SPA1 (Q9SYX2; At2g46340) curation notes

Session 2026-10-05/06 (phytochrome_photomorphogenesis module curation).

• Falcon deep research (just deep-research-falcon ARATH SPA1): the first attempt timed out after 600 s, but a retry produced SPA1-deep-research-falcon.md. It pointed to additional SPA1 kinase substrates, which were verified in primary papers (below).
• Identity check: SPA1_ARATH, Q9SYX2, At2g46340/At2g46350, 1029 aa.

Domain architecture and complex

• N-terminal kinase-like domain, central coiled-coil, C-terminal WD40 PMID:10205059.
• Coiled-coil binds COP1 coiled-coil PMID:11461903.
• CUL4-DDB1-COP1-SPA complexes via WDXR motifs PMID:20061554.
• SPA proteins self-associate / heteromerize PMID:18812498.

Activity

• Stimulates COP1 E3 activity PMID:12827204; PMID:14597662. Chosen MF: GO:0097027 ubiquitin-protein transferase activator activity.
• Kinase activity on PIF1 PMID:31527679. Caveat: Holtkotte et al. 2016 PMID:27310313. Added as NEW (IDA) GO:0004674.
• Further substrates: HY5 PMID:33686674; eIF2alpha C-terminus PMID:38658612. All of these reports involve the Huq group; no independent replication found.

Photoreceptor inhibition

• phyA/phyB bind SPA1 and disrupt COP1-SPA PMID:25627066; PMID:25744387.
• CRY1/CRY2 similar in blue light [PMID:21511871, PMID:21511872, PMID:21514160]. Context only for module.

Decisions

• Protein binding rows: COP1 rows -> MODIFY to GO:0097027; other partners (HFR1, CO/COL1, SPA3/4, CRY1/2, phyB) REMOVE per policy (interactions real, captured in text).
• photomorphogenesis -> MODIFY to negative regulation of photomorphogenesis.
• nuclear speck (IEA) -> MODIFY to nuclear body.
• chloroplast organization (end mutant screen) -> over-annotated.
• Flowering / blue light rows kept as non-core.