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

Nele Merret Hollmann,Pravin Kumar Ankush Jagtap,Pawel Masiewicz,Tanit Guitart,Bernd Simon,Jan Provaznik,Frank Stein,Per Haberkant,Lara Jayne Sweetapple,Laura Villacorta,Dylan Mooijman,Vladimir Benes,Mikhail M Savitski,Fátima Gebauer,Janosch Hennig

doi:10.1016/j.celrep.2020.107930

Abstract

SummaryRNA-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.

Highlights

Current estimates indicate that approximately 10% of the entire human genome codes for RNA-binding proteins (RBPs) (Hentze et al, 2018)
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

Summary

Introduction

Current estimates indicate that approximately 10% of the entire human genome codes for RNA-binding proteins (RBPs) (Hentze et al, 2018). The majority of RBPs contain more than one RBD, resulting in a large combinatorial variety of different domain classes, and diversity of architectures and modes of target RNA sequence binding In many cases these domains are separated by flexible linker regions (Afroz et al, 2015; Gerstberger et al, 2014). There have been a number of efforts to examine structural features that dictate RBP/RNA-binding specificity (Clery and Allain, 2011). These efforts have increased our understanding of how single RBDs engage their target sequences, and in some cases offered insights into the role of multi-domain arrangements in the recognition process. We appreciate that target RNA recognition employs complex binding modes that depend on the target itself, such

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Discussion

Conclusion