Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras

• Published in: Cell reports (Cambridge) Vol. 32; no. 3; p. 107930
• Main Authors: Hollmann, Nele Merret, Jagtap, Pravin Kumar Ankush, Masiewicz, Pawel, Guitart, Tanit, Simon, Bernd, Provaznik, Jan, Stein, Frank, Haberkant, Per, Sweetapple, Lara Jayne, Villacorta, Laura, Mooijman, Dylan, Benes, Vladimir, Savitski, Mikhail M., Gebauer, Fátima, Hennig, Janosch
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.07.2020; Cell Press
• Subjects: Amino Acid Sequence; Animals; cold-shock domains; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; Drosophila melanogaster; Drosophila Proteins - chemistry; Drosophila Proteins - metabolism; integrative structural biology; NMR spectroscopy; Nucleic Acid Conformation; Protein Biosynthesis; Protein Domains; ribonucleoproteins; RNA - chemistry; RNA - metabolism; RNA-binding domains; RNA-binding proteins; translation regulation; cold-shock domains; RNA-binding domains; RNA-binding proteins; translation regulation; integrative structural biology; ribonucleoproteins; NMR spectroscopy
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2020.107930

RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity. [Display omitted] •Discovery of non-canonical cold-shock domains•Non-canonical cold-shock domains do not bind RNA independently•Interdomain contacts mediate RNA structure specificity and impact translation•Determination of an Unr-dependent ribonucleoprotein (RNP) interactome Hollmann et al. show how non-RNA-binding domains within Drosophila Unr, an RNA-binding protein, contribute to its RNA target specificity. The selectivity is mediated by interdomain contacts to the RNA-binding cold-shock domains, which restrict the protein shape.