NUC-1 (C07B5.5) is the major acid deoxyribonuclease of C. elegans and a member of the DNase II family. It is a secreted, glycosylated acid hydrolase with an N-terminal signal peptide. It resides in lysosomes and phagolysosomes and is released in excretory and secretory products. It cleaves double-stranded DNA endonucleolytically and is most active at acidic pH. Loss of nuc-1 removes almost all of the worm's DNase II-type activity. NUC-1 carries out the late step of apoptotic DNA degradation. Its loss leaves TUNEL-reactive DNA ends in cell corpses of the embryo, larva and germline, and it is the predominant of the three worm DNase II paralogs (NUC-1, CRN-6, CRN-7) in this role. Degradation of corpse DNA depends on corpse engulfment, which fits digestion in the phagolysosome of the engulfing cell. NUC-1 also acts non-autonomously after secretion and uptake. Whether it can act inside dying cells is debated. NUC-1 also digests the DNA of ingested bacteria in the intestinal lumen, and secreted NUC-1 degrades extracellular DNA. Undigested apoptotic DNA in nuc-1 mutant gonads goes with raised expression of antimicrobial genes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002785 negative regulation of antimicrobial peptide production | IMP PMID:26251453 Loss of DNase II function in the gonad is associated with a ... | KEEP AS NON CORE | Summary: nuc-1 (and crn-7) mutant gonads show raised transcript levels of antimicrobial genes (abf-2, spp-1, nlp-29, cnc-2, lys-7). The authors attribute this to undigested apoptotic DNA fragments activating ERK signalling. Reason: The phenotype is real and the WormBase curator read the paper (abstract only in our cache), so we do not overrule it. But NUC-1 does not take part in regulating antimicrobial peptide production. It degrades DNA, and accumulation of its undigested substrate triggers an innate immune response. The effect is indirect and downstream of the core nuclease function. The readout was antimicrobial gene expression, not peptide production. Kept as a non-core, indirect consequence. Supporting Evidence: PMID:26251453 loss of NUC-1 and CRN-7 lead to up-regulation of antimicrobial genes (abf-2, spp-1, nlp-29, cnc-2, and lys-7) PMID:26251453 an incomplete digestion of DNA fragments resulting from the absence of NUC-1 or CRN-7 in the gonad could induce the ERK signalling, consequently activating antimicrobial gene expression |
| GO:0004520 DNA endonuclease activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA-derived generic DNA endonuclease activity. Correct but less specific than the DNase II activity the gene already carries from IBA, IEA and IMP evidence. Reason: NUC-1 is an endonuclease (it introduces nicks and double-strand breaks), so the claim is true. GO:0004531 deoxyribonuclease II activity is an is_a descendant of GO:0004520 and is already supported on this gene by direct mutant-extract assays and by the DNase II family assignment. Following the correct-but-general rule, refine to that term. Proposed replacements: deoxyribonuclease II activity Supporting Evidence: PMID:3228446 The DNase functioned as an endonuclease and introduced both single-strand nicks and double-strand breaks into DNA. PMID:10903446 wild-type animals contained a potent endonuclease activity with a cleavage preference similar to DNase II, while nuc-1 mutant worms demonstrated a marked reduction in this nuclease activity |
| GO:0004531 deoxyribonuclease II activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD at the eukaryote-level DNase II node PTN000092274 (PTHR10858). It is seeded by human DNASE2, mouse Dnase2a, rat Dnase2, Drosophila DNaseII and the three worm paralogs, including nuc-1 itself. Reason: NUC-1 sits inside the DNase II clade (PTHR10858:SF31, Pfam PF03265), and there is no sign of catalytic loss. Mutant extracts lack the DNase II-type activity. nuc-1 appearing among the IBD seeds reflects its own experimental grounding, not circularity. This is the core molecular function. Supporting Evidence: file:worm/nuc-1/nuc-1-uniprot.txt Belongs to the DNase II family. PMID:10903446 Our results therefore provide compelling evidence that the C07B5.5 gene encodes the NUC-1 apoptotic nuclease and that this nuclease is related in sequence and activity to DNase II. |
| GO:0004531 deoxyribonuclease II activity | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro IPR004947 (DNase II) / EC 3.1.22.1 mapping to DNase II activity. Reason: The mapping agrees with the IBA and with direct experimental evidence for this gene. Supporting Evidence: file:worm/nuc-1/nuc-1-uniprot.txt Hydrolyzes DNA under acidic conditions with a preference for double-stranded DNA. |
| GO:0004531 deoxyribonuclease II activity | IMP PMID:10903446 The C. elegans apoptotic nuclease NUC-1 is related in sequen... | ACCEPT | Summary: Crude extracts of wild-type worms have a potent DNase II-like endonuclease activity that is markedly reduced in nuc-1(e1392) nonsense mutants, and a wild-type C07B5.5 transgene restores it. Reason: Loss-of-function and complementation evidence ties the DNase II-like activity to the C07B5.5 product. Earlier partial purification showed that three independent nuc-1 alleles reduce this activity to under 1%. Supporting Evidence: PMID:10903446 wild-type animals contained a potent endonuclease activity with a cleavage preference similar to DNase II, while nuc-1 mutant worms demonstrated a marked reduction in this nuclease activity PMID:3228446 Three independent mutations in the nuc-1 gene were shown to reduce nuclease activity to less than 1% of that seen in wild-type organisms. |
| GO:0004531 deoxyribonuclease II activity | IMP PMID:19809494 The roles and acting mechanism of Caenorhabditis elegans DNa... | ACCEPT | Summary: Comparative analysis of the three worm DNase II genes. NUC-1 is the major enzyme resolving 3'-OH DNA breaks in apoptotic cells and the only one degrading bacterial DNA in the intestine. Reason: Mutant, rescue and promoter-swap experiments support NUC-1 as the main functional DNase II enzyme in vivo. They are consistent with the activity annotation. Supporting Evidence: PMID:19809494 nuc-1 plays a major role, crn-6 plays an auxiliary role, and crn-7 plays a negligible role in resolving 3' OH DNA breaks generated in apoptotic cells |
| GO:0004531 deoxyribonuclease II activity | IMP PMID:26182365 Autonomous and non-autonomous roles of DNase II during cell ... | ACCEPT | Summary: The ToLFP probe detects DNase II-generated DNA ends (5'-OH/3'-phosphate). nuc-1 embryos showed the fewest ToLFP signals of the three DNase II mutants. Reason: ToLFP specifically reads out the cleavage products typical of DNase II. Their loss in nuc-1 embryos supports NUC-1 having this activity in vivo. Supporting Evidence: PMID:26182365 Among three DNase II mutant embryos (nuc-1, crn-6 and crn-7), nuc-1 embryos exhibited the least number of ToLFP. The ToLFP results confirmed the previous findings that NUC-1 is the major DNase II for degrading apoptotic DNA. |
| GO:0004531 deoxyribonuclease II activity | IMP PMID:26251453 Loss of DNase II function in the gonad is associated with a ... | ACCEPT | Summary: In vitro and in vivo assays on DNase II mutants show NUC-1 (with CRN-7) is required for degrading apoptotic DNA in the gonad. Reason: Consistent with the other evidence for DNase II activity. The abstract states in vitro nuclease assays on mutants were performed, and the curator read the full text. Supporting Evidence: PMID:26251453 we performed in vitro and in vivo assays on various mutant nematodes to demonstrate that NUC-1 and CRN-7, but not CRN-6, function in germ cell apoptosis |
| GO:0005634 nucleus | TAS PMID:10716942 NUC-1, a caenorhabditis elegans DNase II homolog, functions ... | MARK AS OVER ANNOTATED | Summary: Traceable author statement placing NUC-1 in the nucleus, presumably because its substrate is the chromosomal DNA of apoptotic cells. Reason: No direct evidence places the NUC-1 protein in the nucleus. The cached Wu et al. abstract describes degradation of apoptotic-cell DNA but no localization. NUC-1 is a signal-peptide-bearing, glycosylated acid hydrolase. It is lysosomal (IDA) and secreted, and its secretion signal is needed for function. Completion of corpse DNA degradation requires engulfment. The nuclear location of the substrate does not make the enzyme nuclear. A 2026 preprint (Europe PMC PPR1304135, not cited as support) reports that NUC-1 is absent from nuclei of apoptotic and live cells. Because this is a TAS and not an experimental call, we flag it as an over-annotation and do not remove it. Supporting Evidence: file:worm/nuc-1/nuc-1-uniprot.txt SIGNAL 1..21 PMID:10716942 Completion of DNA degradation did not occur in the absence of cell-corpse engulfment. PMID:19809494 Removal or disruption of NUC-1 secretion signal eliminates NUC-1's ability to mediate DNA degradation across its expression border. |
| GO:0005764 lysosome | IDA PMID:20921409 Sequential action of Caenorhabditis elegans Rab GTPases regu... | ACCEPT | Summary: Guo et al. 2010 used NUC-1 fusion protein as a lysosomal marker in studying phagolysosome formation. NUC-1::mCHERRY is widely used as a C. elegans lysosome marker. Reason: Direct localization evidence (WormBase IDA; the cached abstract does not mention NUC-1, so we defer to the curator). It is corroborated by independent use of NUC-1::mCHERRY to label lysosomes and phagolysosomes, and by the acidic pH optimum of the enzyme. Under the root-organelle policy, the organelle term is informative and is kept. The lumenal sub-compartment is added as a separate NEW row. Supporting Evidence: PMID:22822152 Using NUC-1::mCHERRY, which labels lysosomes (8, 9) PMID:22822152 degradation of apoptotic cells in phagolysosomes (indicated by GFP::RAB-7 or NUC-1::mCHERRY) |
| GO:0006259 DNA metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the DNase II domain to the generic DNA metabolic process. Reason: Correct but too general. NUC-1 degrades DNA, both the chromatin of apoptotic cells and the DNA of ingested bacteria. GO:0006308 DNA catabolic process covers both roles. Its descendant GO:0006309 apoptotic DNA fragmentation, which the gene already carries, covers the apoptotic role. Proposed replacements: DNA catabolic process apoptotic DNA fragmentation Supporting Evidence: PMID:19809494 Therefore, NUC-1 appears to be the only DNase II nuclease that has a function in degrading DNA in post-embryonic apoptotic cells and bacterial DNA in intestine. |
| GO:0006309 apoptotic DNA fragmentation | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBD for apoptotic DNA fragmentation at the DNase II node, seeded by the three C. elegans DNase II genes, including nuc-1. Reason: The seeds are worm genes with experimental evidence, and nuc-1 is the best characterized of them. Its own presence among the seeds marks experimental grounding on the target. DNase II directly cleaves apoptotic DNA (the late step after initial nicking), which fits the term's requirement for direct involvement in fragmenting DNA. Supporting Evidence: PMID:19809494 nuc-1 plays a major role, crn-6 plays an auxiliary role, and crn-7 plays a negligible role in resolving 3' OH DNA breaks generated in apoptotic cells |
| GO:0006309 apoptotic DNA fragmentation | IMP PMID:10716942 NUC-1, a caenorhabditis elegans DNase II homolog, functions ... | ACCEPT | Summary: nuc-1 mutants generate TUNEL-reactive DNA in apoptotic cells but cannot convert it to the TUNEL-unreactive (fully degraded) state. Reason: This is the defining genetic evidence that NUC-1 carries out an intermediate step of apoptotic DNA degradation. Its nuclease activity is the agent of that step, so this is participation and not just requirement. Supporting Evidence: PMID:10716942 Mutations in nuc-1 allowed the generation of TUNEL-reactive DNA but blocked the conversion of TUNEL-reactive DNA to a subsequent TUNEL-unreactive state. |
| GO:0006309 apoptotic DNA fragmentation | IMP PMID:10903446 The C. elegans apoptotic nuclease NUC-1 is related in sequen... | ACCEPT | Summary: nuc-1(e1392) mutants carry persistent undegraded apoptotic DNA, and C07B5.5 transgenes complement the phenotype. Reason: Consistent with the other evidence that NUC-1 is the apoptotic nuclease. Supporting Evidence: PMID:10903446 The Caenorhabditis elegans nuc-1 gene has previously been implicated in programmed cell death due to the presence of persistent undegraded apoptotic DNA in nuc-1 mutant animals. |
| GO:0006309 apoptotic DNA fragmentation | IMP PMID:19809494 The roles and acting mechanism of Caenorhabditis elegans DNa... | ACCEPT | Summary: NUC-1 is the major DNase II resolving 3'-OH DNA breaks in apoptotic cells. It acts non-autonomously after secretion and uptake. Reason: Strong genetic evidence for direct nuclease participation. The site of action (dying cell or engulfing cell) is debated but does not affect this process annotation. Supporting Evidence: PMID:19809494 nuc-1 plays a major role, crn-6 plays an auxiliary role, and crn-7 plays a negligible role in resolving 3' OH DNA breaks generated in apoptotic cells PMID:19809494 elegans DNase II can also act in phagocytes to promote apoptotic DNA degradation, when cell corpse engulfment proceeds normally. |
| GO:0006309 apoptotic DNA fragmentation | IMP PMID:26182365 Autonomous and non-autonomous roles of DNase II during cell ... | ACCEPT | Summary: ToLFP detection of DNase II cleavage products shows NUC-1 is the major DNase II degrading apoptotic DNA in embryos, acting mostly non-autonomously and in a secretion-dependent manner. Reason: Direct visualization of DNase II cleavage products in apoptotic cells, reduced most in nuc-1 embryos. Supporting Evidence: PMID:26182365 anteriorly expressed NUC-1 digests apoptotic DNA in posterior blastomeres in a non-autonomous and secretion-dependent manner |
| GO:0006309 apoptotic DNA fragmentation | IMP PMID:26251453 Loss of DNase II function in the gonad is associated with a ... | ACCEPT | Summary: NUC-1 degrades apoptotic DNA of germ cells at the pachytene zone of the gonad. Reason: Extends the apoptotic DNA degradation role to germline apoptosis. Supporting Evidence: PMID:26251453 nuc-1 and crn-7 play a role in degrading apoptotic DNA in distinct sites of the gonad |
| GO:0043202 lysosomal lumen | IC PMID:20921409 Sequential action of Caenorhabditis elegans Rab GTPases regu... | NEW | Summary: Proposed sub-compartment for the lysosomal localization of NUC-1. Reason: Added beside, not instead of, the lysosome row, following the root-organelle policy. Several independent lines agree that NUC-1 is a soluble lumenal hydrolase. (1) It has an N-terminal signal peptide and no transmembrane segment, and it is secreted. (2) Its activity is gated by acidic pH, which is only met in the lumen. (3) Yu et al. had to fuse the LMP-1 membrane domain to NUC-1 to make a membrane-bound form, so the native protein is soluble. (4) NUC-1::mCHERRY fills lysosomes and phagolysosomes and is used to mark them. Supporting Evidence: file:worm/nuc-1/nuc-1-uniprot.txt Hydrolyzes DNA under acidic conditions with a preference for double-stranded DNA. PMID:26182365 express a different version of fusion protein (NUC-1::LMP-1153–237::GFP) with the insertion of the membrane domain of lysosomal protein LMP-1 between NUC-1 and GFP PMID:22822152 Using NUC-1::mCHERRY, which labels lysosomes (8, 9) PMID:40349596 environmental pH specifically modulates NUC-1 activity rather than expression |
| GO:0005576 extracellular region | IDA PMID:19809494 The roles and acting mechanism of Caenorhabditis elegans DNa... | NEW | Summary: NUC-1 is secreted. Its signal peptide is needed for it to leave the pharynx and act on distant cells, and it is present in worm excretory/secretory products. Reason: Two independent lines show secretion. (1) Lai et al. 2009 found that NUC-1::GFP expressed from the myo-2 promoter left the pharynx, while a signal-peptide-deleted form was retained and failed to rescue. (2) Dong et al. 2023 found NUC-1 DNase II in nematode excretory and secretory products, where it degrades extracellular DNA. Secretion explains non-autonomous action and the degradation of bacterial DNA in the intestinal lumen. Supporting Evidence: PMID:19809494 in which the NUC-1 signal peptide (amino acids 1–21) was deleted and the mutant NUC-1 protein was not secreted PMID:37523858 Deoxyribonuclease (DNase) II encoded by nuc-1 in the excretory and secretory products of nematodes was the primary mechanism. |
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Download this section (compressed HTML)Q: Where does NUC-1 act on apoptotic DNA? Lai et al. 2009 and Yu et al. 2015 report activity in unengulfed dying cells. Wu et al. 2000 and a 2026 preprint (PPR1304135) show that degradation needs engulfment and phagolysosome fusion, and that NUC-1 is absent from nuclei. Can the engulfment-independent signal be explained by residual engulfment or by CRN-6/CRN-7?
Q: Should GO:0032010 phagolysosome (or phagocytic vesicle lumen) be added for NUC-1 once the engulfing-cell phagosomal localization is published in peer-reviewed form?
Q: Should the WormBase TAS nucleus annotation (PMID:10716942) be retired, given that NUC-1 is a secreted lysosomal hydrolase whose substrate, not itself, is nuclear?
Q: How is secreted NUC-1 taken back up by distant cells and delivered to lysosomes? Is it mannose-6-phosphate-independent, and which receptor is involved?
Experiment: CRISPR knock-in of a pH-insensitive fluorescent tag at the nuc-1 locus, with imaging of embryonic cell-corpse phagosomes and dying-cell nuclei in wild-type and engulfment-defective (ced-1; ced-5) backgrounds.
Hypothesis: Endogenous NUC-1 is found in phagolysosomes of engulfing cells and not in apoptotic nuclei.
Type: Endogenous tagging and live imaging
Experiment: Express nuc-1 only in engulfing cells or only in dying cells (for example with ced-1 versus egl-1 promoters) in nuc-1 mutants and quantify TUNEL/ToLFP-positive corpses.
Hypothesis: Only engulfing-cell expression rescues apoptotic DNA degradation.
Type: Cell-type-specific rescue
Experiment: Purify recombinant NUC-1 and determine pH optimum, product ends (3'-phosphate), and the effect of mutating the conserved catalytic histidines of the two PLD-like motifs.
Hypothesis: NUC-1 is a canonical DNase II with 3'-phosphate products and an acidic pH optimum, and needs both PLD-like motifs.
Type: Recombinant enzymology
The nuc-1 gene encodes a DNase II homolog similar to mammalian and Drosophila DNaseII enzymes and is required for DNA degradation during apoptosis as well as for degradation of dietary DNA during normal feeding; during apoptosis, NUC-1 functions in apoptotic cells at an intermediate stage of DNA degradation, after the killing step, but prior to cell-corpse engulfment.
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