Human pumilio proteins use fuzzy multivalent hydrophobic interactions to recruit the CCR4-NOT deadenylase complex to repress mRNAs

Pumilio proteins are conserved RNA-binding proteins that control mRNAs involved in development, proliferation, and differentiation. Human PUM1 and PUM2 repress targets by recruiting the CCR4-NOT deadenylase complex through a metazoan-specific, intrinsically disordered repression domain (RD3). Here we dissect RD3 using functional assays, protein interaction assays, and crosslinking mass spectrometry. We identify multiple RD3 peptides that are sufficient for repression and binding to the CCR4-NOT complex. Crosslinking reveals numerous mutually exclusive contacts between RD3 and CCR4-NOT, consistent with a multivalent “fuzzy” binding mode in which interactions are not defined by a single sequence or structure. Sequence scrambling shows that the linear amino acid order of RD3 is dispensable, whereas its physicochemical composition, in particular aliphatic and aromatic residues, is essential for repression and CCR4-NOT binding. These findings support a model in which multivalent interactions between intrinsically disordered regions and effector complexes, governed by amino acid composition, underlie robust PUM-mediated repression and exemplify general principles by which intrinsically disordered regions recruit CCR4-NOT to regulate gene expression.