SERRATE (SE, At2g27100, UniProt Q9ZVD0) - curation notes

2026-10-19 - initial review (claude-code)

No deep-research provider was available in this environment, so these notes are
based on the cached publications (publications/PMID_*.md), PubMed searches, and the
UniProt record. Abstract-only papers are flagged.

Identity and family

• 720-aa nuclear protein, ARS2 family (PANTHER PTHR13165:SF0; Pfam PF04959 ARS2,
  PF12066 SERRATE_Ars2_N), single C2H2-type zinc finger at 498-523 (UniProt FT),
  extensive disordered N- and C-terminal regions (MobiDB-lite).
• Metazoan ortholog is ARS2/SRRT PMID:30152752. No human SRRT review exists in this
  repo yet. Human SRRT carries IDA protein-macromolecule adaptor activity and mRNA
  cap binding complex binding (QuickGO, PMID:28297668), consistent with a
  family-level "CBC-associated adaptor" framing.

Original cloning and development (abstract-only papers)

• se mutant: defects in organ initiation/elaboration; zinc finger protein
  PMID:11402159. That paper
  speculated on chromatin modification PMID:11402159 - this
  is the source of the ISS DNA binding / TF / transcription regulation annotations. No
  study has shown sequence-specific DNA binding.
• Phase length / juvenile leaves PMID:10607301.
• Leaf polarity and meristem via miR165/166-PHB and KNOX competence
  PMID:16222298.

miRNA biogenesis (core)

• General role in pri-miRNA processing, interacts with HYL1 PMID:16889646; PMID:16977334
• In vitro reconstitution: SE stimulates DCL1 PMID:18632569 SE alone gave a ~6-fold
  stimulation of miR167b release (full text).
• Domain dissection PMID:23921632; PMID:23921632. This is the best direct
  evidence for ribonuclease activator activity (GO:0170054), which the
  plant_mirna_biogenesis module already asserts for SE.
• Crystal structure of SE core 194-543 (PDB 3AX1) PMID:21685453. NOTE: this paper carries a 2021 Expression of
  Concern (Nucleic Acids Res 49:3002); used only as corroborating evidence.
• D-bodies: PMID:17442570; SE is mostly in speckles and only
  transiently in D-bodies PMID:17442570.
• Phase separation (abstract only) PMID:33288888. Supports molecular condensate scaffold activity
  (GO:0140693) as a NEW MF.
• Scaffold role: PMID:23141542 (abstract only).
• CHR2/BRM remodels pri-miRNAs via SE PMID:29769717.
• SE recruits NEXT for pri-miRNA decay PMID:32449937.
• Other partners: HOS5, RS40, RS41 in speckles PMID:26227967; SMA1 PMID:29982637;
  SEAP1 PMID:34449907; PAG1/20S proteasome turnover of SE PMID:32690892.

Splicing / CBC

• PMID:18550839 (abstract only).
• PMID:24137006 and SE affects 5' splice site choice of first introns.
• GOA has SE part_of nuclear cap binding complex (GO:0005846). GO defines that complex
  as the CBP20/CBP80 heterodimer; SE is an interacting partner (CBC-SE, cf. human
  CBC-ARS2). Proposed MODIFY to mRNA cap binding complex binding (GO:0140262), matching
  human SRRT IDA.

Transcription

• PMID:30152752 This is
  Pol II association, not DNA binding; supports positive regulation of Pol II
  transcription as a non-core role.

Decisions summary

• REMOVE: DNA binding (ISS), DNA-binding TF activity (ISS): no evidence; zinc finger
  is a non-canonical protein/RNA-interaction module.
• MODIFY protein binding rows where the paper shows a scaffolding role (CPL1-HYL1,
  CHR2, NEXT) to protein-macromolecule adaptor activity; other bare protein binding
  rows REMOVE (policy).
• NEW: ribonuclease activator activity (GO:0170054) - SE stimulates DCL1; molecular
  condensate scaffold activity (GO:0140693).
• Upstream report candidates: GO:0005846 part_of -> GO:0140262; ISS DNA binding/TF
  rows from 2000-2001 sequence-based speculation.

2026-10-20: ported fixes from the parallel review branch

• The SE-DCL1/SMA1 GO:0005515 row (PMID:29982637, full text cached) changed from REMOVE to MODIFY to GO:0030674 protein-macromolecule adaptor activity, as for the SE-HYL1/CPL1 rows from PMID:23141542 PMID:29982637.
• Source defects recorded for the TAIR ISS rows GO:0003700 (PMID:11118137) and GO:0003677 (PMID:11402159), both without With/From, and for part_of GO:0005846 nuclear cap binding complex (PMID:24137006), which should be enables GO:0140262.