id: MODULE:retinoic_acid_metabolism title: All-trans-retinoic acid metabolism — RBP4/STRA6 retinol delivery, CRBP1 binding, RDH10/DHRS3 retinol-retinal interconversion, ALDH1A1-3 retinal oxidation, CRABP1/2 binding and CYP26A1/B1/C1 catabolism description: >- All-trans-retinoic acid (atRA), the most potent vitamin A metabolite, is made on demand inside target cells from circulating retinol and is cleared by oxidative catabolism, so that its tissue level is set by the balance of local synthesis and local destruction. Retinol travels in plasma bound to retinol-binding protein 4 (RBP4), which circulates as a complex with the transthyretin (TTR) tetramer. The multi-pass membrane receptor STRA6 binds holo-RBP4 and moves retinol into the cell, where it is bound by cellular retinol-binding protein 1 (CRBP1, RBP1). The first and rate-limiting step of synthesis is the reversible, membrane-associated oxidation of all-trans-retinol to all-trans-retinal by the short-chain dehydrogenase/reductase RDH10. RDH10 works together with the retinaldehyde reductase DHRS3: the two proteins activate each other, and DHRS3 reduces retinal back to retinol, so the pair sets the flux of retinal toward acid. Cytosolic medium-chain alcohol dehydrogenases can also oxidise retinol. The second step, the oxidation of retinal to atRA, is irreversible and is catalysed by the NAD+-dependent retinaldehyde dehydrogenases ALDH1A1, ALDH1A2 and ALDH1A3, whose distinct tissue patterns define where atRA is produced in the embryo. Cellular retinoic acid-binding proteins bind atRA in the cytosol: CRABP2 delivers it to the nuclear retinoic acid receptors, and CRABP1 sequesters it and favours its catabolism. atRA is inactivated by the cytochrome P450 retinoic acid hydroxylases CYP26A1, CYP26B1 and CYP26C1, which form 4-hydroxy-, 4-oxo- and 18-hydroxy-atRA in the endoplasmic reticulum; CYP26A1 and DHRS3 are induced by atRA, giving negative feedback on its own level. Retinol not used for synthesis can be stored as retinyl esters, made by LRAT and hydrolysed back to retinol by retinyl ester hydrolases such as the carboxylesterase CES1. Loss of RDH10 or ALDH1A2 in mouse abolishes embryonic atRA synthesis, CYP26B1 deficiency causes craniosynostosis and skeletal anomalies, and STRA6 and RBP4 defects cause microphthalmia and coloboma. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0001004 title: retinoic acid metabolic pathway statement: >- The module boundary follows the RGD Pathway Ontology record and diagram for this term. The diagram draws circulating retinol associated with Rbp4 and Ttr, Rbp4 associated with Stra6, cellular retinol bound to Rbp1 and reversibly converted to retinal, retinal irreversibly converted to all-trans retinoic acid, atRA associated with Crabp1, Crabp2 and Fabp5 and feeding the atRA CYPs and the retinoic acid signaling pathway (PW:0001014), and retinol exchanged with the retinyl ester pool (Lrat, CES1, apo-Rbp1). The RGD human gene set is ALDH1A1, ALDH1A2, ALDH1A3, CES1, CRABP1, CRABP2, CYP26A1, CYP26B1, CYP26C1, DHRS9, FABP5, LRAT, RBP1, RBP4, RDH10, RDH16, STRA6 and TTR. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0001004.yaml). - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0001004.yaml title: RGD PW:0001004 record text (project snapshot) statement: >- The RGD record places the reversible retinol-retinal step before the irreversible retinal dehydrogenase step that commits retinal to atRA. supporting_text: In other cells, retinal is the substrate for retinal dehydrogenases that irreversible convert it to all-trans retinoic acid (atRA) and other derivatives with atRA being the most potent molecule. - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0001004.yaml title: RGD PW:0001004 record text (project snapshot) statement: >- The RGD record assigns CRABP2 to delivery of atRA to the RARs and CRABP1 to atRA catabolism. supporting_text: Crabp1 on the other hand, relates to the processing and catabolism of retinoic acid. - source_id: GO:0042573 title: retinoic acid metabolic process statement: >- The skos:closeMatch GO mapping of PW:0001004 (RGD page GO xref, PW definition xref and lexical match; projects/RGD_PATHWAY_ONTOLOGY/data/module_seeds.yaml). Used as the module-level concept; its children GO:0002138 retinoic acid biosynthetic process and GO:0034653 retinoic acid catabolic process are placed on the synthesis and catabolism steps. - source_id: PMID:17473173 title: RDH10 is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. statement: >- Genetic evidence that retinol oxidation by RDH10, not redundant cytosolic alcohol dehydrogenases, is the first and critical step of embryonic atRA synthesis. supporting_text: Thus, we show that the first oxidative step of Vitamin A metabolism, which is catalyzed in large part by the retinol dehydrogenase RDH10, is critical for the spatiotemporal synthesis of RA. - source_id: PMID:9228017 title: cDNA cloning of human retinoic acid-metabolizing enzyme (hP450RAI) identifies a novel family of cytochromes P450. statement: >- The atRA-inducible CYP26A1 hydroxylase closes a negative feedback loop on atRA level. supporting_text: We conclude that this enzyme plays a key role in RA metabolism, functioning in a feedback loop where RA levels are controlled in an autoregulatory manner. module: id: retinoic_acid_metabolism label: All-trans-retinoic acid metabolism module_type: METABOLIC_PATHWAY concepts: - preferred_term: retinoic acid metabolic process term: id: GO:0042573 label: retinoic acid metabolic process description: >- The closeMatch of PW:0001004. Covers both the synthesis and the catabolism of atRA, which this module models as one life cycle because the two arms together set the local atRA level. context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens cellular_components: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane description: >- Where the membrane-bound steps act: retinol oxidation by RDH10 with DHRS3, and atRA hydroxylation by the CYP26 enzymes. - preferred_term: cytosol term: id: GO:0005829 label: cytosol description: >- Where the soluble steps act: CRBP1 retinol binding, retinal oxidation by the ALDH1A enzymes and atRA binding by the CRABPs. Listed beside the ER membrane because the pathway alternates between the two compartments, not as a refinement of one by the other. parts: - order: 1 role: plasma retinol delivery and receptor-mediated uptake node: id: retinol_delivery_uptake label: RBP4-TTR transport of retinol and STRA6-mediated uptake module_type: TRANSPORT_STEP description: >- Holo-RBP4 carries all-trans-retinol in plasma as a complex with the TTR tetramer, which keeps the small RBP4 from glomerular filtration. STRA6 at the plasma membrane binds holo-RBP4 and transfers retinol into the cell. The visual cycle module starts from retinol already in the RPE and does not model this step, so it is modelled here rather than referenced. concepts: - preferred_term: retinol transport term: id: GO:0034633 label: retinol transport evidence: - source_id: PMID:17255476 statement: STRA6 is the RBP receptor that takes up vitamin A from the vitamin A-RBP complex. supporting_text: STRA6 binds to RBP with high affinity and has robust vitamin A uptake activity from the vitamin A-RBP complex. annotons: - id: rbp4_retinol_carrier label: RBP4 plasma retinol carrier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RBP4 term: id: UniProtKB:P02753 label: Retinol-binding protein 4 function: preferred_term: molecular carrier activity term: id: GO:0140104 label: molecular carrier activity substrates: - preferred_term: all-trans-retinol term: id: CHEBI:17336 label: all-trans-retinol processes: - preferred_term: retinol transport term: id: GO:0034633 label: retinol transport locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Lipocalin that binds one all-trans-retinol (retinol binding, GO:0019841, IDA in human GOA) and carries it from liver to peripheral tissues. The carrier activity follows the mouse GO-CAM that models Rbp4 this way. evidence: - source_id: PMID:571335 statement: Human RBP4 exists as apo and holo forms that differ by bound retinol and binds prealbumin (transthyretin). supporting_text: The anodal of the two bands was therefore probably the apo form and the cathodal the holo form of the same retinol-binding protein. gocam_associations: - model: gomodel:67086be200001721 activity: gomodel:67086be200001721/67086be200001793 title: Retinoid Metabolic Process 2 (Mouse) description: >- Mouse Rbp4 GO:0140104 molecular carrier activity in the extracellular region, downstream of Pnpla2 retinyl ester hydrolysis in hepatic stellate cells. - id: ttr_rbp4_partner label: TTR stabilisation of circulating holo-RBP4 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TTR term: id: UniProtKB:P02766 label: Transthyretin function: preferred_term: molecular sequestering activity term: id: GO:0140313 label: molecular sequestering activity locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- The thyroxine-carrying tetramer that binds holo-RBP4 and so retains it in plasma. Retinol is not its own ligand; TTR is an accessory of the RBP4 carrier. The function term follows the mouse GO-CAM and the Reactome-derived human annotation (TAS); TTR has no experimental molecular function in human GOA other than self-association. evidence: - source_id: PMID:571335 statement: Most urinary RBP binds prealbumin (transthyretin) in vitro. supporting_text: More than 85% of the retinol-binding protein in the urine bound to prealbumin-Sephrose. gocam_associations: - model: gomodel:67086be200001721 activity: gomodel:67086be200001721/67086be200001792 title: Retinoid Metabolic Process 2 (Mouse) description: Mouse Ttr GO:0140313 molecular sequestering activity in the retinoid metabolic process. - id: stra6_retinol_uptake label: STRA6 retinol transmembrane transporter (RBP4 receptor) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: STRA6 term: id: UniProtKB:Q9BX79 label: Receptor for retinol uptake STRA6 function: preferred_term: retinol transmembrane transporter activity term: id: GO:0034632 label: retinol transmembrane transporter activity substrates: - preferred_term: all-trans-retinol (from holo-RBP4) term: id: CHEBI:17336 label: all-trans-retinol processes: - preferred_term: retinol transport term: id: GO:0034633 label: retinol transport locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Multi-pass membrane receptor for holo-RBP4 that transfers retinol into the cell (GO:0034632, IDA, PMID:21901792). Uptake is coupled to intracellular acceptors, CRBP1 and LRAT, which drain the retinol; the uptake is bidirectional in vitro. evidence: - source_id: PMID:21901792 statement: A disease-associated STRA6 mutant is mislocalised and has reduced vitamin A uptake, and the eye phenotype is reproduced by inhibiting RA synthesis. supporting_text: We have shown that the G304K mutant STRA6 protein is mislocalized and has severely reduced vitamin A uptake activity. - order: 2 role: intracellular retinol binding node: id: cellular_retinol_binding label: CRBP1 (RBP1) binding of cellular all-trans-retinol module_type: TRANSPORT_STEP description: >- CRBP1 binds incoming retinol with nanomolar affinity, protects it from non-specific oxidation and presents it to the membrane-bound enzymes, both the RDH10 dehydrogenase and LRAT. The ratio of apo- to holo-CRBP1 steers retinol between atRA synthesis and retinyl ester storage, which is why the RGD diagram draws apo-Rbp1 inhibiting Lrat and favouring ester hydrolysis. annotons: - id: rbp1_retinol_binding label: CRBP1 all-trans-retinol binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RBP1 (CRBP1) term: id: UniProtKB:P09455 label: Retinol-binding protein 1 function: preferred_term: all-trans-retinol binding term: id: GO:1904768 label: all-trans-retinol binding locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Intracellular lipocalin-fold (FABP family) retinol chaperone. GO:1904768 is its experimental molecular function (IDA, PMID:28057518) and the activity the mouse GO-CAMs use. evidence: - source_id: PMID:28057518 statement: Apo-CRBP1 binds retinol stoichiometrically with nanomolar affinity. supporting_text: An approximately stoichiometric binding of retinol to wild type apo-CRBP1 (Kd∼4.5nM) gocam_associations: - model: gomodel:66f5faaa00001204 activity: gomodel:66f5faaa00001204/66f5faaa00001307 title: Retinoid Metabolic Process 1 (Mouse) description: Mouse Rbp1 GO:1904768 all-trans-retinol binding, part of retinoid metabolic process. - order: 3 role: reversible retinol-retinal interconversion (rate-limiting step of synthesis) node: id: retinol_retinal_interconversion label: RDH10-DHRS3 retinol dehydrogenase/retinaldehyde reductase pair module_type: REACTION description: >- RDH10 oxidises all-trans-retinol to all-trans-retinal at the ER and lipid-droplet membrane. DHRS3 reduces all-trans-retinal back to retinol. The two SDRs activate each other when co-expressed: DHRS3 reaches its full reductase activity only with RDH10 present, and RDH10 retinol dehydrogenase activity rises with DHRS3, with neither needing to be catalytically active to activate the other. Because DHRS3 is induced by atRA, the pair forms a feedback loop that limits retinal supply. No GO cellular component term exists for the RDH10-DHRS3 association, so it is modelled as two annotons in one node rather than as a named complex. concepts: - preferred_term: retinol metabolic process term: id: GO:0042572 label: retinol metabolic process evidence: - source_id: PMID:24733397 statement: DHRS3 needs RDH10 for full reductase activity and RDH10 is reciprocally activated by DHRS3. supporting_text: This study demonstrates that DHRS3 requires the presence of retinol dehydrogenase 10 (RDH10) to display its full catalytic activity. - source_id: PMID:24733397 statement: The mutual activation does not depend on the catalytic activity of the activating partner. supporting_text: Neither RDH10 nor DHRS3 has to be itself catalytically active to activate each other. annotons: - id: rdh10_retinol_dehydrogenase label: RDH10 all-trans-retinol dehydrogenase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RDH10 term: id: UniProtKB:Q8IZV5 label: Retinol dehydrogenase 10 function: preferred_term: all-trans-retinol dehydrogenase (NAD+) activity term: id: GO:0004745 label: all-trans-retinol dehydrogenase (NAD+) activity substrates: - preferred_term: all-trans-retinol term: id: CHEBI:17336 label: all-trans-retinol - preferred_term: NAD+ term: id: CHEBI:57540 label: NAD(1-) products: - preferred_term: all-trans-retinal term: id: CHEBI:17898 label: all-trans-retinal - preferred_term: NADH term: id: CHEBI:57945 label: NADH(2-) processes: - preferred_term: retinoic acid biosynthetic process term: id: GO:0002138 label: retinoic acid biosynthetic process locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- The main retinol dehydrogenase for atRA synthesis; the mouse trex mutant lacks retinol oxidase activity and dies at midgestation with RA deficiency. GO:0004745 is its experimental GOA function (IDA, PMID:12407145 and PMID:19458327). Cofactor use is not settled: the first characterisation reported a preference for NADP, while later work found NAD+ more effective; the GOA term is kept. evidence: - source_id: PMID:12407145 statement: Recombinant human RDH10 oxidises all-trans-retinol to all-trans-retinal. supporting_text: Human RDH10 expressed in COS cells oxidized all-trans retinol to all-trans retinal. - source_id: PMID:19458327 statement: RDH10 uses both NAD+ and NADP+, with NAD+ giving more robust activity (11-cis substrate). supporting_text: RDH10 can use both NAD(+) and NADP(+) as cofactors for 11-cis-RDH activity, although NAD(+) cofactor confers more robust activity. - source_id: PMID:17473173 statement: The trex RDH10 mutant cannot oxidise retinol and gives insufficient RA signalling. supporting_text: we determined that RDH10(trex) mutant protein lacks the ability to oxidize retinol to retinal, resulting in insufficient RA signaling. - id: dhrs3_retinaldehyde_reductase label: DHRS3 all-trans-retinaldehyde reductase (RDH10-activated) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DHRS3 term: id: UniProtKB:O75911 label: Short-chain dehydrogenase/reductase 3 function: preferred_term: all-trans-retinol dehydrogenase (NADP+) activity term: id: GO:0052650 label: all-trans-retinol dehydrogenase (NADP+) activity substrates: - preferred_term: all-trans-retinal term: id: CHEBI:17898 label: all-trans-retinal - preferred_term: NADPH term: id: CHEBI:57783 label: NADPH(4-) products: - preferred_term: all-trans-retinol term: id: CHEBI:17336 label: all-trans-retinol - preferred_term: NADP+ term: id: CHEBI:58349 label: NADP(3-) locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- NADPH-dependent reductase working in the reverse direction to RDH10; this activity is the core function in the completed human DHRS3 review. The same DHRS3 role is also drawn, as retinoid buffering, in modules/retinoid_visual_cycle.yaml (node retinoid_buffering); here it is modelled with its RDH10 partner because the mutual activation is what makes it a control point of atRA synthesis. The substrates and products are written in the reduction direction it works in here, although GO names GO:0052650 in the oxidation (dehydrogenase) direction; GO activity terms cover both directions of a reversible reaction, and GOA uses this term for the reductase. evidence: - source_id: file:human/DHRS3/DHRS3-ai-review.yaml statement: Core function GO:0052650, NADPH-dependent all-trans-retinaldehyde reductase buffering retinaldehyde supply for atRA synthesis. - source_id: PMID:24733397 statement: RDH10-activated DHRS3 reduces retinaldehyde back to retinol and slows atRA synthesis. supporting_text: The RDH10-activated DHRS3 acts as a robust high affinity all-trans-retinaldehyde-specific reductase that effectively converts retinaldehyde back to retinol, decreasing the rate of retinoic acid biosynthesis. gocam_associations: - model: gomodel:67086be200002705 activity: gomodel:67086be200002705/67086be200002846 title: Retinoid Metabolic Process 4 (Mouse) description: Mouse Dhrs3 GO:0052650 all-trans-retinol dehydrogenase (NADP+) activity. - order: 4 role: irreversible oxidation of retinal to all-trans-retinoic acid node: id: retinal_oxidation label: Retinaldehyde dehydrogenases ALDH1A1, ALDH1A2 and ALDH1A3 module_type: REACTION description: >- Cytosolic NAD+-dependent class 1 aldehyde dehydrogenases oxidise all-trans-retinal to atRA through a catalytic cysteine. The reaction is irreversible and commits retinal to atRA. The three paralogues catalyse the same reaction and differ in tissue and developmental expression (ALDH1A2 is the main embryonic and testicular enzyme, ALDH1A1 is abundant in liver and also oxidises other aldehydes, ALDH1A3 acts in the developing eye and nasal region), so they are modelled as variants. concepts: - preferred_term: retinoic acid biosynthetic process term: id: GO:0002138 label: retinoic acid biosynthetic process variant_sets: - id: raldh_paralog label: Retinaldehyde dehydrogenase paralogue axis: enzyme paralogue (ALDH1A1/ALDH1A2/ALDH1A3, differing in tissue and developmental expression) selection: ONE_OR_MORE variants: - id: aldh1a2_variant label: ALDH1A2 (RALDH2) module_type: REACTION annotons: - id: aldh1a2_retinal_dehydrogenase label: ALDH1A2 retinal dehydrogenase (NAD+) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ALDH1A2 (RALDH2) term: id: UniProtKB:O94788 label: Retinal dehydrogenase 2 function: preferred_term: retinal dehydrogenase (NAD+) activity term: id: GO:0001758 label: retinal dehydrogenase (NAD+) activity substrates: - preferred_term: all-trans-retinal term: id: CHEBI:17898 label: all-trans-retinal - preferred_term: NAD+ term: id: CHEBI:57540 label: NAD(1-) products: - preferred_term: all-trans-retinoate term: id: CHEBI:35291 label: all-trans-retinoate - preferred_term: NADH term: id: CHEBI:57945 label: NADH(2-) processes: - preferred_term: retinoic acid biosynthetic process term: id: GO:0002138 label: retinoic acid biosynthetic process locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- The dominant embryonic and spermatogenic atRA-synthesising enzyme. GO:0001758 is its experimental GOA function (IDA, PMID:29240402). evidence: - source_id: PMID:29240402 statement: ALDH1A2 is the primary RA-synthesising enzyme in mammalian spermatogenesis. supporting_text: ALDH1A2 is the primary RA-synthesizing enzyme in mammalian spermatogenesis and is therefore considered a viable drug target for male contraceptive development. - id: aldh1a1_variant label: ALDH1A1 (RALDH1) module_type: REACTION annotons: - id: aldh1a1_retinal_dehydrogenase label: ALDH1A1 retinal dehydrogenase (NAD+) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ALDH1A1 (RALDH1) term: id: UniProtKB:P00352 label: Aldehyde dehydrogenase 1A1 function: preferred_term: retinal dehydrogenase (NAD+) activity term: id: GO:0001758 label: retinal dehydrogenase (NAD+) activity substrates: - preferred_term: all-trans-retinal term: id: CHEBI:17898 label: all-trans-retinal - preferred_term: NAD+ term: id: CHEBI:57540 label: NAD(1-) products: - preferred_term: all-trans-retinoate term: id: CHEBI:35291 label: all-trans-retinoate - preferred_term: NADH term: id: CHEBI:57945 label: NADH(2-) locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Broad-specificity cytosolic aldehyde dehydrogenase, abundant in liver, that oxidises retinal to atRA. Its experimental GOA functions are the generic aldehyde dehydrogenase (NAD+) activity (GO:0004029) and 3-deoxyglucosone dehydrogenase activity; GO:0001758 rests on ISS and IEA in human GOA. The more specific term is used here because retinal oxidation is the activity the pathway needs and is a long-established activity of the enzyme, which the 3-deoxyglucosone paper itself states. evidence: - source_id: PMID:17175089 statement: ALDH1A1 is a known retinaldehyde-to-RA enzyme that also oxidises 3-deoxyglucosone. supporting_text: aldehyde dehydrogenase 1A1 (ALDH1A1), an enzyme known to catalyze the oxidation of retinaldehyde to retinoic acid. - id: aldh1a3_variant label: ALDH1A3 (RALDH3) module_type: REACTION annotons: - id: aldh1a3_retinal_dehydrogenase label: ALDH1A3 retinal dehydrogenase (NAD+) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ALDH1A3 (RALDH3) term: id: UniProtKB:P47895 label: Retinaldehyde dehydrogenase 3 function: preferred_term: retinal dehydrogenase (NAD+) activity term: id: GO:0001758 label: retinal dehydrogenase (NAD+) activity substrates: - preferred_term: all-trans-retinal term: id: CHEBI:17898 label: all-trans-retinal - preferred_term: NAD+ term: id: CHEBI:57540 label: NAD(1-) products: - preferred_term: all-trans-retinoate term: id: CHEBI:35291 label: all-trans-retinoate - preferred_term: NADH term: id: CHEBI:57945 label: NADH(2-) processes: - preferred_term: retinoic acid biosynthetic process term: id: GO:0002138 label: retinoic acid biosynthetic process locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Retinal dehydrogenase of the developing eye and nasal region. GO:0001758 and GO:0002138 are both experimental in GOA (IDA, PMID:27759097), from the structure with bound NAD+ and atRA. evidence: - source_id: PMID:27759097 statement: ALDH1A3 oxidises retinal to retinoic acid using NAD+. supporting_text: The aldehyde dehydrogenase family 1 member A3 (ALDH1A3) catalyzes the oxidation of retinal to the pleiotropic factor retinoic acid using NAD+. - order: 5 role: cytosolic atRA binding (delivery or sequestration) node: id: retinoic_acid_binding label: Cellular retinoic acid-binding proteins CRABP1 and CRABP2 module_type: TRANSPORT_STEP description: >- atRA in the cytosol is bound by two small FABP-family proteins with opposite effects on its fate. CRABP2 moves to the nucleus and hands atRA directly to the RARs, increasing signalling; CRABP1 retains atRA in the cytosol and favours its CYP26 catabolism. They are modelled as variants along the axis of what happens to the bound atRA. FABP5, which RGD also draws, is not modelled (see notes). variant_sets: - id: crabp_paralog label: CRABP paralogue axis: fate of bound atRA (nuclear delivery to RARs versus cytosolic retention and catabolism) selection: ONE_OR_MORE variants: - id: crabp2_variant label: CRABP2 (delivery to RAR) module_type: TRANSPORT_STEP annotons: - id: crabp2_retinoic_acid_binding label: CRABP2 retinoic acid binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CRABP2 term: id: UniProtKB:P29373 label: Cellular retinoic acid-binding protein 2 function: preferred_term: retinoic acid binding term: id: GO:0001972 label: retinoic acid binding locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Binds atRA and channels it to RAR in the nucleus. GO:0001972 rests on IBA and IEA in human GOA; no experimental retinoic acid binding row exists, although binding is the defining property of the protein. The same protein appears, without the binding function, in the production part of modules/retinoic_acid_receptor_signaling.yaml. evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0001004.yaml statement: RGD assigns CRABP2 delivery of atRA to the RARs. supporting_text: Crabp2 and Fabp5 deliver atRA to particular nuclear receptors such as retinoid acid receptors (RARs) - id: crabp1_variant label: CRABP1 (cytosolic retention, favours catabolism) module_type: TRANSPORT_STEP annotons: - id: crabp1_retinoic_acid_binding label: CRABP1 retinoic acid binding participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CRABP1 term: id: UniProtKB:P29762 label: Cellular retinoic acid-binding protein 1 function: preferred_term: retinoic acid binding term: id: GO:0001972 label: retinoic acid binding locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Binds atRA in the cytosol and, when overexpressed, raises the rate of atRA catabolism. GO:0001972 rests on IBA and IEA in human GOA. evidence: - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0001004.yaml statement: RGD records that CRABP1 overexpression increases atRA catabolism. supporting_text: its overexpression increases the rate of atRA catabolism. - order: 6 role: oxidative catabolism of atRA node: id: retinoic_acid_catabolism label: CYP26 retinoic acid hydroxylases (CYP26A1, CYP26B1, CYP26C1) module_type: REACTION description: >- ER cytochrome P450s hydroxylate atRA at C4 and C18, forming 4-OH-, 4-oxo- and 18-OH-atRA, which are far less active and are further oxidised and conjugated for elimination. The three enzymes share the chemistry and differ in tissue expression and kinetics: CYP26A1 has the highest capacity and is strongly atRA-inducible, CYP26B1 has the highest affinity and dominates in brain, and CYP26C1 also accepts 9-cis-RA. concepts: - preferred_term: retinoic acid catabolic process term: id: GO:0034653 label: retinoic acid catabolic process variant_sets: - id: cyp26_paralog label: CYP26 paralogue axis: enzyme paralogue (CYP26A1/B1/C1, differing in tissue expression, kinetics and isomer range) selection: ONE_OR_MORE variants: - id: cyp26a1_variant label: CYP26A1 module_type: REACTION annotons: - id: cyp26a1_ra_hydroxylase label: CYP26A1 retinoic acid 4-hydroxylase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CYP26A1 term: id: UniProtKB:O43174 label: Cytochrome P450 26A1 function: preferred_term: retinoic acid 4-hydroxylase activity term: id: GO:0008401 label: retinoic acid 4-hydroxylase activity substrates: - preferred_term: all-trans-retinoate term: id: CHEBI:35291 label: all-trans-retinoate - preferred_term: O2 term: id: CHEBI:15379 label: dioxygen - preferred_term: reduced [NADPH-hemoprotein reductase] products: - preferred_term: all-trans-4-hydroxyretinoate term: id: CHEBI:134178 label: all-trans-4-hydroxyretinoate processes: - preferred_term: retinoic acid catabolic process term: id: GO:0034653 label: retinoic acid catabolic process locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- High-capacity, atRA-inducible atRA hydroxylase, dominant in liver. GO:0008401 is experimental in GOA (IDA, PMID:9228017, PMID:10823918 and others), as is all-trans retinoic acid 18-hydroxylase activity (GO:0062183, IDA, PMID:22020119), which is recorded here in prose. evidence: - source_id: PMID:9228017 statement: CYP26A1 generates 4-OH-RA, 4-oxo-RA and 18-OH-RA. supporting_text: We demonstrate that hP450RAI is responsible for generation of several hydroxylated forms of RA, including 4-OH-RA, 4-oxo-RA, and 18-OH-RA. - source_id: PMID:22020119 statement: CYP26A1 has higher activity than CYP26B1 and seems to clear atRA in barrier tissues. supporting_text: CYP26A1 has higher catalytic activity than CYP26B1 and seems to be responsible for metabolism of atRA in tissues that function as a barrier for atRA exposure. gocam_associations: - model: gomodel:5fce9b7300001742 activity: gomodel:5fce9b7300001742/5fce9b7300001846 title: Strap in alternative splicing-mouse description: >- Mouse Cyp26a1 GO:0008401 retinoic acid 4-hydroxylase activity, part of GO:0034653 retinoic acid catabolic process. The activity matches this annoton; the model as a whole is about Strap and splicing, so it grounds only the CYP26A1 activity. - id: cyp26b1_variant label: CYP26B1 module_type: REACTION annotons: - id: cyp26b1_ra_hydroxylase label: CYP26B1 retinoic acid 4-hydroxylase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CYP26B1 term: id: UniProtKB:Q9NR63 label: Cytochrome P450 26B1 function: preferred_term: retinoic acid 4-hydroxylase activity term: id: GO:0008401 label: retinoic acid 4-hydroxylase activity processes: - preferred_term: retinoic acid catabolic process term: id: GO:0034653 label: retinoic acid catabolic process locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- High-affinity atRA hydroxylase that predominates in cerebellum and pons. GO:0008401 and GO:0034653 are experimental in GOA (IDA, PMID:10823918). evidence: - source_id: PMID:10823918 statement: CYP26B1 (P450RAI-2) converts atRA to 4-oxo-, 4-OH- and 18-OH-atRA. supporting_text: Transiently transfected P450RAI-2 can convert all-trans-RA to more polar metabolites including 4-oxo-, 4-OH-, and 18-OH-all-trans-RA. - source_id: PMID:22020119 statement: CYP26B1 has a lower Km than CYP26A1 for 4-OH-RA formation. supporting_text: CYP26B1 had a lower K(m) (19nM) and V(max) (0.8 pmol/min/pmol) than CYP26A1 - id: cyp26c1_variant label: CYP26C1 module_type: REACTION annotons: - id: cyp26c1_ra_hydroxylase label: CYP26C1 retinoic acid 4-hydroxylase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CYP26C1 term: id: UniProtKB:Q6V0L0 label: Cytochrome P450 26C1 function: preferred_term: retinoic acid 4-hydroxylase activity term: id: GO:0008401 label: retinoic acid 4-hydroxylase activity processes: - preferred_term: retinoic acid catabolic process term: id: GO:0034653 label: retinoic acid catabolic process locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: >- Third CYP26, with restricted adult expression, that metabolises both all-trans- and 9-cis-RA. GO:0008401 and GO:0034653 are experimental in GOA (IDA, PMID:14532297). evidence: - source_id: PMID:14532297 statement: CYP26C1 prefers atRA but also metabolises 9-cis-RA. supporting_text: Specifically, CYP26C1 can also recognize and metabolize 9-cis-RA and is much less sensitive than the other CYP26 family members to the inhibitory effects of ketoconazole. - order: 7 role: retinyl ester storage and mobilisation (buffer of the retinol pool) optional: true node: id: retinyl_ester_storage label: Retinyl ester formation (LRAT) and hydrolysis (CES1) module_type: METABOLIC_PATHWAY description: >- Optional side branch. Cellular retinol not oxidised by RDH10 can be esterified by LRAT and stored as retinyl esters, mainly in hepatic stellate cells, and the esters are hydrolysed back to retinol when needed. It is optional because it buffers the retinol supply rather than being a step on the route from retinol to atRA, and atRA is made in tissues without a large ester store. parts: - order: 1 role: retinol esterification node: id: retinol_esterification_ref label: LRAT esterification of all-trans-retinol description: >- Included by reference to the LRAT step of the retinoid visual cycle module, which models phosphatidylcholine-retinol O-acyltransferase activity on the same all-trans-retinol substrate. The enzyme and reaction are the same in the RPE and in storage tissues, so the step is not re-modelled. module_ref: retinoid_visual_cycle#retinol_esterification - order: 2 role: retinyl ester hydrolysis node: id: retinyl_ester_hydrolysis label: CES1 retinyl ester hydrolase module_type: REACTION annotons: - id: ces1_retinyl_ester_hydrolase label: CES1 retinyl-palmitate esterase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CES1 term: id: UniProtKB:P23141 label: Liver carboxylesterase 1 function: preferred_term: retinyl-palmitate esterase activity term: id: GO:0050253 label: retinyl-palmitate esterase activity substrates: - preferred_term: all-trans-retinyl palmitate term: id: CHEBI:17616 label: all-trans-retinyl palmitate products: - preferred_term: all-trans-retinol term: id: CHEBI:17336 label: all-trans-retinol - preferred_term: hexadecanoate term: id: CHEBI:7896 label: hexadecanoate locations: - preferred_term: endoplasmic reticulum lumen term: id: GO:0005788 label: endoplasmic reticulum lumen role_description: >- The human hepatic retinyl ester hydrolase drawn by RGD. Experimental GOA functions are generic carboxylesterase and sterol ester esterase activities; GO:0050253 rests on IBA. The enzyme purified as liver retinyl ester hydrolase is a non-specific carboxylesterase, and several other lipases and esterases (for example PNPLA2 in stellate cells, in the mouse GO-CAM) also hydrolyse retinyl esters, so CES1 is one representative hydrolase rather than the dedicated enzyme. evidence: - source_id: PMID:9490062 statement: Hepatic retinyl ester hydrolase from pig and human liver is a non-specific carboxylesterase. supporting_text: Hepatic retinyl ester hydrolase (REH) activity was isolated from porcine and human liver and characterized connections: - source: retinol_delivery_uptake target: cellular_retinol_binding connection_type: PROVIDES_INPUT_FOR description: Retinol taken up through STRA6 is bound by CRBP1 in the cytosol. - source: cellular_retinol_binding target: retinol_retinal_interconversion connection_type: PROVIDES_INPUT_FOR description: Holo-CRBP1 retinol is the substrate of the membrane-bound RDH10. - source: retinol_retinal_interconversion target: retinal_oxidation connection_type: PROVIDES_INPUT_FOR description: The all-trans-retinal not reduced back by DHRS3 is oxidised to atRA by the ALDH1A enzymes. - source: retinal_oxidation target: retinoic_acid_binding connection_type: PROVIDES_INPUT_FOR description: Newly made atRA is bound by CRABP2 (delivery to RAR) or CRABP1 (retention). - source: retinoic_acid_binding target: retinoic_acid_catabolism connection_type: PROVIDES_INPUT_FOR description: Unbound and CRABP1-associated atRA is hydroxylated by the CYP26 enzymes. - source: cellular_retinol_binding target: retinyl_ester_storage connection_type: PROVIDES_INPUT_FOR description: Surplus holo-CRBP1 retinol is esterified by LRAT for storage. - source: retinyl_ester_storage target: cellular_retinol_binding connection_type: PROVIDES_INPUT_FOR description: Hydrolysis of stored retinyl esters returns retinol to the cellular pool. notes: >- Derived from the RGD Pathway Ontology record and diagram PW:0001004 (retinoic acid metabolic pathway) through the RGD_PATHWAY_ONTOLOGY project's diagram->module route; GO mapping GO:0042573 retinoic acid metabolic process (skos:closeMatch). The 18-gene RGD human set and the diagram give the boundary: circulating retinol in, atRA made, bound and catabolised, with an output to the retinoic acid signaling pathway (PW:0001014). It is modelled as six required parts and one optional part: (1) RBP4/TTR transport and STRA6 uptake; (2) CRBP1 binding; (3) the RDH10-DHRS3 retinol dehydrogenase/retinaldehyde reductase pair; (4) a variant set of the ALDH1A1, ALDH1A2 and ALDH1A3 retinaldehyde dehydrogenases; (5) a variant set of CRABP2 and CRABP1; (6) a variant set of the CYP26A1, CYP26B1 and CYP26C1 hydroxylases; and (7, optional) retinyl ester storage, with LRAT esterification by module_ref and CES1 hydrolysis. Second RGD pathway considered, PW:0000141 (retinol metabolic pathway, GO:0042572), is NOT listed as an evidence source and is not claimed as covered. Its record and diagram describe dietary vitamin A absorption in the intestine: carotenoid uptake by SCARB1 and CD36, retinyl ester hydrolysis in the gut lumen by PNLIP, PNLIPRP2 and PLB1, central cleavage of beta-carotene to retinal by BCO1, reduction of retinal by AKR1B10, binding by RBP2 (CRBP2), re-esterification by LRAT, chylomicron secretion and ABCA1 efflux, with the ISX feedback on SCARB1 and BCO1. Of its 11 RGD human genes only LRAT (here by reference) and ALDH1A2 fall inside this module. Its content is enterocyte absorption and chylomicron packaging, a distinct module upstream of the plasma RBP4 pool, so it should get its own module rather than be counted as covered here. Boundary decisions. (a) Downstream signalling is not modelled: RAR/RXR activation and coregulator exchange are in modules/retinoic_acid_receptor_signaling.yaml (RGD PW:0001014). That module has a compact retinoic acid production and transport part, with ALDH1A2 and CRABP2 grounded by PAINT nodes, which overlaps parts 4 and 5 here; it could be replaced there by a module_ref to this module's retinal_oxidation and retinoic_acid_binding nodes (not edited here). (b) The retinoid visual cycle (modules/retinoid_visual_cycle.yaml) shares LRAT and DHRS3. LRAT is included by module_ref to its retinol_esterification node, since the reaction and enzyme are the same. DHRS3 is modelled again here, with its RDH10 partner, because the visual-cycle node treats it as a stand-alone buffer and has no RDH10; the activity term (GO:0052650) is the same in both. That module does not contain RBP4 or STRA6, so the plasma delivery step is modelled here. (c) Retinyl ester storage is optional: it buffers the retinol supply rather than being a step from retinol to atRA. CES1 is the RGD-drawn hydrolase; its GO:0050253 rests on IBA, and the purified liver retinyl ester hydrolase is a non-specific carboxylesterase, so it is a representative, not the dedicated enzyme. The mouse GO-CAM gomodel:67086be200001721 uses Pnpla2 for the same step in stellate cells. (d) Context, not participants: cytosolic medium-chain alcohol dehydrogenases (ADH1 class, ADH4, ADH7), which oxidise retinol in vitro and in mouse GO-CAMs gomodel:66f5faaa00001204 and gomodel:67086be200002705 (Adh1 GO:0004745), but whose redundancy RDH10 genetics argues against as the main embryonic route (PMID:17473173); and the other SDR retinol dehydrogenases in the RGD gene list, RDH16 and DHRS9, which have experimental GO:0004745 rows in human GOA but whose contribution to atRA synthesis in vivo is less clear than that of RDH10 and which also act on 3-alpha-hydroxysteroids. They could be added as an optional variant of part 3 if a curator judges the in vivo evidence sufficient. (e) FABP5 is drawn by RGD as delivering atRA to PPARD. It is a broad fatty acid-binding protein (GO:0005504 IDA), and the atRA-PPARD route is contested, so it is not a participant. (f) Not drawn by RGD and not modelled: BCO1 cleavage of beta-carotene (an alternative retinal source, in PW:0000141), RETSAT, the 9-cis-RA routes, and DHRS3/CYP26A1 transcriptional induction by atRA, which is the feedback recorded in the description but which acts through the RAR module and is not drawn as a connection. Molecular functions come from each protein's experimental GO annotations in QuickGO (checked 2026-11-05): RBP4 retinol binding GO:0019841 (IDA, PMID:571335), with GO:0140104 molecular carrier activity used as the annoton function after the mouse GO-CAM; STRA6 GO:0034632 (IDA, PMID:21901792); RBP1 GO:1904768 (IDA, PMID:28057518); RDH10 GO:0004745 (IDA, PMID:12407145, PMID:19458327); DHRS3 GO:0052650 (EXP, PMID:9705317; core function of the completed DHRS3 review); ALDH1A2 GO:0001758 (IDA, PMID:29240402); ALDH1A3 GO:0001758 and GO:0002138 (IDA, PMID:27759097); CYP26A1 GO:0008401 (IDA) and GO:0062183 (IDA, PMID:22020119); CYP26B1 and CYP26C1 GO:0008401 and GO:0034653 (IDA). Exceptions, used without experimental GOA support: ALDH1A1 GO:0001758 (ISS/IEA; experimental rows are the parent GO:0004029); CRABP1 and CRABP2 GO:0001972 (IBA/IEA; CRABP2's only experimental MF row is cyclin binding); TTR GO:0140313 (TAS and mouse GO-CAM); CES1 GO:0050253 (IBA). Possible upstream issue: the RDH10 GO:0004745 (NAD+) IDA row from PMID:12407145 cites a paper whose abstract reports a preference for NADP as cofactor, so the NAD+ term may need checking against the full text. Comparator check for processes: GO:0002138 is placed on RDH10 and the ALDH1A enzymes, which do the chemistry, and not on the binding proteins or STRA6; GO:0034653 only on the CYP26 enzymes. GO-CAM: gocams/index.tsv (checked 2026-11-05) has no human production model for any member. The seed's best_gocam lead is empty for PW:0001004. Mouse models are linked at activity level: Retinoid Metabolic Process 2 (gomodel:67086be200001721; Rbp4, Ttr), Retinoid Metabolic Process 1 (gomodel:66f5faaa00001204; Rbp1) and 4 (gomodel:67086be200002705; Dhrs3), and gomodel:5fce9b7300001742 for Cyp26a1, whose title is about Strap and splicing, so only the Cyp26a1 activity is relevant. These mouse models describe absorption, storage and mobilisation and contain no Rdh10, Aldh1a2/3 or Crabp activity, which is the main GO-CAM gap for this pathway. Gene reviews exist for DHRS3 and LRAT (and RDH11, not a member); the other members have none. PANTHER family ids and PTNs are deliberately not asserted. Most cited publications are abstract-only in the cache; PMID:21901792, PMID:24733397 (PMC), PMID:17473173 (PMC), PMID:29240402, PMID:27759097, PMID:17175089 and PMID:22020119 have full text or a PMC record.