The evolutionary conserved protein-RNA interface formed by the cell-fate regulator Bicaudal-C

Bicaudal-C (Bicc1) is an essential cell-fate regulator that guides the animal body plan during early development and maintains organ homeostasis in adults. It does so by binding specific mRNA targets and regulating their translation, yet the molecular basis of mRNA target selection has remained unclear. Here, we combined experimental and computational approaches to define the Bicc1-RNA interaction. In vitro binding experiments with wild-type and mutant RNA substrates identified the RNA features recognized by Bicc1, while protein-RNA XL-MS—a UV-crosslinking approach coupled to LC-MS/MS—pinpointed Bicc1 amino acids in direct contact with RNA. Deep protein-sequence alignments showed that key RNA contacts are conserved across invertebrates and vertebrates, and binding experiments with recombinant Bicc1 proteins from multiple species confirmed this conservation functionally. AlphaFold 3.0 predictions of Bicc1-RNA complexes generated a structural model that complemented and extended these experimental findings. Together, these data establish that Bicc1 recognizes a bipartite binding site comprising a GAC primary sequence and a stem-loop structure through contacts distributed across both the KH1 and KH2 domains. This interface is conserved from invertebrates to vertebrates. This work thus defines the evolutionarily conserved mechanism by which Bicc1 selects specific mRNAs for translational regulation.