4E-BP1 differentially regulates translation of a subset of human mRNAs

Elevated levels of eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) influence cap-independent translation by forming a complex with eukaryotic initiation factor 4E (eIF4E) (eIF4E•4E-BP1). Certain mRNAs-including those encoding hypoxia-inducible factor-1α (HIF-1α), fibroblast growth factor-9 (FGF-9), and two isoforms of tumor suppressors, p53 (p53_A, and p53_B)-contain structured 5'untranslated regions (UTRs) that enable translation either via cap-independent translation enhancer (CITE)-like or internal ribosomal entry site (IRES)-like mechanisms. However, how 4E-BP1 modulates these mechanisms remains unclear. Using fluorescence-based anisotropy assays, we showed that the eIF4E•4E-BP1 binds more tightly to the 5' m⁷G-cap of these mRNAs than eIF4E alone. Luciferase reporter assays further demonstrated that 4E-BP1 inhibits translation of CITE-like (HIF-1α, and p53_A) more effectively than IRES-like (FGF-9, and p53_B) mRNAs. Although binding affinity of eIF4E•4E-BP1 to each of these mRNAs increased, only CITE-like mRNA translation was significantly inhibited. Importantly, eIF4GI_557-1599 and its binding partner eIF4A, overcomes this inhibition selectively for CITE-like mRNAs, while eIF4E alone has only partial effects. In contrast, IRES-like mRNAs, despite binding to eIF4E•4E-BP1, exhibited only a modest translational repression and were minimally affected by eIF4GI_557-1599•eIF4A or eIF4E. These findings reveal that 4E-BP1 selectively represses cap-independent translation in a transcript-specific manner. Moreover, fluorescence anisotropy revealed that 4E-BP1 enhances eIF4GI_557-1599 recruitment to certain mRNAs, potentially facilitating 43S pre-initiation complex (43S PIC) assembly during stress. These results provide new mechanistic insights into selective translational control with implications for stress response and cancer progression via non-canonical translation.