DNASE2 encodes deoxyribonuclease II alpha (DNase II), a 360-residue glycosylated, signal-peptide-bearing acid endonuclease of the lysosome. Its catalytic domain belongs to the phospholipase D superfamily, and it cleaves double-stranded DNA endonucleolytically at acidic pH, without divalent cations, to 3'-phosphate products. DNase II is expressed ubiquitously and highly in macrophages, where it degrades the DNA of engulfed apoptotic cells and of nuclei extruded by erythroid precursors in phagolysosomes; it also degrades nuclear and mitochondrial DNA delivered to lysosomes by autophagy, and trims endocytosed microbial DNA into ligands for TLR9. DNase II-derived oligonucleotides from apoptotic-cell DNA also serve as a signal for efferocytosis-induced macrophage proliferation in mice. Loss of DNase II leaves undigested self-DNA that activates cGAS-STING and type I interferon responses; in mice this causes lethal anemia and polyarthritis, and biallelic hypomorphic DNASE2 variants in humans cause autoinflammatory-pancytopenia syndrome, a type I interferonopathy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004520 DNA endonuclease activity | IEA GO_REF:0000120 | MODIFY | Summary: IEA (ARBA/ortholog-based) annotation to the general DNA endonuclease activity term. Reason: DNase II is an endonuclease, so the term is correct, but it is less specific than the evidence supports. The enzyme cleaves DNA endonucleolytically to 3'-phosphomononucleotide and 3'-phosphooligonucleotide products (EC 3.1.22.1), exactly captured by GO:0004531 deoxyribonuclease II activity, which the gene already carries by IBA, IEA and two IMP rows. Proposed replacements: deoxyribonuclease II activity Supporting Evidence: PMID:29259162 lysates of fibroblasts from F1:V-1 and F2:II-4 demonstrated a marked reduction of DNase II activity against the same substrate; DNase II activity in these cells could be restored by expression of constructs coding for wild-type protein file:human/DNASE2/DNASE2-uniprot.txt Hydrolyzes DNA under acidic conditions with a preference for double-stranded DNA. Plays a major role in the clearance of nucleic acids generated through apoptosis, hence preventing autoinflammation |
| GO:0004531 deoxyribonuclease II activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from eukaryote-level node PTN000092274 (PTHR10858) propagating deoxyribonuclease II activity; human DNASE2 is itself one of the experimentally grounded seeds alongside mouse Dnase2a, fly DNaseII and worm nuc-1 paralogs. Reason: Core molecular function. DNASE2 is the founding member of the DNase II family; the catalytic PLD-superfamily fold is conserved, and human recombinant and endogenous enzyme show acid DNase II activity. Human O00115 appearing in WITH/FROM reflects its own experimental grounding, not circularity. Supporting Evidence: PMID:29259162 DNase II activity is calculated via linear approximation according to the Kunitz protocol (WT 3108 Ku/mg; G116A 120 Ku/mg; del-Exon4 0 Ku/mg; D121V 19.57 Ku/mg) PMID:16150810 DNase II exhibits a catalytic domain common to the phospholipase D superfamily file:human/DNASE2/DNASE2-uniprot.txt Hydrolyzes DNA under acidic conditions with a preference for double-stranded DNA. Plays a major role in the clearance of nucleic acids generated through apoptosis, hence preventing autoinflammation |
| GO:0004531 deoxyribonuclease II activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA (combined InterPro IPR004947 / EC 3.1.22.1 / mouse ortholog) annotation to deoxyribonuclease II activity. Reason: Consistent with the experimental and phylogenetic evidence; DNase II family membership (Pfam PF03265, IPR004947) and direct activity assays of the human enzyme support this core function. Supporting Evidence: file:human/DNASE2/DNASE2-uniprot.txt Belongs to the DNase II family. PMID:29259162 DNase II activity is calculated via linear approximation according to the Kunitz protocol (WT 3108 Ku/mg; G116A 120 Ku/mg; del-Exon4 0 Ku/mg; D121V 19.57 Ku/mg) |
| GO:0004531 deoxyribonuclease II activity | IMP PMID:29259162 Type I interferon-mediated autoinflammation due to DNase II ... | ACCEPT | Summary: Rodero et al. 2017 showed that recombinant wild-type human DNase II digests plasmid DNA at pH 5, that patient missense/splice variants abolish activity, and that patient fibroblast activity is rescued by wild-type cDNA. Reason: Direct biochemical and genetic (patient variant, siRNA and rescue) evidence for acid DNase activity of human DNASE2. Core function. Supporting Evidence: PMID:29259162 lysates of fibroblasts from F1:V-1 and F2:II-4 demonstrated a marked reduction of DNase II activity against the same substrate; DNase II activity in these cells could be restored by expression of constructs coding for wild-type protein PMID:29259162 DNase II activity is calculated via linear approximation according to the Kunitz protocol (WT 3108 Ku/mg; G116A 120 Ku/mg; del-Exon4 0 Ku/mg; D121V 19.57 Ku/mg) |
| GO:0004531 deoxyribonuclease II activity | IMP PMID:31775019 Janus kinase inhibition for autoinflammation in patients wit... | ACCEPT | Summary: Hong et al. 2020 (JACI letter) described further DNASE2-deficient patients treated with JAK inhibition; the cached record has no abstract or full text. Reason: The cached record is a letter with no abstract, so the curator's evidence (presumably DNase II activity measurements on patient variants; UniProt cites this paper for the catalytic activity) cannot be inspected directly. The function itself is firmly established for human DNASE2 by PMID:29259162, so the annotation is accepted, deferring to the curator. Supporting Evidence: PMID:29259162 DNase II activity is calculated via linear approximation according to the Kunitz protocol (WT 3108 Ku/mg; G116A 120 Ku/mg; del-Exon4 0 Ku/mg; D121V 19.57 Ku/mg) file:human/DNASE2/DNASE2-uniprot.txt Hydrolyzes DNA under acidic conditions with a preference for double-stranded DNA. Plays a major role in the clearance of nucleic acids generated through apoptosis, hence preventing autoinflammation |
| GO:0005515 protein binding | IPI PMID:28514442 Architecture of the human interactome defines protein commun... | REMOVE | Summary: High-throughput interactome mapping detected DNASE2 with calnexin (CANX). Reason: Generic protein binding is uninformative. The only partner is calnexin (CANX, P27824), the ER lectin chaperone that binds newly synthesised N-glycoproteins; DNase II is a glycosylated secretory-pathway protein, so the interaction from high-throughput interactome mapping most likely reflects ER folding quality control of the nascent enzyme rather than a DNase II function. Removal under the protein-binding policy does not imply the interaction is false. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | REMOVE | Summary: High-throughput interactome mapping detected DNASE2 with calnexin (CANX). Reason: Generic protein binding is uninformative. The only partner is calnexin (CANX, P27824), the ER lectin chaperone that binds newly synthesised N-glycoproteins; DNase II is a glycosylated secretory-pathway protein, so the interaction from high-throughput interactome mapping most likely reflects ER folding quality control of the nascent enzyme rather than a DNase II function. Removal under the protein-binding policy does not imply the interaction is false. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | REMOVE | Summary: High-throughput interactome mapping detected DNASE2 with calnexin (CANX). Reason: Generic protein binding is uninformative. The only partner is calnexin (CANX, P27824), the ER lectin chaperone that binds newly synthesised N-glycoproteins; DNase II is a glycosylated secretory-pathway protein, so the interaction from high-throughput interactome mapping most likely reflects ER folding quality control of the nascent enzyme rather than a DNase II function. Removal under the protein-binding policy does not imply the interaction is false. |
| GO:0005764 lysosome | IDA PMID:23516607 Biogenesis and proteolytic processing of lysosomal DNase II. | ACCEPT | Summary: Ohkouchi et al. 2013 showed by subcellular fractionation and immuno-EM that processed DNase II forms reside in lysosomes, with lysosomal processing by cathepsin L, and that DNase II is localized in macrophage lysosomes. Reason: Lysosome is the principal site of DNase II action and is supported directly. The cached abstract describes mouse DNase II (antibody against mouse protein, mouse tissues); the curator applied it to human O00115, which may reflect assays in the full text. The localization is in any case conserved and corroborated for the human enzyme (patient report describes DNASE2 as "the lysosomal DNase") so the annotation is accepted. Whole-organelle fractionation cannot resolve sub-compartment; lumen added separately as NEW. Supporting Evidence: PMID:23516607 These results indicate that DNase II is processed and activated in lysosomes, while cathepsin L is involved in the processing of the enzyme. PMID:29259162 the gene encoding the 360 amino acid lysosomal DNase DNase II |
| GO:0005764 lysosome | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from UniProt subcellular location (Lysosome, by similarity to mouse P56542). Reason: Checked the source: the UniProt location rests on the mouse ortholog, whose lysosomal localization is shown experimentally (PMID:23516607). The organelle claim holds for human DNase II (acid optimum, signal peptide, lysosomal processing), so the row is kept. Supporting Evidence: PMID:23516607 These results indicate that DNase II is processed and activated in lysosomes, while cathepsin L is involved in the processing of the enzyme. |
| GO:0006259 DNA metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping (IPR004947 DNase II) to the broad DNA metabolic process. Reason: True but too general: DNase II acts only catabolically, degrading DNA. The specific supported term is GO:0006308 DNA catabolic process, which the gene already carries. Proposed replacements: DNA catabolic process Supporting Evidence: PMID:29259162 DNase II digests the DNA of apoptotic cells and of nuclei expelled from erythroid precursors. |
| GO:0006308 DNA catabolic process | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara transfer of DNA catabolic process from mouse Dnase2a. Reason: Core process: DNase II degrades DNA of engulfed apoptotic cells, expelled erythroid nuclei, autophagically delivered nuclear and mitochondrial DNA, and endocytosed microbial DNA in lysosomes. Supporting Evidence: PMID:29259162 DNase II digests the DNA of apoptotic cells and of nuclei expelled from erythroid precursors. PMID:12524536 when apoptotic cells were phagocytosed by macrophages, their DNA was degraded by DNase II PMID:25284779 Removal of damaged DNA by Dnase2a required nuclear export and autophagy-mediated delivery of the DNA to lysosomes. |
| GO:0006309 apoptotic DNA fragmentation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA from PTN000092274 seeded by C. elegans nuc-1 and paralogs, which degrade apoptotic-cell DNA. Reason: DNase II does directly cleave the DNA of apoptotic cells, satisfying the GO usage note requiring direct involvement in fragmenting DNA. However, in both worm and mammals this is the engulfment-dependent step performed in the phagocyte (nuc-1; macrophage DNase II), not the cell-autonomous fragmentation by CAD/DFFB in the dying cell. The process the enzyme serves is more fully described by DNA catabolic process and apoptotic cell clearance; this term is kept as non-core. Supporting Evidence: PMID:12524536 when apoptotic cells were phagocytosed by macrophages, their DNA was degraded by DNase II PMID:10716942 Completion of DNA degradation did not occur in the absence of cell-corpse engulfment. |
| GO:0043277 apoptotic cell clearance | IMP PMID:29259162 Type I interferon-mediated autoinflammation due to DNase II ... | ACCEPT | Summary: Patients with hypomorphic DNASE2 variants develop type I interferon-driven autoinflammation attributed to failure to degrade DNA of apoptotic cells and expelled erythroid nuclei, matching Dnase2-null mouse phenotypes. Reason: DNase II performs the DNA-digestion step of corpse degradation inside the phagocyte, so it does part of the work of apoptotic cell clearance (degradation of the engulfed cell), not merely being required for it. Shown in mouse (macrophage lysosomes accumulate undigested DNA) and supported for human by the patient phenotype. Supporting Evidence: PMID:29259162 DNase II digests the DNA of apoptotic cells and of nuclei expelled from erythroid precursors. PMID:12524536 when apoptotic cells were phagocytosed by macrophages, their DNA was degraded by DNase II file:human/DNASE2/DNASE2-uniprot.txt Hydrolyzes DNA under acidic conditions with a preference for double-stranded DNA. Plays a major role in the clearance of nucleic acids generated through apoptosis, hence preventing autoinflammation |
| GO:0043277 apoptotic cell clearance | IMP PMID:31775019 Janus kinase inhibition for autoinflammation in patients wit... | ACCEPT | Summary: Hong et al. 2020 (JACI letter) described DNASE2-deficient patients; cached record has no abstract. Reason: Full text not available in the cache; the claim is consistent with and established by PMID:29259162 and mouse genetics (PMID:12524536), so the annotation is accepted deferring to the curator. Supporting Evidence: PMID:29259162 DNase II digests the DNA of apoptotic cells and of nuclei expelled from erythroid precursors. PMID:12524536 when apoptotic cells were phagocytosed by macrophages, their DNA was degraded by DNase II |
| GO:0070062 extracellular exosome | HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... | KEEP AS NON CORE | Summary: Detected in shotgun proteomics of exosomes from expressed prostatic secretions in urine. Reason: High-throughput exosome proteomics; DNase II is a secreted lysosomal enzyme also found in body fluids (saliva, PMID:39329709), so presence in exosome preparations is plausible but peripheral to its lysosomal function. Supporting Evidence: PMID:23533145 exosome preparations were characterized by a shotgun proteomics procedure |
| GO:0043202 lysosomal lumen | IC PMID:23516607 Biogenesis and proteolytic processing of lysosomal DNase II. | NEW | Summary: Proposed: DNase II is a soluble enzyme of the lysosomal lumen. Reason: Two independent lines agree: (1) an N-terminal signal peptide with no transmembrane segment, giving a soluble secretory-pathway protein; (2) lysosomal fractionation and lumenal proteolytic processing/activation by cathepsin L, with an acidic pH optimum, so the enzyme acts on DNA delivered into the lumen by phagocytosis and autophagy. Added beside the lysosome rows, not replacing them. Supporting Evidence: file:human/DNASE2/DNASE2-uniprot.txt SIGNAL 1..18 PMID:23516607 These results indicate that DNase II is processed and activated in lysosomes, while cathepsin L is involved in the processing of the enzyme. PMID:25284779 Removal of damaged DNA by Dnase2a required nuclear export and autophagy-mediated delivery of the DNA to lysosomes. |
| GO:0032010 phagolysosome | IC PMID:34784501 Efferocytosis induces macrophage proliferation to help resol... | NEW | Summary: Proposed: DNase II acts in the phagolysosome of macrophages on DNA of engulfed apoptotic cells and expelled erythroid nuclei. Reason: DNase II is delivered to phagolysosomes by phagosome-lysosome fusion and is the enzyme that degrades engulfed cell DNA there: in mouse macrophages apoptotic-cell DNA is digested by DNase II only after phagocytosis, and DNase II is described as the phagolysosomal enzyme converting apoptotic-cell DNA to oligonucleotides; degradation requires lysosomal acidification. Inferred by curator (IC) from these functional data in mouse, conserved in human macrophages (patient phenotype). Supporting Evidence: PMID:34784501 the phagolysosomal enzyme that digests AC-DNA into oligonucleotides PMID:12524536 when apoptotic cells were phagocytosed by macrophages, their DNA was degraded by DNase II |
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Download this section (compressed HTML)Q: Should DNase II be annotated to positive regulation of macrophage proliferation (or a future efferocytosis-induced macrophage proliferation term) given that its oligonucleotide products drive DNA-PKcs/mTORC2/MYC signalling, or does it only supply the signal as an enzyme acting on cargo?
Q: Is the reported RNase activity of DNase II (PMID:39329709) physiologically relevant in lysosomes, and does it warrant an RNA endonuclease annotation?
Q: Does human DNase II generate TLR9 ligands from CpG-A and bacterial DNA as shown for mouse dendritic cells (PMID:25600358)?
Experiment: Rescue DNASE2-knockout human monocyte-derived macrophages with wild-type versus catalytically dead (His295 or patient D121V) DNase II and measure EdU incorporation, MYC induction and DNA-PKcs activation after apoptotic-cell feeding.
Hypothesis: DNase II catalytic activity, not protein presence, is required for efferocytosis-induced proliferation of human macrophages.
Experiment: Compare lysosomal RNA turnover and accumulation in DNASE2-null versus wild-type human macrophages using labelled RNA cargo, and assay purified enzyme kinetics on RNA versus DNA substrates at lysosomal pH.
Hypothesis: DNase II hydrolyses RNA in the lysosomal lumen.
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