LIAS encodes mitochondrial lipoyl synthase (EC 2.8.1.8), a radical S-adenosyl-L-methionine (SAM) enzyme that completes de novo synthesis of the lipoyl cofactor. Lipoate is built on its carrier protein: an octanoyl chain from mitochondrial fatty acid synthesis is first attached to a conserved lysine of a lipoyl domain (by LIPT2, mainly onto the glycine cleavage system H protein GCSH), and LIAS then inserts sulfur atoms at C6 and C8 of that octanoyl group to form the dihydrolipoyl group. LIPT1 is thought to pass the lipoyl group on to the E2 subunits of the pyruvate, 2-oxoglutarate and branched-chain 2-oxoacid dehydrogenase complexes. LIAS binds two [4Fe-4S] clusters. The radical SAM cluster reductively cleaves SAM to a 5'-deoxyadenosyl radical that abstracts hydrogen atoms from C6 and C8. An auxiliary cluster supplies the sulfur atoms and is destroyed in each reaction, so sustained activity depends on the mitochondrial iron-sulfur delivery machinery (NFU1, ISCA1/ISCA2, with BOLA3 implicated genetically) to rebuild it, and on ferredoxin FDX1, which binds LIAS and supplies electrons. The enzyme is imported into the mitochondrial matrix by an N-terminal transit peptide. Lipoylation is essential for pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, branched-chain ketoacid dehydrogenase and the glycine cleavage system. Biallelic LIAS variants cause hyperglycinemia, lactic acidosis and seizures (HGCLAS), a neonatal-onset encephalopathy with combined pyruvate oxidation and glycine cleavage defects. Loss of Lias in mice is embryonic lethal.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO root catalytic activity from the radical SAM signatures (IPR006638, IPR007197). True, but it does not say which reaction. Reason: Following the RADICAL_SAM project rule for generic rows: LIAS has a defined reaction, lipoate synthase activity (EC 2.8.1.8), shown directly for the human enzyme (IDA, PMID:36281303), so the root term is replaced by the specific reaction term that the gene already carries. Proposed replacements: lipoate synthase activity Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes PMID:36281303 The inclusion of an excess of NFU1 in the LIAS reaction promotes multiple turnovers and generation of more than 5 equiv of lipoyl product |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: Mitochondrion from the MitoCoP high-confidence human mitochondrial proteome (PMID:34800366). Reason: LIAS has an N-terminal mitochondrial transit peptide (1-27) and works on mitochondrial lipoyl carrier proteins (GCSH and the 2-oxoacid dehydrogenase E2 subunits). Proteomic detection in purified human mitochondria agrees with this. The matrix sub-compartment is recorded separately (GO:0005759). Mitochondrion is as precise as this assay allows. Supporting Evidence: PMID:34800366 defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP) file:human/LIAS/LIAS-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for mitochondrion, from a lipoyl synthase family node (PTN000101947) that includes mouse Lias, Arabidopsis LIP1 and a trypanosomatid lipoyl synthase. Reason: Eukaryotic lipoyl synthases outside plastids work in mitochondria. Human LIAS sits inside that clade, has a transit peptide, and has been detected in human mitochondria (PMID:34800366). Mouse Lias was shown to be imported into mitochondria (PMID:11389890). Supporting Evidence: PMID:11389890 We have shown that the cDNA encodes a lipoic acid synthase by its ability to complement a mutant of Escherichia coli defective in lipoic acid synthase and that mLIP1 is targeted into the mitochondria. file:human/LIAS/LIAS-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Mitochondrion from combined automated methods (UniProt subcellular location, UniRule, Ensembl ortholog projection from mouse). Reason: Consistent with the transit peptide, the HAMAP rule, and the experimental human and mouse localisation evidence. Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion PMID:11389890 We have shown that the cDNA encodes a lipoic acid synthase by its ability to complement a mutant of Escherichia coli defective in lipoic acid synthase and that mLIP1 is targeted into the mitochondria. |
| GO:0005739 mitochondrion | ISS GO_REF:0000024 | ACCEPT | Summary: Mitochondrion transferred by sequence similarity from mouse Lias (Q99M04), which has IDA evidence for mitochondrial targeting (PMID:11389890). Reason: The mouse ortholog is experimentally targeted to mitochondria, and human LIAS is found in the human mitochondrial proteome. Supporting Evidence: PMID:11389890 We have shown that the cDNA encodes a lipoic acid synthase by its ability to complement a mutant of Escherichia coli defective in lipoic acid synthase and that mLIP1 is targeted into the mitochondria. PMID:34800366 defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP) |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6793591 | ACCEPT | Summary: Mitochondrial matrix from the Reactome reaction "LIAS synthesizes lipoyl-GCSH". Reason: LIAS is a soluble matrix enzyme. It has no transmembrane segment, and its substrate octanoyl-GCSH and the downstream lipoylated E2 subunits of PDH, OGDH and BCKDH are matrix proteins. LIAS co-migrates with GCSH and FDX1 in cells (PMID:37453661). This is the site where the core activity is carried out. Supporting Evidence: Reactome:R-HSA-6793591 Mitochondrial lipoyl synthase (LIAS) mediates the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to glycine cleavage system H protein (GCSH) PMID:37453661 Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH |
| GO:0006954 inflammatory response | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Inflammatory response transferred from mouse Lias, based on increased LPS-induced inflammation in Lias+/- mice (PMID:18845616). Reason: Source is a mouse IMP (PMID:18845616, Lias+/- mice) recorded upstream of the phenotype. Heterozygous mice had less tissue lipoic acid, more oxidative stress, and a stronger inflammatory response to LPS. LIAS does not carry out the inflammatory response. The phenotype follows from less lipoate (a cofactor and antioxidant) being available. The transferred claim is a physiological consequence of the core lipoylation activity, not participation, so the annotation overstates what LIAS does. It is not false as a genetic observation, so REMOVE is not used. Supporting Evidence: PMID:18845616 These data demonstrate the importance of endogenously produced LA for preventing leukocyte accumulation and tissue injury that result from LPS-induced inflammation. PMID:18845616 we examined the effect of genetic reduction of LA synthesis on its antioxidant and anti-inflammatory properties |
| GO:0006979 response to oxidative stress | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Response to oxidative stress transferred from mouse Lias, based on higher tissue oxidative stress in Lias+/- mice (PMID:18845616). Reason: Source is a mouse IMP (PMID:18845616, Lias+/- mice) recorded upstream of the phenotype. Heterozygous mice had less tissue lipoic acid, more oxidative stress, and a stronger inflammatory response to LPS. LIAS does not carry out the response to oxidative stress. The phenotype follows from less lipoate (a cofactor and antioxidant) being available. The transferred claim is a physiological consequence of the core lipoylation activity, not participation, so the annotation overstates what LIAS does. It is not false as a genetic observation, so REMOVE is not used. Supporting Evidence: PMID:18845616 Decreased Lias expression was associated with diminished hepatic LA and tissue oxidative stress. PMID:18845616 we examined the effect of genetic reduction of LA synthesis on its antioxidant and anti-inflammatory properties |
| GO:0009107 obsolete lipoate biosynthetic process | IBA GO_REF:0000033 | MODIFY | Summary: PAINT IBA to the obsolete lipoate biosynthetic process term, from the lipoyl synthase family node PTN000101947. Reason: GO:0009107 lipoate biosynthetic process is obsolete (obsoletion comment: inconsistent term usage) and QuickGO lists GO:0009249 protein lipoylation as its replaced_by term. The underlying claim is sound: in mammals lipoate is made de novo on the carrier protein, and LIAS performs the sulfur-insertion step that turns the octanoyl group into a lipoyl group. GO:0009249 explicitly covers de novo assembly on the carrier protein by octanoyl transfer followed by sulfur insertion, and it is the term the gene already carries. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: PANTHER:PTN000101947 SOURCE STALE OR MISSING Human LIAS descends from this lipoyl synthase node as expected. The only problem is that the asserted term GO:0009107 has been obsoleted and replaced by GO:0009249. This is a retired term, not wrong ancestral biology or a loss in the target. Proposed replacements: protein lipoylation Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes PMID:37453661 Second, two sulfurs are added at C-6 and C-8 positions by the lipoyl synthase (LIAS) enzyme, a radical SAM enzyme (23, 24, 25) that uses SAM to initiate the synthesis of lipoic acid on GCSH. |
| GO:0009107 obsolete lipoate biosynthetic process | IEA GO_REF:0000120 | MODIFY | Summary: Combined-method IEA (InterPro IPR003698 Lipoyl_synth, UniRule) to the obsolete lipoate biosynthetic process term. Reason: GO:0009107 lipoate biosynthetic process is obsolete (obsoletion comment: inconsistent term usage) and QuickGO lists GO:0009249 protein lipoylation as its replaced_by term. The underlying claim is sound: in mammals lipoate is made de novo on the carrier protein, and LIAS performs the sulfur-insertion step that turns the octanoyl group into a lipoyl group. GO:0009249 explicitly covers de novo assembly on the carrier protein by octanoyl transfer followed by sulfur insertion, and it is the term the gene already carries. Proposed replacements: protein lipoylation Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes PMID:37453661 Second, two sulfurs are added at C-6 and C-8 positions by the lipoyl synthase (LIAS) enzyme, a radical SAM enzyme (23, 24, 25) that uses SAM to initiate the synthesis of lipoic acid on GCSH. |
| GO:0009107 obsolete lipoate biosynthetic process | ISS GO_REF:0000024 | MODIFY | Summary: Obsolete lipoate biosynthetic process transferred from mouse Lias, which complements an E. coli lipA mutant (IGI, PMID:11389890). Reason: GO:0009107 lipoate biosynthetic process is obsolete (obsoletion comment: inconsistent term usage) and QuickGO lists GO:0009249 protein lipoylation as its replaced_by term. The underlying claim is sound: in mammals lipoate is made de novo on the carrier protein, and LIAS performs the sulfur-insertion step that turns the octanoyl group into a lipoyl group. GO:0009249 explicitly covers de novo assembly on the carrier protein by octanoyl transfer followed by sulfur insertion, and it is the term the gene already carries. Proposed replacements: protein lipoylation Supporting Evidence: PMID:11389890 We have shown that the cDNA encodes a lipoic acid synthase by its ability to complement a mutant of Escherichia coli defective in lipoic acid synthase and that mLIP1 is targeted into the mitochondria. PMID:37453661 Second, two sulfurs are added at C-6 and C-8 positions by the lipoyl synthase (LIAS) enzyme, a radical SAM enzyme (23, 24, 25) that uses SAM to initiate the synthesis of lipoic acid on GCSH. |
| GO:0009249 protein lipoylation | IEA GO_REF:0000120 | ACCEPT | Summary: Protein lipoylation from combined automated methods (UniRule, Ensembl projection from mouse Lias). Reason: LIAS carries out the second and final step of de novo protein lipoylation, inserting the two sulfurs into the octanoyl chain already attached to the carrier lysine. It therefore does part of the work of the process and passes the participation test. Loss of LIAS in patients causes a strong loss of protein-bound lipoamide (PMID:22152680). The human enzyme catalyses the step in vitro (PMID:36281303). Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes PMID:22152680 A pronounced reduction of the prosthetic group lipoamide was found in lipoylated proteins. PMID:37453661 Second, two sulfurs are added at C-6 and C-8 positions by the lipoyl synthase (LIAS) enzyme, a radical SAM enzyme (23, 24, 25) that uses SAM to initiate the synthesis of lipoic acid on GCSH. |
| GO:0016783 sulfurtransferase activity | IEA GO_REF:0000104 | MODIFY | Summary: Sulfurtransferase activity from UniRule-based transfer. Reason: Correct but general. Lipoate synthase activity (GO:0016992) is_a sulfurtransferase activity (QuickGO ancestor chain GO:0016992 -> GO:0016783 -> GO:0016782 -> GO:0016740), and GO:0016992 is supported experimentally for human LIAS and already carried by the gene. Refine to the specific reaction. Proposed replacements: lipoate synthase activity Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes PMID:36281303 LSs contain an additional auxiliary [4Fe-4S] cluster from which sulfur atoms are extracted during turnover, leading to degradation of the cluster |
| GO:0016992 lipoate synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for lipoate synthase activity from the lipoyl synthase family node (PTN000101947), with mouse and Arabidopsis donors. Reason: Lipoyl synthase activity is the defining, conserved function of the LipA/LIAS family. Human LIAS is inside the clade and keeps the radical SAM CxxxCxxC motif and the auxiliary-cluster cysteines. The activity has been shown directly for the human enzyme (PMID:36281303). Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Belongs to the radical SAM superfamily. Lipoyl synthase family. PMID:36281303 The inclusion of an excess of NFU1 in the LIAS reaction promotes multiple turnovers and generation of more than 5 equiv of lipoyl product |
| GO:0016992 lipoate synthase activity | IDA PMID:36281303 In Vitro Demonstration of Human Lipoyl Synthase Catalytic Ac... | ACCEPT | Summary: Warui et al. 2022 purified human LIAS (residues 28-372) with two [4Fe-4S] clusters. With an octanoyllysyl peptide it formed about 1 equivalent of lipoyl product, and with NFU1 present it formed more than 5 equivalents. Reason: Direct biochemical demonstration of the core activity for the human protein. The single turnover without NFU1 matches the sacrifice of the auxiliary cluster as sulfur donor, and NFU1 restores catalytic turnover. Supporting Evidence: PMID:36281303 the protein catalyzes formation of no more than 1 equiv of lipoyl product PMID:36281303 The inclusion of an excess of NFU1 in the LIAS reaction promotes multiple turnovers and generation of more than 5 equiv of lipoyl product PMID:36281303 LSs contain an additional auxiliary [4Fe-4S] cluster from which sulfur atoms are extracted during turnover, leading to degradation of the cluster |
| GO:0016992 lipoate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Lipoate synthase activity from combined automated methods (InterPro IPR003698, Rhea 16585, EC 2.8.1.8, UniRule). Reason: Consistent with the experimental evidence for the human enzyme (PMID:36281303) and the HAMAP family rule. Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes PMID:36281303 The inclusion of an excess of NFU1 in the LIAS reaction promotes multiple turnovers and generation of more than 5 equiv of lipoyl product |
| GO:0016992 lipoate synthase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Lipoate synthase activity transferred from mouse Lias (Q99M04), whose cDNA complements an E. coli lipA mutant (PMID:11389890). Reason: Supported by complementation of the mouse ortholog and by direct biochemistry of human LIAS (PMID:36281303, PMID:33562493). Supporting Evidence: PMID:11389890 We have shown that the cDNA encodes a lipoic acid synthase by its ability to complement a mutant of Escherichia coli defective in lipoic acid synthase and that mLIP1 is targeted into the mitochondria. PMID:33562493 The enzyme contains two [4Fe-4S] centers (reducing and auxiliary clusters) that promote radical formation and sulfur transfer, respectively. |
| GO:0032496 response to lipopolysaccharide | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: Response to lipopolysaccharide transferred from mouse Lias, based on increased LPS sensitivity of Lias+/- mice (PMID:18845616). Reason: Source is a mouse IMP (PMID:18845616, Lias+/- mice) recorded upstream of the phenotype. Heterozygous mice had less tissue lipoic acid, more oxidative stress, and a stronger inflammatory response to LPS. LIAS does not carry out the response to lipopolysaccharide. The phenotype follows from less lipoate (a cofactor and antioxidant) being available. The transferred claim is a physiological consequence of the core lipoylation activity, not participation, so the annotation overstates what LIAS does. It is not false as a genetic observation, so REMOVE is not used. Supporting Evidence: PMID:18845616 These data demonstrate the importance of endogenously produced LA for preventing leukocyte accumulation and tissue injury that result from LPS-induced inflammation. |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO iron-sulfur cluster binding from the radical SAM signatures. Reason: Following the RADICAL_SAM project rule: correct but general. LIAS binds two [4Fe-4S] clusters, the radical SAM cluster and the auxiliary sulfur-donor cluster, shown by Mossbauer and EPR spectroscopy for the human enzyme (PMID:36281303). The descendant GO:0051539 is the precise term and the gene already carries it. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. PMID:33562493 The enzyme contains two [4Fe-4S] centers (reducing and auxiliary clusters) that promote radical formation and sulfur transfer, respectively. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000120 | ACCEPT | Summary: 4 iron, 4 sulfur cluster binding from combined automated methods (InterPro IPR003698, UniRule). Reason: Core cofactor binding. Human LIAS binds two [4Fe-4S] clusters. The radical SAM cluster cleaves SAM to give the 5'-deoxyadenosyl radical, and the auxiliary cluster supplies the two sulfur atoms and is broken down during turnover (PMID:36281303, PMID:33562493). Both clusters are needed for catalysis. Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. PMID:36281303 All radical SAM enzymes have at least one [4Fe-4S] cluster that is used in the reductive cleavage of SAM to generate the 5'-dA· PMID:36281303 LSs contain an additional auxiliary [4Fe-4S] cluster from which sulfur atoms are extracted during turnover, leading to degradation of the cluster PMID:33562493 The enzyme contains two [4Fe-4S] centers (reducing and auxiliary clusters) that promote radical formation and sulfur transfer, respectively. |
| GO:1904047 S-adenosyl-L-methionine binding | IC PMID:36281303 In Vitro Demonstration of Human Lipoyl Synthase Catalytic Ac... | NEW | Summary: LIAS binds SAM as the radical-generating cosubstrate at the unique iron of its radical SAM [4Fe-4S] cluster. Human LIAS turns over an octanoyl peptide only when SAM is present. Reason: GOA has no SAM-binding row for LIAS, although the RADICAL_SAM project treats GO:1904047 as a core cosubstrate-binding function of every active radical SAM enzyme. This is a molecular function, not a process, so the participation test is met directly: LIAS itself binds and cleaves SAM. The HAMAP family rule records SAM as an exchangeable ligand of the radical SAM cluster, and the human enzyme carries out the SAM-dependent reaction in vitro (PMID:36281303). Comparator check, against GOA rather than against this project's own proposals: GOA does annotate GO:1904047 to radical SAM enzymes in exactly this role, by UniRule -- ECOLI/queE (UR000100349), ECOLI/moaA and PSEPK/moaA (UR000101305), METEA/pqqE and PSEPK/pqqE (UR000098303). So the absence here is patchy UniRule coverage, which rules happen to carry the term, not a GO convention against annotating a radical SAM enzyme's own cosubstrate. That is also why those five genes have an existing row to ACCEPT or MODIFY while this one needs a NEW row. Supporting Evidence: file:human/LIAS/LIAS-uniprot.txt Binds 2 [4Fe-4S] clusters per subunit. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. PMID:36281303 All radical SAM enzymes have at least one [4Fe-4S] cluster that is used in the reductive cleavage of SAM to generate the 5'-dA· |
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Download this section (compressed HTML)Q: In human mitochondria, does LIAS act only on octanoyl-GCSH, with LIPT1 then relaying the lipoyl group to the E2 subunits of PDH, OGDH and BCKDH, or can LIAS also lipoylate octanoylated E2 lipoyl domains directly at a physiologically significant rate?
Q: Which iron-sulfur carrier (NFU1 alone, the NFU1-ISCA1 heterodimer, or ISCA2/ISCU) rebuilds the auxiliary cluster of LIAS in vivo, and at which step is BOLA3 required, given that it has no direct effect on cluster transfer in vitro?
Experiment: In LIPT1-knockout human cells expressing an E2 lipoyl domain that is octanoylated in vivo (e.g. by a mitochondrially targeted bacterial LipB), measure whether LIAS converts octanoyl-E2 to lipoyl-E2 by targeted mass spectrometry, and compare with GCSH-knockout cells.
Hypothesis: LIAS lipoylates only GCSH in human cells, and E2 lipoylation depends on LIPT1-mediated transfer.
Experiment: Pulse-chase 57Fe or 34S labelling in NFU1-, ISCA1-, ISCA2- and BOLA3-depleted cells, followed by LIAS immunoprecipitation, Mossbauer or mass-spectrometric cluster analysis, and per-turnover lipoyl product isotope tracking.
Hypothesis: NFU1 is the obligate in vivo donor for the auxiliary cluster of LIAS.
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