Ribosome-associated RNAs trigger prion protein phase separation and aggregation

The conversion of the cellular prion protein (PrP^C) into its pathogenic form (PrP^Sc) is a central event in prion diseases and may be facilitated by cofactors that lower the energy barrier between native and misfolded states. Nucleic acids (NAs) are strong candidates among these cofactors. The interaction between recombinant PrP (rPrP) and total RNA extracted from neuroblastoma cells (N2aRNA) induces significant structural changes. Here, we use rPrP:N2aRNA as a model to identify RNAs capable of inducing full-length murine rPrP phase separation and/or aggregation. Liquid–liquid phase separation (LLPS) is a process increasingly recognized as a precursor to pathological protein aggregation in neurodegenerative diseases. rPrP was incubated with N2aRNA, and the resulting phase transitions and aggregate formation were monitored via turbidity measurements and microscopy. RNAs associated with rPrP-containing condensates and aggregates were recovered and subjected to RNA-seq and bioinformatic analysis to identify candidate RNA motifs. The recovered RNA pool was heterogeneous and predominantly composed of ribosomal RNAs. However, three consensus motifs characterized by low sequence complexity were consistently enriched in transcripts related to ribonucleoprotein complexes. These features suggest that structural properties of specific RNA molecules are critical for their ability to induce rPrP phase transitions. Our findings support a model in which RNAs enriched in low-complexity motifs selectively bind PrP and drive its LLPS and aggregation in a stoichiometry-dependent manner. This RNA-driven mechanism may represent an early molecular event in the formation of PrP^Sc-like species and offers new insights into prion protein biology and pathogenesis.

Funding: FAPERJ, CNPq, CAPES, FAPESP.