Delta (Q8T4N9, Strongylocentrotus purpuratus) — curation notes

Identity

• UniProt Q8T4N9 (unreviewed, TrEMBL) is the S. purpuratus Delta cDNA
  (EMBL AAL71862, gene name Delta, "Delta-like protein"), a 674-aa fragment.
  The record's only literature reference is Sweet, Gehring & Ettensohn 2002
  (PMID:11934860), which is written about the Lytechinus variegatus orthologue
  LvDelta; the companion LvDelta accession is AAL71861 (cited as the probe source
  in Croce & McClay 2010, PMID:20023163), so AAL71861/AAL71862 are the Lv/Sp pair
  deposited by the Ettensohn lab. The S. purpuratus gene is the SpDelta of
  Revilla-i-Domingo et al. 2004 (PMID:15385170) and the delta node of the
  Davidson endomesoderm GRN. No identity doubt.
• Domain architecture (UniProt features): Notch-ligand N-terminal MNNL domain
  (Pfam PF07657), DSL domain (Pfam PF01414; InterPro IPR001774, residues 182-226),
  eight EGF-like repeats (291-552, several calcium-binding-type), a single
  transmembrane helix at 594-616 and a short C-terminal cytoplasmic tail — the
  canonical single-pass type I Delta ligand topology. The UniProt CAUTION line
  notes that one EGF domain lacks residues required for ProRule feature
  propagation (PRU00076); this concerns feature annotation only.
• PANTHER placement is PTHR24033 / PTHR24033:SF232 (a laminin-gamma-2-related
  subfamily), which reflects EGF-repeat similarity of a fragment rather than the
  Delta subfamily; not asserted anywhere in the review (CLAUDE.md rule).

What the gene does (GRN placement)

Delta is a signaling ligand, not a transcription factor: a cell-surface
Notch ligand that acts strictly on contiguous neighbours.
PMID:22306924

Inputs: the double-negative gate

• delta is one of the direct targets of the pmar1–hesC double-negative gate.
  It is activated by ubiquitous factors and repressed everywhere by HesC; Pmar1
  represses hesC only in the micromeres, so delta transcription is confined
  to the skeletogenic micromere lineage.
  [PMID:17636127 "every cell of the embryo expressed either hesC (purple) or δ
  (orange), but no cell expressed both genes"; "in hesC MASO embryos, it is
  detected throughout the whole embryo"]
  PMID:12027443
• Timing: PMID:19104065
  PMID:22306924
• cis-regulation. Two CRMs: R11, ~13-16 kb downstream of the last exon, drives
  micromere-lineage expression and responds to the pmar1 repression system
  PMID:15385170, with Ets1 sites required for
  activity PMID:19104065. A proximal
  CRM (−90 to +484, in the 5'UTR) reproduces the entire pregastrular pattern
  (SM, NSM, apical plate), is activated by Runx and directly repressed by HesC
  through a class-C E-box.
  PMID:19104065
• Second phase: when skeletogenic cells ingress, delta turns off in them and
  is activated in the NSM (Blimp1 has by then repressed hesC there), so that
  Notch signaling moves outward to the veg2 endoderm ring.
  PMID:19104065 The NSM phase itself depends on the
  earlier skeletogenic Delta signal PMID:22306924.

Outputs: Notch-mediated induction of non-skeletogenic mesoderm

• Micromere-descendant Delta is the signal that makes the adjacent veg2 ring
  mesodermal. PMID:18413610
  PMID:12027443
  PMID:19104065
• Loss of function in S. purpuratus (Materna & Davidson 2012, full text):
  Delta MASO, Notch MASO, dominant-negative Su(H) and DAPT gave the same result
  on a 205-gene regulome panel. PMID:22306924 Direct
  pregastrular targets are few and mesodermal: PMID:22306924; PMID:22306924; the NSM phase feeds foxY in the small micromeres
  PMID:22306924
• Direct transcriptional target in the receiving cell: gcm, via Su(H) sites.
  PMID:16925988
• Blocking the ligand or the pathway abolishes pigment cells.
  PMID:18413610
• Orthologue evidence in Lytechinus variegatus (necessity AND sufficiency):
  PMID:11934860; PMID:11934860;
  PMID:20023163 Croce & McClay also show a continuous Delta
  input of >2 cleavages (~2.5 h) is needed before gcm becomes Delta-independent.
  The receptor side was established by Sherwood & McClay 1999 in Lv
  PMID:10079232.

Second, non-core role: lateral inhibition in the neurogenic ectoderm

• Delta/Notch signaling also restricts neural progenitor number in the
  gastrula-stage ectoderm and ciliary band (Mellott, Thompson & Burke 2017,
  abstract only). PMID:28851710; PMID:28851710 This is a classical
  lateral-inhibition role and is the only sea urchin evidence bearing on the
  ARBA "neuron development" transfer; it argues for a negative-regulation-of-
  neurogenesis term rather than the vague parent, and it is not the core
  (endomesoderm GRN) function of the gene.

Curation decisions (summary)

• Electronic rows: Notch signaling pathway (InterPro) — ACCEPT, with IMP support
  from PMID:22306924 (Sp) and PMID:11934860 (Lv). Plasma membrane / membrane —
  ACCEPT (type I TM ligand; surface presentation is how it signals). Calcium ion
  binding — KEEP_AS_NON_CORE (structural cbEGF repeats). Cell communication —
  MODIFY to the Notch pathway term (too general). Extracellular region and
  cytoplasm (ARBA subcellular mapping from vertebrate family members) — REMOVE:
  a membrane-tethered, contact-dependent ligand is neither secreted nor
  cytoplasmic. ARBA gliogenesis and cell morphogenesis are vertebrate Dll1-derived
  transfers with no sea urchin evidence: REMOVE. ARBA neuron development —
  MODIFY to GO:0050768 negative regulation of neurogenesis on the strength of
  PMID:28851710 (non-core).
• NEW: GO:0048018 receptor ligand activity (IMP; Delta MASO, Notch MASO,
  dominant-negative Su(H) and DAPT give the same regulome phenotype, i.e. the
  ligand acts through the Notch receptor; this is the MF used for Drosophila Dl
  in the production GO-CAM 60ad85f700000309, gocams/index.tsv);
  GO:0007501 mesodermal cell fate specification (IMP); GO:0050768 negative
  regulation of neurogenesis (IMP, non-core).
• Comparator check (QuickGO, 2026-09): mouse Dll1 (Q61483) carries GO:0005112
  Notch binding (IPI), GO:0007219 (IMP), GO:0007267 cell-cell signaling (IDA),
  GO:0045747 (IDA/IMP), GO:0050767 regulation of neurogenesis and GO:0045665
  negative regulation of neuron differentiation (IMP), and tissue-specific fate
  terms by IMP; the Drosophila FGF ligands pyr and ths carry GO:0007501 by IMP.
  Lineage-fate terms on an inductive ligand are therefore within GO convention.
  GO:0045168 "cell-cell signaling involved in cell fate commitment" was
  considered and dropped: only two experimental annotations exist (both plant
  peptides), so it is not the conventional term.
• Participation test: the ligand is the inductive signal itself, i.e. it
  performs the intercellular step of the specification (Delta on the micromere
  surface activates Notch on the veg2 cell, whose Su(H) then activates gcm),
  not merely a prerequisite.
• Not proposed: GO:0005112 Notch binding (no direct binding assay for the sea
  urchin protein; raised as a question), endoderm specification (Materna &
  Davidson found no endoderm regulatory gene activated by Delta before
  gastrulation), pigment cell differentiation (downstream of gcm), positive
  regulation of Notch signaling (the ligand is a pathway component, not a
  regulator of it).