protein binding GO:0005515 (IPI, two refs) — uninformative per guidelines; KEEP_AS_NON_CORE (real interactions: 14-3-3 / ADA2), but note these are regulatory, not core MF. Avoid as core.Source: file:ARATH/CBF1/CBF1-deep-research-falcon.md. The Falcon report corroborates and strengthens the existing review without overturning any decision:
- MF (DNA-binding TF activity / activator): corroborates the activator-not-just-binder distinction [falcon "CBF1 encodes an AP2-domain transcriptional activator that binds CRT/DRE motifs and can activate CRT/DRE-containing reporters in heterologous assays (yeast), supporting that it acts as a bona fide transcriptional activator rather than merely binding DNA."]. Used as supported_by on GO:0003700 (IEA, ISS), GO:0045893 (IDA), GO:0006355, and core_function 1.
- DNA binding (GO:0003677): [falcon "recombinant CBF1 binds the CRT/DRE sequence by gel-shift assays"]. Added to the IEA and IDA DNA-binding annotations.
- Nucleus (GO:0005634): report confirms localization rests on a predicted NLS + TF function, not direct imaging [falcon "multiple primary sources identify a putative nuclear localization sequence in the protein sequence, consistent with its function as a transcription factor acting on nuclear DNA."]; report's Limitations section explicitly notes no CBF1-GFP imaging was retrieved, so the open question on direct localization stands.
- Cold acclimation / response to cold: kinetics [falcon "CBF-family transcripts rise rapidly following cold shift (minutes), and COR gene expression follows within hours"] and quantitative loss-of-function effect [falcon "antisense downregulation of CBF1 and CBF3 reduces cold-induced freezing tolerance by about 60%"] and the core-regulator framing [falcon "CBF1 is a core regulator of cold acclimation."].
- Water deprivation (kept NON_CORE): report reinforces that the cold/drought link is via the shared cis-element [falcon "The CRT/DRE element is a shared regulatory node for cold- and dehydration-responsive gene expression, and CBF/DREB-type factors are widely used to connect these stress responses."], consistent with KEEP_AS_NON_CORE (CBF1 transcript is cold-induced, not osmotic-induced).
- ADA2/GCN5 (protein binding, NON_CORE): report adds the SAGA-like coactivator mechanism [falcon "Stockinger et al. (2001) report physical interaction (in vitro pull-down) between CBF1 and Arabidopsis homologs of Ada/SAGA-like complex components ADA2a/ADA2b and GCN5 (a histone acetyltransferase)."]. Still uninformative as bare protein binding; retained NON_CORE per guidelines.
- New mechanistic context not annotatable to existing GOA/UniProt IDs (recorded for reference, no NEW GO term added): SVALKA (SVK) lncRNA cis-antisense fine-tuning of CBF1 mRNA stability/termination; upstream ICE1-CBF-COR cascade, CAMTA activation, MYB15 repression, circadian control. These concern regulation OF CBF1 rather than CBF1's own activity, so no new MF/BP annotation is warranted.
- No action: UNDECIDED entries existed; none required resolution.
Reviewer (ai4c-agent) flagged that proposed_new_terms listed GO:0000977 and GO:0043565, which are EXISTING GO terms (not terms requiring creation). Verified via QuickGO REST API:
- GO:0000977 "RNA polymerase II transcription regulatory region sequence-specific DNA binding" — molecular_function, not obsolete.
- GO:0043565 "sequence-specific DNA binding" — molecular_function, not obsolete.
Action taken:
- Removed the entire proposed_new_terms block (both GO:0000977 and GO:0043565).
- Added GO:0000977 as a NEW entry under existing_annotations with evidence_type: IDA, original_reference_id: PMID:9023378, qualifier enables. This is the single most informative MF term: CBF1 binds the C-repeat/DRE (a Pol II promoter regulatory region) sequence-specifically. Supported by verbatim gel-shift/EMSA quote ["Binding of CBF1 to the C-repeat/DRE was demonstrated in gel shift assays using recombinant CBF1 protein expressed in Escherichia coli."] plus the specificity-vs-mutant-element quote ["expression of CBF1 in yeast was found to activate transcription of reporter genes containing the C-repeat/DRE as an upstream activator sequence but not mutant versions of the DNA element."], both exact substrings of PMID:9023378.
- Did not separately add GO:0043565 (sequence-specific DNA binding); GO:0000977 is its more specific child and already captures the Pol II promoter context, so a single NEW annotation suffices.
- Also fixed two directly_involved_in: fields in core_functions that were single mappings instead of YAML lists (added - list-item syntax for GO:0045893 and GO:0009631).
- Validation: uv run ai-gene-review validate genes/ARATH/CBF1/CBF1-ai-review.yaml → ✓ Valid.