clk-1 encodes the C. elegans ortholog of COQ7 (human COQ7), a mitochondrial carboxylate-bridged di-iron monooxygenase (hydroxylase) that catalyzes the penultimate step of ubiquinone (coenzyme Q) biosynthesis: hydroxylation of 5-demethoxyubiquinone (DMQ) to 3-demethylubiquinone, using NAD(P)H and molecular oxygen (EC 1.14.13.253). The mature protein is a peripheral protein of the inner mitochondrial membrane on the matrix side and acts within the multi-subunit CoQ biosynthetic (COQ) machinery. Loss of clk-1 abolishes synthesis of ubiquinone (UQ9) and causes accumulation of the DMQ9 precursor, which can partially substitute as a respiratory-chain electron carrier. clk-1 is the founding "Clk" (clock) longevity gene: reduction-of-function mutants show an average slowing of developmental, behavioral, respiratory and metabolic rates and a markedly extended lifespan; these organismal phenotypes arise downstream of altered quinone content and mitochondrial reactive-oxygen-species output rather than from the hydroxylation step itself. A distinct, debated nuclear pool of CLK-1/COQ7 has additionally been reported to modulate mitochondrial retrograde stress signalling (the mitochondrial unfolded protein response), ROS-responsive gene expression, and longevity independently of ubiquinone biosynthesis.
Definition: A protein-containing complex, located at the matrix face of the inner mitochondrial membrane, that carries out the later membrane-associated steps of ubiquinone (coenzyme Q) biosynthesis; in eukaryotes it comprises multiple COQ polypeptides (including the COQ7/CLK-1 hydroxylase) that are mutually stabilizing.
Justification: CLK-1/COQ7 and its orthologs function within, and structurally stabilize, a multi-subunit CoQ biosynthetic complex, but GO has no cellular-component term for this complex.
Parent term: protein-containing complex
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005743 mitochondrial inner membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Core localization. CLK-1 is a peripheral inner-mitochondrial-membrane protein (matrix side) where it catalyzes DMQ hydroxylation in CoQ biosynthesis. Reason: Phylogenetic (IBA) placement in the inner mitochondrial membrane is consistent with direct experimental evidence that active CLK-1-GFP is found in worm mitochondria and with UniProt's peripheral/matrix-side membrane assignment. Supporting Evidence: PMID:10202142 CLK-1 is fully active when fused to green fluorescent protein and is found in the mitochondria of all somatic cells. |
| GO:0160224 3-demethoxyubiquinone 3-hydroxylase (NADH) activity | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function: the di-iron ubiquinone/CoQ biosynthetic monooxygenase catalyzing the DMQ to demethylubiquinone hydroxylation. Reason: This is the direct, evolutionarily conserved molecular function of clk-1/COQ7, matching EC 1.14.13.253 and supported experimentally in the worm. Supporting Evidence: PMID:14517217 clk-1 encodes a hydroxylase involved in the biosynthesis of the redox-active lipid ubiquinone (co-enzyme Q), and in clk-1 mutants, ubiquinone is replaced by its biosynthetic precursor demethoxyubiquinone. |
| GO:0006744 ubiquinone biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: Core biological process; the pathway in which the clk-1 hydroxylase acts. Reason: clk-1 is required for ubiquinone biosynthesis; loss abolishes UQ9 and leads to accumulation of the DMQ9 intermediate. Supporting Evidence: PMID:11244089 This result demonstrates that CLK-1 is absolutely required for the biosynthesis of UQ(9) in C. elegans. |
| GO:2000377 regulation of reactive oxygen species metabolic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Non-core regulatory role tied to the debated nuclear function; clk-1 mutants have altered ROS and a ROS-responsive gene-expression program. Reason: This IBA propagation reflects the reported nuclear CLK-1/COQ7 role in ROS metabolism rather than the direct hydroxylase activity; retain as a non-core downstream/moonlighting function. Supporting Evidence: PMID:25961505 the pathway regulates both mitochondrial reactive oxygen species metabolism and the mitochondrial unfolded protein response. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Debated secondary nuclear localization propagated by phylogeny; treat as non-core. Reason: A nuclear pool of CLK-1/COQ7 has been reported (GFP in both compartments), but this localization and its functional significance remain debated; it is not the core mitochondrial site of the enzyme. Supporting Evidence: PMID:25961505 adult transgenic worms expressing CLK-1 fused to green fluorescent protein (GFP) also display fluorescence in both compartments |
| GO:0008340 determination of adult lifespan | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Classic longevity phenotype; a downstream organismal consequence of altered quinone content, not the core molecular function. Reason: clk-1 loss extends lifespan, but this is a pleiotropic downstream effect of reduced ubiquinone/altered mitochondrial metabolism; keep as non-core. Supporting Evidence: PMID:10202142 the reduced respiration of the long-lived clk-1 mutants suggests that longevity is promoted by the age-dependent decrease in mitochondrial function |
| GO:0004497 monooxygenase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Correct but general parent of the specific 3-demethoxyubiquinone 3-hydroxylase activity; captures the core monooxygenase function. Reason: InterPro2GO assigns the general monooxygenase parent; it is accurate for the di-iron hydroxylase but less informative than GO:0160224, which is also annotated. Supporting Evidence: PMID:14517217 clk-1 encodes a hydroxylase involved in the biosynthesis of the redox-active lipid ubiquinone (co-enzyme Q) |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Debated nuclear localization propagated from the UniProt subcellular vocabulary. Reason: This IEA derives from the UniProt Nucleus subcellular-location term, which is itself based on the single (debated) report of nuclear CLK-1/COQ7; retain as non-core. Supporting Evidence: PMID:25961505 We have uncovered a distinct nuclear form of CLK-1 that independently regulates lifespan. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Core localization; the enzyme's primary compartment. Reason: Mitochondrial localization is strongly established experimentally for CLK-1. Supporting Evidence: PMID:10202142 CLK-1 is fully active when fused to green fluorescent protein and is found in the mitochondria of all somatic cells. |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Core localization; peripheral inner-membrane, matrix side. Reason: Consistent with UniProt's inner-membrane (peripheral, matrix-side) assignment and the phylogenetic annotation. |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Core biological process (electronic support for the pathway role). Reason: Automated multi-method IEA correctly assigns the ubiquinone biosynthetic process, consistent with experimental evidence. Supporting Evidence: PMID:11244089 This result demonstrates that CLK-1 is absolutely required for the biosynthesis of UQ(9) in C. elegans. |
| GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen | IEA GO_REF:0000104 | ACCEPT | Summary: Correct general MF parent corresponding to the EC 1.14.13 mechanism (NAD(P)H, one oxygen atom incorporated). Reason: Accurately describes the mechanistic class of the clk-1 hydroxylation reaction; less specific than GO:0160224 but not incorrect. |
| GO:0031314 extrinsic component of mitochondrial inner membrane | IEA GO_REF:0000104 | ACCEPT | Summary: Accurate refinement of the localization: CLK-1 is a peripheral (extrinsic) inner-membrane protein on the matrix face. Reason: Matches UniProt's "Peripheral membrane protein; Matrix side" assignment and is more precise than the plain inner-membrane term. |
| GO:0160224 3-demethoxyubiquinone 3-hydroxylase (NADH) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function (electronic/RHEA-EC support). Reason: Automated RHEA/EC-based assignment of the specific hydroxylase activity, the direct molecular function of clk-1. Supporting Evidence: PMID:11244089 clk-1 mutants mitochondria do not contain detectable levels of UQ(9). Instead, the UQ(9) biosynthesis intermediate, demethoxyubiquinone (DMQ(9)), is present at high levels. |
| GO:0000122 negative regulation of transcription by RNA polymerase II | IMP PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | KEEP AS NON CORE | Summary: Non-core, debated nuclear moonlighting function; nuclear CLK-1 suppresses a subset of ROS/UPRmt genes. Reason: Based on the reported nuclear role in which CLK-1 abrogates the elevated transcript levels of stress genes in clk-1 null worms. This is an experimental IMP but reflects a debated non-mitochondrial activity; retain as non-core. Supporting Evidence: PMID:25961505 The expression of nuclear CLK-1 in clk-1 null worms abrogated the increased transcript levels of these genes |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | KEEP AS NON CORE | Summary: Non-core, debated nuclear moonlighting function; nuclear CLK-1 promotes expression of some target genes (e.g. glna-1/GLS2). Reason: Same nuclear study: loss of nuclear CLK-1/COQ7 decreases glna-1/GLS2 expression, which is rescued by nuclear CLK-1. Experimental IMP but a debated non-core function. Supporting Evidence: PMID:25961505 glna-1 transcript levels were decreased compared to wild type animals, an effect that was rescued in the presence of CLK-1nuc(+) |
| GO:0008340 determination of adult lifespan | IMP PMID:17277769 eIF4E function in somatic cells modulates ageing in Caenorha... | KEEP AS NON CORE | Summary: Longevity phenotype; clk mutants used in a genetic study of translation and ageing. Downstream/non-core. Reason: Supports clk-1's role in lifespan determination as a pleiotropic downstream effect. The cached abstract names "clk" mutants; the curator read the full text. Supporting Evidence: PMID:17277769 lack of IFE-2 enhances the long-lived phenotype of clk and dietary-restricted eat mutant animals. |
| GO:0008340 determination of adult lifespan | IGI PMID:17277769 eIF4E function in somatic cells modulates ageing in Caenorha... | KEEP AS NON CORE | Summary: Genetic-interaction evidence for the longevity phenotype (with ife-2). Downstream/non-core. Reason: IGI supporting the pleiotropic lifespan role; a non-core organismal phenotype. Supporting Evidence: PMID:17277769 lack of IFE-2 enhances the long-lived phenotype of clk and dietary-restricted eat mutant animals. |
| GO:0008340 determination of adult lifespan | IGI PMID:19783783 Life-span extension by dietary restriction is mediated by NL... | KEEP AS NON CORE | Summary: Genetic-interaction lifespan evidence (electron-transport-chain longevity pathway). Downstream/non-core. Reason: The cached abstract discusses long-lived electron-transport-chain mutants rather than naming clk-1 explicitly; the full-text curator classed clk-1 in this group. clk-1's lifespan role is well established, so retain as non-core rather than remove. Supporting Evidence: PMID:19783783 has no effect on the life span of long-lived mutants resulting from reduced insulin/IGF-1 signaling or dysfunction of the mitochondrial electron transport chain. |
| GO:0008340 determination of adult lifespan | IMP PMID:19783783 Life-span extension by dietary restriction is mediated by NL... | KEEP AS NON CORE | Summary: Longevity phenotype (mutant); downstream/non-core. Reason: IMP for the pleiotropic lifespan phenotype; retain as a non-core downstream effect of altered mitochondrial quinone metabolism. Supporting Evidence: PMID:19783783 has no effect on the life span of long-lived mutants resulting from reduced insulin/IGF-1 signaling or dysfunction of the mitochondrial electron transport chain. |
| GO:0005634 nucleus | IDA PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | KEEP AS NON CORE | Summary: Direct (GFP/immunostaining) evidence for a nuclear pool of CLK-1/COQ7; a debated secondary localization, kept as non-core. Reason: Genuine experimental IDA (CLK-1-GFP in both compartments; endogenous COQ7 in nuclei), but the endogenous, physiologically significant nuclear pool remains debated and is not the core enzymatic site. Per curation guidance the experimental annotation is retained (not removed), marked non-core. Supporting Evidence: PMID:25961505 adult transgenic worms expressing CLK-1 fused to green fluorescent protein (GFP) also display fluorescence in both compartments |
| GO:0005739 mitochondrion | IDA PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | ACCEPT | Summary: Core localization; direct evidence for mitochondrial CLK-1. Reason: Direct imaging shows CLK-1-GFP in mitochondria (and nucleus); mitochondrion is the primary/core site of the enzyme. Supporting Evidence: PMID:25961505 adult transgenic worms expressing CLK-1 fused to green fluorescent protein (GFP) also display fluorescence in both compartments |
| GO:0006744 ubiquinone biosynthetic process | IMP PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | ACCEPT | Summary: Core biological process; full-length CLK-1 rescues UQ biosynthesis. Reason: This study confirms the mitochondrial CLK-1 requirement for ubiquinone biosynthesis (full-length, but not nuclear-only, CLK-1 rescues UQ). Supporting Evidence: PMID:25961505 full length CLK-1 was able to rescue ubiquinone biosynthesis in these worms, however, CLK-1nuc(+) could not |
| GO:0008340 determination of adult lifespan | IMP PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | KEEP AS NON CORE | Summary: Longevity phenotype; here attributed partly to the debated nuclear CLK-1 pool. Downstream/non-core. Reason: clk-1 modulates lifespan; this study assigns part of that effect to nuclear CLK-1 independent of ubiquinone. A non-core downstream/moonlighting phenotype. Supporting Evidence: PMID:25961505 the expression of CLK-1nuc(+) in clk-1 null worms caused a decrease in their enhanced longevity phenotype |
| GO:2000377 regulation of reactive oxygen species metabolic process | IMP PMID:25961505 A nuclear role for the respiratory enzyme CLK-1 in regulatin... | KEEP AS NON CORE | Summary: Non-core regulatory role; nuclear CLK-1 modulates cellular ROS levels and ROS-responsive gene expression. Reason: Experimental IMP for ROS regulation via the debated nuclear pathway; a downstream/moonlighting function rather than the direct hydroxylase activity. Supporting Evidence: PMID:25961505 Expression of CLK-1nuc(+) in clk-1 null worms partially rescued the increased ROS levels observed in these animals |
| GO:0000976 transcription cis-regulatory region binding | IDA PMID:11959146 CLK-1 protein has DNA binding activity specific to O(L) regi... | KEEP AS NON CORE | Summary: Isolated in-vitro report that CLK-1 binds the O_L region of mitochondrial DNA; a debated possible moonlighting activity, kept as non-core. Reason: The single (2002) in-vitro study shows sequence-specific binding to the mitochondrial-DNA O_L region, not a nuclear cis-regulatory region; it is not widely replicated and is unrelated to the core hydroxylase function. As an experimental IDA it is retained rather than removed, but flagged as a debated, possibly over-annotated moonlighting activity. Supporting Evidence: PMID:11959146 C. elegans CLK-1 as well as its mouse homologue have DNA binding activity that is specific to the O(L) region of mitochondrial DNA. |
| GO:0005739 mitochondrion | IDA PMID:17189267 Knockdown of mitochondrial heat shock protein 70 promotes pr... | ACCEPT | Summary: Core localization; CLK-1 treated as a mitochondrial protein. Reason: This study monitors CLK-1 as a mitochondrial protein whose levels drop upon hsp-6 (mtHSP70) knockdown, consistent with mitochondrial localization. Supporting Evidence: PMID:17189267 Knockdown of HSP-6 by RNA interference in young adult nematodes caused a reduction in the levels of ATP-2, HSP-60 and CLK-1 |
| GO:0006744 ubiquinone biosynthetic process | IMP PMID:14517217 Molecular mechanism of maternal rescue in the clk-1 mutants ... | ACCEPT | Summary: Core biological process; clk-1 hydroxylase required for UQ, replaced by DMQ in mutants. Reason: Directly supports the ubiquinone biosynthetic role; in clk-1 mutants UQ is replaced by the DMQ precursor. Supporting Evidence: PMID:14517217 clk-1 encodes a hydroxylase involved in the biosynthesis of the redox-active lipid ubiquinone (co-enzyme Q), and in clk-1 mutants, ubiquinone is replaced by its biosynthetic precursor demethoxyubiquinone. |
| GO:0008340 determination of adult lifespan | IMP PMID:14517217 Molecular mechanism of maternal rescue in the clk-1 mutants ... | KEEP AS NON CORE | Summary: Longevity/developmental-timing phenotype; downstream/non-core. Reason: Supports the pleiotropic ageing phenotype; a downstream consequence of altered quinone metabolism, not the core function. Supporting Evidence: PMID:14517217 The clk-1 mutants of Caenorhabditis elegans display an average slowing down of physiological rates, including those of development, various behaviors, and aging. |
| GO:0008340 determination of adult lifespan | IGI PMID:14517217 Molecular mechanism of maternal rescue in the clk-1 mutants ... | KEEP AS NON CORE | Summary: Genetic interaction with daf-2 for lifespan; downstream/non-core longevity phenotype. Reason: The daf-2 clk-1 double-mutant synergy underlies this IGI; a non-core organismal longevity phenotype. Supporting Evidence: PMID:14517217 the very long lifespan observed in daf-2 clk-1 double mutants is not abolished by the maternal effect |
| GO:0040010 positive regulation of growth rate | IMP PMID:14517217 Molecular mechanism of maternal rescue in the clk-1 mutants ... | KEEP AS NON CORE | Summary: Developmental-timing/growth-rate phenotype (the "Clk" slowing); downstream and non-core. Reason: clk-1 loss slows post-embryonic growth and development; a pleiotropic timing phenotype rather than the direct molecular function. Supporting Evidence: PMID:14517217 The clk-1 mutants of Caenorhabditis elegans display an average slowing down of physiological rates, including those of development, various behaviors, and aging. |
| GO:0048520 positive regulation of behavior | IMP PMID:14517217 Molecular mechanism of maternal rescue in the clk-1 mutants ... | KEEP AS NON CORE | Summary: Behavioral-rate ("clock") phenotype (e.g. defecation/pumping rhythms); downstream/non-core. Reason: Slowed rhythmic behaviors are a hallmark Clk phenotype but a downstream consequence of altered mitochondrial metabolism. Supporting Evidence: PMID:14517217 The clk-1 mutants of Caenorhabditis elegans display an average slowing down of physiological rates, including those of development, various behaviors, and aging. |
| GO:0051094 positive regulation of developmental process | IMP PMID:14517217 Molecular mechanism of maternal rescue in the clk-1 mutants ... | KEEP AS NON CORE | Summary: Developmental-timing phenotype; downstream/non-core. Reason: clk-1 loss slows embryonic and post-embryonic development; a pleiotropic timing phenotype, not the core function. Supporting Evidence: PMID:14517217 The clk-1 mutants of Caenorhabditis elegans display an average slowing down of physiological rates, including those of development, various behaviors, and aging. |
| GO:0006119 oxidative phosphorylation | IMP PMID:16920626 Mitochondrial complex I function modulates volatile anesthet... | KEEP AS NON CORE | Summary: Non-core; clk-1 mutation alters respiratory-chain (OXPHOS) function via changed quinone content. Reason: OXPHOS effects are a downstream consequence of DMQ-for-UQ substitution at the respiratory chain, not a direct clk-1 molecular function. Supporting Evidence: PMID:16920626 a clear correlation between complex I-dependent oxidative phosphorylation capacity and volatile anesthetic sensitivity. |
| GO:0009410 response to xenobiotic stimulus | IMP PMID:16920626 Mitochondrial complex I function modulates volatile anesthet... | KEEP AS NON CORE | Summary: Altered volatile-anesthetic (xenobiotic) sensitivity of the mutant; an indirect downstream phenotype, non-core. Reason: The anesthetic-sensitivity phenotype arises indirectly from altered complex-I/ OXPHOS function in quinone-pathway mutants; a distal phenotype rather than a direct clk-1 function (borderline over-annotation), kept as non-core. Supporting Evidence: PMID:16920626 a clear correlation between complex I-dependent oxidative phosphorylation capacity and volatile anesthetic sensitivity. |
| GO:0005739 mitochondrion | IDA PMID:10202142 CLK-1 controls respiration, behavior and aging in the nemato... | ACCEPT | Summary: Core localization; direct evidence that active CLK-1-GFP is mitochondrial. Reason: Foundational direct evidence for mitochondrial localization of functional CLK-1. Supporting Evidence: PMID:10202142 CLK-1 is fully active when fused to green fluorescent protein and is found in the mitochondria of all somatic cells. |
| GO:0006744 ubiquinone biosynthetic process | IDA PMID:11244089 Altered quinone biosynthesis in the long-lived clk-1 mutants... | ACCEPT | Summary: Core biological process; biochemical demonstration that CLK-1 is required for UQ9 synthesis (DMQ9 accumulates in mutants). Reason: Strong direct biochemical evidence for the ubiquinone biosynthetic role. Supporting Evidence: PMID:11244089 clk-1 mutants mitochondria do not contain detectable levels of UQ(9). Instead, the UQ(9) biosynthesis intermediate, demethoxyubiquinone (DMQ(9)), is present at high levels. |
| GO:0006744 ubiquinone biosynthetic process | IMP PMID:12709403 Silencing of ubiquinone biosynthesis genes extends life span... | ACCEPT | Summary: Core biological process; RNAi of clk-1 (with other COQ genes) reduces Q and extends lifespan. Reason: RNAi phenotype confirms clk-1's role in ubiquinone biosynthesis. Supporting Evidence: PMID:12709403 We have identified by RNA interference (RNAi) eight genes, including clk-1, involved in ubiquinone biosynthesis in C. elegans |
| GO:0008340 determination of adult lifespan | IMP PMID:10202142 CLK-1 controls respiration, behavior and aging in the nemato... | KEEP AS NON CORE | Summary: Longevity phenotype (foundational); downstream/non-core. Reason: Foundational demonstration that clk-1 controls aging; a pleiotropic downstream phenotype rather than the core molecular function. Supporting Evidence: PMID:10202142 Overexpression of CLK-1 activity in wild-type worms can increase mitochondrial activity, accelerate behavioral rates during aging and shorten life span |
| GO:0030534 adult behavior | IMP PMID:10202142 CLK-1 controls respiration, behavior and aging in the nemato... | KEEP AS NON CORE | Summary: Rhythmic adult-behavior ("clock") phenotype; downstream/non-core. Reason: The slowed rhythmic behaviors of clk-1 mutants are a downstream Clk phenotype, not the direct function. Supporting Evidence: PMID:10202142 Mutations in the clk-1 gene of the nematode Caenorhabditis elegans result in an average slowing of a variety of developmental and physiological processes, including the cell cycle, embryogenesis, post-embryonic growth, rhythmic behaviors and aging. |
| GO:0045333 cellular respiration | TAS PMID:10202142 CLK-1 controls respiration, behavior and aging in the nemato... | KEEP AS NON CORE | Summary: clk-1 controls respiration via its role in ubiquinone supply; a closely-linked but downstream process, non-core. Reason: Respiration is affected because ubiquinone (or the DMQ surrogate) feeds the electron transport chain; this is a consequence of the biosynthetic function rather than the molecular function itself. Supporting Evidence: PMID:10202142 the reduced respiration of the long-lived clk-1 mutants |
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Download this section (compressed HTML)Q: Is the pro-longevity signal in clk-1 mutants driven by the accumulated DMQ species, by lowered ubiquinone, or by an altered ROS output, and are these separable?
Q: Does an endogenous nuclear pool of CLK-1 exist at physiologically relevant levels in C. elegans, and if so how is it targeted given the non-conserved N-terminus?
Experiment: Rescue clk-1 nulls with graded dietary ubiquinone versus DMQ analogs while measuring quinone pools, mitochondrial ROS, respiration, and lifespan, to determine which change is causal for lifespan extension.
Hypothesis: The longevity of clk-1 mutants is set by the quinone species/ROS output rather than by ATP-level respiratory deficiency.
Type: metabolite-rescue and phenotype assay
Experiment: Use endogenously tagged CLK-1 and separation-of-function alleles (nuclear- targeting-impaired vs catalytically-dead) with imaging, subcellular fractionation, and ChIP to test for a reproducible, sequence-specific nuclear/ chromatin role in the worm.
Hypothesis: CLK-1 has a separable nuclear function distinct from its mitochondrial hydroxylase activity.
Type: genetics and localization
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: How the quinone change in clk-1 mutants (loss of ubiquinone UQ9, accumulation of the DMQ9 precursor) is transduced into the pro-longevity signal is undetermined: it is unclear whether the signal comes from DMQ itself, from altered respiratory-chain electron flow, from changed mitochondrial ROS output, or from a ubiquinone-independent route, and which of these is causal for lifespan extension.
OPEN BIOLOGY BP_DARK
What is known: It is firmly established that CLK-1 catalyzes DMQ hydroxylation in ubiquinone biosynthesis, that clk-1 nulls lack UQ9 and accumulate DMQ9, that DMQ9 can partially substitute as a respiratory-chain electron carrier, and that clk-1 loss extends lifespan. The mechanistic link between the specific quinone species and the longevity output is what remains open.
Significance: clk-1 is a flagship mitochondrial-longevity ("Clk") gene; resolving how quinone identity sets lifespan would clarify a central, conserved model of how mitochondrial metabolism controls ageing.
What would resolve it: Uncouple the candidate signals experimentally (e.g. dietary UQ rescue vs DMQ supplementation; quinone-pool and ROS measurements combined with lifespan) to establish which change is causal.
Provenance (the field's own admissions):
Gap: Whether CLK-1 has a genuine, physiologically significant non-mitochondrial (nuclear) function in C. elegans is unresolved: how a nuclear pool is targeted (the worm N-terminus lacks the COQ7 nuclear-targeting residues), whether it binds DNA sequence-specifically, and whether its effect on transcription of ROS/UPRmt genes is a direct molecular activity or an indirect consequence, remain open and debated.
OPEN BIOLOGY MF_DARK
What is known: A nuclear pool of CLK-1/COQ7 and a ubiquinone-independent effect on ROS metabolism, the mitochondrial unfolded protein response, and longevity have been reported (Nat Cell Biol 2015), and an older in-vitro study reports CLK-1 binding the O_L region of mitochondrial DNA. What is unresolved is the mechanism, endogenous relevance, and reproducibility of a nuclear/DNA-associated role.
Significance: If real, a moonlighting nuclear/retrograde-signalling function would redefine CLK-1/COQ7 beyond a metabolic enzyme; if not, several transcription/ROS annotations rest on a contested model.
What would resolve it: Independent replication with endogenous, tagged CLK-1 (localization, ChIP, and separation-of-function alleles that disable nuclear but not mitochondrial CLK-1) in the worm.
Provenance (the field's own admissions):
Gap: There is no Gene Ontology cellular-component term for the multi-subunit ubiquinone-biosynthetic (COQ) complex ("CoQ synthome") of which CLK-1/COQ7 is a component and which it is proposed to structurally stabilize, so this membership cannot be expressed as a GO annotation.
OPEN ONTOLOGY CC_DARK
What is known: CLK-1/COQ7 is described (by similarity to characterized orthologs) as part of a multi-subunit COQ enzyme complex with a structural stabilizing role, but GO provides only the ubiquinone biosynthetic process and membrane-location terms, not a complex term.
Significance: Capturing COQ-complex membership would let curation record the structural role of COQ7 family members alongside their catalytic activity.
What would resolve it: Add a "coenzyme Q biosynthesis complex" (or "CoQ synthome") cellular-component term to GO.
Proposed term (ontology gap):
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