cup (Q9VMA3) review notes

Module context: dmel_eif4e_cup_complex (Cup with eIF4E1).

Deep research: the first falcon attempt failed (timeout/killed; perplexity unavailable); a retry produced cup-deep-research-falcon.md after the review was drafted. It agrees with this review: Cup is described as a cytoplasmic mRNP adaptor and translational repressor, not an enzyme, acting in germline P bodies; it also notes newer roles in cycA/cycB mRNA partitioning and CTLH-mediated clearance at the maternal-to-zygotic transition (not in GOA).

Molecular function

• Cup is an eIF4E-binding protein (4E-BP) of the 4E-T family. PMID:14685270
• Binding uses a canonical and a non-canonical motif on two faces of eIF4E. PMID:22832024; PMID:25179781
• eIF4E-independent effector domain: PMID:21937713; PMID:21937713
• Smaug complex reconstitution: PMID:36951092
• No RNA-binding domain; recruited indirectly: PMID:14685270; PMID:37553798

Biological roles

• oskar repression: PMID:14723848; mechanism PMID:16469699
• oskar localization / Barentsz recruitment: PMID:14691132
• gurken: PMID:18082158
• NMJ: PMID:26102195

Localization

• Shuttling: PMID:15465908
• P bodies: PMID:37553798
• The NOT P-body annotation (PMID:24335285) is from GFP-Cup in HeLa cells: PMID:24335285 -- removed as heterologous and contradicted by native-context data.

Decisions

• Protein binding rows: eIF4E partners -> MODIFY to GO:0008190; others REMOVE (uninformative).
• RNA binding IDA (PMID:16469699, abstract only) -> UNDECIDED; mRNA binding IBA -> over-annotation.
• protein-RNA adaptor activity -> over-annotation (Cup bridges Bru1/Smaug to eIF4E, protein-protein).