SHR (SHORT-ROOT) curation notes

UniProt: Q9SZF7 (SHR_ARATH); locus AT4G37650; GRAS family (GRAS-26 / SGR7).
531 aa. GRAS domain 134-529 (LRI, VHIID, LRII, PFYRE, SAW subdomains). N-terminus disordered.

Core biology

SHR is a GRAS-family transcriptional regulator that is transcribed only in the
stele but moves cell-to-cell (via plasmodesmata, endosome/SIEL-dependent) into
the adjacent cell layer, where it enters the nucleus and, together with
SCARECROW (SCR), specifies endodermis/ground-tissue identity, the quiescent
centre, and drives the asymmetric (formative) division of the cortex/endodermis
initial.

• PMID:10850497
• PMID:11565032
• PMID:15498493 (Thr289 mutant: loss of export and activity)

Molecular function — DNA binding vs cofactor (key decision)

SHR was historically annotated as a DNA-binding transcription factor
(GO:0003700) and as having sequence-specific DNA binding (GO:0043565). The
structural work strongly argues that SHR does NOT bind DNA directly and instead
acts as a transcription cofactor recruited to target promoters by DNA-binding
BIRD/IDD zinc-finger transcription factors.

• PMID:28211915
• PMID:28211915
• PMID:28211915 (i.e. DNA contact is by the IDD partner, not SHR)
• PMID:28211915

The original IDA "sequence-specific DNA binding" came from in vivo ChIP, which
detects promoter occupancy but not direct sequence-specific contact:
- PMID:16640459
The ChIP occupancy is fully consistent with indirect recruitment via IDD TFs.
The cleaner MF terms are therefore transcription coregulator activity
(GO:0003712) and DNA-binding transcription factor binding (GO:0140297) /
transcription factor binding (GO:0008134), rather than GO:0003700/GO:0043565.

The cis-regulatory-region binding (GO:0000976) IPI annotation comes from an
enhanced yeast-one-hybrid secondary-cell-wall GRN where SHR scored against
several promoters:
- PMID:25533953
Y1H reports promoter association but, in light of the structural data, this is
most plausibly indirect; kept as non-core with that caveat.

Protein–protein interactions (central function)

SHR's defining biochemical activity is heterodimerization with SCR via the GRAS
α-helical caps, and binding of the SHR–SCR dimer to BIRD/IDD zinc-finger TFs
(JKD/IDD10, MGP/IDD3, etc.).

• PMID:17446396
• PMID:28211915
• PMID:28211915
• PMID:17785527 (SHR interacts with JKD/AT1G03840 and MGP/AT5G03150)
• PMID:18500650
• PMID:22921914 (IntAct WITH = SCR Q9M384)
• [PMID:28746306 in vivo FRET-FLIM: SHR forms cell-type-specific complexes with SCR and JKD in roots]

The "protein binding" (GO:0005515) IPI entries are all SHR–SCR / SHR–IDD
interactions; the specific informative MF is DNA-binding transcription factor
binding (GO:0140297) for the IDD partners and protein homo/heterodimerization
for SCR.

Downstream / non-core processes

• Radial pattern formation, asymmetric (formative) cell division of CEI: core developmental output PMID:10850497.
• Leaf growth / S-phase progression (general cell proliferation in leaves), distinct from root role:
  PMID:20739610 — KEEP_AS_NON_CORE (leaf development, negative regulation of mitotic cell cycle).
• Bundle sheath cell fate in leaves PMID:24517883.
• Iron homeostasis (GO:0060586, IMP PMID:19726572): the iron paper does not actually study or mention SHR; it identifies the endodermal vacuole as the embryo iron store. The link to SHR is indirect (SHR specifies endodermis). Treat as non-core / over-annotated downstream consequence. The TAIR IMP appears to be an inferred connection, not a direct SHR experiment in that paper.
• Regulation of hormone metabolic process (GO:0032350, NAS PMID:16640459): the paper reports SHR pathway intersects GA/BR/auxin pathways via indirect targets (e.g. SNE, BR6ox2); NAS, peripheral.

Subcellular location

Cytoplasm + nucleus in the stele; restricted to nucleus in adjacent (endodermis)
cells (SCR sequesters it). Endosome (early/late/recycling) localization is part
of the SIEL-dependent intercellular trafficking machinery.
- PMID:25124761
Nucleus is the functional compartment (transcriptional regulation); cytoplasm
and endosomes are part of the movement/trafficking route.

Annotation action summary

• protein binding (GO:0005515) x6 → MODIFY to GO:0140297 (DNA-binding TF binding) where partner is an IDD; for SCR-only interactions, capture as protein dimerization / KEEP. Avoid bare "protein binding" as core.
• GO:0003700 (DNA-binding TF activity) TAS/ISS x3 → MODIFY to GO:0003712 transcription coregulator activity.
• GO:0043565 (sequence-specific DNA binding) IDA x2 → MARK_AS_OVER_ANNOTATED / MODIFY (no direct DNA binding per structure).
• GO:0000976 (cis-reg region binding) IPI → KEEP_AS_NON_CORE (Y1H; likely indirect).
• GO:0006355 (regulation of DNA-templated transcription) IBA → ACCEPT (core, correct level).
• Locations: nucleus ACCEPT (core); cytoplasm ACCEPT (trafficking); endosomes KEEP_AS_NON_CORE.
• Developmental BP: radial pattern formation ACCEPT; asymmetric cell division ACCEPT; leaf development / neg reg mitotic cell cycle / iron homeostasis / hormone metabolic = KEEP_AS_NON_CORE.

Deep research synthesis (Falcon / Edison Scientific report)

The Falcon deep-research report (file:ARATH/SHR/SHR-deep-research-falcon.md)
corroborates and extends the existing review without contradicting any decision.
No UNDECIDED annotations were present; none required resolution. Key points:

• Mobile, non-cell-autonomous GRAS TF: "SHR is synthesized in one tissue domain
  but acts in neighboring cells after intercellular movement through
  plasmodesmata, thereby delivering positional information." Reinforces ACCEPT for
  nucleus and the trafficking/movement framing (cytoplasm, endosomes). Added as
  supported_by on the nucleus (PMID:11565032 IDA) annotation.
• Acts via protein complexes, not direct DNA binding: "SHR functions through
  protein–protein interactions forming cell-type-specific complexes. In roots,
  SHR interacts with SCR ... SCL23 ... and JKD (JACKDAW; a BIRD/IDD TF)." Consistent
  with the MODIFY decisions (coregulator / DNA-binding TF binding / dimerization),
  and used to enrich the SCL23 (PMID:18500650) and FRET-FLIM (PMID:28746306) entries
  plus the SCR-dimerization and IDD-binding core functions.
• Transcriptional output: SHR/SCR "activate or coordinate transcription of
  developmental regulators and cell-cycle components in recipient cells." Added to
  the regulation-of-transcription (GO:0006355) annotation.
• Core developmental phenotypes: "Loss-of-function shr mutants show characteristic
  defects including loss of correct ground tissue layering (single layer instead of
  cortex+endodermis) and stem-cell niche abnormalities" and SHR/SCR "trigger the
  formative (asymmetric) division that generates separate cortex and endodermis
  lineages." Added to radial pattern formation (GO:0009956) and asymmetric cell
  division (GO:0008356).
• Shoot/leaf redeployment: SHR network is reused in the SAM and leaves (bundle
  sheath, lateral-organ initiation), consistent with KEEP_AS_NON_CORE for leaf
  development. Added to the leaf-development (PMID:24517883) entry.

New evidence beyond the current review (not added as new GO annotations because
no verifiable GO IDs are present in GOA/UniProt for them, recorded here only):
- SHR → MYB36 → CASP1 Casparian-strip / endodermal-differentiation cascade (Li et al.
2018, Curr Biol). Plausible downstream BP (endodermis differentiation / Casparian
strip), but the GO IDs are not in the current GOA/UniProt set, so not added.
- 2024 Nature (Winter et al.): SHR/SCR act via transient early-cell-cycle dynamics
(not a stable bistable switch) to orient formative division — refines mechanism but
does not change any existing annotation action.
- Auxin/MONOPTEROS-linked SHR expression in the SAM; promoter repressor motifs
(ZML1/DDF1) sharpening the SHR domain — regulation OF SHR rather than functions OF
SHR; not annotated.
No NEW GO annotation was added because no additional GO ID verifiable from the
existing GOA/UniProt could be supported by the deep-research evidence alone.