De novo design of RNA-binding proteins with a prion-like domain related to ALS/FTD proteinopathies

Abstract

Aberrant RNA-binding proteins form the core of the neurodegeneration cascade in spectrums of disease, such as amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Six ALS-related molecules, TDP-43, FUS, TAF15, EWSR1, heterogeneous nuclear (hn)RNPA1 and hnRNPA2 are RNA-binding proteins containing candidate mutations identified in ALS patients and those share several common features, including harboring an aggregation-prone prion-like domain (PrLD) containing a glycine/serine-tyrosine-glycine/serine (G/S-Y-G/S)-motif-enriched low-complexity sequence and rich in glutamine and/or asparagine. Additinally, these six molecules are components of RNA granules involved in RNA quality control and become mislocated from the nucleus to form cytoplasmic inclusion bodies (IBs) in the ALS/FTD-affected brain. To reveal the essential mechanisms involved in ALS/FTD-related cytotoxicity associated with RNA-binding proteins containing PrLDs, we designed artificial RNA-binding proteins harboring G/S-Y-G/S-motif repeats with and without enriched glutamine residues and nuclear-import/export-signal sequences and examined their cytotoxicity in vitro. These proteins recapitulated features of ALS-linked molecules, including insoluble aggregation, formation of cytoplasmic IBs and components of RNA granules, and cytotoxicity instigation. These findings indicated that these artificial RNA-binding proteins mimicked features of ALS-linked molecules and allowed the study of mechanisms associated with gain of toxic functions related to ALS/FTD pathogenesis.

From Prions to Stress Granules: Defining the Compositional Features of Prion-Like Domains That Promote Different Types of Assemblies

“…The fact that sequence scrambling did not block stress granule recruitment suggests that specific interactions with primary sequence motifs are not a dominant driver of recruitment. This is consistent with the findings of a previous study showing that simple SYGQ repeats are sufficient to promote stress granule recruitment in mammalian cells [ 148 ], and demonstrates that rather generic compositional features can nonetheless lead to specific targeting. The strong enrichment of charged residues suggests that the formation of labile amyloid-like gels is likely not a principal driver of recruitment for these PrLDs, as charged residues should disrupt the in-register parallel β-sheet interactions thought to underlie these gels [ 138 , 139 , 140 ].…”

Formation of Toxic Oligomeric Assemblies of RNA-binding Protein: Musashi in Alzheimer’s disease

“…Over the past decades, RBPs, their dysregulation and toxic roles in neurodegenerative diseases are being actively investigated. Aggregation of many RBPs, such as TIA-1 [ 18 ], FUS, TDP43, hnRNPA1 and hnRNPA2 in Amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) proteinopathies are mediated by prion-related domain (PRD) [ 29 , 39 ]. RBPs also possess RNA-Recognition Motifs (RRMs) by which they interact with RNA molecules.…”

Cprp—An Unusual, Repetitive Protein Which Impacts Pleuromutilin Biosynthesis in the Basidiomycete Clitopilus passeckerianus

“…Aromatic residues such as tyrosine, which is at the core of the repetitive motif of all Cprp-like proteins, are thought to be particularly important for LLPS (Lin et al, 2017). The S-Y-G motif provides another tentative link to RNA granules, as a similar motif has been characterized in a family of RNA-binding proteins from humans which are known to be components of RNA granules and which are implicated in a spectrum of diseases (Mitsuhashi et al, 2017). A potential role for DDR48 proteins in RNA-mediated regulation is consistent with a study which found that DDR48 overexpression in S. cerevisiae resulted in a 63% decrease in RNA accumulation (Li et al, 2008).…”