Delta is the single-pass type I transmembrane Notch ligand of the purple sea urchin embryo, built of an N-terminal MNNL domain, a DSL domain, eight EGF-like repeats (several of the calcium-binding type), a transmembrane helix and a short cytoplasmic tail. It is not secreted: it stays tethered to the surface of the cell that expresses it and signals only to cells in direct contact, by activating the Notch receptor and thereby Su(H)-dependent transcription in the neighbour. Zygotic delta transcription begins at about 8-9 h after fertilization in the large micromere (skeletogenic mesoderm) lineage at the center of the vegetal plate, where its transcription is permitted by the Pmar1-HesC double-negative gate (HesC represses delta everywhere else, through a class C E-box in the 5' UTR proximal module, while Runx and Ets1 activate it). Delta presented by the micromere descendants is the inductive signal that makes the immediately adjacent ring of veg2 cells non-skeletogenic mesoderm: it drives the Notch/Su(H)-dependent activation of gcm and of gataE, foxA and foxY in those cells, and blocking the ligand, the receptor or Su(H) abolishes pigment cells and other pregastrular mesoderm derivatives. When the skeletogenic cells ingress at the mesenchyme blastula stage, delta is switched off in them and turned on in the non-skeletogenic mesoderm itself, moving the signal outward to the veg2 endoderm ring and to the small micromeres. In the Lytechinus orthologue the micromere ligand is both necessary and sufficient for pigment and blastocoelar cell formation, and macromere-derived Delta is needed for blastocoelar and muscle cells. Later, in the gastrula ectoderm, Delta/Notch signaling restricts the number of neural progenitors by lateral inhibition; Delta knockdown or CRISPR mutation gives supernumerary neurons.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000902 cell morphogenesis | IEA GO_REF:0000117 | REMOVE | Summary: ARBA machine-learning transfer of a very general morphogenesis term, presumably from vertebrate Delta-like ligands. No sea urchin study attributes a cell-morphogenesis role to Delta; its demonstrated roles are inductive signaling for mesodermal fate and lateral inhibition in neurogenesis. Reason: Uninformative and unsupported for this gene; the specific processes Delta participates in (Notch signaling pathway, mesodermal cell fate specification, negative regulation of neurogenesis) are captured by other rows. |
| GO:0005509 calcium ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the calcium-binding EGF-like repeat signatures. The protein carries eight EGF-like repeats, several of the cbEGF type, so calcium binding by these structural repeats is plausible, but it is a structural property of the extracellular stalk rather than the gene product's function. Reason: The mapping is sequence-correct (cbEGF consensus present), and there is no evidence against it, but the function of the protein is Notch-receptor ligand activity; calcium binding by the EGF repeats is not what the gene does in the embryo. |
| GO:0005576 extracellular region | IEA GO_REF:0000044 | REMOVE | Summary: Subcellular-location keyword mapping ('Secreted', from ARBA transfer). Delta has a transmembrane helix at residues 594-616 and, as the sea urchin literature states explicitly, is bound to the surface of the expressing cell and not secreted; it signals only to contiguous neighbours. Reason: Contradicted by the domain architecture (single-pass type I membrane protein) and by the contact-dependent mode of signaling described for this gene. The correct location is the plasma membrane. Supporting Evidence: PMID:22306924 In contrast to many other signaling ligands it is bound to the cell surface of the delta expressing cell and not secreted. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | REMOVE | Summary: ARBA-derived 'Cytoplasm' subcellular-location keyword, transferred from vertebrate family members (where a cleaved intracellular fragment has been reported). No cytoplasmic localization or function is described for the sea urchin protein. Reason: A single-pass type I membrane ligand acting at the cell surface; nothing in the sea urchin literature supports a cytoplasmic pool, and the mapping reflects a vertebrate-specific observation at best. |
| GO:0005886 plasma membrane | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA plasma membrane location. Correct and core; the protein is a single-pass transmembrane ligand whose presentation on the surface of the micromere descendants is how it signals to adjacent cells. Reason: Consistent with the transmembrane helix (594-616), with the DSL/EGF ectodomain topology of Notch ligands, and with the explicit statement in the sea urchin literature that the ligand stays bound to the surface of the expressing cell. Supporting Evidence: PMID:22306924 In contrast to many other signaling ligands it is bound to the cell surface of the delta expressing cell and not secreted. |
| GO:0007154 cell communication | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping of the DSL domain to the generic 'cell communication'. True but far too general; the DSL domain is the Notch-binding module and the specific process is the Notch signaling pathway, already present as a separate row. Reason: Replace with the specific pathway term GO:0007219, which is supported in S. purpuratus by the concordant phenotypes of Delta MASO, Notch MASO, dominant-negative Su(H) and gamma-secretase inhibition. Proposed replacements: Notch signaling pathway Supporting Evidence: PMID:22306924 These were injection of morpholino-substituted antisense oligonucleotides (MASO) to block translation of the Delta ligand; injection of MASO targeting the Notch receptor; expression of a dominant negative form of the Suppressor of Hairless (Su(H)) |
| GO:0007219 Notch signaling pathway | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping of the Notch-ligand N-terminal (MNNL) domain to the Notch signaling pathway. This is the core function of the gene. In S. purpuratus, blocking Delta translation gives the same 205-gene regulome phenotype as blocking the Notch receptor, Su(H) or gamma-secretase, and gcm in the receiving cells is a direct Su(H) target of the signal; in Lytechinus the ligand was identified as the Notch ligand of the micromeres. Reason: Experimentally confirmed in this species (IMP-level evidence) and in the Lytechinus orthologue; the gene product is the ligand that initiates the pathway. Supporting Evidence: PMID:22306924 These were injection of morpholino-substituted antisense oligonucleotides (MASO) to block translation of the Delta ligand; injection of MASO targeting the Notch receptor; expression of a dominant negative form of the Suppressor of Hairless (Su(H)) PMID:16925988 confirming that spgcm is a direct target of canonical N signaling mediated through Su(H) inputs PMID:11934860 we demonstrate that these micromere descendants express LvDelta, a ligand for the Notch receptor |
| GO:0016020 membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA 'membrane' from the DSL/MNNL domain signatures and the UniProt keyword. Correct; the more specific plasma membrane row is also accepted. Reason: Single-pass type I membrane protein with a predicted transmembrane helix; redundant with, but not contradictory to, the plasma membrane annotation. Supporting Evidence: PMID:22306924 In contrast to many other signaling ligands it is bound to the cell surface of the delta expressing cell and not secreted. |
| GO:0042063 gliogenesis | IEA GO_REF:0000117 | REMOVE | Summary: ARBA transfer of a vertebrate Dll1 phenotype (Notch-dependent glial fate choice). Nothing in the sea urchin literature connects Delta with glia, and the term is a vertebrate-nervous-system process. Reason: Over-propagated machine-learning transfer with no organism-appropriate evidence; the neural role that is documented for sea urchin Delta is lateral inhibition of neural progenitors, captured under negative regulation of neurogenesis. |
| GO:0048666 neuron development | IEA GO_REF:0000117 | MODIFY | Summary: ARBA transfer of a neural role. There is genuine S. purpuratus evidence for a neural role of Delta, but it is lateral inhibition, i.e. restriction of neural progenitor number in the gastrula ectoderm, not participation in neuron development itself; Sp-Delta morpholino or CRISPR mutation produces supernumerary neural progenitors and neurons. Reason: The gene product is the ligand of a signal that limits neurogenesis, so the appropriate term is a regulation term (GO:0050768 negative regulation of neurogenesis, proposed as a NEW row), not the direct neuron development term. This is a secondary, non-core role relative to the endomesoderm signaling function. Proposed replacements: negative regulation of neurogenesis Supporting Evidence: PMID:28851710 Inhibition of Ξ³-secretase, injection of Sp-Delta morpholinos or CRISPR/Cas9-induced mutation of Sp-Delta results in supernumerary neural progenitors and neurons. |
| GO:0048018 receptor ligand activity | IMP PMID:22306924 A comprehensive analysis of Delta signaling in pre-gastrular... | NEW | Summary: Proposed. Delta is the cell-surface ligand of the Notch receptor. In S. purpuratus, translation blockade of the ligand, translation blockade of the receptor, a dominant-negative Su(H) and gamma-secretase inhibition all give the same regulome phenotype, showing that the ligand acts through Notch; in Lytechinus the micromere ligand was identified as the Notch ligand and is necessary and sufficient for the induced fates. Reason: This is the molecular function that GO uses for Notch ligands (Drosophila Dl carries GO:0048018 as its activity in the production Notch signaling GO-CAM 60ad85f700000309, listed in gocams/index.tsv; mouse Dll1 carries it by ISO). The activity is inferred from concordant loss-of-function of ligand, receptor and transducer in this species (IMP); no direct binding assay exists for the sea urchin protein, so the more specific GO:0005112 Notch binding is not asserted here. Supporting Evidence: PMID:22306924 These were injection of morpholino-substituted antisense oligonucleotides (MASO) to block translation of the Delta ligand; injection of MASO targeting the Notch receptor; expression of a dominant negative form of the Suppressor of Hairless (Su(H)) PMID:22306924 In contrast to many other signaling ligands it is bound to the cell surface of the delta expressing cell and not secreted. PMID:11934860 we demonstrate that these micromere descendants express LvDelta, a ligand for the Notch receptor PMID:11934860 expression of LvDelta by micromere descendants is both necessary and sufficient for the development of two mesodermal cell types, pigment cells and blastocoelar cells |
| GO:0007501 mesodermal cell fate specification | IMP PMID:22306924 A comprehensive analysis of Delta signaling in pre-gastrular... | NEW | Summary: Proposed. Delta presented by the skeletogenic micromere lineage is the inductive signal that specifies the immediately adjacent ring of veg2 cells as non-skeletogenic mesoderm. Loss of the ligand abolishes pregastrular specification of all NSM derivatives and pigment cells, and the direct targets in the receiving cells are the mesodermal regulatory genes gcm, gataE, foxA and foxY. Reason: Participation test: the ligand itself performs the intercellular step of the specification; it is the signal, presented on the micromere surface, that activates Notch/Su(H) in the veg2 cell and thereby gcm. Comparator check (QuickGO): the Drosophila FGF ligands pyr and ths carry GO:0007501 by IMP, and mouse Dll1 carries lineage fate terms by IMP, so a specification term on an inductive ligand is within GO convention. Not an ancestor or descendant of any other term on the gene. Downstream pigment-cell differentiation and endoderm terms are deliberately not proposed (executed by gcm and its targets; no endoderm regulatory gene responds to Delta before gastrulation). Supporting Evidence: PMID:22306924 The expression of the Delta signaling ligand is required for pregastrular specification of all mesoderm derivatives in the adjacent NSM. PMID:22306924 In our data set, gcm, gataE, foxA, and foxY are significantly affected in their expression level in repeat experiments PMID:18413610 blockade of the micromere lineage expression of delta or of the reception and transduction of this signal by the Notch pathway in the adjacent cells severely affects their mesodermal specification and abolishes pigment cell differentiation PMID:18413610 from seventh cleavage, the Notch ligand Delta. Reception of this signal causes the ring of cells then immediately adjacent to the micromere lineage to assume mesodermal fate PMID:19104065 The early SM Delta signal is critical for specification of the adjacent ring of cells as NSM beginning at the early blastula stage. PMID:11934860 expression of LvDelta by micromere descendants is both necessary and sufficient for the development of two mesodermal cell types, pigment cells and blastocoelar cells PMID:20023163 Initially, Delta is expressed exclusively in the micromeres, where it is necessary for the most vegetal endomesoderm cell descendants to express Gcm and become mesoderm. PMID:12027443 they express Delta, a Notch ligand which triggers the conditional specification of the central mesodermal domain of the vegetal plate |
| GO:0050768 negative regulation of neurogenesis | IMP PMID:28851710 Notch signaling patterns neurogenic ectoderm and regulates t... | NEW | Summary: Proposed, non-core. In the gastrula-stage ectoderm and ciliary band, Delta/Notch signaling restricts the number of neural progenitors recruited; morpholino knockdown or CRISPR/Cas9 mutation of Sp-Delta yields supernumerary neural progenitors and neurons, with Notch activity detected in the cells adjacent to SoxC-expressing progenitors. Reason: Classical lateral inhibition mediated by the ligand; mouse Dll1 carries regulation-of-neurogenesis and negative regulation of neuron differentiation terms by IMP, so this is the conventional way to represent the role. Replaces the vague ARBA 'neuron development' transfer. Not part of the core endomesoderm signaling function. Supporting Evidence: PMID:28851710 Inhibition of Ξ³-secretase, injection of Sp-Delta morpholinos or CRISPR/Cas9-induced mutation of Sp-Delta results in supernumerary neural progenitors and neurons. PMID:28851710 Thus, Notch signaling restricts the number of neural progenitors recruited and regulates the fate of progeny of the asymmetric division. |
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Download this section (compressed HTML)Q: Should GO:0005112 Notch binding be asserted for the sea urchin protein? It is the expected activity of a DSL-domain ligand and mouse Dll1 carries it by IPI, but no direct Delta-Notch binding assay has been reported for S. purpuratus; the current review stops at receptor ligand activity inferred from concordant ligand/receptor/Su(H) perturbations.
Q: Is the ARBA 'cytoplasm' location a transfer of the vertebrate Dll1 intracellular-domain observation, and if so should the ARBA rule be restricted to vertebrate members? Nothing in the sea urchin literature supports a cytoplasmic pool.
Q: The second (NSM) phase of delta expression signals to the veg2 endoderm ring and small micromeres; should any endoderm-directed process be annotated, given that no endoderm regulatory gene responds to Delta before gastrulation?
Experiment: Immunolocalization or a tagged Delta BAC to document surface presentation on the micromere descendants and the SM-to-NSM switch at the protein level, and to test whether the ligand is endocytosed or cleaved in the signaling cell.
Type: localization
Experiment: In vitro or cell-based binding assay between the sea urchin Delta DSL/EGF ectodomain and the Sp-Notch EGF repeats to convert the inferred receptor ligand activity into direct Notch binding evidence.
Type: biochemical
Experiment: Lineage-restricted rescue (micromere-only delta mRNA in a Delta-CRISPR background) to separate the contribution of the first (SM) and second (NSM) phases of expression to pigment, blastocoelar, muscle and coelomic pouch fates.
Type: genetic
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