Characterization of Amyloid Cores in Prion Domains

Ricardo Sant’Anna,Susanna Navarro,Cristina Batlle,Maria Rosario Fernández,Louise Serpell,Salvador Ventura,Natalia S De Groot

doi:10.1038/srep34274

Ricardo Sant’Anna, Susanna Navarro + Show 5 more

Open Access

https://doi.org/10.1038/srep34274

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Abstract

Amyloids consist of repetitions of a specific polypeptide chain in a regular cross-β-sheet conformation. Amyloid propensity is largely determined by the protein sequence, the aggregation process being nucleated by specific and short segments. Prions are special amyloids that become self-perpetuating after aggregation. Prions are responsible for neuropathology in mammals, but they can also be functional, as in yeast prions. The conversion of these last proteins to the prion state is driven by prion forming domains (PFDs), which are generally large, intrinsically disordered, enriched in glutamines/asparagines and depleted in hydrophobic residues. The self-assembly of PFDs has been thought to rely mostly on their particular amino acid composition, rather than on their sequence. Instead, we have recently proposed that specific amyloid-prone sequences within PFDs might be key to their prion behaviour. Here, we demonstrate experimentally the existence of these amyloid stretches inside the PFDs of the canonical Sup35, Swi1, Mot3 and Ure2 prions. These sequences self-assemble efficiently into highly ordered amyloid fibrils, that are functionally competent, being able to promote the PFD amyloid conversion in vitro and in vivo. Computational analyses indicate that these kind of amyloid stretches may act as typical nucleating signals in a number of different prion domains.

Highlights

Because PFDs are intrinsically disordered, in case those highly aggregating regions would be present, they would be exposed to solvent and ready to aggregate, precluding prion proteins to remain in their soluble and functional conformation under physiological conditions
We have shown that the implementation of this concept in our in house pWALTZ algorithm allows classifying Q/N rich sequences according to their prionic behaviour with better accuracy than methods relying only on composition17,19. pWALTZ aims to predict the 21 residues long sequence stretch with the average highest amyloidogenic potential in a Q/N rich sequential context, a length that has been shown to suffice for the formation of transmissible β-folds in the case of the HET-s prion domain[20] and corresponding to minimal core size allowing maximal discrimination between prionic and non-prionic sequences bearing similar Q/N content[17]
We provide experimental evidence for the existence of such Q/N rich amyloid stretches in the PFDs of four of the best-characterized yeast prion proteins: Sup[35], Swi[1], Mot[3] and Ure2. pWALTZ identified potential, previously uncharacterized, 21 residues long amyloid stretches in the PFDs of the four proteins

Summary

Introduction

Because PFDs are intrinsically disordered, in case those highly aggregating regions would be present, they would be exposed to solvent and ready to aggregate, precluding prion proteins to remain in their soluble and functional conformation under physiological conditions. We have suggested that in PFDs, the amyloid stretches should be longer and less hydrophobic, in such a way that the amyloid potential is less concentrated, making their aggregation sensitive to protein concentration and seeding[17]. They should cluster in the same sequence region amino acid residues with a significant amyloid propensity with residues promoting structural disorder. This suggests that these relatively short sequences may act as important amyloid nucleating signals in prion domains

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