CED-1 is the C. elegans engulfment receptor for apoptotic cell corpses, a single-pass transmembrane protein of the CED-1/Draper/MEGF10 family with an EMI domain, extracellular EGF-like repeats and a cytoplasmic tail carrying NPXY and YXXL motifs. Expressed on engulfing cells, it clusters around neighbouring corpses and recognizes them through the secreted bridging protein TTR-52, which binds exposed phosphatidylserine. Its NPXY motif recruits the PTB-domain adaptor CED-6/GULP and, with the ABC transporter CED-7 and dynamin DYN-1, it drives pseudopod extension, actin reorganization and internalization, then initiates phagosome maturation through PI(3)P and RAB-7. After engulfment it is recycled to the plasma membrane by retromer. Engulfing cells also use it to promote the death of cells that receive weak death signals, and it contributes to defense against bacterial pathogens.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000132 establishment of mitotic spindle orientation | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MARK AS OVER ANNOTATED | Summary: Establishment of mitotic spindle orientation (IGI with mom-5, Cabello et al. 2010). Reason: In the full text, spindle orientation needs MOM-5/Frizzled, GSK-3 and beta-catenins. Spindle defects appear only in a small fraction of ced-1; ced-5 double mutants, and the authors write that they 'cannot exclude' a role. This does not show that CED-1 orients spindles. Supporting Evidence: PMID:20126385 we did observe spindle defects in a small fraction of ced-1; ced-5 double mutants |
| GO:0001845 phagolysosome assembly | IMP PMID:18351800 Phagocytic receptor CED-1 initiates a signaling pathway for ... | ACCEPT | Summary: CED-1 initiates phagosome maturation and phagolysosome formation (Yu et al. 2008). Reason: IMP with full text. The CED-1/CED-6/DYN-1 pathway sets the rate of PI(3)P and RAB-7 enrichment on phagosomes and the formation of phagolysosomes. The receptor that initiates engulfment also drives degradation of the engulfed corpse. Supporting Evidence: PMID:18351800 One of the pathways, composed of CED-1, the adaptor protein CED-6, and DYN-1, controls the rate of enrichment of PI(3)P and RAB-7 on phagosomal surfaces and the formation of phagolysosomes |
| GO:0001891 phagocytic cup | IDA PMID:20133524 Retromer is required for apoptotic cell clearance by phagocy... | ACCEPT | Summary: CED-1 at the phagocytic cup (IDA, Chen et al. 2010). Reason: The cached record is abstract-only. CED-1::GFP marks budding pseudopods and phagocytic cups in time-lapse imaging, so the location is well established. Supporting Evidence: PMID:18351800 the CED-1::GFP signal rapidly disappeared from phagosomal surface after the enclosure of the phagocytic cup PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses |
| GO:0005044 scavenger receptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Scavenger receptor activity (IBA (PTN009076277, sources MEGF10 and ced-1)). Reason: CED-1 is the founding member of the CED-1/Draper/MEGF10 scavenger-receptor family. Through its EMI domain it binds the bridging molecule TTR-52, which binds phosphatidylserine on apoptotic cells. Core molecular function. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses PMID:20526330 binds to both PtdSer and the extracellular domain of CED-1 in vitro |
| GO:0005044 scavenger receptor activity | IEA GO_REF:0000002 | ACCEPT | Summary: Scavenger receptor activity (InterPro2GO (MEGF10/SREC1/2-like family)). Reason: CED-1 is the founding member of the CED-1/Draper/MEGF10 scavenger-receptor family. Through its EMI domain it binds the bridging molecule TTR-52, which binds phosphatidylserine on apoptotic cells. Core molecular function. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses PMID:20526330 binds to both PtdSer and the extracellular domain of CED-1 in vitro |
| GO:0005044 scavenger receptor activity | IPI PMID:20526330 Caenorhabditis elegans transthyretin-like protein TTR-52 med... | ACCEPT | Summary: CED-1 extracellular domain binds the bridging molecule TTR-52 (IPI, Wang et al. 2010). Reason: CED-1 is the founding member of the CED-1/Draper/MEGF10 scavenger-receptor family. Through its EMI domain it binds the bridging molecule TTR-52, which binds phosphatidylserine on apoptotic cells. The IPI with TTR-52 is the ligand-recognition step. Supporting Evidence: PMID:20526330 binds to both PtdSer and the extracellular domain of CED-1 in vitro PMID:22713871 CED-1 binds TTR-52 through its N-terminal EMI domain |
| GO:0005044 scavenger receptor activity | ISS PMID:11163239 CED-1 is a transmembrane receptor that mediates cell corpse ... | ACCEPT | Summary: Scavenger receptor activity by similarity to SREC (ISS). Reason: CED-1 is the founding member of the CED-1/Draper/MEGF10 scavenger-receptor family. Through its EMI domain it binds the bridging molecule TTR-52, which binds phosphatidylserine on apoptotic cells. Supporting Evidence: PMID:11163239 ced-1 encodes a transmembrane protein similar to human SREC (Scavenger Receptor from Endothelial Cells) PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses |
| GO:0005515 protein binding | IPI PMID:11729193 Interaction of CED-6/GULP, an adapter protein involved in en... | MODIFY | Summary: CED-1 cytoplasmic NPXY motif binds the PTB domain of CED-6/GULP (Su et al. 2002). Reason: 'Protein binding' is uninformative. The interaction is how the CED-1 receptor passes its signal to its adaptor, and the intracellular PTB/SH2-binding motifs are needed for engulfment but not for clustering. The informative activity is signaling receptor activity. Proposed replacements: signaling receptor activity Supporting Evidence: PMID:11729193 we present evidence for a physical interaction between GULP/CED-6 and one of the two motifs (NPXY motif) in the cytoplasmic tail of CED-1 PMID:11163239 Motifs in the intracellular domain of CED-1 known to interact with PTB and SH2 domains were necessary for engulfment but not for clustering |
| GO:0005515 protein binding | IPI PMID:11729193 Interaction of CED-6/GULP, an adapter protein involved in en... | MODIFY | Summary: CED-1 cytoplasmic NPXY motif binds the PTB domain of CED-6/GULP (Su et al. 2002). Reason: 'Protein binding' is uninformative. The interaction is how the CED-1 receptor passes its signal to its adaptor, and the intracellular PTB/SH2-binding motifs are needed for engulfment but not for clustering. The informative activity is signaling receptor activity. Proposed replacements: signaling receptor activity Supporting Evidence: PMID:11729193 we present evidence for a physical interaction between GULP/CED-6 and one of the two motifs (NPXY motif) in the cytoplasmic tail of CED-1 PMID:11163239 Motifs in the intracellular domain of CED-1 known to interact with PTB and SH2 domains were necessary for engulfment but not for clustering |
| GO:0005515 protein binding | IPI PMID:22713871 Structural study of TTR-52 reveals the mechanism by which a ... | MODIFY | Summary: CED-1 EMI domain binds TTR-52 (Kang et al. 2012). Reason: 'Protein binding' is uninformative. The binding partner is a phosphatidylserine-bridging ligand, so the interaction is the receptor's ligand-recognition activity, captured by scavenger receptor activity. Proposed replacements: scavenger receptor activity Supporting Evidence: PMID:22713871 CED-1 binds TTR-52 through its N-terminal EMI domain PMID:20526330 binds to both PtdSer and the extracellular domain of CED-1 in vitro |
| GO:0005886 plasma membrane | EXP PMID:35929733 trim-21 promotes proteasomal degradation of CED-1 for apopto... | ACCEPT | Summary: Plasma membrane. Reason: CED-1 is a single-pass transmembrane receptor at the engulfing-cell surface and is recycled back to the plasma membrane from phagosomes. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:35929733 CED-1 is recycled from phagosome membranes to plasma membranes via the retromer complex |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Plasma membrane. Reason: CED-1 is a single-pass transmembrane receptor at the engulfing-cell surface and is recycled back to the plasma membrane from phagosomes. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:35929733 CED-1 is recycled from phagosome membranes to plasma membranes via the retromer complex |
| GO:0005886 plasma membrane | IDA PMID:11163239 CED-1 is a transmembrane receptor that mediates cell corpse ... | ACCEPT | Summary: Plasma membrane. Reason: CED-1 is a single-pass transmembrane receptor at the engulfing-cell surface and is recycled back to the plasma membrane from phagosomes. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:35929733 CED-1 is recycled from phagosome membranes to plasma membranes via the retromer complex |
| GO:0005886 plasma membrane | IDA PMID:20133524 Retromer is required for apoptotic cell clearance by phagocy... | ACCEPT | Summary: Plasma membrane. Reason: CED-1 is a single-pass transmembrane receptor at the engulfing-cell surface and is recycled back to the plasma membrane from phagosomes. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:35929733 CED-1 is recycled from phagosome membranes to plasma membranes via the retromer complex |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Plasma membrane. Reason: CED-1 is a single-pass transmembrane receptor at the engulfing-cell surface and is recycled back to the plasma membrane from phagosomes. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:35929733 CED-1 is recycled from phagosome membranes to plasma membranes via the retromer complex |
| GO:0009986 cell surface | IDA PMID:11163239 CED-1 is a transmembrane receptor that mediates cell corpse ... | ACCEPT | Summary: Cell surface (IDA). Reason: CED-1 is displayed on the engulfing-cell surface, where it clusters around corpses. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses |
| GO:0012501 programmed cell death | IMP PMID:6857247 Mutations affecting programmed cell deaths in the nematode C... | MARK AS OVER ANNOTATED | Summary: Programmed cell death (IMP, Hedgecock et al. 1983). Reason: The source paper concludes that cells programmed to die still die in engulfment mutants, so engulfment is not needed for most deaths. Engulfment genes do promote death in sensitized backgrounds (Reddien et al. 2001), but that is a regulatory role, captured here by positive regulation of apoptotic process involved in development. CED-1 is not part of the death program itself. Supporting Evidence: PMID:6857247 With few exceptions, these cells still die, suggesting that, in nematodes, engulfment is not necessary for most programmed deaths PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants |
| GO:0016192 vesicle-mediated transport | IEA GO_REF:0000108 | MARK AS OVER ANNOTATED | Summary: Vesicle-mediated transport (inferred from scavenger receptor activity). Reason: Correct but uninformative parent of receptor-mediated engulfment. Engulfment of apoptotic cell is already annotated. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses |
| GO:0030036 actin cytoskeleton organization | IDA PMID:15744306 Two pathways converge at CED-10 to mediate actin rearrangeme... | KEEP AS NON CORE | Summary: Actin reorganization around corpses requires CED-1 (Kinchen et al. 2005). Reason: IDA. Actin rearrangement around the corpse is a step within engulfment and is downstream of CED-1 signaling, so it is kept as a non-core component of the engulfment role. Supporting Evidence: PMID:15744306 CED-1, CED-6 and CED-7 are required for actin reorganization around the apoptotic cell corpse |
| GO:0030670 phagocytic vesicle membrane | IDA PMID:16740477 C. elegans Dynamin mediates the signaling of phagocytic rece... | ACCEPT | Summary: CED-1 on the phagosome membrane (IDA, Yu et al. 2006). Reason: The cached record is abstract-only. Time-lapse imaging shows CED-1::GFP on the nascent phagosome surface, from which it is then recycled. Supporting Evidence: PMID:18351800 the CED-1::GFP signal rapidly disappeared from phagosomal surface after the enclosure of the phagocytic cup PMID:35929733 CED-1 is recycled from phagosome membranes to plasma membranes via the retromer complex |
| GO:0030670 phagocytic vesicle membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Phagocytic vesicle membrane (electronic). Reason: Consistent with the experimental data. Supporting Evidence: PMID:18351800 the CED-1::GFP signal rapidly disappeared from phagosomal surface after the enclosure of the phagocytic cup |
| GO:0031260 pseudopodium membrane | IDA PMID:16740477 C. elegans Dynamin mediates the signaling of phagocytic rece... | ACCEPT | Summary: CED-1 on extending pseudopods around corpses. Reason: CED-1 clusters on the engulfing-cell membrane around corpses, including the pseudopods that wrap them. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:16740477 DYN-1 transiently accumulates to the surface of pseudopods in a manner dependent on ced-1, ced-6, and ced-7 |
| GO:0031260 pseudopodium membrane | IDA PMID:21148288 Three sorting nexins drive the degradation of apoptotic cell... | ACCEPT | Summary: CED-1 on extending pseudopods around corpses. Reason: CED-1 clusters on the engulfing-cell membrane around corpses, including the pseudopods that wrap them. Supporting Evidence: PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses PMID:16740477 DYN-1 transiently accumulates to the surface of pseudopods in a manner dependent on ced-1, ced-6, and ced-7 |
| GO:0034620 cellular response to unfolded protein | IDA PMID:18606143 Unfolded protein response genes regulated by CED-1 are requi... | MARK AS OVER ANNOTATED | Summary: Cellular response to unfolded protein (IDA, Haskins et al. 2008). Reason: CED-1 is needed for expression of pqn/abu genes, which the authors class as a noncanonical unfolded protein response during infection. No study shows CED-1 responding to unfolded protein. The finding is about immune gene expression and is covered by defense response to bacterium. Supporting Evidence: PMID:18606143 CED-1 functions to activate the expression of pqn/abu genes |
| GO:0042742 defense response to bacterium | IMP PMID:18606143 Unfolded protein response genes regulated by CED-1 are requi... | KEEP AS NON CORE | Summary: ced-1 mutants are killed faster by Salmonella (Haskins et al. 2008). Reason: IMP with full text. This is a real but secondary role of CED-1 in innate immunity, separate from its engulfment function. Supporting Evidence: PMID:18606143 loss-of-function ced-1 mutants are immunocompromised animals and are rapidly killed by live bacteria PMID:18606143 CED-1 functions to activate the expression of pqn/abu genes |
| GO:0043652 engulfment of apoptotic cell | IBA GO_REF:0000033 | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants |
| GO:0043652 engulfment of apoptotic cell | IDA PMID:11163239 CED-1 is a transmembrane receptor that mediates cell corpse ... | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses PMID:11163239 ced-1 is expressed in and functions in engulfing cells |
| GO:0043652 engulfment of apoptotic cell | IDA PMID:15744306 Two pathways converge at CED-10 to mediate actin rearrangeme... | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:15744306 CED-1, CED-6 and CED-7 are required for actin reorganization around the apoptotic cell corpse |
| GO:0043652 engulfment of apoptotic cell | IMP PMID:11163239 CED-1 is a transmembrane receptor that mediates cell corpse ... | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:11163239 ced-1 is expressed in and functions in engulfing cells PMID:1936965 mutations in each of these genes prevent engulfment |
| GO:0043652 engulfment of apoptotic cell | IMP PMID:18351800 Phagocytic receptor CED-1 initiates a signaling pathway for ... | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:18351800 One of the pathways, composed of CED-1, the adaptor protein CED-6, and DYN-1, controls the rate of enrichment of PI(3)P and RAB-7 on phagosomal surfaces and the formation of phagolysosomes |
| GO:0043652 engulfment of apoptotic cell | IMP PMID:1936965 Genes required for the engulfment of cell corpses during pro... | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:1936965 mutations in each of these genes prevent engulfment |
| GO:0043652 engulfment of apoptotic cell | IMP PMID:19461656 An essential role for calcium flux in phagocytes for apoptot... | ACCEPT | Summary: Engulfment of apoptotic cell. Reason: CED-1 is the engulfing-cell receptor of the CED-1/CED-6/CED-7 corpse-clearance pathway: it recognizes cell corpses, signals through CED-6 and DYN-1, and initiates phagosome maturation. Core process. Supporting Evidence: PMID:19461656 This result was quite comparable to the phenotype seen with knockdown of ced-1 |
| GO:0043654 recognition of apoptotic cell | IDA PMID:11163239 CED-1 is a transmembrane receptor that mediates cell corpse ... | ACCEPT | Summary: Recognition of apoptotic cell (IDA, Zhou et al. 2001). Reason: CED-1 recognizes cell corpses as the phagocytic receptor of the CED-1 pathway. Supporting Evidence: PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses PMID:11163239 The CED-1 protein localizes to cell membranes and clusters around neighboring cell corpses |
| GO:0045184 establishment of protein localization | IDA PMID:16740477 C. elegans Dynamin mediates the signaling of phagocytic rece... | MARK AS OVER ANNOTATED | Summary: Establishment of protein localization (IDA, Yu et al. 2006). Reason: The observation is that DYN-1 recruitment to pseudopods depends on CED-1. That is a downstream step of CED-1 signaling within engulfment, not a protein-localization function of CED-1. The term is too generic to be informative. Supporting Evidence: PMID:16740477 DYN-1 transiently accumulates to the surface of pseudopods in a manner dependent on ced-1, ced-6, and ced-7 |
| GO:0070986 left/right axis specification | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MARK AS OVER ANNOTATED | Summary: Left/right axis specification (IGI, Cabello et al. 2010). Reason: The left/right and spindle phenotypes in this paper depend on MOM-5/Frizzled, GSK-3 and beta-catenins. ced-1 shows at most rare spindle defects in double mutants. Supporting Evidence: PMID:20126385 we did observe spindle defects in a small fraction of ced-1; ced-5 double mutants |
| GO:1901076 positive regulation of engulfment of apoptotic cell | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MODIFY | Summary: Positive regulation of engulfment of apoptotic cell (Cabello et al. 2010). Reason: CED-1 does not regulate engulfment from outside: it is the receptor that carries it out, and ced-1 single mutants have engulfment defects in this paper. The direct process term is the accurate one. Proposed replacements: engulfment of apoptotic cell Supporting Evidence: PMID:20126385 ced-1, ced-7, or ced-6 single mutants showed a weaker engulfment defect PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses |
| GO:1901076 positive regulation of engulfment of apoptotic cell | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MODIFY | Summary: Positive regulation of engulfment of apoptotic cell (Cabello et al. 2010). Reason: CED-1 does not regulate engulfment from outside: it is the receptor that carries it out, and ced-1 single mutants have engulfment defects in this paper. The direct process term is the accurate one. Proposed replacements: engulfment of apoptotic cell Supporting Evidence: PMID:20126385 ced-1, ced-7, or ced-6 single mutants showed a weaker engulfment defect PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses |
| GO:1901076 positive regulation of engulfment of apoptotic cell | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MODIFY | Summary: Positive regulation of engulfment of apoptotic cell (Cabello et al. 2010). Reason: CED-1 does not regulate engulfment from outside: it is the receptor that carries it out, and ced-1 single mutants have engulfment defects in this paper. The direct process term is the accurate one. Proposed replacements: engulfment of apoptotic cell Supporting Evidence: PMID:20126385 ced-1, ced-7, or ced-6 single mutants showed a weaker engulfment defect PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses |
| GO:1901076 positive regulation of engulfment of apoptotic cell | IMP PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MODIFY | Summary: Positive regulation of engulfment of apoptotic cell (Cabello et al. 2010). Reason: CED-1 does not regulate engulfment from outside: it is the receptor that carries it out, and ced-1 single mutants have engulfment defects in this paper. The direct process term is the accurate one. Proposed replacements: engulfment of apoptotic cell Supporting Evidence: PMID:20126385 ced-1, ced-7, or ced-6 single mutants showed a weaker engulfment defect PMID:11163239 CED-1 is a cell surface phagocytic receptor that recognizes cell corpses |
| GO:1902742 apoptotic process involved in development | IGI PMID:24225442 Caspase-mediated activation of Caenorhabditis elegans CED-8 ... | MODIFY | Summary: Apoptotic process involved in development (Chen et al. 2013, CED-8 paper). Reason: In the full text, ced-1(e1735) is used as a background that blocks engulfment so that corpses persist and can be counted; the paper tests ced-8, not ced-1. Separately, engulfment genes including ced-1 promote cell death when killing is weakened (Reddien 2001; Hoeppner 2001), and ced-1 expressed in engulfing cells rescues that. CED-1 therefore promotes death from the engulfing cell rather than taking part in the dying cell's apoptotic program. The replacement is GO:0043065 positive regulation of apoptotic process, without the developmental context of its precomposed child GO:1904747. Proposed replacements: positive regulation of apoptotic process Context of precomposed term: context dropped The replacement is unfolded from GO:1904747 positive regulation of apoptotic process involved in development to GO:0043065 (projects/INVOLVED_IN_PRECOMPOSITION.md, round 6); the sign correction (regulation, not participation) is unchanged. The developmental context is not carried: it is where the engulfment genes' pro-death role was measured (Reddien 2001; Hoeppner 2001), not a mechanism, and the role is non-core for this gene. Supporting Evidence: PMID:24225442 ced-1(e1735) blocks cell corpse engulfment and sensitizes PMID:11449278 mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants PMID:11449279 genes that mediate corpse removal can also function to actively kill cells |
| GO:1902742 apoptotic process involved in development | IMP PMID:24225442 Caspase-mediated activation of Caenorhabditis elegans CED-8 ... | MODIFY | Summary: Apoptotic process involved in development (Chen et al. 2013, CED-8 paper). Reason: In the full text, ced-1(e1735) is used as a background that blocks engulfment so that corpses persist and can be counted; the paper tests ced-8, not ced-1. Separately, engulfment genes including ced-1 promote cell death when killing is weakened (Reddien 2001; Hoeppner 2001), and ced-1 expressed in engulfing cells rescues that. CED-1 therefore promotes death from the engulfing cell rather than taking part in the dying cell's apoptotic program. The replacement is GO:0043065 positive regulation of apoptotic process, without the developmental context of its precomposed child GO:1904747. Proposed replacements: positive regulation of apoptotic process Context of precomposed term: context dropped The replacement is unfolded from GO:1904747 positive regulation of apoptotic process involved in development to GO:0043065 (projects/INVOLVED_IN_PRECOMPOSITION.md, round 6); the sign correction (regulation, not participation) is unchanged. The developmental context is not carried: it is where the engulfment genes' pro-death role was measured (Reddien 2001; Hoeppner 2001), not a mechanism, and the role is non-core for this gene. Supporting Evidence: PMID:24225442 ced-1(e1735) blocks cell corpse engulfment and sensitizes PMID:11449278 mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants PMID:11449279 genes that mediate corpse removal can also function to actively kill cells |
| GO:1903356 positive regulation of distal tip cell migration | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MARK AS OVER ANNOTATED | Summary: Positive regulation of distal tip cell migration (Cabello et al. 2010). Reason: The source paper's own conclusion is that the CED-1/6/7 pathway plays at most a minor role, if any, in distal tip cell migration, which instead depends on the CED-2/5/12 branch. Supporting Evidence: PMID:20126385 we found that the CED-1/6/7 pathway appears to play at most a minor role, if any, in this process |
| GO:1903356 positive regulation of distal tip cell migration | IGI PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MARK AS OVER ANNOTATED | Summary: Positive regulation of distal tip cell migration (Cabello et al. 2010). Reason: The source paper's own conclusion is that the CED-1/6/7 pathway plays at most a minor role, if any, in distal tip cell migration, which instead depends on the CED-2/5/12 branch. Supporting Evidence: PMID:20126385 we found that the CED-1/6/7 pathway appears to play at most a minor role, if any, in this process |
| GO:1903356 positive regulation of distal tip cell migration | IMP PMID:20126385 The Wnt pathway controls cell death engulfment, spindle orie... | MARK AS OVER ANNOTATED | Summary: Positive regulation of distal tip cell migration (Cabello et al. 2010). Reason: The source paper's own conclusion is that the CED-1/6/7 pathway plays at most a minor role, if any, in distal tip cell migration, which instead depends on the CED-2/5/12 branch. Supporting Evidence: PMID:20126385 we found that the CED-1/6/7 pathway appears to play at most a minor role, if any, in this process |
| GO:1904747 positive regulation of apoptotic process involved in development | IGI PMID:23505386 Both the caspase CSP-1 and a caspase-independent pathway pro... | MODIFY | Summary: Positive regulation of apoptotic process involved in development (Denning et al. 2013). Reason: The cited paper uses ced-1 as a background and attributes the extra corpses to an engulfment defect, so it does not itself show this. The term is still supported elsewhere: engulfment genes, including ced-1 acting in engulfing cells, promote death of cells receiving weak death signals (Reddien 2001; Hoeppner 2001), which the Denning paper also states. The role is non-core, a consequence of the engulfment role. The claim is positive regulation of apoptotic process (GO:0043065); the precomposed term's developmental context is dropped. Proposed replacements: positive regulation of apoptotic process Context of precomposed term: context dropped Decomposed from the precomposed GO:1904747 positive regulation of apoptotic process involved in development (projects/INVOLVED_IN_PRECOMPOSITION.md, round 6), which positively regulates GO:1902742 apoptotic process involved in development, to the regulation genus GO:0043065. The developmental context is not carried: it is where the engulfment genes' pro-death role was measured (Reddien 2001; Hoeppner 2001), not a mechanism, and the role is non-core for this gene. Supporting Evidence: PMID:23505386 the extra cell corpses in ced-1 mutant larvae likely reflected an engulfment defect PMID:23505386 Given that ced-1 and other genes that function in cell-corpse engulfment promote programmed cell death PMID:11449278 mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants PMID:11449279 genes that mediate corpse removal can also function to actively kill cells |
| GO:1904747 positive regulation of apoptotic process involved in development | IGI PMID:23505386 Both the caspase CSP-1 and a caspase-independent pathway pro... | MODIFY | Summary: Positive regulation of apoptotic process involved in development (Denning et al. 2013). Reason: The cited paper uses ced-1 as a background and attributes the extra corpses to an engulfment defect, so it does not itself show this. The term is still supported elsewhere: engulfment genes, including ced-1 acting in engulfing cells, promote death of cells receiving weak death signals (Reddien 2001; Hoeppner 2001), which the Denning paper also states. The role is non-core, a consequence of the engulfment role. The claim is positive regulation of apoptotic process (GO:0043065); the precomposed term's developmental context is dropped. Proposed replacements: positive regulation of apoptotic process Context of precomposed term: context dropped Decomposed from the precomposed GO:1904747 positive regulation of apoptotic process involved in development (projects/INVOLVED_IN_PRECOMPOSITION.md, round 6), which positively regulates GO:1902742 apoptotic process involved in development, to the regulation genus GO:0043065. The developmental context is not carried: it is where the engulfment genes' pro-death role was measured (Reddien 2001; Hoeppner 2001), not a mechanism, and the role is non-core for this gene. Supporting Evidence: PMID:23505386 the extra cell corpses in ced-1 mutant larvae likely reflected an engulfment defect PMID:23505386 Given that ced-1 and other genes that function in cell-corpse engulfment promote programmed cell death PMID:11449278 mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants PMID:11449279 genes that mediate corpse removal can also function to actively kill cells |
| GO:1904747 positive regulation of apoptotic process involved in development | IGI PMID:23505386 Both the caspase CSP-1 and a caspase-independent pathway pro... | MODIFY | Summary: Positive regulation of apoptotic process involved in development (Denning et al. 2013). Reason: The cited paper uses ced-1 as a background and attributes the extra corpses to an engulfment defect, so it does not itself show this. The term is still supported elsewhere: engulfment genes, including ced-1 acting in engulfing cells, promote death of cells receiving weak death signals (Reddien 2001; Hoeppner 2001), which the Denning paper also states. The role is non-core, a consequence of the engulfment role. The claim is positive regulation of apoptotic process (GO:0043065); the precomposed term's developmental context is dropped. Proposed replacements: positive regulation of apoptotic process Context of precomposed term: context dropped Decomposed from the precomposed GO:1904747 positive regulation of apoptotic process involved in development (projects/INVOLVED_IN_PRECOMPOSITION.md, round 6), which positively regulates GO:1902742 apoptotic process involved in development, to the regulation genus GO:0043065. The developmental context is not carried: it is where the engulfment genes' pro-death role was measured (Reddien 2001; Hoeppner 2001), not a mechanism, and the role is non-core for this gene. Supporting Evidence: PMID:23505386 the extra cell corpses in ced-1 mutant larvae likely reflected an engulfment defect PMID:23505386 Given that ced-1 and other genes that function in cell-corpse engulfment promote programmed cell death PMID:11449278 mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants PMID:11449279 genes that mediate corpse removal can also function to actively kill cells |
| GO:1904747 positive regulation of apoptotic process involved in development | IMP PMID:23505386 Both the caspase CSP-1 and a caspase-independent pathway pro... | MODIFY | Summary: Positive regulation of apoptotic process involved in development (Denning et al. 2013). Reason: The cited paper uses ced-1 as a background and attributes the extra corpses to an engulfment defect, so it does not itself show this. The term is still supported elsewhere: engulfment genes, including ced-1 acting in engulfing cells, promote death of cells receiving weak death signals (Reddien 2001; Hoeppner 2001), which the Denning paper also states. The role is non-core, a consequence of the engulfment role. The claim is positive regulation of apoptotic process (GO:0043065); the precomposed term's developmental context is dropped. Proposed replacements: positive regulation of apoptotic process Context of precomposed term: context dropped Decomposed from the precomposed GO:1904747 positive regulation of apoptotic process involved in development (projects/INVOLVED_IN_PRECOMPOSITION.md, round 6), which positively regulates GO:1902742 apoptotic process involved in development, to the regulation genus GO:0043065. The developmental context is not carried: it is where the engulfment genes' pro-death role was measured (Reddien 2001; Hoeppner 2001), not a mechanism, and the role is non-core for this gene. Supporting Evidence: PMID:23505386 the extra cell corpses in ced-1 mutant larvae likely reflected an engulfment defect PMID:23505386 Given that ced-1 and other genes that function in cell-corpse engulfment promote programmed cell death PMID:11449278 mutations in engulfment genes alone allow the survival and differentiation of some cells that would normally die PMID:11449278 the expression in engulfing cells of ced-1, which encodes a receptor that recognizes cell corpses, rescues the cell-killing defects of ced-1 mutants PMID:11449279 genes that mediate corpse removal can also function to actively kill cells |
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Download this section (compressed HTML)Q: Does CED-1 bind phosphatidylserine directly, or only through TTR-52 and other bridging molecules?
Q: How do engulfing cells, through CED-1, push cells that have received a weak death signal into death, and what signal passes back to the dying cell?
Q: Should the PANTHER family for CED-1 follow PANTHER's own classification (PTHR24035:SF109, which holds the CED-1/Draper/MEGF10 PAINT nodes) rather than the UniProt/InterPro cross-reference (PTHR24043:SF8)? See projects/PANTHER_FAMILY_ASSIGNMENT_DISCREPANCIES.md.
Experiment: In a weak ced-3 background, compare survival of specific cells when ced-1 is restored only in the engulfing cell versus with NPXY or YXXL tail mutants, scoring survival with cell-type reporters.
Hypothesis: CED-1 promotes death of weakly signalled cells through direct contact-dependent signalling from the engulfing cell.
Type: genetic
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