Regulation by the RNA-binding protein Unkempt at its effector interface [Ribo]

How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of ‘dual-purpose’ peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface. We performed ribosome profiling experiments to assess changes in ribosome occupancy upon induction of UNKWT, UNKdPAM2, or UNK3M for 24 hours in inducible wild-type HeLa cells, and upon induction of UNKWT for 24 hours in inducible CNOT9 knockout (CNOT9KO) HeLa cells. We processed two biological replicates from either Dox-induced or uninduced cells. Comparisons between uninduced and WT, 3M, or dPAM2 UNK-expressing cells were performed. The log2FoldChange between the conditions were expressed as log2(Translation efficiency ratio): log2TER.