by cholesterol triggers a signaling that promotes GLI1 transcription activator activity and inhibits the smoothened signaling inhibitor GPR161 (Human). evidence: - source_id: Reactome:R-HSA-5635839 title: "ULK3:SUFU dissociates" statement: Release of the GLI:SUFU complex is curated as a discrete activation event. - id: fused_family_kinase label: Fused-family kinase participant: selector_type: FAMILY family: preferred_term: Fused-family Ser/Thr kinases (Fu, STK36, ULK3) family_terms: - id: PANTHER:PTHR22983 label: PROTEIN KINASE RELATED - id: PANTHER:PTHR24348 label: SERINE/THREONINE-PROTEIN KINASE UNC-51-RELATED description: >- Drosophila Fused and the vertebrate kinases STK36 and ULK3 phosphorylate conserved sites on Ci/GLI. No single family id fits: Drosophila fu and human STK36 share one PANTHER subfamily, PTHR22983:SF6, which is direct classification support for the orthology, while ULK3 sits in a different family. The activity is shared across a classification boundary, so both families are recorded. representative_members: - preferred_term: STK36 (human) term: id: UniProtKB:Q9NRP7 label: Serine/threonine-protein kinase 36 - preferred_term: ULK3 (human) term: id: UniProtKB:Q6PHR2 label: Serine/threonine-protein kinase ULK3 - preferred_term: fu (Drosophila melanogaster) term: id: UniProtKB:P23647 label: Serine/threonine-protein kinase fused function: preferred_term: activating phosphorylation of Ci/GLI term: id: GO:0004674 label: protein serine/threonine kinase activity targets: - preferred_term: full-length Ci/GLI transcription factor processes: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway role_description: >- Converts released Ci/GLI into the activator form; the one pan-metazoan positive kinase input documented for this step. gocam_associations: - model: gomodel:696022cd00001645 activity: gomodel:696022cd00001645/696022cd00001720 title: >- Smoothened (SMO) activation by cholesterol triggers a signaling that promotes (1) GLI2 transcription activator activity via phosphorylation of GLI2 by STK36 and (2) inhibits the smoothened signaling inhibitor GPR161 (Human). - model: gomodel:696022cd00001523 activity: gomodel:696022cd00001523/696022cd00001634 title: >- Smoothened (SMO) activation by cholesterol triggers a signaling that promotes (1) GLI2 transcription activator activity via phosphorylation of GLI2 by ULK3 and (2) inhibits the smoothened signaling inhibitor GPR161 (Human). variant_sets: - id: gli_activation_compartment_axis label: Compartment in which the Ci/GLI processing-activation complex operates axis: taxon / subcellular compartment of the Ci/GLI regulatory complex selection: EXACTLY_ONE notes: >- A kinesin scaffold organizes the Ci/GLI complex in both lineages: Drosophila Costal-2 (PTHR24115:SF949) and vertebrate KIF7 (PTHR24115:SF445) are sister subfamilies of one PANTHER family, which is the classification evidence that these are one ancestral role realized in two compartments rather than two inventions. Both have also lost the motor function the family is named for: purified KIF7 binds microtubules but is immotile, as is Costal-2, so the shared role is scaffolding rather than transport and the annotons below are typed as adaptors rather than motors. evidence: - source_id: PMID:19592253 title: >- The mammalian Cos2 homolog Kif7 plays an essential role in modulating Hh signal transduction during development. statement: >- KIF7 is the mammalian Costal-2 counterpart and acts at the ciliary tip, where Costal-2 acts on a cytoplasmic complex. supporting_text: >- We show that Kif7 accumulates at the distal tip of the primary cilia in a Hh-dependent manner. variants: - id: vertebrate_ciliary_variant label: Vertebrate primary-cilium implementation module_type: REGULATORY_STEP description: >- Vertebrates run the step inside the primary cilium. In the off state the orphan receptor GPR161 sits in the ciliary membrane and raises cAMP through Gs and adenylate cyclase, sustaining PKA activity; activated Smoothened enters the cilium and GPR161 leaves it, KIF7 accumulates at the ciliary tip, and intraflagellar transport moves GLI:SUFU complexes between base and tip. context: taxa: - preferred_term: vertebrates term: id: NCBITaxon:7742 label: Vertebrata cellular_components: - preferred_term: non-motile primary cilium term: id: GO:0097730 label: non-motile cilium annotons: - id: gpr161_camp_brake label: GPR161 ciliary cAMP brake participant: selector_type: GENE_PRODUCT gene_product: preferred_term: GPR161 (human) term: id: UniProtKB:Q8N6U8 label: G-protein coupled receptor 161 function: preferred_term: constitutive Gs-coupled receptor activity sustaining ciliary cAMP term: id: GO:0004930 label: G protein-coupled receptor activity processes: - preferred_term: adenylate cyclase-activating G protein-coupled receptor signaling pathway term: id: GO:0007189 label: adenylate cyclase-activating G protein-coupled receptor signaling pathway - preferred_term: negative regulation of smoothened signaling pathway term: id: GO:0045879 label: negative regulation of smoothened signaling pathway locations: - preferred_term: non-motile cilium membrane term: id: GO:0098804 label: non-motile cilium membrane role_description: >- Keeps PKA active in the resting cilium; its Hedgehog-induced exit is part of pathway activation and has no known Drosophila counterpart. gocam_associations: - model: gomodel:693b3c0900000157 activity: gomodel:693b3c0900000157/693b3c0900000212 title: >- GPR161 acts as a negative regulator of smoothened pathway by promoting protein processing of GLI3 into transcription repressor GLI3R (Human). - model: gomodel:693b3c0900000716 title: >- GPR161 is exported from primary cilium in response to smoothened signaling via a beta-arrestin, BBSome and IFT-B complex-dependent mechanism (Human). - id: ciliary_adenylate_cyclase label: Ciliary adenylate cyclase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ADCY3 (human) term: id: UniProtKB:O60266 label: Adenylate cyclase type 3 function: preferred_term: cAMP synthesis in the ciliary membrane term: id: GO:0004016 label: adenylate cyclase activity processes: - preferred_term: adenylate cyclase-activating G protein-coupled receptor signaling pathway term: id: GO:0007189 label: adenylate cyclase-activating G protein-coupled receptor signaling pathway locations: - preferred_term: non-motile cilium membrane term: id: GO:0098804 label: non-motile cilium membrane role_description: Supplies the cAMP that keeps PKA phosphorylating GLI in the off state. gocam_associations: - model: gomodel:693b3c0900000157 activity: gomodel:693b3c0900000157/693b3c0900000233 title: >- GPR161 acts as a negative regulator of smoothened pathway by promoting protein processing of GLI3 into transcription repressor GLI3R (Human). - id: kif7_ciliary_scaffold label: KIF7 ciliary-tip scaffold participant: selector_type: FAMILY family: preferred_term: KIF7 kinesin-4 scaffold term: id: PANTHER:PTHR24115:SF445 label: KINESIN-LIKE PROTEIN KIF7 description: >- Vertebrate counterpart of Drosophila Costal-2; both sit in PANTHER family PTHR24115. representative_members: - preferred_term: KIF7 (human) term: id: UniProtKB:Q2M1P5 label: Kinesin-like protein KIF7 function: preferred_term: scaffolding of the GLI regulatory complex at the ciliary tip term: id: GO:0030674 label: protein-macromolecule adaptor activity targets: - preferred_term: GLI transcription factor - preferred_term: SUFU processes: - preferred_term: regulation of smoothened signaling pathway term: id: GO:0008589 label: regulation of smoothened signaling pathway locations: - preferred_term: ciliary tip term: id: GO:0097542 label: ciliary tip role_description: >- Organizes GLI processing and activation at the ciliary tip; loss causes both gain and loss of signaling because it serves the off and on states. - id: ift_gli_transport label: Intraflagellar transport of the GLI:SUFU complex participant: selector_type: FAMILY family: preferred_term: Kinesin-2 anterograde intraflagellar transport motor representative_members: - preferred_term: KIF3A (human) term: id: UniProtKB:Q9Y496 label: Kinesin-like protein KIF3A function: preferred_term: motor-driven movement of pathway components within the cilium term: id: GO:0003777 label: microtubule motor activity processes: - preferred_term: protein localization to non-motile cilium term: id: GO:0097499 label: protein localization to non-motile cilium locations: - preferred_term: non-motile cilium term: id: GO:0097730 label: non-motile cilium role_description: >- Makes the cilium a functional compartment for the pathway; this requirement is absent from the Drosophila variant. gocam_associations: - model: gomodel:696022cd00000124 activity: gomodel:696022cd00000124/696022cd00000163 title: SMO is translocated in primary cilium via a beta-arrestin and KIF3A-dependent mechanism (Human). evidence: - source_id: Reactome:R-HSA-5610767 title: >- The intraflagellar transport B (IFT-B) complex is required for the transit of GLI:SUFU complexes to the ciliary tip statement: Anterograde transport delivers GLI:SUFU to the tip. - source_id: Reactome:R-HSA-5610766 title: >- The intraflagellar transport A (IFT-A) complex is required for the transit of GLI:SUFU complexes to the ciliary base statement: Retrograde transport returns GLI:SUFU to the base. - id: drosophila_cytoplasmic_variant label: Drosophila cytoplasmic Hedgehog signaling complex implementation module_type: REGULATORY_STEP description: >- In its developmental epithelia, which are unciliated, Drosophila runs the same step without a cilium. The Costal-2 kinesin tethers Ci, Fused, and the processing kinases to the cytoplasmic face of the plasma membrane, and the Smoothened C-terminal tail recruits that complex when the pathway turns on. Phosphorylation of the Smoothened tail, rather than ciliary entry, is the readout of activation in this lineage. The cilium-independence is a property of those tissues rather than of the lineage: Drosophila olfactory sensory neurons are ciliated, and there Smoothened localizes to the cilium and signals through intraflagellar transport much as the vertebrate receptor does, which is why the ciliary assertion at the Smoothened ancestral node rests on protostome evidence too. context: taxa: - preferred_term: Drosophila melanogaster term: id: NCBITaxon:7227 label: Drosophila melanogaster cellular_components: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm evidence: - source_id: PMID:28195188 title: SUMO regulates the activity of Smoothened and Costal-2 in Drosophila Hedgehog signaling. statement: >- In Drosophila, activation is read out as cell-surface accumulation and post-translational modification of Smoothened, with Costal-2 acting as a modified inhibitory partner. supporting_text: >- Binding of Hh to Ptc alleviates Ptc-mediated inhibition of Smo, allowing Smo to activate Cubitus interuptus (Ci)/Gli transcription factors and ultimately induce the expression of Hh target genes annotons: - id: cos2_cytoplasmic_scaffold label: Costal-2 cytoplasmic scaffold participant: selector_type: FAMILY family: preferred_term: Costal-2 kinesin-4 scaffold term: id: PANTHER:PTHR24115:SF949 label: KINESIN-LIKE PROTEIN COSTA description: >- Drosophila Costal-2 and vertebrate KIF7 are sister subfamilies of PANTHER family PTHR24115, which is the classification evidence that the scaffold role is one ancestral role rather than two inventions. representative_members: - preferred_term: cos (Drosophila melanogaster) term: id: UniProtKB:O16844 label: Kinesin-like protein costa function: preferred_term: scaffolding of the cytoplasmic Ci regulatory complex term: id: GO:0030674 label: protein-macromolecule adaptor activity targets: - preferred_term: Ci transcription factor - preferred_term: Fused kinase processes: - preferred_term: regulation of smoothened signaling pathway term: id: GO:0008589 label: regulation of smoothened signaling pathway locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- Holds Ci, Fused, and the processing kinases together at the membrane; the compartmental counterpart of the vertebrate ciliary tip. - id: smo_tail_recruitment label: Smoothened C-terminal tail recruitment of the complex participant: selector_type: GENE_PRODUCT gene_product: preferred_term: smo (Drosophila melanogaster) term: id: UniProtKB:P91682 label: Protein smoothened function: preferred_term: recruitment of the Costal-2/Fused complex to the activated receptor term: id: GO:0030674 label: protein-macromolecule adaptor activity targets: - preferred_term: Costal-2 scaffold processes: - preferred_term: positive regulation of smoothened signaling pathway term: id: GO:0045880 label: positive regulation of smoothened signaling pathway locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- The long Drosophila Smoothened tail, progressively phosphorylated on activation, is the docking site that the vertebrate receptor largely replaces with ciliary compartmentalization. - order: 6 role: Transcriptional output node: id: ci_gli_transcriptional_output label: Ci/GLI activator-driven target-gene expression module_type: REGULATORY_STEP description: >- The activator form of Ci/GLI enters the nucleus and induces Hedgehog target genes, among them the pathway's own negative regulators (patched, and HHIP in vertebrates) and, in vertebrates, the amplifying paralog GLI1. The balance between activator and repressor forms, not the presence of ligand alone, is what the target genes read. annotons: - id: ci_gli_activator label: Ci/GLI activator form participant: selector_type: FAMILY family: preferred_term: Ci/GLI zinc-finger transcription factor family (activator form) term: id: PANTHER:PTHR45718 label: TRANSCRIPTIONAL ACTIVATOR CUBITUS INTERRUPTUS representative_members: - preferred_term: GLI1 (human) term: id: UniProtKB:P08151 label: Transcription activator GLI1 - preferred_term: GLI2 (human) term: id: UniProtKB:P10070 label: Transcription activator GLI2 - preferred_term: ci (Drosophila melanogaster) term: id: UniProtKB:P19538 label: Transcriptional activator cubitus interruptus ancestral_nodes: - preferred_term: PAINT Ci/GLI node PTN001836086 term: id: PANTHER:PTN001836086 label: PTN001836086 description: >- PTHR45718 node with IBD support for the smoothened signaling pathway (P:GO:0007224). The node is stamped Deuterostomia (NCBITaxon:33511) and seeded by the mouse and human GLI paralogs and zebrafish gli genes, so it supports the vertebrate effector tier only. Drosophila ci sits in the same family but outside that clade, and carries no IBA from this node: its pathway role rests on its own experimental record, which is extensive, and the family membership carries the deeper homology. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN001836086 in PTHR45718. function: preferred_term: activation of Hedgehog target-gene transcription term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: smoothened signaling pathway term: id: GO:0007224 label: smoothened signaling pathway locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: >- The terminal effector of the module; its dose and duration are what downstream patterning programs interpret. gocam_associations: - model: gomodel:693b3c0900001389 activity: gomodel:693b3c0900001389/693b3c0900001475 title: >- Smoothened (SMO) activation by cholesterol triggers a signaling that promotes GLI1 transcription activator activity and inhibits the smoothened signaling inhibitor GPR161 (Human). connections: - source: hh_ligand_biogenesis target: hh_reception connection_type: PROVIDES_INPUT_FOR description: The released dually lipidated ligand is the input to the receiving cell. - source: hh_reception target: smo_activation connection_type: CAUSES description: >- Ligand-bound Patched stops restricting Smoothened, which is what activates the transducer. - source: patched_receptor target: smo_transducer connection_type: NEGATIVELY_REGULATES description: >- Unliganded Patched holds Smoothened off; this is the edge the ligand removes, and it is the reason the pathway is drawn as de-repression. - source: smo_activation target: ci_gli_repressor_processing connection_type: NEGATIVELY_REGULATES description: >- Active Smoothened shuts down the PKA-primed processing cassette, chiefly by inhibiting PKA. - source: smo_activation target: ci_gli_activation connection_type: CAUSES description: Active Smoothened drives SUFU release and Fused-family phosphorylation. - source: ci_gli_repressor_processing target: ci_gli_transcriptional_output connection_type: NEGATIVELY_REGULATES description: The repressor form silences the same target genes the activator induces. - source: ci_gli_activation target: ci_gli_transcriptional_output connection_type: CAUSES description: The activator form induces Hedgehog target genes. - source: ci_gli_transcriptional_output target: hh_reception connection_type: NEGATIVELY_REGULATES description: >- Target-gene feedback: patched is itself a Hedgehog target gene, and in vertebrates so is HHIP, so output raises the reception threshold.