ELF3 (At2g25930; UniProt O82804) curation notes

2026-10-06: initial review (module plant_circadian_clock_oscillator)

• Fetched with just fetch-gene ARATH O82804 --alias ELF3. Falcon deep research failed; review based on cached publications.

Key findings

• Evening complex scaffold PMID:21753751; LUX targets the EC to PIF4/PIF5 promoters PMID:21753751.
• No DNA-binding domain PMID:32165537.
• ELF4 recruits ELF3 into nuclear foci; ELF3 associates with the PRR9 promoter PMID:22327739.
• Thermosensor prion-like domain PMID:32848244; EC target binding is temperature-dependent PMID:28650433.
• Zeitnehmer that antagonises nocturnal light input PMID:11402162; required for clock function under thermocycles PMID:20133619.
• COP1 substrate adaptor for GI degradation PMID:19061637.

Decisions

• DNA-binding TF activity ISS (PYK20 paper, Q-rich domain only): MODIFY to transcription corepressor activity.
• Protein binding with ELF4: MODIFY to protein-macromolecule adaptor activity. With PHYB: REMOVE.
• IEP auxin/ABA: MARK_AS_OVER_ANNOTATED. Cold IEP: KEEP_AS_NON_CORE.
• Flowering, stomata, circumnutation and hypocotyl phenotypes: KEEP_AS_NON_CORE (clock outputs).
• NEW: response to temperature stimulus (GO:0009266), from Jung et al. 2020 thermosensing.

2026-10-19: literature update (2022-2026)

• Searched PubMed for ELF3 / evening-complex papers from 2022 onward (about 45 hits). None were cited in the review or behind any GOA row; the newest experimental GOA reference is from 2011 (PMID:21753751).
• Cached 17 priority papers with just fetch-pmid. Abstract only: PMID:40737553, PMID:36883592, PMID:34698833, PMID:41292294, PMID:40913711, PMID:39192577. The rest have full text.

Key findings added

• Chromatin mechanism of EC repression PMID:39880018; SWR1/H2A.Z at PIF4 PMID:38816994; H2A.Z at GI PMID:38327058.
• Temperature input to the clock [PMID:34698833 "ELF3 is essential for delivering temperature input to the clock"; "Genetic analyses suggest that the evening complex is not required for ELF3-controlled thermoresponsiveness"].
• PrLD biophysics PMID:37399408; condensate hysteresis PMID:35234947; Ser364 site outside the PrD and ELF4-dependent ELF3 stability PMID:41292294; PrLD mainly in Brassicales PMID:39391982.
• ABA signalling PMID:40737553.
• ELF3β from an alternative promoter in intron 2 PMID:36883592; natural SNP near the ELF3β start site PMID:42315129. ELF3β is not UniProt isoform O82804-2, which is a C-terminal truncation (1-339).
• Regulators of ELF3 (not annotated to ELF3): SA reduces ELF3 LLPS PMID:40913711; BBX24/BBX25 bind and suppress ELF3 PMID:40443038; phyB-ELF3-HEMERA complex PMID:39192577; light-quality-dependent localization PMID:35191492; XCT and COP1 lower ELF3 abundance PMID:41522720. Phototropism output PMID:40995069 noted but not annotated.

Decisions

• Response to abscisic acid (IEP): MARK_AS_OVER_ANNOTATED changed to MODIFY → GO:0009788 negative regulation of abscisic acid-activated signaling pathway, based on the Tang et al. 2025 abstract. Full text still to be checked.
• Kept NEW GO:0009266 response to temperature stimulus rather than GO:0016048 detection of temperature stimulus. Comparator check: TAIR annotates PHYB (the canonical plant thermosensor) to GO:0009266, and no ARATH gene in this repo carries GO:0016048. Outside plants, the C. elegans AFD thermoreceptor guanylyl cyclases gcy-8, gcy-18 and gcy-23 do carry GO:0016048 (accepted and core in their reviews), which is a precedent pointing towards GO:0016048 for direct thermosensors. Kept GO:0009266 for consistency with PHYB and raised the choice as a suggested question.
• Added supporting evidence to: DNA-binding TF → corepressor MODIFY (JMJ17/18), entrainment IMP (Zhu et al. 2022), and the thermosensor NEW row and core function (PNAS 2023, Plant Cell 2022).

2026-10-20: PR review follow-up (ai4curation/ai-gene-review#5221)

• Moved the PMID:34698833 quote out of the EC corepressor core function into a new core function for EC-independent temperature input to the oscillator (GO:0009649).
• Qualified the description: chromatin-based repression has been shown at PIF4, PIF5 and GI only.
• Cited PMID:35191492 (light-quality-dependent ELF3 localization) on the nucleus IDA row.
• Checked OLS: GO:0009788 is not an is_a/part_of descendant of GO:0009737 (its ancestors are under regulation of signal transduction and regulation of response to alcohol), so the ABA MODIFY is a lateral move rather than a refinement. Decision on restructuring (KEEP_AS_NON_CORE on GO:0009737 plus NEW GO:0009788) left to the curator.
• GO:0034720 histone H3-K4 demethylation is obsolete; raised the ELF3-JMJ targeting question without a term id.