Existing Annotations Review

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

Core Functions

Mitochondrial di-iron ubiquinone (coenzyme Q) biosynthetic monooxygenase. CLK-1 (COQ7 ortholog) uses a carboxylate-bridged di-iron center and NAD(P)H to hydroxylate 5-demethoxyubiquinone (DMQ) to 3-demethylubiquinone, the penultimate step of ubiquinone biosynthesis, acting as a peripheral protein on the matrix face of the inner mitochondrial membrane. Loss of this activity abolishes UQ9 and causes DMQ9 accumulation.

Molecular Function:

3-demethoxyubiquinone 3-hydroxylase (NADH) activity

Directly Involved In:

ubiquinone biosynthetic process

Cellular Locations:

mitochondrial inner membrane mitochondrion

Supporting Evidence:

PMID:11244089
This result demonstrates that CLK-1 is absolutely required for the biosynthesis of UQ(9) in C. elegans.
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.
PMID:9020081
clk-1 complemented the phenotype of cat5/coq7 null mutants, demonstrating that clk-1 and CAT5/COQ7 share biochemical function
file:worm/clk-1/clk-1-deep-research-falcon.md
CLK-1 (UniProt P48376) is a mitochondrial diiron carboxylate hydroxylase that catalyzes the C5 hydroxylation of DMQ9 to produce UQ9, the penultimate step in coenzyme Q biosynthesis.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000104

Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:9020081

Structural and functional conservation of the Caenorhabditis elegans timing gene clk-1.

PMID:10202142

CLK-1 controls respiration, behavior and aging in the nematode Caenorhabditis elegans.

PMID:11244089

Altered quinone biosynthesis in the long-lived clk-1 mutants of Caenorhabditis elegans.

PMID:11959146

CLK-1 protein has DNA binding activity specific to O(L) region of mitochondrial DNA.

PMID:12709403

Silencing of ubiquinone biosynthesis genes extends life span in Caenorhabditis elegans.

PMID:14517217

Molecular mechanism of maternal rescue in the clk-1 mutants of Caenorhabditis elegans.

PMID:16920626

Mitochondrial complex I function modulates volatile anesthetic sensitivity in C. elegans.

PMID:17189267

Knockdown of mitochondrial heat shock protein 70 promotes progeria-like phenotypes in caenorhabditis elegans.

PMID:17277769

eIF4E function in somatic cells modulates ageing in Caenorhabditis elegans.

PMID:19783783

Life-span extension by dietary restriction is mediated by NLP-7 signaling and coelomocyte endocytosis in C. elegans.

PMID:25961505

A nuclear role for the respiratory enzyme CLK-1 in regulating mitochondrial stress responses and longevity.

file:worm/clk-1/clk-1-deep-research-falcon.md

Deep research report (Edison/falcon): C. elegans CLK-1 (COQ7)

Suggested Experiments

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

Knowledge Gaps

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):

"it has not been possible to identify biochemical changes that might underlie the extension of life span observed in clk-1 mutants, and therefore the function of CLK-1 in C. elegans remains unknown." — PMID:11244089
"extended lifespans through a pathway that appears to be independent of ubiquinone biosynthesis and ATP production" — PMID:25961505

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):

"the N-terminal residues we identified as being critical for nuclear localisation of COQ7 do not appear to be conserved in CLK-1" — PMID:25961505
"in addition to its enzymatic function in ubiquinone biosynthesis, CLK-1 is involved in the regulation of mtDNA replication or transcription." — PMID:11959146

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):

coenzyme Q biosynthesis complex

Deep Research

Falcon

(clk-1-deep-research-falcon.md)

Comprehensive Research Report: *C. elegans* CLK-1 (COQ7) — Gene ID: clk-1, UniProt: P48376 Falcon Edison Scientific Literature 40 citations 1 artifacts 2026-07-04T15:46:09.357765

Edison artifact artifact-00 (text/markdown)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive Research Report: C. elegans CLK-1 (COQ7) — Gene ID: clk-1, UniProt: P48376

Gene Identity Verification

The gene symbol clk-1 unambiguously corresponds to the Caenorhabditis elegans Clock abnormal protein 1, also known as ubiquinone biosynthesis monooxygenase COQ7 (UniProt: P48376). This protein belongs to the COQ7 family of diiron carboxylate hydroxylases and contains the expected Ferritin-like superfamily fold (IPR009078) and the Ubq_synth_Coq7 domain (IPR011566; PF03232). The gene is encoded at locus ZC395.2 and is orthologous to yeast COQ7/CAT5, mouse Mclk1, and human COQ7 (wang2013moleculargeneticsof pages 4-6, jonassen1998yeastclk1homologue pages 1-1).

The following table summarizes the core properties of CLK-1:

Property	Details/Description
Gene name	clk-1 (C. elegans clock abnormal protein 1 / COQ7 ortholog) (wang2013moleculargeneticsof pages 4-6, jonassen1998yeastclk1homologue pages 1-1)
UniProt accession	P48376
Protein name	NADPH-dependent 3-demethoxyubiquinone 3-hydroxylase, mitochondrial; also called protein CLK-1 or ubiquinone biosynthesis monooxygenase COQ7 (wang2013moleculargeneticsof pages 6-7, stefely2017biochemistryofmitochondrial pages 21-22)
Enzymatic function	Catalyzes hydroxylation of demethoxyubiquinone during coenzyme Q biosynthesis; in C. elegans, loss of clk-1 prevents endogenous UQ9 production and causes DMQ9 accumulation, establishing CLK-1 as the DMQ hydroxylase step in the pathway (wang2013moleculargeneticsof pages 6-7, haynes2022mitochondrialdysfunctionaging pages 1-2, haynes2022mitochondrialdysfunctionaging pages 12-12)
EC number	EC 1.14.13.253
Substrate	DMQ9 / 5-demethoxyubiquinone-9 (demethoxyubiquinone precursor of ubiquinone-9) (wang2013moleculargeneticsof pages 6-7, haynes2022mitochondrialdysfunctionaging pages 1-2, wang2013moleculargeneticsof pages 12-14)
Product	UQ9 / ubiquinone-9 (coenzyme Q9); some descriptions also refer to formation of the hydroxylated intermediate en route to mature ubiquinone (haynes2022mitochondrialdysfunctionaging pages 1-2, haynes2022mitochondrialdysfunctionaging pages 12-12)
Cofactor / active site	Carboxylate-bridged diiron center that activates dioxygen for aromatic ring hydroxylation; catalytic activity is iron-sensitive and disrupted by manganese mismetallation (wang2013moleculargeneticsof pages 6-7, diessl2022manganesedrivencoqdeficiency pages 3-5, diessl2022manganesedrivencoqdeficiency pages 1-2)
Protein family	COQ7 family; conserved eukaryotic ubiquinone-biosynthetic hydroxylase family (wang2013moleculargeneticsof pages 4-6, jonassen1998yeastclk1homologue pages 1-1)
Structural features	Predicted/characterized four-helix bundle diiron protein with an additional membrane-associating helix; membrane-bound or peripherally membrane-associated hydroxylase (wang2022predictingandunderstanding pages 34-38, awad2018coenzymeq10deficiencies pages 7-8)
Subcellular localization	Primarily mitochondrial, associated with the inner mitochondrial membrane on the matrix side for CoQ biosynthesis; evidence also supports nuclear localization under stress/ROS conditions, where CLK-1/COQ7 may regulate gene expression (awad2018coenzymeq10deficiencies pages 7-8, lionaki2016differentialproteindistribution pages 8-9, jonassen2001adietarysource pages 5-6)
Pathway	Coenzyme Q (ubiquinone) biosynthesis; CLK-1/COQ7 functions in the late aromatic ring-modification steps and participates with COQ3/4/5/6/7/9 in the COQ metabolon / CoQ synthome (awad2018coenzymeq10deficiencies pages 8-10, nicoll2024invitroconstruction pages 1-2)
Organism	Caenorhabditis elegans (worm)
Orthologs	Conserved across eukaryotes: yeast Coq7p/Cat5p, mouse MCLK1, human COQ7; functional complementation data support strong conservation (haynes2022mitochondrialdysfunctionaging pages 12-12, wang2013moleculargeneticsof pages 4-6, diazcasado2019theparadoxof pages 7-9, jonassen1998yeastclk1homologue pages 1-1)

Table: This table summarizes the core identity, enzymatic role, localization, structure, and pathway context of C. elegans CLK-1/COQ7. It is useful as a compact reference for functional annotation and for distinguishing clk-1 from unrelated similarly named genes.

1. Enzymatic Function and Catalytic Mechanism

1.1 Primary Reaction

CLK-1 is an NADH-dependent hydroxylase (EC 1.14.13.253) that catalyzes the hydroxylation of 5-demethoxyubiquinone-9 (DMQ9) to produce ubiquinone-9 (UQ9/coenzyme Q9) in C. elegans. This reaction represents the penultimate step in the coenzyme Q biosynthetic pathway, specifically the C5 hydroxylation of the quinone ring (wang2013moleculargeneticsof pages 6-7, stefely2017biochemistryofmitochondrial pages 21-22, haynes2022mitochondrialdysfunctionaging pages 1-2, haynes2022mitochondrialdysfunctionaging pages 12-12). Loss-of-function mutations in clk-1 (such as the qm30 null allele) abolish endogenous UQ9 production and lead to accumulation of DMQ9, the direct substrate of CLK-1, firmly establishing this enzymatic assignment (haynes2022mitochondrialdysfunctionaging pages 1-2, wang2013moleculargeneticsof pages 12-14, wang2013moleculargeneticsof pages 4-6).

1.2 Active Site and Cofactor

CLK-1/COQ7 is a member of the carboxylate-bridged diiron protein family, which also includes methane monooxygenase, ribonucleotide reductase, and phenol hydroxylase (awad2018coenzymeq10deficiencies pages 7-8). The protein employs a diiron center to activate molecular oxygen (O₂) for the aromatic ring hydroxylation reaction. Spectroscopic characterization of the purified mouse ortholog MCLK1 confirmed the presence of this diiron center, which serves as the catalytic active site for dioxygen activation and subsequent demethoxyubiquinone hydroxylation (wang2013moleculargeneticsof pages 6-7). The enzymatic activity is sensitive to iron availability, and the diiron center can be reduced by substrate-mediated processes in the presence of NADH and oxygen. In vitro assays using substrate analogs DMQ0 and DMQ2 demonstrated binding to the diiron site and NADH-mediated reduction (stefely2017biochemistryofmitochondrial pages 21-22, awad2018coenzymeq10deficiencies pages 8-10).

1.3 Structural Features

COQ7 is predicted—and partially confirmed experimentally—to adopt a four-helix bundle architecture, with an additional α-helix mediating peripheral association with the mitochondrial inner membrane (wang2022predictingandunderstanding pages 34-38, awad2018coenzymeq10deficiencies pages 7-8). The iron-liganding motif has been refined as E–X₆–Y–X₂₂–E–X₂–H–X₄₈–E–X₆–Y–X₂₈–E–X₂–H, with key residues (E60, Y67, E90, H93, E142, Y149, E178, H181 in human COQ7 numbering) predicted to coordinate the two Fe(II) atoms within the bundle. However, experimentally determined structures have not yet captured metals in the active site, so the metal-liganding assignments remain based on structural analogy to other diiron proteins (wang2022predictingandunderstanding pages 34-38, wang2022predictingandunderstanding pages 38-41).

A particularly notable finding is that the diiron center of Coq7 is uniquely sensitive to manganese mismetallation. Under conditions of manganese overload, Mn²⁺ ions erroneously occupy the diiron binding sites, inactivating the enzyme and triggering its proteolytic degradation. This mismetallation selectively disrupts CoQ biosynthesis while leaving respiratory chain complexes intact, establishing Coq7 as the molecular target of manganese-induced bioenergetic failure (diessl2022manganesedrivencoqdeficiency pages 3-5, diessl2022manganesedrivencoqdeficiency pages 5-6, diessl2022manganesedrivencoqdeficiency pages 1-2, diessl2022manganesedrivencoqdeficiency pages 2-3).

2. Subcellular Localization

2.1 Mitochondrial Localization

The primary site of CLK-1 function is the mitochondria. CLK-1 contains a mitochondrial targeting sequence (MTS) and is peripherally associated with the inner mitochondrial membrane on the matrix side (awad2018coenzymeq10deficiencies pages 7-8, jonassen2001adietarysource pages 5-6). This localization is consistent with the established site of coenzyme Q biosynthesis in eukaryotic cells and with the mitochondrial localization of the yeast homolog Coq7p (jonassen2001adietarysource pages 5-6, jonassen1998yeastclk1homologue pages 1-1). CLK-1 is expressed ubiquitously throughout the worm, consistent with the observation that Q biosynthesis occurs in essentially all tissues (jonassen2001adietarysource pages 5-6).

2.2 Dual Localization to the Nucleus

Evidence supports a dual mitochondrial-nuclear distribution for CLK-1/COQ7. The protein contains nuclear localization signals in addition to its MTS, and nuclear accumulation has been observed under conditions of mitochondrial stress and elevated reactive oxygen species (ROS) (lionaki2016differentialproteindistribution pages 8-9, lionaki2016differentialproteindistribution pages 7-8). In the nucleus, CLK-1/COQ7 has been reported to bind chromatin and regulate oxidative stress response genes while suppressing genes associated with the mitochondrial unfolded protein response (UPRmt). Importantly, restricting CLK-1 exclusively to the nucleus inhibits ubiquinone biosynthesis, demonstrating that its nuclear role is distinct from its enzymatic function in the mitochondria (lionaki2016differentialproteindistribution pages 8-9). However, these nuclear "moonlighting" functions remain an area of active investigation and require further confirmation (haynes2022mitochondrialdysfunctionaging pages 12-13).

3. Pathway Context: The CoQ Biosynthetic Pathway and the COQ Metabolon

3.1 CoQ Biosynthesis

Coenzyme Q (ubiquinone) is an essential redox-active lipid composed of a benzoquinone ring and a polyisoprenyl tail. It functions primarily as a mobile electron carrier in the mitochondrial electron transport chain and as a membrane-soluble antioxidant (guerra2023coenzymeqbiochemistry pages 1-3). The biosynthesis of CoQ involves multiple enzymatic modifications of the aromatic ring, including decarboxylation, hydroxylation, and methylation reactions. CLK-1/COQ7 catalyzes the late-stage C5 hydroxylation that converts DMQ to UQ (haynes2022mitochondrialdysfunctionaging pages 12-12, guerra2023coenzymeqbiochemistry pages 3-4).

3.2 The COQ Metabolon (CoQ Synthome)

CLK-1/COQ7 does not function in isolation but rather as part of a multi-protein complex called the COQ metabolon (also termed the CoQ synthome or Complex Q). This complex comprises at least six core proteins: COQ3, COQ4, COQ5, COQ6, COQ7, and COQ9, all located at the matrix side of the inner mitochondrial membrane (awad2018coenzymeq10deficiencies pages 8-10, nicoll2024invitroconstruction pages 1-2). The metabolon coordinates sequential ring-modification reactions, facilitating substrate channeling among its component enzymes.

A landmark 2024 study by Nicoll et al. in Nature Catalysis achieved the first in vitro reconstitution of the complete COQ metabolon using ancestral sequence reconstruction, capturing the entire biosynthetic pathway in vitro and revealing enzymes responsible for previously uncharacterized steps (nicoll2024invitroconstruction pages 1-2, mattevi2023invitroconstruction pages 1-4). This work also demonstrated that COQ8, a kinase, increases and streamlines coenzyme Q production by phosphorylating metabolon components such as COQ3, thereby regulating metabolon assembly and disassembly (nicoll2024invitroconstruction pages 1-2, nicoll2024invitroconstruction pages 8-8).

3.3 The COQ7–COQ9 Interaction

A particularly well-characterized interaction within the metabolon is the COQ7:COQ9 complex. COQ9 is a lipid-binding auxiliary protein that physically associates with COQ7 and is essential for both the stability and catalytic activity of COQ7 (diazcasado2019theparadoxof pages 3-5, staiano2023biosynthesisdeficiencyand pages 4-5). The two proteins form a double heterodimer that reshapes the mitochondrial inner membrane to allow substrate accessibility to their lipid-binding sites (staiano2023biosynthesisdeficiencyand pages 4-5). COQ9 binds aromatic isoprene intermediates and is proposed to present these directly to COQ7 for hydroxylation (diazcasado2019theparadoxof pages 3-5). In COQ9-deficient cells and mice, COQ7 levels decrease and the COQ7 substrate DMQ accumulates, confirming the functional coupling of these two proteins (diazcasado2019theparadoxof pages 3-5).

4. Phenotypes of clk-1 Mutants and Relationship to Aging

4.1 Pleiotropic Phenotypes

clk-1 loss-of-function mutants in C. elegans display a constellation of pleiotropic phenotypes collectively described as the "Clock" (Clk) phenotype: slowed development, reduced rates of pharyngeal pumping, defecation, and swimming, as well as increased UV stress resistance and extended adult lifespan (jonassen2001adietarysource pages 5-6, jonassen1998yeastclk1homologue pages 1-1). The clk-1 mutant was among the first genetic demonstrations that mitochondrial dysfunction can paradoxically extend lifespan (haynes2022mitochondrialdysfunctionaging pages 1-1, haynes2022mitochondrialdysfunctionaging pages 12-12).

4.2 DMQ9 Accumulation and UQ9 Deficiency

clk-1 null mutants lack endogenous UQ9 and instead accumulate its biosynthetic precursor DMQ9 (haynes2022mitochondrialdysfunctionaging pages 1-2, wang2013moleculargeneticsof pages 12-14). DMQ9 differs from UQ9 by lacking one methoxy group and appears to act as a non-functional competitor at CoQ-binding sites in mitochondrial respiratory complexes, particularly at Complex I, further reducing electron transport chain efficiency (diazcasado2019theparadoxof pages 7-9, wang2013moleculargeneticsof pages 12-14). Despite lacking endogenous UQ9, clk-1 mutants survive because they can absorb bacterial UQ8 from their E. coli food source, which partially substitutes for endogenous UQ9 but does not fully restore wild-type phenotypes (haynes2022mitochondrialdysfunctionaging pages 1-1, haynes2022mitochondrialdysfunctionaging pages 1-2). Critically, clk-1 mutant larvae die on CoQ-deficient diets, indicating that a minimum level of dietary CoQ is essential for development and fertility (diazcasado2019theparadoxof pages 7-9).

4.3 Mechanism of Lifespan Extension

The lifespan extension in clk-1 mutants is intimately tied to deficient UQ synthesis. Treatment with 2,4-dihydroxybenzoic acid (2,4-DHB), a biosynthetic intermediate that bypasses the CLK-1 enzymatic step, rescues all clk-1 mutant phenotypes including the aging effect, even without any CLK-1 protein present (haynes2022mitochondrialdysfunctionaging pages 1-2, haynes2022mitochondrialdysfunctionaging pages 12-12). This demonstrates that all phenotypes result from the lack of UQ9 rather than from loss of any alternative CLK-1 function. The precise mechanism by which reduced UQ biosynthesis extends lifespan remains under investigation, but it is proposed to involve reduced electron flow through the respiratory chain, altered ROS production, and adaptive mitohormetic responses (diazcasado2019theparadoxof pages 7-9, haynes2022mitochondrialdysfunctionaging pages 12-12). Notably, the lifespan extension in clk-1 mutants is not suppressed by loss of the apoptotic pathway component CED-4, and in fact CED-4 loss further extends clk-1 mutant lifespan, distinguishing the clk-1 longevity mechanism from those of other mitochondrial mutants such as isp-1 and nuo-6 (haynes2022mitochondrialdysfunctionaging pages 12-13).

5. Evolutionary Conservation

CLK-1/COQ7 is highly conserved across eukaryotes, from Saccharomyces cerevisiae (yeast Coq7p/Cat5p) to C. elegans (CLK-1), mouse (MCLK1), and human (COQ7) (wang2013moleculargeneticsof pages 4-6, diazcasado2019theparadoxof pages 7-9, jonassen1998yeastclk1homologue pages 1-1). Functional conservation has been demonstrated through cross-species complementation experiments: the rat and C. elegans CLK-1 homologs can rescue yeast coq7/cat5 mutants, restoring growth on nonfermentable carbon sources (jonassen1998yeastclk1homologue pages 1-1). Similarly, mammalian COQ7 cDNA can partially complement yeast coq7 mutations (wang2013moleculargeneticsof pages 4-6). Both yeast coq7 and C. elegans clk-1 mutants accumulate the same class of biosynthetic intermediate (DMQ6 and DMQ9, respectively), and heterozygous Mclk1 mice also display extended lifespan, paralleling the C. elegans phenotype (wang2013moleculargeneticsof pages 4-6, diazcasado2019theparadoxof pages 7-9). Treatment with 2,4-DHB restores UQ biosynthesis in CLK-1-deficient mouse cells and Mclk1 knockout mice, confirming conservation of the bypass mechanism (haynes2022mitochondrialdysfunctionaging pages 12-12).

6. Recent Developments (2022–2024)

Several important advances have furthered our understanding of COQ7/CLK-1:

In vitro reconstitution of the COQ metabolon (2024): Nicoll et al. used ancestral sequence reconstruction to create stable, experimentally tractable COQ proteins and achieved the first complete in vitro reconstitution of the CoQ biosynthetic metabolon, revealing the determinants of substrate channeling and the regulatory role of COQ8 kinase (nicoll2024invitroconstruction pages 1-2, mattevi2023invitroconstruction pages 1-4, nicoll2024invitroconstruction pages 8-8).
Manganese mismetallation of Coq7 (2022): Diessl et al. demonstrated that manganese overload selectively inactivates Coq7 through mismetallation of its diiron center, revealing a conserved molecular mechanism for manganese-induced bioenergetic failure (diessl2022manganesedrivencoqdeficiency pages 3-5, diessl2022manganesedrivencoqdeficiency pages 5-6, diessl2022manganesedrivencoqdeficiency pages 1-2).
COQ7:COQ9 double heterodimer characterization (2023): Staiano et al. described the COQ7–COQ9 complex as a double heterodimer that reshapes the mitochondrial inner membrane for substrate accessibility, advancing understanding of the lipid-binding and substrate delivery mechanisms (staiano2023biosynthesisdeficiencyand pages 4-5).
CoQ biochemistry review (2023): Guerra and Pagliarini provided a comprehensive review highlighting persisting knowledge gaps in CoQ biosynthesis, distribution, and transport, while emphasizing the central role of the COQ metabolon in which COQ7 participates (guerra2023coenzymeqbiochemistry pages 12-14, guerra2023coenzymeqbiochemistry pages 1-3).

Summary

C. elegans CLK-1 (UniProt P48376) is a mitochondrial diiron carboxylate hydroxylase that catalyzes the C5 hydroxylation of DMQ9 to produce UQ9, the penultimate step in coenzyme Q biosynthesis. It functions at the matrix face of the inner mitochondrial membrane as part of the COQ metabolon, in close partnership with the lipid-binding protein COQ9. Loss of CLK-1 abolishes endogenous UQ9 production, leading to pleiotropic phenotypes including slowed development and extended lifespan—effects that are entirely attributable to UQ deficiency and can be rescued by biosynthetic bypass compounds. CLK-1 is highly conserved across eukaryotes, and its diiron active site is uniquely vulnerable to manganese mismetallation. Evidence also supports a secondary, stress-responsive nuclear localization where CLK-1 may modulate gene expression, though this function requires further confirmation.

References

(wang2013moleculargeneticsof pages 4-6): Ying Wang and Siegfried Hekimi. Molecular genetics of ubiquinone biosynthesis in animals. Critical Reviews in Biochemistry and Molecular Biology, 48:69-88, Jan 2013. URL: https://doi.org/10.3109/10409238.2012.741564, doi:10.3109/10409238.2012.741564. This article has 90 citations and is from a peer-reviewed journal.
(jonassen1998yeastclk1homologue pages 1-1): Tanya Jonassen, Markus Proft, Francisca Randez-Gil, Jeffery R. Schultz, B. Noelle Marbois, Karl-Dieter Entian, and Catherine F. Clarke. Yeast clk-1 homologue (coq7/cat5) is a mitochondrial protein in coenzyme q synthesis*. The Journal of Biological Chemistry, 273:3351-3357, Feb 1998. URL: https://doi.org/10.1074/jbc.273.6.3351, doi:10.1074/jbc.273.6.3351. This article has 182 citations.
(wang2013moleculargeneticsof pages 6-7): Ying Wang and Siegfried Hekimi. Molecular genetics of ubiquinone biosynthesis in animals. Critical Reviews in Biochemistry and Molecular Biology, 48:69-88, Jan 2013. URL: https://doi.org/10.3109/10409238.2012.741564, doi:10.3109/10409238.2012.741564. This article has 90 citations and is from a peer-reviewed journal.
(stefely2017biochemistryofmitochondrial pages 21-22): Jonathan A. Stefely and David J. Pagliarini. Biochemistry of mitochondrial coenzyme q biosynthesis. Trends in biochemical sciences, 42 10:824-843, Oct 2017. URL: https://doi.org/10.1016/j.tibs.2017.06.008, doi:10.1016/j.tibs.2017.06.008. This article has 401 citations and is from a domain leading peer-reviewed journal.
(haynes2022mitochondrialdysfunctionaging pages 1-2): Cole M Haynes and Siegfried Hekimi. Mitochondrial dysfunction, aging, and the mitochondrial unfolded protein response in caenorhabditis elegans. Genetics, Nov 2022. URL: https://doi.org/10.1093/genetics/iyac160, doi:10.1093/genetics/iyac160. This article has 40 citations and is from a domain leading peer-reviewed journal.
(haynes2022mitochondrialdysfunctionaging pages 12-12): Cole M Haynes and Siegfried Hekimi. Mitochondrial dysfunction, aging, and the mitochondrial unfolded protein response in caenorhabditis elegans. Genetics, Nov 2022. URL: https://doi.org/10.1093/genetics/iyac160, doi:10.1093/genetics/iyac160. This article has 40 citations and is from a domain leading peer-reviewed journal.
(wang2013moleculargeneticsof pages 12-14): Ying Wang and Siegfried Hekimi. Molecular genetics of ubiquinone biosynthesis in animals. Critical Reviews in Biochemistry and Molecular Biology, 48:69-88, Jan 2013. URL: https://doi.org/10.3109/10409238.2012.741564, doi:10.3109/10409238.2012.741564. This article has 90 citations and is from a peer-reviewed journal.
(diessl2022manganesedrivencoqdeficiency pages 3-5): Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F.-Nora Vögtle, Fabien Pierrel, Martin Ott, and Sabrina Büttner. Manganese-driven coq deficiency. Nature Communications, Oct 2022. URL: https://doi.org/10.1038/s41467-022-33641-x, doi:10.1038/s41467-022-33641-x. This article has 26 citations and is from a highest quality peer-reviewed journal.
(diessl2022manganesedrivencoqdeficiency pages 1-2): Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F.-Nora Vögtle, Fabien Pierrel, Martin Ott, and Sabrina Büttner. Manganese-driven coq deficiency. Nature Communications, Oct 2022. URL: https://doi.org/10.1038/s41467-022-33641-x, doi:10.1038/s41467-022-33641-x. This article has 26 citations and is from a highest quality peer-reviewed journal.
(wang2022predictingandunderstanding pages 34-38): Sining Wang, Akash Jain, Noelle Alexa Novales, Audrey N. Nashner, Fiona Tran, and Catherine F. Clarke. Predicting and understanding the pathology of single nucleotide variants in human coq genes. Antioxidants, 11:2308, Nov 2022. URL: https://doi.org/10.3390/antiox11122308, doi:10.3390/antiox11122308. This article has 7 citations.
(awad2018coenzymeq10deficiencies pages 7-8): Agape M. Awad, Michelle C. Bradley, Lucía Fernández-del-Río, Anish Nag, Hui S. Tsui, and Catherine F. Clarke. Coenzyme q10 deficiencies: pathways in yeast and humans. Essays in Biochemistry, 62:361-376, Jul 2018. URL: https://doi.org/10.1042/ebc20170106, doi:10.1042/ebc20170106. This article has 185 citations and is from a peer-reviewed journal.
(lionaki2016differentialproteindistribution pages 8-9): Eirini Lionaki, Ilias Gkikas, and Nektarios Tavernarakis. Differential protein distribution between the nucleus and mitochondria: implications in aging. Frontiers in Genetics, Sep 2016. URL: https://doi.org/10.3389/fgene.2016.00162, doi:10.3389/fgene.2016.00162. This article has 57 citations and is from a peer-reviewed journal.
(jonassen2001adietarysource pages 5-6): Tanya Jonassen, Pamela L. Larsen, and Catherine F. Clarke. A dietary source of coenzyme q is essential for growth of long-lived caenorhabditis elegans clk-1 mutants. Proceedings of the National Academy of Sciences of the United States of America, 98 2:421-6, Jan 2001. URL: https://doi.org/10.1073/pnas.98.2.421, doi:10.1073/pnas.98.2.421. This article has 249 citations and is from a highest quality peer-reviewed journal.
(awad2018coenzymeq10deficiencies pages 8-10): Agape M. Awad, Michelle C. Bradley, Lucía Fernández-del-Río, Anish Nag, Hui S. Tsui, and Catherine F. Clarke. Coenzyme q10 deficiencies: pathways in yeast and humans. Essays in Biochemistry, 62:361-376, Jul 2018. URL: https://doi.org/10.1042/ebc20170106, doi:10.1042/ebc20170106. This article has 185 citations and is from a peer-reviewed journal.
(nicoll2024invitroconstruction pages 1-2): Callum R. Nicoll, Laura Alvigini, Andrea Gottinger, Domiziana Cecchini, Barbara Mannucci, Federica Corana, María Laura Mascotti, and Andrea Mattevi. In vitro construction of the coq metabolon unveils the molecular determinants of coenzyme q biosynthesis. Nature catalysis, 7:148-160, Jan 2024. URL: https://doi.org/10.1038/s41929-023-01087-z, doi:10.1038/s41929-023-01087-z. This article has 27 citations and is from a domain leading peer-reviewed journal.
(diazcasado2019theparadoxof pages 7-9): M. E. Díaz-Casado, J. Quiles, Eliana Barriocanal-Casado, Pilar González-García, Maurizio Battino, M. Battino, Maurizio Battino, L. López, and A. Varela-López. The paradox of coenzyme q10 in aging. Sep 2019. URL: https://doi.org/10.3390/nu11092221, doi:10.3390/nu11092221. This article has 105 citations.
(wang2022predictingandunderstanding pages 38-41): Sining Wang, Akash Jain, Noelle Alexa Novales, Audrey N. Nashner, Fiona Tran, and Catherine F. Clarke. Predicting and understanding the pathology of single nucleotide variants in human coq genes. Antioxidants, 11:2308, Nov 2022. URL: https://doi.org/10.3390/antiox11122308, doi:10.3390/antiox11122308. This article has 7 citations.
(diessl2022manganesedrivencoqdeficiency pages 5-6): Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F.-Nora Vögtle, Fabien Pierrel, Martin Ott, and Sabrina Büttner. Manganese-driven coq deficiency. Nature Communications, Oct 2022. URL: https://doi.org/10.1038/s41467-022-33641-x, doi:10.1038/s41467-022-33641-x. This article has 26 citations and is from a highest quality peer-reviewed journal.
(diessl2022manganesedrivencoqdeficiency pages 2-3): Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F.-Nora Vögtle, Fabien Pierrel, Martin Ott, and Sabrina Büttner. Manganese-driven coq deficiency. Nature Communications, Oct 2022. URL: https://doi.org/10.1038/s41467-022-33641-x, doi:10.1038/s41467-022-33641-x. This article has 26 citations and is from a highest quality peer-reviewed journal.
(lionaki2016differentialproteindistribution pages 7-8): Eirini Lionaki, Ilias Gkikas, and Nektarios Tavernarakis. Differential protein distribution between the nucleus and mitochondria: implications in aging. Frontiers in Genetics, Sep 2016. URL: https://doi.org/10.3389/fgene.2016.00162, doi:10.3389/fgene.2016.00162. This article has 57 citations and is from a peer-reviewed journal.
(haynes2022mitochondrialdysfunctionaging pages 12-13): Cole M Haynes and Siegfried Hekimi. Mitochondrial dysfunction, aging, and the mitochondrial unfolded protein response in caenorhabditis elegans. Genetics, Nov 2022. URL: https://doi.org/10.1093/genetics/iyac160, doi:10.1093/genetics/iyac160. This article has 40 citations and is from a domain leading peer-reviewed journal.
(guerra2023coenzymeqbiochemistry pages 1-3): Rachel M. Guerra and David J. Pagliarini. Coenzyme q biochemistry and biosynthesis. Trends in Biochemical Sciences, 48:463-476, May 2023. URL: https://doi.org/10.1016/j.tibs.2022.12.006, doi:10.1016/j.tibs.2022.12.006. This article has 142 citations and is from a domain leading peer-reviewed journal.
(guerra2023coenzymeqbiochemistry pages 3-4): Rachel M. Guerra and David J. Pagliarini. Coenzyme q biochemistry and biosynthesis. Trends in Biochemical Sciences, 48:463-476, May 2023. URL: https://doi.org/10.1016/j.tibs.2022.12.006, doi:10.1016/j.tibs.2022.12.006. This article has 142 citations and is from a domain leading peer-reviewed journal.
(mattevi2023invitroconstruction pages 1-4): Andrea Mattevi, Callum Nicoll, Laura Alvigini, Andrea Gottinger, Domiziana Cecchini, Barbara Mannucci, Federica Corana, and Maria Laura Mascotti. In vitro construction of the coq metabolon unveils the molecular determinants of coenzyme q biosynthesis. Nov 2023. URL: https://doi.org/10.21203/rs.3.rs-2845141/v1, doi:10.21203/rs.3.rs-2845141/v1.
(nicoll2024invitroconstruction pages 8-8): Callum R. Nicoll, Laura Alvigini, Andrea Gottinger, Domiziana Cecchini, Barbara Mannucci, Federica Corana, María Laura Mascotti, and Andrea Mattevi. In vitro construction of the coq metabolon unveils the molecular determinants of coenzyme q biosynthesis. Nature catalysis, 7:148-160, Jan 2024. URL: https://doi.org/10.1038/s41929-023-01087-z, doi:10.1038/s41929-023-01087-z. This article has 27 citations and is from a domain leading peer-reviewed journal.
(diazcasado2019theparadoxof pages 3-5): M. E. Díaz-Casado, J. Quiles, Eliana Barriocanal-Casado, Pilar González-García, Maurizio Battino, M. Battino, Maurizio Battino, L. López, and A. Varela-López. The paradox of coenzyme q10 in aging. Sep 2019. URL: https://doi.org/10.3390/nu11092221, doi:10.3390/nu11092221. This article has 105 citations.
(staiano2023biosynthesisdeficiencyand pages 4-5): Carmine Staiano, Laura García-Corzo, David Mantle, Nadia Turton, Lauren E. Millichap, Gloria Brea-Calvo, and Iain Hargreaves. Biosynthesis, deficiency, and supplementation of coenzyme q. Antioxidants, 12:1469, Jul 2023. URL: https://doi.org/10.3390/antiox12071469, doi:10.3390/antiox12071469. This article has 25 citations.
(haynes2022mitochondrialdysfunctionaging pages 1-1): Cole M Haynes and Siegfried Hekimi. Mitochondrial dysfunction, aging, and the mitochondrial unfolded protein response in caenorhabditis elegans. Genetics, Nov 2022. URL: https://doi.org/10.1093/genetics/iyac160, doi:10.1093/genetics/iyac160. This article has 40 citations and is from a domain leading peer-reviewed journal.
(guerra2023coenzymeqbiochemistry pages 12-14): Rachel M. Guerra and David J. Pagliarini. Coenzyme q biochemistry and biosynthesis. Trends in Biochemical Sciences, 48:463-476, May 2023. URL: https://doi.org/10.1016/j.tibs.2022.12.006, doi:10.1016/j.tibs.2022.12.006. This article has 142 citations and is from a domain leading peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

wang2013moleculargeneticsof pages 6-7
jonassen2001adietarysource pages 5-6
lionaki2016differentialproteindistribution pages 8-9
haynes2022mitochondrialdysfunctionaging pages 12-13
guerra2023coenzymeqbiochemistry pages 1-3
staiano2023biosynthesisdeficiencyand pages 4-5
diazcasado2019theparadoxof pages 3-5
diazcasado2019theparadoxof pages 7-9
wang2013moleculargeneticsof pages 4-6
haynes2022mitochondrialdysfunctionaging pages 12-12
stefely2017biochemistryofmitochondrial pages 21-22
haynes2022mitochondrialdysfunctionaging pages 1-2
wang2013moleculargeneticsof pages 12-14
diessl2022manganesedrivencoqdeficiency pages 3-5
diessl2022manganesedrivencoqdeficiency pages 1-2
wang2022predictingandunderstanding pages 34-38
nicoll2024invitroconstruction pages 1-2
wang2022predictingandunderstanding pages 38-41
diessl2022manganesedrivencoqdeficiency pages 5-6
diessl2022manganesedrivencoqdeficiency pages 2-3
lionaki2016differentialproteindistribution pages 7-8
guerra2023coenzymeqbiochemistry pages 3-4
mattevi2023invitroconstruction pages 1-4
nicoll2024invitroconstruction pages 8-8
haynes2022mitochondrialdysfunctionaging pages 1-1
guerra2023coenzymeqbiochemistry pages 12-14
https://doi.org/10.3109/10409238.2012.741564,
https://doi.org/10.1074/jbc.273.6.3351,
https://doi.org/10.1016/j.tibs.2017.06.008,
https://doi.org/10.1093/genetics/iyac160,
https://doi.org/10.1038/s41467-022-33641-x,
https://doi.org/10.3390/antiox11122308,
https://doi.org/10.1042/ebc20170106,
https://doi.org/10.3389/fgene.2016.00162,
https://doi.org/10.1073/pnas.98.2.421,
https://doi.org/10.1038/s41929-023-01087-z,
https://doi.org/10.3390/nu11092221,
https://doi.org/10.1016/j.tibs.2022.12.006,
https://doi.org/10.21203/rs.3.rs-2845141/v1,
https://doi.org/10.3390/antiox12071469,

📚 Additional Documentation

Notes

(clk-1-notes.md)

clk-1 (COQ7 ortholog) — research notes

UniProt: P48376 (COQ7_CAEEL). WormBase: WBGene00000536 / ZC395.2. Gene symbol clk-1
("clock abnormal / clk"). Human ortholog: COQ7. 187 aa precursor with an N-terminal
mitochondrial transit peptide (1–8) cleaved to a mature 9–187 chain.

Summary of what is KNOWN (with provenance)

Direct molecular function: di-iron ubiquinone/CoQ biosynthetic monooxygenase

clk-1/COQ7 catalyzes the penultimate step of ubiquinone (coenzyme Q) biosynthesis: the
hydroxylation of 5-demethoxyubiquinone (DMQ) at the C6 (C5 in some numbering) position,
producing 3-demethylubiquinone. EC 1.14.13.253; RHEA:81211. It uses a carboxylate-bridged
di-iron center and NAD(P)H (UniProt P48376 CATALYTIC ACTIVITY / COFACTOR: "Binds 2 iron
ions per subunit"; FT BINDING residues 30/60/63/112/148/151 to Fe cation).
The enzyme belongs to the COQ7 family / ferritin-like di-iron superfamily
(Pfam PF03232 COQ7; InterPro IPR011566; PANTHER PTHR11237 "COENZYME Q10 BIOSYNTHESIS
PROTEIN 7"; HAMAP MF_01658/MF_03194).
Founding paper established structural + functional conservation of clk-1 as a "timing gene"
and did mutagenesis of the catalytic Glu148: PMID:9020081 (Science 1997). (Not in GOA
annotation set but is the founding functional reference; cited in UniProt.)
Biochemical proof that CLK-1 is required for UQ biosynthesis in the worm:
PMID:11244089 Also: DMQ9 can substitute as an electron carrier —
PMID:11244089.
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" PMID:14517217.

Subcellular location: mitochondrion (inner membrane, matrix face)

UniProt SUBCELLULAR LOCATION: "Mitochondrion inner membrane; Peripheral membrane protein;
Matrix side" (so a genuine "extrinsic component of mitochondrial inner membrane",
GO:0031314, not an integral membrane protein).
CLK-1-GFP is fully active and localizes to mitochondria of all somatic cells:
PMID:10202142
Mitochondrial localization independently observed: PMID:25961505 (mitochondria and nucleus).

Downstream / mutant-phenotype (NON-CORE) biology

The mutant phenotypes are consequences of altered Q/DMQ, not the direct molecular activity.

Longevity ("Clk" clock phenotype): clk-1 mutations extend lifespan and slow developmental
and behavioral rates. PMID:10202142 Overexpression shortens
lifespan and accelerates behavior PMID:10202142.
Lifespan extension by RNAi of UQ-biosynthesis genes incl. clk-1: PMID:12709403
Maternal rescue / developmental-timing: PMID:14517217.
Genetic-interaction lifespan modulation with translation / DR pathways (clk-1 used as a
long-lived ETC/"clk" mutant partner): PMID:17277769; PMID:19783783 (DR / NLP-7,
clk-1 as ETC-mutant control; IGI/IMP determination of adult lifespan).
Oxidative phosphorylation / anesthetic (xenobiotic) sensitivity: complex I–dependent OXPHOS
correlates with volatile-anesthetic sensitivity, tested across ETC/CoQ mutants including
clk-1: PMID:16920626
CLK-1 protein level tracks mitochondrial biogenesis; used as a mito marker reduced on hsp-6
knockdown: PMID:17189267.

DEBATED / secondary nuclear moonlighting role — treat cautiously

A distinct nuclear pool of CLK-1/COQ7 was reported to regulate mitochondrial stress
responses and longevity independently of UQ biosynthesis: PMID:25961505; the nuclear-only,
MTS-deleted CLK-1 "localised predominantly to the nucleus" and "CLK-1nuc(+) could not" rescue
UQ biosynthesis PMID:25961505, yet partially rescued ROS, UPRmt, and
longevity phenotypes. Nuclear COQ7 associates with chromatin PMID:25961505 and modulates
transcription of ROS/UPRmt genes (sod-2, skn-1, hsp-6, hsp-60, spg-7; human SOD2/NRF2/HMOX1,
HSPA9/HSPD1/AFG3L2 etc.). This underlies the WormBase IMP annotations to
negative/positive regulation of transcription by RNA Pol II, regulation of ROS metabolic
process, and determination of adult lifespan on PMID:25961505.
An older, isolated in-vitro report: CLK-1 binds the O_L region of mitochondrial DNA:
PMID:11959146 This is the basis of the IDA
"transcription cis-regulatory region binding" (GO:0000976) annotation. Note the binding is to
mtDNA (a replication/transcription origin), a single in-vitro study, not widely replicated —
a possible moonlighting activity, not the core enzymatic function.

Caveat on the nuclear model: the nuclear localization/role is a genuine experimental report
(Nat Cell Biol 2015) but remains debated in the field; CLK-1's N-terminus and human COQ7's NTS
are not conserved (PMID:25961505), and independent
confirmation of an endogenous, functionally significant nuclear pool in the worm is limited.

What is NOT known (knowledge gaps)

How DMQ-vs-Q levels produce the longevity signal. clk-1 mutants accumulate DMQ9 and lack
UQ9 yet respire near-normally (DMQ9 substitutes as an electron carrier) PMID:11244089, and
lifespan extension appears "independent of ubiquinone biosynthesis and ATP production"
PMID:25961505. The mechanistic chain from the specific quinone species (DMQ vs Q, ROS
output) to the pro-longevity signal is not established.
The disputed nuclear/non-mitochondrial role. Whether an endogenous nuclear CLK-1 pool of
physiological significance exists in the worm, how it is targeted (worm N-terminus lacks the
COQ7 NTS), whether it binds DNA sequence-specifically, and whether "transcription regulation"
is a direct molecular function or an indirect consequence, are unresolved.
Ontology gap: CLK-1/COQ7 is described as a component of a multi-subunit COQ enzyme
("CoQ synthome") complex with a structural stabilizing role (UniProt, By similarity), but GO
has no "coenzyme Q biosynthesis complex" cellular-component term to capture this membership.

Provenance note on deep research

Falcon deep research (just deep-research-falcon worm clk-1 --fallback perplexity-lite) took
~29 min on the congested shared Edison endpoint and the wrapper recipe ultimately reported a
timeout, but the Edison run did land a real report at the boundary:
clk-1-deep-research-falcon.md (provider: falcon, model: Edison Scientific Literature,
cached: false, 40 cited sources). It was verified as genuine and on-target (di-iron DMQ9->UQ9
hydroxylase, COQ metabolon/CoQ-synthome membership, debated nuclear moonlighting "requires
further confirmation", 2,4-DHB bypass showing phenotypes are attributable to UQ deficiency) and
is committed as corroborating context. The review itself is grounded in the UniProt record, the
GOA TSV, and the 11 cached primary publications (PMID_9020081, 10202142, 11244089, 11959146,
12709403, 14517217, 16920626, 17189267, 17277769, 19783783, 25961505); every supporting_text
is a verbatim PMID quote. The falcon file is cited only once (core_functions corroboration) with
a verbatim quote from the committed file. There are no UNDECIDED calls.

Annotation-review plan (core vs non-core)

CORE (keep, ACCEPT): 3-demethoxyubiquinone 3-hydroxylase (NADH) activity (GO:0160224);
ubiquinone biosynthetic process (GO:0006744); mitochondrion (GO:0005739); mitochondrial inner
membrane (GO:0005743); extrinsic component of mitochondrial inner membrane (GO:0031314);
general MF parents monooxygenase activity (GO:0004497) and oxidoreductase...NAD(P)H one-oxygen
(GO:0016709) are correct but less-informative parents — keep, flag as non-core/general.
NON-CORE (KEEP_AS_NON_CORE): determination of adult lifespan (all evidence); cellular
respiration; oxidative phosphorylation; adult behavior; positive regulation of behavior;
positive regulation of growth rate; positive regulation of developmental process; response to
xenobiotic stimulus; regulation of ROS metabolic process; nucleus (all); neg/pos regulation
of transcription by RNA Pol II; transcription cis-regulatory region binding (debated in-vitro
mtDNA-binding moonlighting).
No REMOVE actions: all experimental annotations are defensible; the debated nuclear/DNA
functions are experimental (IDA/IMP) so are retained as non-core with caveats rather than
removed.

📄 View Raw YAML

id: P48376
gene_symbol: clk-1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: >-
  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.
existing_annotations:
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Core localization. CLK-1 is a peripheral inner-mitochondrial-membrane protein
      (matrix side) where it catalyzes DMQ hydroxylation in CoQ biosynthesis.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        CLK-1 is fully active when fused to green fluorescent protein and is found in
        the mitochondria of all somatic cells.
- term:
    id: GO:0160224
    label: 3-demethoxyubiquinone 3-hydroxylase (NADH) activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Core molecular function: the di-iron ubiquinone/CoQ biosynthetic monooxygenase
      catalyzing the DMQ to demethylubiquinone hydroxylation.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        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.
- term:
    id: GO:0006744
    label: ubiquinone biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Core biological process; the pathway in which the clk-1 hydroxylase acts.
    action: ACCEPT
    reason: >-
      clk-1 is required for ubiquinone biosynthesis; loss abolishes UQ9 and leads to
      accumulation of the DMQ9 intermediate.
    supported_by:
    - reference_id: PMID:11244089
      supporting_text: >-
        This result demonstrates that CLK-1 is absolutely required for the
        biosynthesis of UQ(9) in C. elegans.
- term:
    id: GO:2000377
    label: regulation of reactive oxygen species metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Non-core regulatory role tied to the debated nuclear function; clk-1 mutants
      have altered ROS and a ROS-responsive gene-expression program.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        the pathway regulates both mitochondrial reactive oxygen species metabolism
        and the mitochondrial unfolded protein response.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Debated secondary nuclear localization propagated by phylogeny; treat as
      non-core.
    action: KEEP_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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        adult transgenic worms expressing CLK-1 fused to green fluorescent protein
        (GFP) also display fluorescence in both compartments
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Classic longevity phenotype; a downstream organismal consequence of altered
      quinone content, not the core molecular function.
    action: KEEP_AS_NON_CORE
    reason: >-
      clk-1 loss extends lifespan, but this is a pleiotropic downstream effect of
      reduced ubiquinone/altered mitochondrial metabolism; keep as non-core.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        the reduced respiration of the long-lived clk-1 mutants suggests that
        longevity is promoted by the age-dependent decrease in mitochondrial function
- term:
    id: GO:0004497
    label: monooxygenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      Correct but general parent of the specific 3-demethoxyubiquinone 3-hydroxylase
      activity; captures the core monooxygenase function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        clk-1 encodes a hydroxylase involved in the biosynthesis of the redox-active
        lipid ubiquinone (co-enzyme Q)
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Debated nuclear localization propagated from the UniProt subcellular vocabulary.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        We have uncovered a distinct nuclear form of CLK-1 that independently
        regulates lifespan.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Core localization; the enzyme's primary compartment.
    action: ACCEPT
    reason: >-
      Mitochondrial localization is strongly established experimentally for CLK-1.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        CLK-1 is fully active when fused to green fluorescent protein and is found in
        the mitochondria of all somatic cells.
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Core localization; peripheral inner-membrane, matrix side.
    action: ACCEPT
    reason: >-
      Consistent with UniProt's inner-membrane (peripheral, matrix-side) assignment
      and the phylogenetic annotation.
- term:
    id: GO:0006744
    label: ubiquinone biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: Core biological process (electronic support for the pathway role).
    action: ACCEPT
    reason: >-
      Automated multi-method IEA correctly assigns the ubiquinone biosynthetic
      process, consistent with experimental evidence.
    supported_by:
    - reference_id: PMID:11244089
      supporting_text: >-
        This result demonstrates that CLK-1 is absolutely required for the
        biosynthesis of UQ(9) in C. elegans.
- term:
    id: GO:0016709
    label: 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
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  qualifier: enables
  review:
    summary: >-
      Correct general MF parent corresponding to the EC 1.14.13 mechanism (NAD(P)H,
      one oxygen atom incorporated).
    action: ACCEPT
    reason: >-
      Accurately describes the mechanistic class of the clk-1 hydroxylation reaction;
      less specific than GO:0160224 but not incorrect.
- term:
    id: GO:0031314
    label: extrinsic component of mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  qualifier: located_in
  review:
    summary: >-
      Accurate refinement of the localization: CLK-1 is a peripheral (extrinsic)
      inner-membrane protein on the matrix face.
    action: ACCEPT
    reason: >-
      Matches UniProt's "Peripheral membrane protein; Matrix side" assignment and is
      more precise than the plain inner-membrane term.
- term:
    id: GO:0160224
    label: 3-demethoxyubiquinone 3-hydroxylase (NADH) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Core molecular function (electronic/RHEA-EC support).
    action: ACCEPT
    reason: >-
      Automated RHEA/EC-based assignment of the specific hydroxylase activity, the
      direct molecular function of clk-1.
    supported_by:
    - reference_id: PMID:11244089
      supporting_text: >-
        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.
- term:
    id: GO:0000122
    label: negative regulation of transcription by RNA polymerase II
  evidence_type: IMP
  original_reference_id: PMID:25961505
  qualifier: involved_in
  review:
    summary: >-
      Non-core, debated nuclear moonlighting function; nuclear CLK-1 suppresses a
      subset of ROS/UPRmt genes.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        The expression of nuclear CLK-1 in clk-1 null worms abrogated the increased
        transcript levels of these genes
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IMP
  original_reference_id: PMID:25961505
  qualifier: involved_in
  review:
    summary: >-
      Non-core, debated nuclear moonlighting function; nuclear CLK-1 promotes
      expression of some target genes (e.g. glna-1/GLS2).
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        glna-1 transcript levels were decreased compared to wild type animals, an
        effect that was rescued in the presence of CLK-1nuc(+)
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IMP
  original_reference_id: PMID:17277769
  qualifier: involved_in
  review:
    summary: >-
      Longevity phenotype; clk mutants used in a genetic study of translation and
      ageing. Downstream/non-core.
    action: KEEP_AS_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.
    supported_by:
    - reference_id: PMID:17277769
      supporting_text: >-
        lack of IFE-2 enhances the long-lived phenotype of clk and dietary-restricted
        eat mutant animals.
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IGI
  original_reference_id: PMID:17277769
  qualifier: involved_in
  review:
    summary: >-
      Genetic-interaction evidence for the longevity phenotype (with ife-2).
      Downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      IGI supporting the pleiotropic lifespan role; a non-core organismal phenotype.
    supported_by:
    - reference_id: PMID:17277769
      supporting_text: >-
        lack of IFE-2 enhances the long-lived phenotype of clk and dietary-restricted
        eat mutant animals.
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IGI
  original_reference_id: PMID:19783783
  qualifier: involved_in
  review:
    summary: >-
      Genetic-interaction lifespan evidence (electron-transport-chain longevity
      pathway). Downstream/non-core.
    action: KEEP_AS_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.
    supported_by:
    - reference_id: PMID:19783783
      supporting_text: >-
        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.
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IMP
  original_reference_id: PMID:19783783
  qualifier: involved_in
  review:
    summary: Longevity phenotype (mutant); downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      IMP for the pleiotropic lifespan phenotype; retain as a non-core downstream
      effect of altered mitochondrial quinone metabolism.
    supported_by:
    - reference_id: PMID:19783783
      supporting_text: >-
        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.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:25961505
  qualifier: located_in
  review:
    summary: >-
      Direct (GFP/immunostaining) evidence for a nuclear pool of CLK-1/COQ7; a
      debated secondary localization, kept as non-core.
    action: KEEP_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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        adult transgenic worms expressing CLK-1 fused to green fluorescent protein
        (GFP) also display fluorescence in both compartments
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:25961505
  qualifier: located_in
  review:
    summary: Core localization; direct evidence for mitochondrial CLK-1.
    action: ACCEPT
    reason: >-
      Direct imaging shows CLK-1-GFP in mitochondria (and nucleus); mitochondrion is
      the primary/core site of the enzyme.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        adult transgenic worms expressing CLK-1 fused to green fluorescent protein
        (GFP) also display fluorescence in both compartments
- term:
    id: GO:0006744
    label: ubiquinone biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:25961505
  qualifier: involved_in
  review:
    summary: Core biological process; full-length CLK-1 rescues UQ biosynthesis.
    action: ACCEPT
    reason: >-
      This study confirms the mitochondrial CLK-1 requirement for ubiquinone
      biosynthesis (full-length, but not nuclear-only, CLK-1 rescues UQ).
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        full length CLK-1 was able to rescue ubiquinone biosynthesis in these worms,
        however, CLK-1nuc(+) could not
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IMP
  original_reference_id: PMID:25961505
  qualifier: involved_in
  review:
    summary: >-
      Longevity phenotype; here attributed partly to the debated nuclear CLK-1 pool.
      Downstream/non-core.
    action: KEEP_AS_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.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        the expression of CLK-1nuc(+) in clk-1 null worms caused a decrease in their
        enhanced longevity phenotype
- term:
    id: GO:2000377
    label: regulation of reactive oxygen species metabolic process
  evidence_type: IMP
  original_reference_id: PMID:25961505
  qualifier: involved_in
  review:
    summary: >-
      Non-core regulatory role; nuclear CLK-1 modulates cellular ROS levels and
      ROS-responsive gene expression.
    action: KEEP_AS_NON_CORE
    reason: >-
      Experimental IMP for ROS regulation via the debated nuclear pathway; a
      downstream/moonlighting function rather than the direct hydroxylase activity.
    supported_by:
    - reference_id: PMID:25961505
      supporting_text: >-
        Expression of CLK-1nuc(+) in clk-1 null worms partially rescued the increased
        ROS levels observed in these animals
- term:
    id: GO:0000976
    label: transcription cis-regulatory region binding
  evidence_type: IDA
  original_reference_id: PMID:11959146
  qualifier: enables
  review:
    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.
    action: KEEP_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.
    supported_by:
    - reference_id: PMID:11959146
      supporting_text: >-
        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.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:17189267
  qualifier: located_in
  review:
    summary: Core localization; CLK-1 treated as a mitochondrial protein.
    action: ACCEPT
    reason: >-
      This study monitors CLK-1 as a mitochondrial protein whose levels drop upon
      hsp-6 (mtHSP70) knockdown, consistent with mitochondrial localization.
    supported_by:
    - reference_id: PMID:17189267
      supporting_text: >-
        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
- term:
    id: GO:0006744
    label: ubiquinone biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:14517217
  qualifier: involved_in
  review:
    summary: Core biological process; clk-1 hydroxylase required for UQ, replaced by DMQ in mutants.
    action: ACCEPT
    reason: >-
      Directly supports the ubiquinone biosynthetic role; in clk-1 mutants UQ is
      replaced by the DMQ precursor.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        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.
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IMP
  original_reference_id: PMID:14517217
  qualifier: involved_in
  review:
    summary: Longevity/developmental-timing phenotype; downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      Supports the pleiotropic ageing phenotype; a downstream consequence of altered
      quinone metabolism, not the core function.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        The clk-1 mutants of Caenorhabditis elegans display an average slowing down
        of physiological rates, including those of development, various behaviors, and
        aging.
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IGI
  original_reference_id: PMID:14517217
  qualifier: involved_in
  review:
    summary: >-
      Genetic interaction with daf-2 for lifespan; downstream/non-core longevity
      phenotype.
    action: KEEP_AS_NON_CORE
    reason: >-
      The daf-2 clk-1 double-mutant synergy underlies this IGI; a non-core
      organismal longevity phenotype.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        the very long lifespan observed in daf-2 clk-1 double mutants is not
        abolished by the maternal effect
- term:
    id: GO:0040010
    label: positive regulation of growth rate
  evidence_type: IMP
  original_reference_id: PMID:14517217
  qualifier: involved_in
  review:
    summary: >-
      Developmental-timing/growth-rate phenotype (the "Clk" slowing); downstream and
      non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      clk-1 loss slows post-embryonic growth and development; a pleiotropic timing
      phenotype rather than the direct molecular function.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        The clk-1 mutants of Caenorhabditis elegans display an average slowing down
        of physiological rates, including those of development, various behaviors, and
        aging.
- term:
    id: GO:0048520
    label: positive regulation of behavior
  evidence_type: IMP
  original_reference_id: PMID:14517217
  qualifier: involved_in
  review:
    summary: >-
      Behavioral-rate ("clock") phenotype (e.g. defecation/pumping rhythms);
      downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      Slowed rhythmic behaviors are a hallmark Clk phenotype but a downstream
      consequence of altered mitochondrial metabolism.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        The clk-1 mutants of Caenorhabditis elegans display an average slowing down
        of physiological rates, including those of development, various behaviors, and
        aging.
- term:
    id: GO:0051094
    label: positive regulation of developmental process
  evidence_type: IMP
  original_reference_id: PMID:14517217
  qualifier: involved_in
  review:
    summary: Developmental-timing phenotype; downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      clk-1 loss slows embryonic and post-embryonic development; a pleiotropic timing
      phenotype, not the core function.
    supported_by:
    - reference_id: PMID:14517217
      supporting_text: >-
        The clk-1 mutants of Caenorhabditis elegans display an average slowing down
        of physiological rates, including those of development, various behaviors, and
        aging.
- term:
    id: GO:0006119
    label: oxidative phosphorylation
  evidence_type: IMP
  original_reference_id: PMID:16920626
  qualifier: involved_in
  review:
    summary: >-
      Non-core; clk-1 mutation alters respiratory-chain (OXPHOS) function via changed
      quinone content.
    action: KEEP_AS_NON_CORE
    reason: >-
      OXPHOS effects are a downstream consequence of DMQ-for-UQ substitution at the
      respiratory chain, not a direct clk-1 molecular function.
    supported_by:
    - reference_id: PMID:16920626
      supporting_text: >-
        a clear correlation between complex I-dependent oxidative phosphorylation
        capacity and volatile anesthetic sensitivity.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IMP
  original_reference_id: PMID:16920626
  qualifier: involved_in
  review:
    summary: >-
      Altered volatile-anesthetic (xenobiotic) sensitivity of the mutant; an indirect
      downstream phenotype, non-core.
    action: KEEP_AS_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.
    supported_by:
    - reference_id: PMID:16920626
      supporting_text: >-
        a clear correlation between complex I-dependent oxidative phosphorylation
        capacity and volatile anesthetic sensitivity.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:10202142
  qualifier: located_in
  review:
    summary: Core localization; direct evidence that active CLK-1-GFP is mitochondrial.
    action: ACCEPT
    reason: >-
      Foundational direct evidence for mitochondrial localization of functional CLK-1.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        CLK-1 is fully active when fused to green fluorescent protein and is found in
        the mitochondria of all somatic cells.
- term:
    id: GO:0006744
    label: ubiquinone biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:11244089
  qualifier: involved_in
  review:
    summary: >-
      Core biological process; biochemical demonstration that CLK-1 is required for
      UQ9 synthesis (DMQ9 accumulates in mutants).
    action: ACCEPT
    reason: >-
      Strong direct biochemical evidence for the ubiquinone biosynthetic role.
    supported_by:
    - reference_id: PMID:11244089
      supporting_text: >-
        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.
- term:
    id: GO:0006744
    label: ubiquinone biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:12709403
  qualifier: involved_in
  review:
    summary: Core biological process; RNAi of clk-1 (with other COQ genes) reduces Q and extends lifespan.
    action: ACCEPT
    reason: >-
      RNAi phenotype confirms clk-1's role in ubiquinone biosynthesis.
    supported_by:
    - reference_id: PMID:12709403
      supporting_text: >-
        We have identified by RNA interference (RNAi) eight genes, including clk-1,
        involved in ubiquinone biosynthesis in C. elegans
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IMP
  original_reference_id: PMID:10202142
  qualifier: involved_in
  review:
    summary: Longevity phenotype (foundational); downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      Foundational demonstration that clk-1 controls aging; a pleiotropic downstream
      phenotype rather than the core molecular function.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        Overexpression of CLK-1 activity in wild-type worms can increase
        mitochondrial activity, accelerate behavioral rates during aging and shorten
        life span
- term:
    id: GO:0030534
    label: adult behavior
  evidence_type: IMP
  original_reference_id: PMID:10202142
  qualifier: involved_in
  review:
    summary: >-
      Rhythmic adult-behavior ("clock") phenotype; downstream/non-core.
    action: KEEP_AS_NON_CORE
    reason: >-
      The slowed rhythmic behaviors of clk-1 mutants are a downstream Clk phenotype,
      not the direct function.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        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.
- term:
    id: GO:0045333
    label: cellular respiration
  evidence_type: TAS
  original_reference_id: PMID:10202142
  qualifier: involved_in
  review:
    summary: >-
      clk-1 controls respiration via its role in ubiquinone supply; a
      closely-linked but downstream process, non-core.
    action: KEEP_AS_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.
    supported_by:
    - reference_id: PMID:10202142
      supporting_text: >-
        the reduced respiration of the long-lived clk-1 mutants
core_functions:
- description: >-
    Mitochondrial di-iron ubiquinone (coenzyme Q) biosynthetic monooxygenase. CLK-1
    (COQ7 ortholog) uses a carboxylate-bridged di-iron center and NAD(P)H to
    hydroxylate 5-demethoxyubiquinone (DMQ) to 3-demethylubiquinone, the penultimate
    step of ubiquinone biosynthesis, acting as a peripheral protein on the matrix
    face of the inner mitochondrial membrane. Loss of this activity abolishes UQ9
    and causes DMQ9 accumulation.
  molecular_function:
    id: GO:0160224
    label: 3-demethoxyubiquinone 3-hydroxylase (NADH) activity
  directly_involved_in:
  - id: GO:0006744
    label: ubiquinone biosynthetic process
  locations:
  - id: GO:0005743
    label: mitochondrial inner membrane
  - id: GO:0005739
    label: mitochondrion
  supported_by:
  - reference_id: PMID:11244089
    supporting_text: >-
      This result demonstrates that CLK-1 is absolutely required for the biosynthesis
      of UQ(9) in C. elegans.
  - reference_id: PMID:14517217
    supporting_text: >-
      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.
  - reference_id: PMID:9020081
    supporting_text: >-
      clk-1 complemented the phenotype of cat5/coq7 null mutants, demonstrating that
      clk-1 and CAT5/COQ7 share biochemical function
  - reference_id: file:worm/clk-1/clk-1-deep-research-falcon.md
    supporting_text: >-
      CLK-1 (UniProt P48376) is a mitochondrial diiron carboxylate hydroxylase that
      catalyzes the C5 hydroxylation of DMQ9 to produce UQ9, the penultimate step in
      coenzyme Q biosynthesis.
knowledge_gaps:
- gap_statement: >-
    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.
  boundary: >-
    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.
  gap_kind:
  - BIOLOGY
  dark_aspect: BP_DARK
  status: 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.
  resolution: >-
    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:
  - reference_id: PMID:11244089
    supporting_text: >-
      it has not been possible to identify biochemical changes that might underlie
      the extension of life span observed in clk-1 mutants, and therefore the function
      of CLK-1 in C. elegans remains unknown.
  - reference_id: PMID:25961505
    supporting_text: >-
      extended lifespans through a pathway that appears to be independent of
      ubiquinone biosynthesis and ATP production
- gap_statement: >-
    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.
  boundary: >-
    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.
  gap_kind:
  - BIOLOGY
  dark_aspect: MF_DARK
  status: OPEN
  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.
  resolution: >-
    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:
  - reference_id: PMID:25961505
    supporting_text: >-
      the N-terminal residues we identified as being critical for nuclear
      localisation of COQ7 do not appear to be conserved in CLK-1
  - reference_id: PMID:11959146
    supporting_text: >-
      in addition to its enzymatic function in ubiquinone biosynthesis, CLK-1 is
      involved in the regulation of mtDNA replication or transcription.
- gap_statement: >-
    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.
  boundary: >-
    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.
  gap_kind:
  - ONTOLOGY
  dark_aspect: CC_DARK
  status: OPEN
  significance: >-
    Capturing COQ-complex membership would let curation record the structural role of
    COQ7 family members alongside their catalytic activity.
  resolution: >-
    Add a "coenzyme Q biosynthesis complex" (or "CoQ synthome") cellular-component
    term to GO.
  proposed_terms:
  - proposed_name: coenzyme Q biosynthesis complex
    proposed_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.
    proposed_parent:
      id: GO:0032991
      label: protein-containing complex
proposed_new_terms:
- proposed_name: coenzyme Q biosynthesis complex
  proposed_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.
  proposed_parent:
    id: GO:0032991
    label: protein-containing complex
suggested_questions:
- question: >-
    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?
- question: >-
    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?
suggested_experiments:
- hypothesis: >-
    The longevity of clk-1 mutants is set by the quinone species/ROS output rather
    than by ATP-level respiratory deficiency.
  description: >-
    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.
  experiment_type: metabolite-rescue and phenotype assay
- hypothesis: >-
    CLK-1 has a separable nuclear function distinct from its mitochondrial hydroxylase
    activity.
  description: >-
    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.
  experiment_type: genetics and localization
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations
    between related proteins based on shared sequence features
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:9020081
  title: Structural and functional conservation of the Caenorhabditis elegans timing
    gene clk-1.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Founding paper: cloned clk-1, showed conservation to yeast Cat5p/Coq7p, and
      demonstrated shared biochemical function by cross-complementation. PubMed
      title-verified; supports the core CoQ7-family molecular function.
- id: PMID:10202142
  title: CLK-1 controls respiration, behavior and aging in the nematode Caenorhabditis
    elegans.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Direct evidence that active CLK-1-GFP localizes to mitochondria; establishes
      the respiration/behavior/aging phenotypes. Title-verified.
- id: PMID:11244089
  title: Altered quinone biosynthesis in the long-lived clk-1 mutants of Caenorhabditis
    elegans.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Biochemical proof that clk-1 is required for UQ9 synthesis and that DMQ9
      accumulates and can substitute as an electron carrier; anchors the DMQ-vs-Q
      knowledge gap. Title-verified.
- id: PMID:11959146
  title: CLK-1 protein has DNA binding activity specific to O(L) region of mitochondrial
    DNA.
  findings: []
  reference_review:
    relevance: LOW
    correctness: LOW_QUALITY
    review_notes: >-
      Correctly cited but an isolated 2002 in-vitro study of mtDNA (O_L) binding, not
      widely replicated; basis for the debated transcription cis-regulatory region
      binding annotation. Treated as a possible moonlighting activity, non-core.
- id: PMID:12709403
  title: Silencing of ubiquinone biosynthesis genes extends life span in Caenorhabditis
    elegans.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      RNAi of clk-1 (among eight CoQ genes) lowers quinone and extends lifespan;
      supports the ubiquinone biosynthetic role. Title-verified.
- id: PMID:14517217
  title: Molecular mechanism of maternal rescue in the clk-1 mutants of Caenorhabditis
    elegans.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      clk-1 encodes the UQ-biosynthesis hydroxylase; UQ replaced by DMQ in mutants;
      establishes maternal rescue and uncoupling of longevity from developmental
      phenotypes. Title-verified.
- id: PMID:16920626
  title: Mitochondrial complex I function modulates volatile anesthetic sensitivity
    in C. elegans.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      clk-1 is one of several ETC/CoQ mutants tested; supports the indirect OXPHOS/
      anesthetic-sensitivity (xenobiotic-response) annotations as downstream effects.
- id: PMID:17189267
  title: Knockdown of mitochondrial heat shock protein 70 promotes progeria-like phenotypes
    in caenorhabditis elegans.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Uses CLK-1 as a mitochondrial protein whose level falls with hsp-6 knockdown;
      supports mitochondrial localization only.
- id: PMID:17277769
  title: eIF4E function in somatic cells modulates ageing in Caenorhabditis elegans.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      clk mutants used as long-lived partners in a translation/ageing study; supports
      the non-core lifespan-determination annotations.
- id: PMID:19783783
  title: Life-span extension by dietary restriction is mediated by NLP-7 signaling
    and coelomocyte endocytosis in C. elegans.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Cached abstract discusses long-lived electron-transport-chain mutants without
      naming clk-1; full-text curator classed clk-1 in this group. Supports the
      non-core lifespan annotations; not removed on abstract-only grounds.
- id: PMID:25961505
  title: A nuclear role for the respiratory enzyme CLK-1 in regulating mitochondrial
    stress responses and longevity.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: DISPUTED
    review_notes: >-
      Full-text primary paper reporting a distinct nuclear CLK-1/COQ7 pool that
      regulates ROS metabolism, the UPRmt, transcription, and longevity independently
      of ubiquinone. The data are genuine but the nuclear/non-mitochondrial model is
      debated (worm N-terminus lacks the COQ7 NTS; limited independent confirmation).
      Underlies the nucleus, ROS-regulation, and transcription-regulation annotations,
      which are retained as non-core.
- id: file:worm/clk-1/clk-1-deep-research-falcon.md
  title: "Deep research report (Edison/falcon): C. elegans CLK-1 (COQ7)"
  reference_review:
    relevance: MEDIUM
    correctness: UNVERIFIED
    review_notes: >-
      AI-generated Edison/falcon deep-research synthesis (40 cited sources) used only
      as corroborating context. It independently reproduces the di-iron DMQ9->UQ9
      hydroxylase function, the COQ metabolon/CoQ-synthome membership, and the debated
      (explicitly unconfirmed) nuclear moonlighting role. Its underlying citations were
      not individually verified, so it is marked UNVERIFIED; every review claim is
      anchored to cached primary PMIDs, not to this file.

clk-1

Gene Description

Proposed New Ontology Terms

coenzyme Q biosynthesis complex

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Knowledge Gaps

Deep Research

Falcon

Comprehensive Research Report: C. elegans CLK-1 (COQ7) — Gene ID: clk-1, UniProt: P48376

Gene Identity Verification

1. Enzymatic Function and Catalytic Mechanism

1.1 Primary Reaction

1.2 Active Site and Cofactor

1.3 Structural Features

2. Subcellular Localization

2.1 Mitochondrial Localization

2.2 Dual Localization to the Nucleus

3. Pathway Context: The CoQ Biosynthetic Pathway and the COQ Metabolon

3.1 CoQ Biosynthesis

3.2 The COQ Metabolon (CoQ Synthome)

3.3 The COQ7–COQ9 Interaction

4. Phenotypes of clk-1 Mutants and Relationship to Aging

4.1 Pleiotropic Phenotypes

4.2 DMQ9 Accumulation and UQ9 Deficiency

4.3 Mechanism of Lifespan Extension

5. Evolutionary Conservation

6. Recent Developments (2022–2024)

Summary

Artifacts

Citations

📚 Additional Documentation

Notes

clk-1 (COQ7 ortholog) — research notes

Summary of what is KNOWN (with provenance)

Direct molecular function: di-iron ubiquinone/CoQ biosynthetic monooxygenase

Subcellular location: mitochondrion (inner membrane, matrix face)

Downstream / mutant-phenotype (NON-CORE) biology

DEBATED / secondary nuclear moonlighting role — treat cautiously

What is NOT known (knowledge gaps)

Provenance note on deep research

Annotation-review plan (core vs non-core)

📄 View Raw YAML