SQLE encodes squalene monooxygenase (squalene epoxidase; EC 1.14.14.17), an FAD-dependent flavoprotein monooxygenase that catalyzes the stereospecific oxidation of squalene to (S)-2,3-epoxysqualene (2,3-oxidosqualene), consuming molecular oxygen and using reducing equivalents supplied by NADPH via NADPH-cytochrome P450 reductase. This is the first oxygenation step of sterol biosynthesis and the second rate-limiting step of the cholesterol biosynthetic pathway, acting downstream of HMG-CoA reductase and between squalene synthase (FDFT1) and lanosterol synthase (LSS). The enzyme is an endoplasmic reticulum (microsome) membrane protein associated peripherally with the membrane through N-terminal and C-terminal hydrophobic regions rather than transmembrane helices. Its N-terminal regulatory domain senses cholesterol and mediates cholesterol-accelerated, MARCHF6-dependent ubiquitin- proteasome degradation, providing feedback control of flux through the pathway. SQLE is a validated antifungal and anticancer drug target.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005783 endoplasmic reticulum | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred endoplasmic reticulum localization. SQLE is a well-established ER/microsome membrane enzyme, so this is correct but broader than the specific ER membrane location captured by the IDA/IEA annotations. Reason: IBA localization consistent with all experimental evidence. ER is a correct compartment; the more specific and preferred CC term is endoplasmic reticulum membrane (GO:0005789), captured elsewhere in this record. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt Endoplasmic reticulum membrane Reactome:R-HSA-191299 Squalene monooxygenase (squalene epoxidase, SE) is located on the endoplamic reticulum. |
| GO:0004506 squalene monooxygenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred squalene monooxygenase activity. This is the core, defining molecular function of SQLE across eukaryotes and is directly supported by human enzymology and crystal structures. Reason: IBA correctly identifies the core catalytic function. Human recombinant enzyme was purified and kinetically characterized (PMID:10666321), and the catalytic domain structure with FAD was solved (PMID:30626872). Represents the core function of the gene. Supporting Evidence: PMID:30626872 SQLE is a flavin adenosine dinucleotide (FAD)–dependent epoxidase that catalyzes stereospecific conversion of non-sterol intermediate squalene to 2,3(S)-oxidosqualene file:human/SQLE/SQLE-uniprot.txt Catalyzes the stereospecific oxidation of squalene to |
| GO:0016126 sterol biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred involvement in sterol biosynthesis. SQLE catalyzes the first oxygenation step of the sterol pathway, so this BP annotation is correct. Reason: Correct and well-supported. In humans the specific downstream product pathway is cholesterol biosynthesis (GO:0006695); sterol biosynthetic process is the conserved, broader biological process appropriate for the pan-eukaryotic IBA. Core function. Supporting Evidence: PMID:30626872 the first oxygenation step in cholesterol synthesis |
| GO:0004506 squalene monooxygenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic assignment of squalene monooxygenase activity (ARBA/RHEA:25282/EC:1.14.14.17). Matches the experimentally established core function. Reason: The IEA mapping (RHEA:25282, EC 1.14.14.17) corresponds exactly to the reaction catalyzed by human SQLE and is corroborated by experimental evidence. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt EC=1.14.14.17 |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic CC annotation from UniProt Subcellular Location mapping (SL-0097). Matches the experimentally determined ER membrane localization. Reason: Correct and specific. SQLE is a peripheral ER/microsome membrane protein; supported by experimental topology work and by the IDA annotation from PMID:26434806. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt Endoplasmic reticulum membrane |
| GO:0016020 membrane | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO electronic annotation to the generic term membrane. Correct but far less informative than the specific ER membrane location. Reason: Not wrong (SQLE is membrane-associated), but membrane is an uninformative parent of the specific and preferred endoplasmic reticulum membrane (GO:0005789) already annotated. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt Endoplasmic reticulum membrane |
| GO:0016126 sterol biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO electronic annotation to sterol biosynthetic process, matching the enzyme family's conserved role. Reason: Correct BP for the squalene monooxygenase family; consistent with the IBA and experimental IDA annotations to the same term. Supporting Evidence: PMID:30626872 the first oxygenation step in cholesterol synthesis |
| GO:0050660 flavin adenine dinucleotide binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO electronic annotation for FAD binding. SQLE is an FAD-dependent flavoprotein; FAD is a required, structurally resolved cofactor. Reason: Correct cofactor-binding MF (equivalent to the IDA FAD binding annotation GO:0071949). FAD binding is a supporting molecular function of the catalytic activity rather than the core function itself. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt Name=FAD; Xref=ChEBI:CHEBI:57692; |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Binary-interactome (HuRI) protein-protein interactions. UniProt records the corresponding partners as CREB3L1 (Q96BA8), REEP4 (Q9H6H4) and TMEM14B (Q9NUH8). The bare protein binding term is uninformative about SQLE's function. Reason: Per curation guidelines, the generic protein binding (GO:0005515) term does not convey a specific molecular function. These high-throughput two-hybrid interactions (CREB3L1, REEP4, TMEM14B) are retained as recorded but flagged as over-annotation; they should not be treated as a core function. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt Q14534; Q96BA8: CREB3L1; NbExp=3; IntAct=EBI-3905171, EBI-6942903; |
| GO:0008203 cholesterol metabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation (ARBA) to the broad cholesterol metabolic process. SQLE participates in cholesterol metabolism via its role in cholesterol biosynthesis. Reason: Correct but general. The specific role is cholesterol biosynthetic process (GO:0006695), of which this is a parent; retained as accurate non-core context. Supporting Evidence: PMID:33791309 two rate-limiting enzymes, 3-hydroxy-3-methylglutarylcoenzyme A reductase (HMGCR) and squalene monooxygenase (SQLE) |
| GO:1904614 response to biphenyl | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: Electronic ortholog transfer (Ensembl Compara, from rat Sqle P52020) of a narrow "response to biphenyl" phenotype. There is no human evidence and no clear connection to SQLE's core enzymatic function. Reason: Over-propagated ortholog-transferred response term based solely on a single rodent dataset; it does not represent a core or well-supported human function. Retained but flagged as over-annotation rather than removed, as it is an electronic ortholog inference. Supporting Evidence: GO_REF:0000107 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara |
| GO:0006695 cholesterol biosynthetic process | IC PMID:30626872 Structure and inhibition mechanism of the catalytic domain o... | ACCEPT | Summary: Curator inference (from the squalene monooxygenase activity, GO:0004506) that SQLE is involved in cholesterol biosynthesis. This is the specific human pathway role. Reason: SQLE catalyzes the first oxygenation (epoxidation) step of the cholesterol biosynthetic pathway; the IC from the catalytic activity is sound and represents a core biological process for this gene. Supporting Evidence: PMID:30626872 the first oxygenation step in cholesterol synthesis |
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:26434806 The Regulatory Domain of Squalene Monooxygenase Contains a R... | ACCEPT | Summary: Direct experimental determination that the sterol-responsive N-terminal domain of SQLE is integrally associated with the ER membrane, localizing the active enzyme to the ER membrane. Reason: Topology mapping of SM N100-GFP by cysteine-accessibility placed SQLE in the ER membrane; the enzyme functions at this location. Core cellular location for the protein. Supporting Evidence: PMID:26434806 We have identified a region integrally associated with the endoplasmic reticulum membrane |
| GO:0006695 cholesterol biosynthetic process | IDA PMID:33791309 MYC Enhances Cholesterol Biosynthesis and Supports Cell Prol... | ACCEPT | Summary: Direct experimental evidence that SQLE controls cellular cholesterol levels: SQLE knockdown lowers cholesterol and SQLE overexpression raises it, and SQLE is required for MYC-driven cholesterol production. Reason: Functional genetic manipulation (siRNA/overexpression, cholesterol quantification) directly implicates SQLE in cholesterol biosynthesis. Core biological process. Supporting Evidence: PMID:33791309 Through transcriptional upregulation of SQLE, a rate-limiting enzyme in cholesterol synthesis pathway, MYC increases cholesterol production and promotes tumor cell growth. |
| GO:0004506 squalene monooxygenase activity | EXP PMID:10666321 Cloning, heterologous expression, and enzymological characte... | ACCEPT | Summary: Experimental enzymology: human squalene monooxygenase was cloned, expressed in E. coli, purified, and kinetically characterized, confirming squalene monooxygenase activity with FAD and NADPH-cytochrome P450 reductase as partners. Reason: Gold-standard biochemical demonstration of the core catalytic activity (Km squalene 7.7 uM, Km FAD 0.3 uM). Core molecular function. Supporting Evidence: PMID:10666321 The cDNA for human squalene monooxygenase, a key enzyme in the committed pathway for cholesterol biosynthesis, was amplified from a human liver cDNA library and cloned, and the protein was expressed in Escherichia coli and purified. |
| GO:0005515 protein binding | IPI PMID:29765154 The cancer-associated microprotein CASIMO1 controls cell pro... | MARK AS OVER ANNOTATED | Summary: Physical interaction of SQLE with the cancer-associated microprotein CASIMO1/SMIM22 (isoform K7EJ46). The interaction modulates SQLE protein accumulation and lipid droplet formation, but the bare protein binding term is uninformative. Reason: Genuine, experimentally supported interaction with CASIMO1 (SMIM22), but per curation guidelines protein binding (GO:0005515) is too generic to be a molecular function. Retained as recorded and flagged; the functional consequences are captured by the associated lipid droplet / proliferation BP annotations. Supporting Evidence: PMID:29765154 CASIMO1 microprotein interacts with squalene epoxidase (SQLE), a key enzyme in cholesterol synthesis and a known oncogene in breast cancer. file:human/SQLE/SQLE-uniprot.txt SMIM22; this interaction modulates lipid droplet formation |
| GO:0042127 regulation of cell population proliferation | IMP PMID:29765154 The cancer-associated microprotein CASIMO1 controls cell pro... | KEEP AS NON CORE | Summary: SQLE knockdown mimics the CASIMO1 knockdown proliferation phenotype and SQLE overexpression rescues it, implicating SQLE in the control of cell proliferation in breast cancer cells. Reason: Experimentally supported but a downstream, cell-context (cancer) consequence of altered cholesterol/lipid metabolism rather than the core molecular function of the enzyme. Keep as a valid non-core process annotation. Supporting Evidence: PMID:29765154 SQLE knockdown mimicked the CASIMO1 knockdown phenotype and in turn SQLE overexpression fully rescued the effect of CASIMO1 knockdown. |
| GO:0140042 lipid droplet formation | IMP PMID:29765154 The cancer-associated microprotein CASIMO1 controls cell pro... | KEEP AS NON CORE | Summary: Modulation of CASIMO1 (which interacts with SQLE) alters lipid droplet clustering, and the SQLE-CASIMO1 interaction is reported to modulate lipid droplet formation. Reason: Supported by the CASIMO1/SQLE study, but a peripheral, context-specific role linked to the interaction with SMIM22 rather than the core sterol-biosynthetic enzyme activity. Retain as non-core. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt SMIM22; this interaction modulates lipid droplet formation PMID:29765154 increased lipid droplet clustering |
| GO:0004506 squalene monooxygenase activity | IDA PMID:30626872 Structure and inhibition mechanism of the catalytic domain o... | ACCEPT | Summary: Direct assay of squalene monooxygenase activity across recombinant catalytic domain, full-length baculosome, and human liver microsome systems, with FAD/squalene kinetics and an LC-MS 2,3-oxidosqualene product assay. Reason: High-quality direct biochemical demonstration of the core catalytic function alongside crystal structures. Core molecular function. Supporting Evidence: PMID:30626872 SQLE is a flavin adenosine dinucleotide (FAD)–dependent epoxidase that catalyzes stereospecific conversion of non-sterol intermediate squalene to 2,3(S)-oxidosqualene |
| GO:0016020 membrane | IDA PMID:30626872 Structure and inhibition mechanism of the catalytic domain o... | MARK AS OVER ANNOTATED | Summary: Membrane association observed for SQLE, consistent with its C-terminal hydrophobic membrane-binding helices. Generic membrane term. Reason: Correct but uninformative; the specific location is the endoplasmic reticulum membrane (GO:0005789), and SQLE is a peripheral membrane protein without transmembrane helices. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt mediate interaction with membranes |
| GO:0016126 sterol biosynthetic process | IDA PMID:30626872 Structure and inhibition mechanism of the catalytic domain o... | ACCEPT | Summary: Direct evidence linking SQLE catalytic activity to sterol (cholesterol) biosynthesis via production of 2,3-oxidosqualene, the first oxygenation intermediate. Reason: Well-supported core BP; the enzyme's catalytic step is committed to sterol/cholesterol biosynthesis. Supporting Evidence: PMID:30626872 the first oxygenation step in cholesterol synthesis |
| GO:0043231 intracellular membrane-bounded organelle | IDA PMID:30626872 Structure and inhibition mechanism of the catalytic domain o... | MARK AS OVER ANNOTATED | Summary: Generic organelle localization consistent with ER (a membrane-bounded organelle) localization. Reason: Correct but very general parent of the specific endoplasmic reticulum membrane location; uninformative as an independent annotation. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt Endoplasmic reticulum membrane |
| GO:0071949 FAD binding | IDA PMID:30626872 Structure and inhibition mechanism of the catalytic domain o... | ACCEPT | Summary: Crystal structures of the SQLE catalytic domain were solved in complex with FAD, with multiple defined FAD-binding residues, directly demonstrating FAD binding. Reason: Direct structural evidence of the FAD cofactor and its binding pocket. FAD binding is a supporting molecular function enabling the core squalene monooxygenase catalysis. Supporting Evidence: file:human/SQLE/SQLE-uniprot.txt X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 118-574 IN COMPLEXES WITH FAD AND |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-1655844 | ACCEPT | Summary: Reactome traceable-author-statement placing SQLE at the ER membrane (Expression of Squalene Monooxygenase module). Consistent with all other evidence. Reason: Correct and specific ER membrane localization, corroborated by IDA and IEA annotations. Supporting Evidence: Reactome:R-HSA-191299 Squalene monooxygenase (squalene epoxidase, SE) is located on the endoplamic reticulum. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-191299 | ACCEPT | Summary: Reactome TAS for the reaction "Squalene is oxidized to its epoxide", placing squalene monooxygenase at the ER membrane. Reason: Correct ER membrane localization tied to the catalytic reaction module; consistent with experimental evidence. Supporting Evidence: Reactome:R-HSA-191299 It catalyzes the oxidation of squalene (SQNE) to squalene 2,3-epoxide (SQNX) |
| GO:0004506 squalene monooxygenase activity | NAS PMID:9286711 Localization of the squalene epoxidase gene (SQLE) to human ... | ACCEPT | Summary: Non-traceable author statement (gene-mapping paper) asserting the squalene epoxidase function. The catalytic function is independently confirmed experimentally. Reason: Although only NAS in this reference, the core squalene monooxygenase activity is firmly established by EXP/IDA evidence (PMID:10666321, PMID:30626872). Accept as consistent. Supporting Evidence: PMID:9286711 Squalene epoxidase (EC 1.14.99.7) catalyzes the first oxygenation step in sterol biosynthesis |
| GO:0016126 sterol biosynthetic process | NAS PMID:9286711 Localization of the squalene epoxidase gene (SQLE) to human ... | ACCEPT | Summary: Non-traceable author statement that squalene epoxidase acts in sterol biosynthesis. This is correct and supported by experimental evidence elsewhere. Reason: Consistent with the established role of SQLE in sterol/cholesterol biosynthesis; corroborated by IBA and experimental IDA annotations. Supporting Evidence: PMID:9286711 catalyzes the first oxygenation step in sterol biosynthesis and is suggested to be one of the rate-limiting enzymes in this pathway |
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Download this section (compressed HTML)Q: Beyond MARCHF6-mediated cholesterol-dependent degradation, what other post-translational inputs (e.g. unsaturated fatty acids, ERAD partners) tune SQLE stability in vivo?
Q: Is the SQLE-CASIMO1 (SMIM22) interaction relevant to normal (non-cancer) lipid droplet biology, or is it specific to tumor cell contexts?
Experiment: Reconstitute human SQLE with NADPH-cytochrome P450 reductase and measure epoxidation of squalene to (S)-2,3-epoxysqualene to formally confirm the physiological electron-donor coupling and stoichiometry.
Type: in vitro enzymatic reconstitution
Experiment: Structure-guided mutagenesis of the N-terminal cholesterol-sensing degron (residues 62-73) combined with degradation assays to map the cholesterol-responsive turnover mechanism.
Type: mutagenesis and protein degradation assay
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