The cooperative binding of TDP-43 to GU-rich RNA repeats antagonizes TDP-43 aggregation.

Juan Carlos Rengifo-Gonzalez,Emilie Steiner,Dominique Durand,David Pastré,Krystel El Hage,Pierrick Craveur,Ahmed Bouhss,Vandana Joshi,Marie-Jeanne Clément

doi:10.7554/elife.67605

Abstract

TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA recognition motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.

Highlights

In comparison to other proteins, many RNA-binding proteins (RBP) harbor low complexity domains (LCD) that initiate weak multivalent interactions leading to the assembly of liquid-like membrane-less organelles, notably in the mammalian cell nucleus (1-4)
Through a structural analysis by NMR spectroscopy of the intermolecular interface between two RRM-1 and -2 (RRM1-2) monomers, we identified the residues driving the cooperative binding of TAR DNA-binding protein 43 (TDP-43) on long GU-rich sequences
To understand through which molecular mechanisms TDP-43 targets pyrimidine-rich introns in cells as revealed by CLIP experiments, we considered whether a cooperative association of TDP-43 may take place in long GU-rich repeats to secure the binding of several TDP-43 proteins

Summary

Introduction

In comparison to other proteins, many RNA-binding proteins (RBP) harbor low complexity domains (LCD) that initiate weak multivalent interactions leading to the assembly of liquid-like membrane-less organelles, notably in the mammalian cell nucleus (1-4). The majority of pathological mutations associated with TDP-43 are located in its self-adhesive C-terminal LCD (16). Many structural in vitro analyses focused on pathological TDP-43 mutations have indicated a critical role of the TDP-43 LCD in the aggregation process (7, 17-20). In recent in vitro studies, the dimerization of the structured N-terminal was proposed to promote a head-to-tail aggregation of TDP-43 in cells, together with the self-adhesive LCD (21-23). As proposed in recent studies, the recruitment of TDP-43 in mRNA-rich stress granules may preserve the solubility of TDP-43 in the cytoplasm (32, 33), like nuclear RNA under physiological conditions (27, 34). A pathological mutation, K181E, located in the linker between RRM1 and RRM2 domains, leads to TDP-43 aggregation and to a reduced affinity for its RNA targets (36)

Methods

Results

Conclusion