RNA-Binding and Prion Domains: The Yin and Yang of Phase Separation

Abstract

Biomolecular condensates are membrane-less organelles mainly composed of proteins and RNAs that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to phase separate is encoded in their sequences, yet it is still unknown which domains drive the process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting biomolecular condensation. Using advanced computational models to predict the phase separation propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-Binding Domains (RBDs). We found that while just one PrLD is sufficient to drive protein condensation, multiple RBDs are needed to modulate the dynamicity of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.

New lessons on TDP‐43 from old N. furzeri killifish

“…We have demonstrated that other regions, including the RRM motifs, can play an important role in aggregation and pathology (Zacco et al, 2019). This evidence agrees with a role of RNA in the aggregation properties of this protein (Gotor et al, 2020;Loganathan et al, 2020). We also demonstrated that binding to short RNA aptamers can efficiently prevent TDP-43 aggregation (Zacco et al, 2019).…”

Structural analysis of SARS-CoV-2 genome and predictions of the human interactome

“…To further investigate the propensity of these proteins to phase separate, we used the cat GRANULE algorithm (Material and Methods) ( 32 ). Differently from other methods to predict solid-like aggregation ( 79 , 80 ), cat GRANULE estimates the propensity of proteins to form liquid-like assemblies such as stress granules ( 81 ). We found that the 274 proteins binding to the 5′ end (fragment 1) with Z score ≥1.5 are highly prone to accumulate in assemblies similar to stress-granules (274 proteins with the lowest Z score are used in the comparison; P -value <0.0001; Kolmogorov−Smirnoff; Figure 5C ; Supplementary Table S6 ).…”

A novel SATB1 protein isoform with different biophysical properties

“…LLPS is mostly driven by weak multivalent interactions between the protein’s intrinsically disordered regions (IDRs) and is often accompanied by interactions with RNA 2,3 . Low-complexity prion-like domains (PrLDs) and RNA binding domains are known features that affect a protein’s biophysical properties 4,5 . Glutamine-rich proteins and proteins harboring a poly-Q domain also display prion-like characteristics 6 .…”

“…Glutamine-rich proteins and proteins harboring a poly-Q domain also display prionlike characteristics 6 . Moreover, proteins with poly-Q domains and/or PrLDs are known to undergo LLPS 4,5,[7][8][9][10] . However, such proteins are also prone to abnormalities and their phase transitions frequently result in fibrous amyloids or other rigid aggregates, which are associated to several pathologies 8,11 .…”